gmx Namespace Reference

Description

Generic GROMACS namespace.

Test helper utilities for generating frame data.

Functionality for testing whether calls to mdrun produce the same energy and force quantities when they should do so.

Convenience macro to help us avoid ifdefs each time we use sysconf.

Declarations of H5md utility functions.

Declarations of H5md data type utility routines.

Declares the topology utility functions for H5MD.

Definition of the topology utility functions for H5MD.

Declarations of H5md time data block manipulation routines.

Definitions of H5md time data block manipulation routines.

Declarations of H5md particle data block routines.

Definitions of H5md particle data block routines.

Helper functions for managing scope guards in the H5md module.

Declarations of utility functions for working with H5MD groups.

Definitions of utility functions for working with H5MD groups.

Declarations of H5md frame data set builder routines.

Declarations of H5md frame data set manipulation routines.

Definitions of H5md frame data set manipulation routines.

Declarations of H5md fixed data set class.

Definitions of H5md fixed data set class.

Declarations of H5md data set builder routines.

Declarations of H5md data set base class.

Definitions of H5md data set base class.

Declarations of utility functions for working with H5MD attributes.

Definitions of utility functions for working with H5MD attributes.

I/o interface to H5MD HDF5 files.

Declaration of H5MD exception class and helper macros.

Definitions for H5MD exception class.

Author

Magnus Lundborg lundb.nosp@m.org..nosp@m.magnu.nosp@m.s@gm.nosp@m.ail.c.nosp@m.om

Petter Johansson pettj.nosp@m.oha@.nosp@m.kth.s.nosp@m.e

Petter Johansson pettj.nosp@m.oha@.nosp@m.kth.s.nosp@m.e

Magnus Lundborg lundb.nosp@m.org..nosp@m.magnu.nosp@m.s@gm.nosp@m.ail.c.nosp@m.om

Yang Zhang yang..nosp@m.zhan.nosp@m.g@sci.nosp@m.life.nosp@m.lab.s.nosp@m.e

Magnus Lundborg lundb.nosp@m.org..nosp@m.magnu.nosp@m.s@gm.nosp@m.ail.c.nosp@m.om

Petter Johansson pettj.nosp@m.oha@.nosp@m.kth.s.nosp@m.e

Yang Zhang yang..nosp@m.zhan.nosp@m.g@sci.nosp@m.life.nosp@m.lab.s.nosp@m.e

Petter Johansson pettj.nosp@m.oha@.nosp@m.kth.s.nosp@m.e

Magnus Lundborg lundb.nosp@m.org..nosp@m.magnu.nosp@m.s@gm.nosp@m.ail.c.nosp@m.om

Yang Zhang yang..nosp@m.zhan.nosp@m.g@sci.nosp@m.life.nosp@m.lab.s.nosp@m.e

Petter Johansson pettj.nosp@m.oha@.nosp@m.kth.s.nosp@m.e

Yang Zhang yang..nosp@m.zhan.nosp@m.g@sci.nosp@m.life.nosp@m.lab.s.nosp@m.e

Namespaces
	compat
	Compatibility aliases for standard library features.
	test
	Testing utilities namespace.

Classes
class	AnalysisDataModuleManager
	Encapsulates handling of data modules attached to AbstractAnalysisData. More...
class	AnalysisDataStorageFrame
	Allows assigning values for a data frame in AnalysisDataStorage. More...
class	AnalysisDataStorage
	Helper class that implements storage of data. More...
class	ArrayRef
	STL-like interface to a C array of T (or part of a std container of T). More...
class	AnalysisDataParallelOptions
	Parallelization options for analysis data objects. More...
class	Awh
	Coupling of the accelerated weight histogram method (AWH) with the system. More...
struct	DensityFittingModuleInfo
	Information about the density fitting module. More...
class	INNPotModel
	NNPot Module. More...
class	TorchModel
	Class responsible for loading and evaluating a TorchScript-compiled neural network model. Inherits from NNPotModel. More...
class	CommandLineHelpContext
	Context information for writing out command-line help. More...
class	GlobalCommandLineHelpContext
	Helper for passing CommandLineHelpContext into parse_common_args(). More...
class	CommandLineHelpWriter
	Writes help information for Options. More...
class	ICommandLineModule
	Module that can be run from command line using CommandLineModuleManager. More...
class	CommandLineModuleManager
	Implements a wrapper command-line interface for multiple modules. More...
class	CommandLineModuleGroup
	Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More...
class	CommandLineModuleSettings
	Settings to pass information between a module and the general runner. More...
class	ICommandLineOptionsModuleSettings
	Settings to pass information between a CommandLineOptionsModule and generic code that runs it. More...
class	ICommandLineOptionsModule
	Module that can be run from a command line and uses gmx::Options for argument processing. More...
class	CommandLineParser
	Implements command-line parsing for Options objects. More...
class	IExecutableEnvironment
	Allows customization of the way various directories are found by CommandLineProgramContext. More...
class	CommandLineProgramContext
	Program context implementation for command line programs. More...
class	TrajectoryFileOpener
	Low level method to take care of only file opening and closing. More...
class	TrajectoryFrameWriter
	Writes coordinate frames to a sink, e.g. a trajectory file. More...
class	ProcessFrameConversion
	ProcessFrameConversion class for handling the running of several analysis steps. More...
class	IFrameConverter
	IFrameConverter interface for manipulating coordinate information. More...
class	IOutputAdapter
	OutputAdapter class for handling trajectory file flag setting and processing. More...
class	OutputAdapterContainer
	Storage for output adapters that modify the state of a t_trxframe object. More...
class	OutputSelector
	OutputSelector class controls setting which coordinates are actually written. More...
class	SetAtoms
	SetAtoms class controls availability of atoms data. More...
class	SetBox
	Allows changing box information when writing a coordinate file. More...
class	SetForces
	SetForces class allows changing writing of forces to file. More...
class	SetPrecision
	SetPrecision class allows changing file writing precision. More...
class	SetStartTime
	SetStartTime class allows changing trajectory time information. More...
class	SetTimeStep
	SetTimeStep class allows changing trajectory time information. More...
class	SetVelocities
	SetVelocities class allows changing writing of velocities to file. More...
class	OutputRequirementOptionDirector
	Container for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer. More...
struct	OutputRequirements
	Finalized version of requirements after processing. More...
class	DomainDecompositionBuilder
	Builds a domain decomposition management object. More...
struct	ZoneCorners
	The upper corners of a zone, used for computing which halo clusters need to be sent. More...
class	FixedCapacityVector
	Vector that behaves likes std::vector but has fixed capacity. More...
class	HashedMap
	Unordered key to value mapping. More...
class	FusedGpuHaloExchange
	NVSHMEM-based fused GPU halo exchange. More...
class	GpuHaloExchange
	Manages GPU Halo Exchange object. More...
class	GpuHaloExchangeNvshmemHelper
	Handles NVSHMEM aspects of GPU Halo exchange. More...
struct	HaloMpiRequests
	Storage for MPI request for halo MPI receive and send operations. More...
class	HaloExchange
	Handles the halo communication of coordinates and forces. More...
class	LocalAtomSet
	A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator. More...
class	LocalAtomSetManager
	Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...
class	LocalTopologyChecker
	Has responsibility for checking that the local topology distributed across domains describes a total number of bonded interactions that matches the system topology. More...
struct	DomdecOptions
	Structure containing all (command line) options for the domain decomposition. More...
class	EnergyAnalysisFrame
	Class describing an energy frame, that is the all the data stored for one energy term at one time step in an energy file. More...
class	EnergyTerm
	Class describing the whole time series of an energy term. More...
struct	EnergyNameUnit
	Convenience structure for keeping energy name and unit together. More...
class	IEnergyAnalysis
	Interface class overloaded by the separate energy modules. More...
class	PmeStepWorkload
	Describes the work PME performs during one simulation step. More...
class	SeparatePmeRanksPermitted
	Class for managing usage of separate PME-only ranks. More...
class	PmeOnlySimulationWorkload
	Describes simulation-wide work performed by a PME-only rank. More...
class	PmeCoordinateReceiverGpu
	Manages receiving coordinates on PME-only ranks from their PP ranks. More...
class	PmeForceSenderGpu
	Manages sending forces from PME-only ranks to their PP ranks. More...
class	PmeLoadBalancing
	Object to manage PME load balancing. More...
class	PmePpComm
	Coordinate communication from PP rank with its PME-only rank. More...
class	PmePpCommGpu
	Manages communication related to GPU buffers between this PP rank and its PME rank. More...
struct	PmePpCommSettings
	Holds PmePpComm configuration from DomainDecompositionBuilder until they can be used to make the PmePpComm. More...
class	RocfftInitializer
	Provides RAII-style initialization of rocFFT library. More...
struct	RocfftPlan
	All the persistent data for planning an executing a 3D FFT. More...
struct	PlanSetupData
	Helper struct to reduce repetitive code setting up a 3D FFT plan. More...
struct	CheckpointHeaderContents
	Header explaining the context of a checkpoint file. More...
class	H5mdError
	Exception class for H5MD errors. More...
class	H5md
	Manager of an H5MD filehandle. The class is designed to read/write data according to de Buyl et al., 2014 (https://doi.org/10.1016/j.cpc.2014.01.018) and https://www.nongnu.org/h5md/h5md.html. More...
class	BasicVector
	C++ class for 3D vectors. More...
class	H5mdDataSetBuilder
	Builder class for H5md data sets. More...
class	H5mdDataSetBase
	Class which manages a HDF5 data set handle and associated data. More...
class	H5mdFixedDataSet
	Class which provides an interface for reading and writing data to data sets of fixed size. More...
class	H5mdFrameDataSet
	Class which provides an interface for reading and writing frame data to H5mdDataSet objects. More...
class	H5mdScalarFrameDataSet
	Class which provides an interface for reading and writing scalar frame data to H5mdDataSetBase objects. More...
class	H5mdFrameDataSetBuilder
	Builder class for framed H5md data sets. More...
class	H5mdCloser
	Bound closing function created by scope guard helper functions. More...
class	H5mdParticleBlock
	Class which manages trajectory data inside of a H5md particle group. More...
class	H5mdParticleBlockBuilder
	Builder class for H5mdParticleBlock objects. More...
class	H5mdTimeDataBlockBuilder
	Builder class to create new H5mdTimeDataBlock objects. More...
class	H5mdTimeDataBlock
	Class which manages time-dependent data sets of the templated ValueType. More...
class	MrcDensityMapOfFloatReader
	Read an mrc/ccp4 file that contains float values. More...
class	MrcDensityMapOfFloatFromFileReader
	Read an mrc density map from a given file. More...
class	MrcDensityMapOfFloatWriter
	Write an mrc/ccp4 file that contains float values. More...
struct	MrcDataStatistics
	Statistics about mrc data arrays. More...
struct	MrcDensitySkewData
	Skew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014". More...
struct	CrystallographicLabels
	Crystallographic labels for mrc data. More...
struct	MrcDensityMapHeader
	A container for the data in mrc density map file formats. More...
struct	TimeControl
	Controls when to start and stop reading trajectory data from files. More...
class	FmmMdpOptions
	MDP option provider that manages all FMM backends. More...
class	FmmMdpValidator
	Validates FMM-related MDP settings during preprocessing. More...
class	FmmForceProviderBuilder
	Helper class to configure and construct FMM Force Provider. More...
struct	IFmmOptions
	Interface for FMM option sets used in MDP handling. More...
struct	VsiteTypeAndSign
	Struct for handling vsite information for vsite generation inside grompp. More...
class	PreprocessingAtomTypes
	Storage of all atom types used during preprocessing of a simulation input. More...
class	PreprocessingBondAtomType
	Storage for all bonded atomtypes during simulation preprocessing. More...
class	ListOfLists
	A list of lists, optimized for performance. More...
class	InteractionOfType
	Describes an interaction of a given type, plus its parameters. More...
struct	InteractionsOfType
	A set of interactions of a given type (found in the enumeration in ifunc.h), complete with atom indices and force field function parameters. More...
struct	MoleculeInformation
	Holds the molecule information during preprocessing. More...
struct	BondedInteraction
	Information about single bonded interaction. More...
struct	BondedInteractionList
	Accumulation of different bonded types for preprocessing. More...
struct	PreprocessResidue
	Information about preprocessing residues. More...
struct	MoleculePatch
	Block to modify individual residues. More...
struct	MoleculePatchDatabase
	A set of modifications to apply to atoms. More...
struct	inputrec_strings
	Storage for preprocessing-only string parameters from MDP files. More...
struct	GpuConfigurationCapabilities
	Collection of GPU capabilities for this configuration. More...
class	ClfftInitializer
	Handle clFFT library init and tear down in RAII style also with mutual exclusion. More...
class	DeviceStreamManager
	Device stream and context manager. More...
class	HostAllocationPolicy
	Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers. More...
class	NvshmemManager
	Duplicates the communicator and initializes NVSHMEM over it. This is a collective call for all the ranks in the given MPI comm. After NVSHMEM initialization all NVSHMEM APIs can be safely used. More...
struct	OpenClTraits
	Stub for OpenCL type traits. More...
struct	OpenClTraitsBase
	Implements common trait infrastructure for OpenCL types. More...
struct	OpenClTraits< cl_context >
	Implements traits for cl_context. More...
struct	OpenClTraits< cl_command_queue >
	Implements traits for cl_command_queue. More...
struct	OpenClTraits< cl_program >
	Implements traits for cl_program. More...
struct	OpenClTraits< cl_kernel >
	Implements traits for cl_kernel. More...
class	ClHandle
	Wrapper of OpenCL type cl_type to implement RAII. More...
class	CpuInfo
	Detect CPU capabilities and basic logical processor info. More...
class	HardwareTopology
	Information about packages, cores, processing units, numa, caches. More...
struct	InteractiveMolecularDynamicsModuleInfo
	Information about the interactive molecular dynamics module. More...
struct	EnumerationArray
	Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type. More...
class	ArrayRefWithPadding
	Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses. More...
class	TranslateAndScale
	Transform coordinates in three dimensions by first translating, then scaling them. More...
class	AffineTransformation
	Affine transformation of three-dimensional coordinates. More...
class	DensitySimilarityMeasure
	Measure similarity and gradient between densities. More...
class	DensityFittingForce
	Manages evaluation of density-fitting forces for particles that were spread with a kernel. More...
struct	ExponentialMovingAverageState
	Store the state of exponential moving averages. More...
class	ExponentialMovingAverage
	Evaluate the exponential moving average with bias correction. More...
struct	GaussianSpreadKernelParameters
	Parameters for density spreading kernels. More...
class	GaussTransform3D
	Sums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as . More...
class	MultiDimArray
	Multidimensional array that manages its own memory. More...
class	PaddedVector
	PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS. More...
class	CheckpointHandler
	Class handling the checkpoint signal. More...
class	Constraints
	Handles constraints. More...
struct	AtomPair
	A pair of atoms indexes. More...
class	MDAtoms
	Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators. More...
class	ResetHandler
	Class handling the reset of counters. More...
struct	SettleWaterTopology
	Composite data for settle initialization. More...
class	SettleData
	Data for executing SETTLE constraining. More...
struct	shakedata
	Working data for the SHAKE algorithm. More...
class	SimulationSignal
	POD-style object used by mdrun ranks to set and receive signals within and between simulations. More...
class	SimulationSignaller
	Object used by mdrun ranks to signal to each other at this step. More...
class	StopHandler
	Class handling the stop signal. More...
class	StopConditionSignal
	Class setting the stop signal based on gmx_get_stop_condition() More...
class	StopConditionTime
	Class setting the stop signal based on maximal run time. More...
class	StopHandlerBuilder
	Class preparing the creation of a StopHandler. More...
class	Update
	Contains data for update phase. More...
class	UpdateGroups
	Owns the update grouping and related data. More...
class	Range
	Defines a range of integer numbers and accompanying operations. More...
class	UpdateGroupsCog
	Class for managing and computing centers of geometry of update groups. More...
class	VirtualSitesHandler
	Class that handles construction of vsites and spreading of vsite forces. More...
class	WholeMoleculeTransform
	This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules. More...
class	BinaryInformationSettings
	Settings for printBinaryInformation(). More...
class	LegacyMdrunOptions
	This class provides the same command-line option functionality to both CLI and API sessions. More...
class	MDModules
	Manages the collection of all modules used for mdrun. More...
class	MembedHolder
	Membed SimulatorBuilder parameter type. More...
struct	ReplicaExchangeParameters
	The parameters for the replica exchange algorithm. More...
class	Mdrunner
	Runner object for supporting setup and execution of mdrun. More...
class	MdrunnerBuilder
	Build a Mdrunner. More...
class	SimulationContext
	Simulation environment and configuration. More...
struct	SimulatorConfig
	Simulation configuation settings. More...
struct	SimulatorStateData
	Data for a specific simulation state. More...
class	SimulatorEnv
	Collection of environmental information for a simulation. More...
class	Profiling
	Collection of profiling information. More...
class	ConstraintsParam
	Collection of constraint parameters. More...
class	LegacyInput
	Collection of legacy input information. More...
class	InteractiveMD
	SimulatorBuilder parameter type for InteractiveMD. More...
class	IonSwapping
	Parameter type for IonSwapping SimulatorBuilder component. More...
class	TopologyData
	Collection of handles to topology information. More...
class	BoxDeformationHandle
	Handle to information about the box. More...
class	SimulatorBuilder
	Class preparing the creation of Simulator objects. More...
class	MDModulesNotifier
	Organizes notifications about an event of interest to modules. More...
struct	BuildMDModulesNotifier< CurrentCallParameter, CallParameter...>
	Template specialization to assemble MDModulesNotifier. More...
struct	MDModulesCheckpointReadingDataOnMain
	Provides the MDModules with the checkpointed data on the main rank. More...
struct	MDModulesCheckpointReadingBroadcast
	Provides the MDModules with the communication record to broadcast. More...
struct	MDModulesWriteCheckpointData
	Writing the MDModules data to a checkpoint file. More...
struct	MDModulesAtomsRedistributedSignal
	Notification that atoms may have been redistributed. More...
struct	MDModulesPairlistConstructedSignal
	Notification that the atom pair list has be (re)constructed. More...
struct	MDModulesEnergyOutputToDensityFittingRequestChecker
	Check if module outputs energy to a specific field. More...
struct	MDModulesEnergyOutputToQMMMRequestChecker
	Check if QMMM module outputs energy to a specific field. More...
struct	MDModulesEnergyOutputToNNPotRequestChecker
	Check if NNPot module outputs energy to a specific field. More...
struct	MDModulesDirectProvider
	Indicates whether an MD module is a direct (short-range coulomb interactions) provider. More...
class	EnergyCalculationFrequencyErrors
	Collect errors for the energy calculation frequency. More...
struct	SimulationTimeStep
	Provides the simulation time step in ps. More...
struct	CoordinatesAndBoxPreprocessed
	Provides coordinates and simulation box. More...
struct	MdRunInputFilename
	Mdrun input filename. More...
struct	EdrOutputFilename
	Energy trajectory output filename from Mdrun. More...
struct	QMInputFileName
	Notification for QM program input filename provided by user as command-line argument for grompp. More...
struct	PlumedInputFilename
	Notification for the optional plumed input filename provided by user as command-line argument for mdrun. More...
struct	EnsembleTemperature
	Provides the constant ensemble temperature. More...
struct	MdModulesCoulombTypeInfo
	Provides Coulomb interaction type info to MD modules. More...
struct	MDModulesNotifiers
	Group of notifers to organize that MDModules can receive callbacks they subscribe to. More...
class	PlainPairlistRanges
	Gathers pairlist range requests from different MDModules. More...
class	accessor_basic
	The most basic memory access model for mdspan. More...
class	extents
	Multidimensional extents with static and dynamic dimensions. More...
class	layout_right
	Right-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number. More...
class	basic_mdspan
	Multidimensional array indexing and memory access with flexible mapping and access model. More...
class	CheckpointData
	} More...
struct	IsSerializableEnum
	{ More...
class	ReadCheckpointDataHolder
	Holder for read checkpoint data. More...
class	WriteCheckpointDataHolder
	Holder for write checkpoint data. More...
class	ForceBuffersView
	A view of the force buffer. More...
class	ForceBuffers
	Object that holds the force buffers. More...
class	ForceWithShiftForces
	Container for force and virial for algorithms that compute shift forces for virial calculation. More...
class	ForceWithVirial
	Container for force and virial for algorithms that provide their own virial tensor contribution. More...
class	ForceOutputs
	Force and virial output buffers for use in force computation. More...
class	ForceProviderInput
	Helper struct that bundles data for passing it over to the force providers. More...
class	ForceProviderOutput
	Helper struct bundling the output data of a force provider. More...
class	IForceProvider
	Interface for a component that provides forces during MD. More...
class	ForceProviders
	Evaluates forces from a collection of gmx::IForceProvider. More...
class	IMDModule
	Extension module for GROMACS simulations. More...
class	IMDOutputProvider
	Interface for handling additional output files during a simulation. More...
class	IMdpOptionProvider
	Interface for handling mdp/tpr input to a mdrun module. More...
struct	MtsLevel
	Setting for a single level for multiple time step integration. More...
struct	GromppMtsOpts
	Struct for passing the MTS mdp options to setupMtsLevels() More...
class	ObservablesReducerBuilder
	Builder for ObservablesReducer. More...
class	ObservablesReducer
	Manage reduction of observables for registered subscribers. More...
class	StepWorkload
	Describes work done on this domain by the current rank that may change per-step. More...
class	DomainLifetimeWorkload
	Describes work done on this domain on every step of its lifetime, but which might change after the next domain partitioning. More...
class	SimulationWorkload
	Manage what computation is required during the simulation. More...
class	ModularSimulator
	The modular simulator. More...
class	ElementNotFoundError
	Exception class signalling that a requested element was not found. More...
class	MissingElementConnectionError
	Exception class signalling that elements were not connected properly. More...
class	SimulationAlgorithmSetupError
	Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way. More...
class	CheckpointError
	Exception class signalling an error in reading or writing modular checkpoints. More...
class	EnergyAccumulator
	Base energy accumulator class, only specializations are used. More...
class	AtomPairlist
	A plain atom pair list, used only for perturbed non-bonded interactions. More...
struct	BenchmarkSystem
	Description of the system used for benchmarking. More...
struct	EnergyFunctionProperties
	Set of boolean constants mimicking preprocessor macros. More...
struct	GridDimensions
	The physical dimensions of a grid. More...
struct	PlainPairlist
	A plain pairlist that can contain both normal and excluded pairs. More...
struct	nonbonded_verlet_t
	Top-level non-bonded data structure for the Verlet-type cut-off scheme. More...
struct	FusedXToXqGridParams
	Per-grid parameters passed to the fused X-to-Xq kernel. More...
struct	FusedXToXqLaunchParams
	All parameters needed to launch the fused X-to-Xq kernel, computed once at pair-list setup and stored per interaction locality in NbnxmGpu. More...
struct	gmx_cache_protect_t
	Cache-line protection buffer. More...
struct	nbnxm_cj_t
	This is the actual cluster-pair list j-entry. More...
class	JClusterList
	Simple j-cluster list. More...
struct	nbnxm_sci_t
	Grouped pair-list i-unit. More...
struct	nbnxm_im_ei_t
	Interaction data for a j-group for one warp. More...
struct	nbnxm_cj_packed_t
	Packed j-cluster list element. More...
class	PackedJClusterList
	Packed j-cluster list. More...
struct	nbnxm_excl_t
	Struct for storing the atom-pair interaction bits for a cluster pair in a GPU pairlist. More...
struct	NbnxmPairlistCpu
	Cluster pairlist type for use on CPUs. More...
class	PairlistSets
	Contains sets of pairlists. More...
struct	NbnxmPairlistCpuWork
	Working data for the actual i-supercell during pair search. More...
class	nbnxm_cycle_t
	Local cycle count struct for profiling. More...
struct	PairsearchWork
	Thread-local work struct, contains working data for Grid. More...
class	PairSearch
	Main pair-search struct, contains the grid(s), not the pair-list(s) More...
class	CoulombCalculator
	Base Coulomb calculator class, only specializations are used. More...
class	CoulombCalculator< KernelCoulombType::RF >
	Specialized calculator for RF. More...
class	CoulombCalculator< KernelCoulombType::EwaldAnalytical >
	Specialized calculator for Ewald using an analytic approximation. More...
class	CoulombCalculator< KernelCoulombType::EwaldTabulated >
	Specialized calculator for Ewald using tabulated functions. More...
class	DiagonalMasker
	Base Coulomb calculator class, only specializations are used. More...
class	DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize >
	Specialized masker for JSizeEqualsISize. More...
class	DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize >
	Specialized masker for JSizeIsDoubleISize. More...
class	DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize >
	Specialized masker for JSizeIsHalfISize. More...
class	EnergyAccumulator< useEnergyGroups, false >
	Specialized energy accumulator class for no energy calculation. More...
class	EnergyAccumulator< false, true >
	Specialized energy accumulator class for energy accumulation without energy groups. More...
class	EnergyAccumulator< true, true >
	Specialized energy accumulator class for energy accumulation with energy groups. More...
class	EnergyGroupsPerCluster
	Holds energy group indices for use in EnergyAccumulator<true, true> More...
class	LennardJonesCalculator
	Base LJ calculator class, only specializations are used. More...
class	LennardJonesCalculator< false, InteractionModifiers::PotShift >
	Specialized calculator for LJ with potential shift and no energy calculation. More...
class	LennardJonesCalculator< true, InteractionModifiers::PotShift >
	Specialized calculator for LJ with potential shift and energy calculation. More...
class	LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch >
	Specialized calculator for LJ with force switch. More...
class	LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch >
	Specialized calculator for LJ with potential switch. More...
class	NbnxmKernel
	Class name for NBNXM kernel. More...
class	TextTableFormatter
	Formats rows of a table for text output. More...
class	HelpManager
	Helper for providing interactive online help. More...
class	AbstractSimpleHelpTopic
	Abstract base class for help topics that have simple text and no subtopics. More...
class	AbstractCompositeHelpTopic
	Abstract base class for help topics that have simple text and subtopics. More...
class	SimpleHelpTopic
	Template for simple implementation of AbstractSimpleHelpTopic. More...
class	CompositeHelpTopic
	Template for simple implementation of AbstractCompositeHelpTopic. More...
class	HelpLinks
	Hyperlink data for writing out help. More...
class	HelpWriterContext
	Context information for writing out help. More...
class	IHelpTopic
	Provides a single online help topic. More...
class	AbstractOptionStorage
	Abstract base class for converting, validating, and storing option values. More...
class	AbstractOptionSection
	Base class for specifying option section properties. More...
class	AbstractOptionSectionHandle
	Base class for handles to option sections. More...
class	OptionsBehaviorCollection
	Container for IOptionsBehavior objects. More...
class	OptionManagerContainer
	Container to keep managers added with Options::addManager() and pass them to options. More...
class	OptionsAssigner
	Decorator class for assigning values to Options. More...
class	OptionSection
	Declares a simple option section. More...
class	OptionSectionHandle
	Allows adding options to an OptionSection. More...
class	OptionStorageTemplate
	Templated base class for constructing option value storage classes. More...
class	OptionStorageTemplateSimple
	Simplified option storage template for options that have one-to-one value conversion. More...
class	OptionsVisitor
	Pure interface for visiting options in a Options object. More...
class	OptionsTypeVisitor
	Abstract base class for visiting options of a particular type. More...
class	OptionsIterator
	Decorator class for visiting options in a Options object. More...
class	OptionsModifyingVisitor
	Pure interface for visiting options in a Options object, allowing modifications. More...
class	OptionsModifyingTypeVisitor
	Abstract base class for visiting options of a particular type, allowing modifications. More...
class	OptionsModifyingIterator
	Decorator class for visiting options in a Options object, allowing changes. More...
class	RepeatingOptionSectionHandle
	Allows adding options to an RepeatingOptionSection. More...
class	RepeatingOptionSection
	Declares an option section that creates a structure for each instance. More...
class	OptionValueConverterSimple
	Helper for converting from Any to a given type. More...
class	PullCoordExpressionParser
	Class with a mathematical expression and parser. More...
class	ExponentialDistribution
	Exponential distribution. More...
class	GammaDistribution
	Gamma distribution. More...
class	NormalDistribution
	Normal distribution. More...
class	TabulatedNormalDistribution
	Tabulated normal random distribution. More...
class	UniformIntDistribution
	Uniform integer distribution. More...
class	UniformRealDistribution
	Uniform real distribution. More...
class	RestraintManager
	Manage the Restraint potentials available for Molecular Dynamics. More...
class	RestraintMDModule
	MDModule wrapper for Restraint implementations. More...
class	Site
	Abstraction for a restraint interaction site. More...
class	SelectionFileOption
	Specifies a special option that provides selections from a file. More...
class	SelectionFileOptionInfo
	Wrapper class for accessing and modifying selection file option information. More...
class	ISerializer
	Interface for types that convert standard data types into a form suitable for storage or transfer. More...
class	Simd4Double
	SIMD4 double type. More...
class	Simd4DBool
	SIMD4 variable type to use for logical comparisons on doubles. More...
class	Simd4Float
	SIMD4 float type. More...
class	Simd4FBool
	SIMD4 variable type to use for logical comparisons on floats. More...
class	SimdDouble
	Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1. More...
class	SimdDInt32
	Integer SIMD variable type to use for conversions to/from double. More...
class	SimdDBool
	Boolean type for double SIMD data. More...
class	SimdDIBool
	Boolean type for integer datatypes corresponding to double SIMD. More...
class	SimdFloat
	Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1. More...
class	SimdFInt32
	Integer SIMD variable type to use for conversions to/from float. More...
class	SimdFBool
	Boolean type for float SIMD data. More...
class	SimdFIBool
	Boolean type for integer datatypes corresponding to float SIMD. More...
struct	SimdFloatTag
	Tag type to select to load SimdFloat with simdLoad(U) More...
struct	SimdDoubleTag
	Tag type to select to load SimdDouble with simdLoad(U) More...
struct	SimdFInt32Tag
	Tag type to select to load SimdFInt32 with simdLoad(U) More...
struct	SimdDInt32Tag
	Tag type to select to load SimdDInt32 with simdLoad(U) More...
struct	AlignedArray< float, N >
	Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual). More...
struct	AlignedArray< double, N >
	Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual). More...
class	SimdSetZeroProxy
	Proxy object to enable setZero() for SIMD and real types. More...
class	CubicSplineTable
	Cubic spline interpolation table. More...
class	QuadraticSplineTable
	Quadratic spline interpolation table. More...
struct	AnalyticalSplineTableInput
	Specification for analytical table function (name, function, derivative) More...
struct	NumericalSplineTableInput
	Specification for vector table function (name, function, derivative, spacing) More...
struct	DevelopmentFeatureFlags
	Structure that holds boolean flags corresponding to the development features present enabled through environment variables. More...
struct	GpuTaskMapping
	Specifies the GPU deviceID_ available for task_ to use. More...
class	GpuTaskAssignmentsBuilder
	Builder for the GpuTaskAssignments for all ranks on this node. More...
class	GpuTaskAssignments
	Contains the GPU task assignment for all ranks on this physical node. More...
class	ConvertTprInfo
	Declares gmx convert-tpr. More...
struct	ExclusionBlock
	Describes exclusions for a single atom. More...
class	UnionFinder
	Union-find data structure for keeping track of disjoint sets. More...
class	MappedUnionFinder
	Extension of UnionFind that supports non-consecutive integer indices as items. More...
class	AlignedAllocationPolicy
	Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code. More...
class	PageAlignedAllocationPolicy
	Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices. More...
class	Allocator
	Policy-based memory allocator. More...
class	Any
	Represents a dynamically typed value of an arbitrary type - deprecated. More...
struct	BoolType
	A clone of a bool as a workaround on the template specialization of std::vector<bool> that is incompatible with ArrayRef. More...
class	DataFileOptions
	Search parameters for DataFileFinder. More...
struct	DataFileInfo
	Information about a data file found by DataFileFinder::enumerateFiles(). More...
class	DataFileFinder
	Searches data files from a set of paths. More...
class	DefaultInitializationAllocator
	Allocator adaptor that interposes construct() calls to convert value initialization into default initialization. More...
class	DirectoryEnumerator
	Lists files in a directory. More...
class	IFileInputRedirector
	Allows overriding file existence checks from code that supports it. More...
class	IFileOutputRedirector
	Allows capturing stdout and file output from code that supports it. More...
class	StandardInputStream
	Text input stream implementation for reading from stdin. More...
class	TextInputFile
	Text input stream implementation for reading from a file. More...
class	TextOutputFile
	Text output stream implementation for writing to a file. More...
class	KeyValueTreePath
	Identifies an entry in a key-value tree. More...
class	KeyValueTreeBuilder
	Root builder for creating trees that have an object at the root. More...
class	KeyValueTreeValueBuilder
	Builder for KeyValueTreeValue objects. More...
class	KeyValueTreeUniformArrayBuilder
	Builder for KeyValueTreeArray objects where all elements are of type T. More...
class	KeyValueTreeObjectArrayBuilder
	Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects. More...
class	KeyValueTreeObjectBuilder
	Builder for KeyValueTreeObject objects. More...
class	IKeyValueTreeTransformRules
	Interface to declare rules for transforming key-value trees. More...
class	KeyValueTreeTransformRulesScoped
	Helper object returned from IKeyValueTreeTransformRules::scopedTransform(). More...
class	KeyValueTreeTransformRuleBuilder
	Provides methods to specify one transformation rule. More...
class	ILogTarget
	Target where log output can be written. More...
class	LogEntryWriter
	Helper class for creating log entries with GMX_LOG. More...
class	LogLevelHelper
	Represents a single logging level. More...
class	MDLogger
	Declares a logging interface. More...
class	LoggerBuilder
	Initializes loggers. More...
class	LoggerOwner
	Manages memory for a logger built with LoggerBuilder. More...
class	MessageStringCollector
	Helper class for collecting message strings, optionally with context. More...
class	MessageStringContext
	Convenience class for creating a message context. More...
class	PhysicalNodeCommunicator
	Holds a communicator for the physical node of this rank. More...
class	StringCompare
	Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare. More...
class	StringOutputStream
	Text output stream implementation for writing to an in-memory string. More...
class	StringInputStream
	Helper class to convert static string data to a stream. More...
class	StringToEnumValueConverter
	A class to convert a string to an enum value of type EnumType. More...
class	TextReader
	Reads text from a TextInputStream. More...
class	TextInputStream
	Interface for reading text. More...
class	TextOutputStream
	Interface for writing text. More...
class	ScopedIndenter
	Helper class to increase the indentation of a TextWriter for the lifetime of this object. More...
class	TextWriter
	Writes text into a TextOutputStream. More...
struct	isIntegralConstant
	Is true if type is a std::integral_constant. More...
class	MpiComm
	MPI communicator with optimized reduction functionality. More...
struct	no_delete
	Deleter for std::shared_ptr that does nothing. More...
class	NonbondedBenchmarkInfo
	Declares gmx nonbonded-bench. More...
class	BasicMatrix3x3
	Three-by-three matrix of ElementType. More...
class	AbstractAnalysisData
	Abstract base class for all objects that provide data. More...
class	AnalysisData
	Parallelizable data container for raw data. More...
class	AnalysisDataHandle
	Handle for inserting data into AnalysisData. More...
class	AbstractAnalysisArrayData
	Abstract base class for data objects that present in-memory data. More...
class	AnalysisArrayData
	Simple in-memory data array. More...
class	AnalysisDataValue
	Value type for representing a single value in analysis data objects. More...
class	AnalysisDataFrameHeader
	Value type for storing frame-level information for analysis data. More...
class	AnalysisDataPointSetRef
	Value type wrapper for non-mutable access to a set of data column values. More...
class	AnalysisDataFrameRef
	Value type wrapper for non-mutable access to a data frame. More...
class	IAnalysisDataModule
	Interface for a module that gets notified whenever data is added. More...
class	AnalysisDataModuleSerial
	Convenience base class for serial analysis data modules. More...
class	AnalysisDataModuleParallel
	Convenience base class for parallel analysis data modules. More...
class	AnalysisDataAverageModule
	Data module for independently averaging each column in input data. More...
class	AnalysisDataFrameAverageModule
	Data module for averaging of columns for each frame. More...
class	AnalysisDataDisplacementModule
	Data module for calculating displacements. More...
class	AnalysisHistogramSettingsInitializer
	Provides "named parameter" idiom for constructing histograms. More...
class	AnalysisHistogramSettings
	Contains parameters that specify histogram bin locations. More...
class	AbstractAverageHistogram
	Base class for representing histograms averaged over frames. More...
class	AnalysisDataSimpleHistogramModule
	Data module for per-frame histograms. More...
class	AnalysisDataWeightedHistogramModule
	Data module for per-frame weighted histograms. More...
class	AnalysisDataBinAverageModule
	Data module for bin averages. More...
class	AnalysisDataLifetimeModule
	Data module for computing lifetime histograms for columns in input data. More...
class	AnalysisDataPlotSettings
	Common settings for data plots. More...
class	AbstractPlotModule
	Abstract data module for writing data into a file. More...
class	AnalysisDataPlotModule
	Plotting module for straightforward plotting of data. More...
class	AnalysisDataVectorPlotModule
	Plotting module specifically for data consisting of vectors. More...
struct	StaticLog2
	Evaluate log2(n) for integer n statically at compile time. More...
struct	StaticLog2< 1 >
	Specialization of StaticLog2<n> for n==1. More...
struct	StaticLog2< 0 >
	Specialization of StaticLog2<n> for n==0. More...
struct	OutputControl
	Output control parameters. More...
class	AbstractOption
	Abstract base class for specifying option properties. More...
class	OptionTemplate
	Templated base class for constructing concrete option settings classes. More...
class	OptionInfo
	Gives information and allows modifications to an option after creation. More...
class	BooleanOption
	Specifies an option that provides boolean values. More...
class	IntegerOption
	Specifies an option that provides 32-bit integer values. More...
class	UnsignedIntegerOption
	Specifies an option that provides unsigned 32-bit integer values. More...
class	Int64Option
	Specifies an option that provides 64-bit integer values. More...
class	UnsignedInt64Option
	Specifies an option that provides 64-bit unsigned integer values. More...
class	DoubleOption
	Specifies an option that provides floating-point (double) values. More...
class	FloatOption
	Specifies an option that provides floating-point (float) values. More...
class	StringOption
	Specifies an option that provides string values. More...
class	EnumOption
	Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an enum variable. More...
class	LegacyEnumOption
	Specifies an option that accepts enumerated string values and writes the selected index into an enum variable. More...
class	BooleanOptionInfo
	Wrapper class for accessing boolean option information. More...
class	IntegerOptionInfo
	Wrapper class for accessing 32-bit integer option information. More...
class	UnsignedIntegerOptionInfo
	Wrapper class for accessing unsigned 32-bit integer option information. More...
class	Int64OptionInfo
	Wrapper class for accessing 64-bit integer option information. More...
class	UnsignedInt64OptionInfo
	Wrapper class for accessing 64-bit unsigned integer option information. More...
class	DoubleOptionInfo
	Wrapper class for accessing floating-point option information. More...
class	FloatOptionInfo
	Wrapper class for accessing floating-point option information. More...
class	StringOptionInfo
	Wrapper class for accessing string option information. More...
class	EnumOptionInfo
	Wrapper class for accessing enum option information. More...
class	FileNameOption
	Specifies an option that provides file names. More...
class	FileNameOptionInfo
	Wrapper class for accessing file name option information. More...
class	FileNameOptionManager
	Handles interaction of file name options with global options. More...
class	IOptionsBehavior
	Interface to provide extension points for options parsing. More...
class	IOptionsContainer
	Interface for adding input options. More...
class	IOptionsContainerWithSections
	Interface for adding input options with sections. More...
class	IOptionManager
	Base class for option managers. More...
class	Options
	Collection of options. More...
class	TimeUnitManager
	Provides common functionality for time unit conversions. More...
class	TimeUnitBehavior
	Options behavior to add a time unit option. More...
class	PotentialPointData
	Structure to hold the results of IRestraintPotential::evaluate(). More...
class	IRestraintPotential
	Interface for Restraint potentials. More...
class	AnalysisNeighborhoodPositions
	Input positions for neighborhood searching. More...
class	AnalysisNeighborhood
	Neighborhood searching for analysis tools. More...
class	AnalysisNeighborhoodPair
	Value type to represent a pair of positions found in neighborhood searching. More...
class	AnalysisNeighborhoodSearch
	Initialized neighborhood search with a fixed set of reference positions. More...
class	AnalysisNeighborhoodPairSearch
	Initialized neighborhood pair search with a fixed set of positions. More...
class	Selection
	Provides access to a single selection. More...
class	SelectionPosition
	Provides access to information about a single selected position. More...
class	SelectionCollection
	Collection of selections. More...
struct	SelectionTopologyProperties
	Describes topology properties required for selection evaluation. More...
class	SelectionOption
	Specifies an option that provides selection(s). More...
class	SelectionOptionInfo
	Wrapper class for accessing and modifying selection option information. More...
class	ITopologyProvider
	Provides topology information to SelectionOptionBehavior. More...
class	SelectionOptionBehavior
	Options behavior to allow using SelectionOptions. More...
class	SelectionOptionManager
	Handles interaction of selection options with other options and user input. More...
class	RangePartitioning
	Division of a range of indices into consecutive blocks. More...
class	TrajectoryAnalysisModuleData
	Base class for thread-local data storage during trajectory analysis. More...
class	TrajectoryAnalysisModule
	Base class for trajectory analysis modules. More...
class	TrajectoryAnalysisSettings
	Trajectory analysis module configuration object. More...
class	TrajectoryAnalysisCommandLineRunner
	Runner for command-line trajectory analysis tools. More...
class	TopologyInformation
	Topology information available to a trajectory analysis module. More...
class	EnumerationIterator
	Allows iterating sequential enumerators. More...
class	EnumerationWrapper
	Allows constructing iterators for looping over sequential enumerators. More...
class	EnumClassSuitsEnumerationArray
	Helper class to determine whether a template type that is an enum class has a Count field. More...
class	ExceptionInfo
	Stores additional context information for exceptions. More...
class	ExceptionInitializer
	Provides information for Gromacs exception constructors. More...
class	GromacsException
	Base class for all exception objects in Gromacs. More...
class	FileIOError
	Exception class for file I/O errors. More...
class	UserInputError
	Exception class for user input errors. More...
class	InvalidInputError
	Exception class for situations where user input cannot be parsed/understood. More...
class	InconsistentInputError
	Exception class for situations where user input is inconsistent. More...
class	ToleranceError
	Exception class when a specified tolerance cannot be achieved. More...
class	SimulationInstabilityError
	Exception class for simulation instabilities. More...
class	InternalError
	Exception class for internal errors. More...
class	APIError
	Exception class for incorrect use of an API. More...
class	RangeError
	Exception class for out-of-range values or indices. More...
class	NotImplementedError
	Exception class for use of an unimplemented feature. More...
class	ParallelConsistencyError
	Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion. More...
class	ModularSimulatorError
	Exception class for modular simulator. More...
class	MDModuleSetupError
	Exception class for MD module setup/initialization failures. More...
class	FlagsTemplate
	Template class for typesafe handling of combination of flags. More...
struct	InstallationPrefixInfo
	Provides information about installation prefix (see IProgramContext::installationPrefix()). More...
class	IProgramContext
	Provides context information about the program that is calling the library. More...
class	StringFormatter
	Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms. More...
class	IdentityFormatter
	Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further. More...
class	EqualCaseInsensitive
	Function object for comparisons with equalCaseInsensitive. More...
class	TextLineWrapperSettings
	Stores settings for line wrapping. More...
class	TextLineWrapper
	Wraps lines to a predefined length. More...
struct	CompileTimeStringJoin
	Combines string literals at compile time to final string. More...

Typedefs
typedef double	awh_dvec [c_biasMaxNumDim]
	A real vector in AWH coordinate space.
typedef int	awh_ivec [c_biasMaxNumDim]
	An integer vector in AWH coordinate space.
using	PairlistEntry = std::pair< std::pair< int, int >, int >
typedef int	force_env_t
	Type for CP2K force environment handle.
typedef std::unique_ptr < ICommandLineModule >	CommandLineModulePointer
	Smart pointer type for managing a ICommandLineModule.
typedef std::map< std::string, CommandLineModulePointer >	CommandLineModuleMap
	Container type for mapping module names to module objects.
typedef std::unique_ptr < CommandLineModuleGroupData >	CommandLineModuleGroupDataPointer
	Smart pointer type for managing a CommandLineModuleGroup.
typedef std::vector < CommandLineModuleGroupDataPointer >	CommandLineModuleGroupList
	Container type for keeping a list of module groups.
typedef std::unique_ptr < ICommandLineOptionsModule >	ICommandLineOptionsModulePointer
	Smart pointer to manage an ICommandLineOptionsModule.
typedef std::unique_ptr < IExecutableEnvironment >	ExecutableEnvironmentPointer
	Shorthand for a smart pointer to IExecutableEnvironment.
using	TrajectoryFrameWriterPointer = std::unique_ptr< TrajectoryFrameWriter >
	Smart pointer to manage the TrajectoryFrameWriter object.
using	ProcessFrameConversionPointer = std::unique_ptr< ProcessFrameConversion >
	Smart pointer to manage the analyse object.
using	FrameConverterPointer = std::unique_ptr< IFrameConverter >
	Typedef to have direct access to the individual FrameConverter modules.
using	OutputAdapterPointer = std::unique_ptr< IOutputAdapter >
	Smart pointer to manage the frame adapter object.
using	OutputSelectorPointer = std::unique_ptr< OutputSelector >
	Smart pointer to manage the object.
using	SetAtomsPointer = std::unique_ptr< SetAtoms >
	Smart pointer to manage the object.
using	SetBoxPointer = std::unique_ptr< SetBox >
	Smart pointer to manage the object.
using	SetForcesPointer = std::unique_ptr< SetForces >
	Smart pointer to manage the object.
using	SetPrecisionPointer = std::unique_ptr< SetPrecision >
	Smart pointer to manage the outputselector object.
using	SetStartTimePointer = std::unique_ptr< SetStartTime >
	Smart pointer to manage the object.
using	SetTimeStepPointer = std::unique_ptr< SetTimeStep >
	Smart pointer to manage the object.
using	SetVelocitiesPointer = std::unique_ptr< SetVelocities >
	Smart pointer to manage the object.
using	EnergyAnalysisFrameIterator = std::vector< EnergyAnalysisFrame >::const_iterator
	Typedef for looping over EnergyFrame.
using	IEnergyAnalysisPointer = std::unique_ptr< IEnergyAnalysis >
	Pointer to the EnergyAnalysisModule classes.
typedef struct gmx::edpar	t_edpar
using	hid_t = int64_t
using	DataSetDims = std::vector< hsize_t >
	Dimensions of a HDF5 data set. More...
using	H5mdCloseType = herr_t(*)(hid_t)
	Function signature for HDF5 closing functions (H5Gclose, etc.)
using	H5mdGuard = sg::detail::scope_guard< H5mdCloser >
	Alias for scope guards used in the H5md module.
using	IndexMap = std::unordered_map< int32_t, int32_t >
	Map the global indices of the selection to the local indices within the selection.
using	BondPairs = std::vector< std::pair< int64_t, int64_t >>
	List of bond representations as pairs of atom indices.
typedef bool(*	peq )(const InteractionOfType &p1, const InteractionOfType &p2)
typedef char	t_dirname [STRLEN]
typedef struct CPreProcessor *	CPreProcessor_t
using	Atom2VsiteConnection = std::vector< int >
	Convenience type def for virtual site connections.
using	CommandGroupHandler = sycl::handler &
template<class T >
using	HostAllocator = Allocator< T, HostAllocationPolicy >
	Memory allocator that uses HostAllocationPolicy. More...
template<class T >
using	HostVector = std::vector< T, HostAllocator< T >>
	Convenience alias for std::vector that uses HostAllocator.
template<class T >
using	PaddedHostVector = PaddedVector< T, HostAllocator< T >>
	Convenience alias for PaddedVector that uses HostAllocator.
template<typename T >
using	AlignedVector = std::vector< T, AlignedAllocator< T >>
	Convenience type for vector with aligned memory.
using	mode = sycl::access_mode
typedef std::array < SimulationSignal, eglsNR >	SimulationSignals
	Convenience typedef for the group of signals used.
using	UpdateSimdReal = real
using	VirialHandling = VirtualSitesHandler::VirialHandling
	VirialHandling is often used outside VirtualSitesHandler class members.
typedef std::array < std::vector< int > , numFtypes >	VsitePbc
	Type for storing PBC atom information for all vsite types in the system.
using	SimulatorFunctionType ) = void(
	Function type for simulator code.
typedef struct gmx_repl_ex *	gmx_repl_ex_t
	Abstract type for replica exchange.
using	LogFilePtr = std::unique_ptr< t_fileio, functor_wrapper< t_fileio, closeLogFile >>
	Simple guard pointer See unique_cptr for details.
using	dynamicExtents2D = extents< dynamic_extent, dynamic_extent >
	Convenience type for often-used two dimensional extents.
using	dynamicExtents3D = extents< dynamic_extent, dynamic_extent, dynamic_extent >
	Convenience type for often-used three dimensional extents.
template<class T , ptrdiff_t... Indices>
using	mdspan = basic_mdspan< T, extents< Indices...>, layout_right, accessor_basic< T >>
	basic_mdspan with wrapped indices, basic_accessor policiy and right-aligned memory layout.
using	ReadCheckpointData = CheckpointData< CheckpointDataOperation::Read >
	Convenience shortcut for reading checkpoint data.
using	WriteCheckpointData = CheckpointData< CheckpointDataOperation::Write >
	Convenience shortcut for writing checkpoint data.
using	Step = int64_t
	Step number.
typedef std::function< void()>	CheckBondedInteractionsCallback
	The function type allowing to request a check of the number of bonded interactions.
using	EnergyContribution = std::function< real(Step, Time)>
	Function type for elements contributing energy.
using	Time = double
	Simulation time.
typedef std::function< void()>	SimulatorRunFunction
	The function type that can be scheduled to be run during the simulator run.
typedef std::function< void(SimulatorRunFunction)>	RegisterRunFunction
	The function type that allows to register run functions.
typedef std::function< void(Step, Time, const RegisterRunFunction &)>	SchedulingFunction
	The function type scheduling run functions for a step / time using a RegisterRunFunction reference.
typedef std::function< void(Step, Time)>	SignallerCallback
	The function type that can be registered to signallers for callback.
typedef std::function< void(gmx_mdoutf *, Step, Time, bool, bool)>	ITrajectoryWriterCallback
	Function type for trajectory writing clients.
typedef std::function< void(Step)>	PropagatorCallback
	Generic callback to the propagator.
typedef std::function< void()>	DomDecCallback
	Callback used by the DomDecHelper object to inform clients about system re-partitioning.
using	ReferenceTemperatureCallback = std::function< void(ArrayRef< const real >, ReferenceTemperatureChangeAlgorithm algorithm)>
	Callback updating the reference temperature.
typedef void(*	KernelFunction )(const AtomPairlist &nlist, const ArrayRefWithPadding< const RVec > &coords, const int ntype, const interaction_const_t &interactionParameters, ArrayRef< const RVec > shiftvec, ArrayRef< const real > nbfp, ArrayRef< const real > nbfp_grid, ArrayRef< const real > chargeA, ArrayRef< const real > chargeB, ArrayRef< const int > typeA, ArrayRef< const int > typeB, const bool computeForeignLambda, const StepWorkload *stepWork, ArrayRef< const real > lambda, t_nrnb *gmx_restrict nrnb, ArrayRefWithPadding< RVec > threadForceBuffer, rvec *threadForceShiftBuffer, ArrayRef< real > threadVCoul, ArrayRef< real > threadVVdw, ArrayRef< real > threadDvdl)
using	GpuPairlistByLocality = EnumerationArray< InteractionLocality, std::unique_ptr< GpuPairlist >>
using	GpuFeplistByLocality = EnumerationArray< InteractionLocality, std::unique_ptr< GpuFeplist >>
typedef struct gmx::cl_nbparam_params	cl_nbparam_params_t
typedef SimdReal	SimdBitMask
	Define SimdBitMask as a real SIMD register.
using	FCiFloat3 = Float3
typedef std::unique_ptr < AbstractCompositeHelpTopic >	CompositeHelpTopicPointer
	Smart pointer type to manage a AbstractCompositeHelpTopic object.
typedef std::unique_ptr < IHelpTopic >	HelpTopicPointer
	Smart pointer type to manage a IHelpTopic object.
typedef std::shared_ptr < IOptionsBehavior >	OptionsBehaviorPointer
	Smart pointer for behaviors stored in OptionsBehaviorCollection.
typedef std::random_device	RandomDevice
	Random device. More...
typedef std::list < SelectionParserValue >	SelectionParserValueList
	Container for a list of SelectionParserValue objects.
typedef std::unique_ptr < SelectionParserValueList >	SelectionParserValueListPointer
	Smart pointer type for managing a SelectionParserValueList.
typedef std::list < SelectionParserParameter >	SelectionParserParameterList
	Container for a list of SelectionParserParameter objects.
typedef std::unique_ptr < SelectionParserParameterList >	SelectionParserParameterListPointer
	Smart pointer type for managing a SelectionParserParameterList.
typedef std::unique_ptr < internal::SelectionData >	SelectionDataPointer
	Smart pointer for managing an internal selection data object.
typedef std::vector < SelectionDataPointer >	SelectionDataList
	Container for storing a list of selections internally.
typedef std::shared_ptr < SelectionTreeElement >	SelectionTreeElementPointer
	Smart pointer type for selection tree element pointers.
typedef struct stats *	stats_t
	Abstract container type.
typedef struct gmx::swap_compartment	t_compartment
typedef double(*	real_space_grid_contribution_computer )(double, double)
	Function pointer to calculate the grid contribution for coulomb/LJ. More...
using	GpuTasksOnRanks = std::vector< std::vector< GpuTask >>
	Container of compute tasks suitable to run on a GPU e.g. on each rank of a node.
using	GpuTaskAssignment = std::vector< GpuTaskMapping >
	Container of GPU tasks on a rank, specifying the task type and GPU device ID, e.g. potentially ready for consumption by the modules on that rank.
template<class T >
using	AlignedAllocator = Allocator< T, AlignedAllocationPolicy >
	Aligned memory allocator. More...
template<class T >
using	PageAlignedAllocator = Allocator< T, PageAlignedAllocationPolicy >
	PageAligned memory allocator. More...
template<typename T >
using	FastVector = std::vector< T, DefaultInitializationAllocator< T >>
	Convenience type for vector that avoids initialization at resize()
using	MPI_Comm_ptr = gmx::unique_cptr< MPI_Comm, MPI_Comm_free_wrapper >
	Make a smart pointer for MPI communicators.
typedef std::shared_ptr < TextInputStream >	TextInputStreamPointer
	Shorthand for a smart pointer to a TextInputStream.
typedef std::shared_ptr < TextOutputStream >	TextOutputStreamPointer
	Shorthand for a smart pointer to a TextOutputStream.
typedef std::shared_ptr < IAnalysisDataModule >	AnalysisDataModulePointer
	Smart pointer for managing a generic analysis data module.
typedef ArrayRef< const AnalysisDataValue >	AnalysisDataValuesRef
	Shorthand for reference to an array of data values.
typedef std::shared_ptr < AnalysisDataAverageModule >	AnalysisDataAverageModulePointer
	Smart pointer to manage an AnalysisDataAverageModule object.
typedef std::shared_ptr < AnalysisDataFrameAverageModule >	AnalysisDataFrameAverageModulePointer
	Smart pointer to manage an AnalysisDataFrameAverageModule object.
typedef std::shared_ptr < AnalysisDataDisplacementModule >	AnalysisDataDisplacementModulePointer
	Smart pointer to manage an AnalysisDataDisplacementModule object.
typedef std::unique_ptr < AbstractAverageHistogram >	AverageHistogramPointer
	Smart pointer to manage an AbstractAverageHistogram object.
typedef std::shared_ptr < AnalysisDataSimpleHistogramModule >	AnalysisDataSimpleHistogramModulePointer
	Smart pointer to manage an AnalysisDataSimpleHistogramModule object.
typedef std::shared_ptr < AnalysisDataWeightedHistogramModule >	AnalysisDataWeightedHistogramModulePointer
	Smart pointer to manage an AnalysisDataWeightedHistogramModule object.
typedef std::shared_ptr < AnalysisDataBinAverageModule >	AnalysisDataBinAverageModulePointer
	Smart pointer to manage an AnalysisDataBinAverageModule object.
typedef std::shared_ptr < AnalysisDataLifetimeModule >	AnalysisDataLifetimeModulePointer
	Smart pointer to manage an AnalysisDataLifetimeModule object.
typedef std::shared_ptr < AnalysisDataPlotModule >	AnalysisDataPlotModulePointer
	Smart pointer to manage an AnalysisDataPlotModule object.
typedef std::shared_ptr < AnalysisDataVectorPlotModule >	AnalysisDataVectorPlotModulePointer
	Smart pointer to manage an AnalysisDataVectorPlotModule object.
typedef FloatOption	RealOption
	Typedef for either DoubleOption or FloatOption, depending on precision. More...
typedef FloatOptionInfo	RealOptionInfo
	Typedef for either DoubleOptionInfo or FloatOptionInfo, depending on precision. More...
typedef FlagsTemplate< OptionFlag >	OptionFlags
	Holds a combination of OptionFlag values.
using	Vector = ::gmx::RVec
	Provide a vector type name with a more stable interface than RVec and a more stable implementation than vec3<>. More...
typedef std::vector< Selection >	SelectionList
	Container of selections used in public selection interfaces.
typedef std::unique_ptr < TrajectoryAnalysisModuleData >	TrajectoryAnalysisModuleDataPointer
	Smart pointer to manage a TrajectoryAnalysisModuleData object.
typedef std::unique_ptr < TrajectoryAnalysisModule >	TrajectoryAnalysisModulePointer
	Smart pointer to manage a TrajectoryAnalysisModule.
using	Index = std::ptrdiff_t
	Integer type for indexing into arrays or vectors. More...
typedef ExceptionInfo< struct ExceptionInfoErrno_, int >	ExceptionInfoErrno
	Stores errno value that triggered the exception.
typedef ExceptionInfo< struct ExceptionInfoApiFunc_, const char * >	ExceptionInfoApiFunction
	Stores the function name that returned the errno in ExceptionInfoErrno.
typedef ExceptionInfo< struct ExceptionInfoLocation_, ThrowLocation >	ExceptionInfoLocation
	Stores the location where the exception was thrown.
using	FilePtr = std::unique_ptr< FILE, functor_wrapper< FILE, fclose_wrapper >>
	Simple guard pointer which calls fclose. See unique_cptr for details.
using	Matrix3x3 = BasicMatrix3x3< real >
	Three-by-three real number matrix. More...
template<typename T , void D = sfree_wrapper>
using	unique_cptr = std::unique_ptr< T, functor_wrapper< T, D >>
	unique_ptr which takes function pointer (has to return void) as template argument
typedef unique_cptr< void >	sfree_guard
	Simple guard which calls sfree. See unique_cptr for details.
typedef BasicVector< real >	RVec
	Shorthand for C++ rvec-equivalent type.
typedef BasicVector< double >	DVec
	Shorthand for C++ dvec-equivalent type.
typedef BasicVector< int >	IVec
	Shorthand for C++ ivec-equivalent type.
using	ClContext = ClHandle< cl_context >
	Convenience declarations.
using	ClCommandQueue = ClHandle< cl_command_queue >
using	ClProgram = ClHandle< cl_program >
using	ClKernel = ClHandle< cl_kernel >

Enumerations
enum	AwhOutputEntryType {   AwhOutputEntryType::MetaData, AwhOutputEntryType::CoordValue, AwhOutputEntryType::Pmf, AwhOutputEntryType::Bias,   AwhOutputEntryType::Visits, AwhOutputEntryType::Weights, AwhOutputEntryType::Target, AwhOutputEntryType::SharedForceCorrelationVolume,   AwhOutputEntryType::SharedFrictionTensor }
	Enum with the AWH variables to write. More...
enum	AwhOutputMetaData { AwhOutputMetaData::NumBlock, AwhOutputMetaData::TargetError, AwhOutputMetaData::ScaledSampleWeight, AwhOutputMetaData::Count }
	Enum with the types of metadata to write. More...
enum	Normalization { Normalization::None, Normalization::Coordinate, Normalization::FreeEnergy, Normalization::Distribution }
	Enum with different ways of normalizing the output. More...
enum	DensityFittingAmplitudeMethod : int { DensityFittingAmplitudeMethod::Unity, DensityFittingAmplitudeMethod::Mass, DensityFittingAmplitudeMethod::Charge, Count }
	The methods that determine how amplitudes are spread on a grid in density guided simulations. More...
enum	NNPotEmbedding { NNPotEmbedding::Mechanical, NNPotEmbedding::ElectrostaticModel, Count }
	Enum to specify embedding scheme used for NNP/MM interaction. More...
enum	QMMMQMMethod {   QMMMQMMethod::PBE, QMMMQMMethod::PBE_D3, QMMMQMMethod::BLYP, QMMMQMMethod::BLYP_D3,   QMMMQMMethod::PBE0, QMMMQMMethod::PBE0_D3, QMMMQMMethod::B3LYP, QMMMQMMethod::B3LYP_D3,   QMMMQMMethod::CAM_B3LYP, QMMMQMMethod::CAM_B3LYP_D3, QMMMQMMethod::WB97X, QMMMQMMethod::WB97X_D3,   QMMMQMMethod::SCC_DFTB, QMMMQMMethod::GFN1_XTB, QMMMQMMethod::GFN2_XTB, QMMMQMMethod::INPUT,   Count }
	Enumerator for supported QM methods Also could be INPUT which means external input file provided with the name determined by QMMMParameters::qminputfilename_. More...
enum	QMMMElectrostaticCoupling { QMMMElectrostaticCoupling::PointCharge, QMMMElectrostaticCoupling::Gauss, Count }
	Enumerator for the QM/MM electrostatic coupling generated for tight-binding CP2K. More...
enum	CoordinateFileFlags : unsigned long {   CoordinateFileFlags::Base = 1 << 0, CoordinateFileFlags::RequireForceOutput = 1 << 1, CoordinateFileFlags::RequireVelocityOutput = 1 << 2, CoordinateFileFlags::RequireAtomConnections = 1 << 3,   CoordinateFileFlags::RequireAtomInformation = 1 << 4, CoordinateFileFlags::RequireChangedOutputPrecision = 1 << 5, CoordinateFileFlags::RequireNewFrameStartTime = 1 << 6, CoordinateFileFlags::RequireNewFrameTimeStep = 1 << 7,   CoordinateFileFlags::RequireNewBox = 1 << 8, CoordinateFileFlags::RequireCoordinateSelection = 1 << 9, CoordinateFileFlags::Count }
	The enums here define the flags specifying the requirements of different outputadapter modules. More...
enum	ChangeSettingType : int { PreservedIfPresent, Always, Never, Count }
	Enum class for setting basic flags in a t_trxframe.
enum	ChangeAtomsType {   PreservedIfPresent, AlwaysFromStructure, Never, Always,   Count }
	Enum class for t_atoms settings.
enum	ChangeFrameInfoType { PreservedIfPresent, Always, Count }
	Enum class for setting fields new or not.
enum	ChangeFrameTimeType {   PreservedIfPresent, StartTime, TimeStep, Both,   Count }
	Enum class for setting frame time from user input.
enum	FrameConverterFlags : unsigned long {   FrameConverterFlags::NoGuarantee = 1 << 0, FrameConverterFlags::MoleculesAreWhole = 1 << 1, FrameConverterFlags::NoPBCJumps = 1 << 2, FrameConverterFlags::MoleculeCOMInBox = 1 << 3,   FrameConverterFlags::ResidueCOMInBox = 1 << 4, FrameConverterFlags::AtomsInBox = 1 << 5, FrameConverterFlags::UnitCellIsRectangular = 1 << 6, FrameConverterFlags::UnitCellIsTriclinic = 1 << 7,   FrameConverterFlags::UnitCellIsCompact = 1 << 8, FrameConverterFlags::SystemIsCenteredInBox = 1 << 9, FrameConverterFlags::FitToReferenceRotTrans = 1 << 10, FrameConverterFlags::FitToReferenceRotTransXY = 1 << 11,   FrameConverterFlags::FitToReferenceTranslation = 1 << 12, FrameConverterFlags::FitToReferenceTranslationXY = 1 << 13, FrameConverterFlags::FitToReferenceProgressive = 1 << 14, FrameConverterFlags::NewSystemCenter = 1 << 15,   FrameConverterFlags::Count }
	The enums here define the guarantees provided by frameconverters concerning the modifications they provide. More...
enum	HaloMpiTag {   HaloMpiTag::X, HaloMpiTag::F, HaloMpiTag::ZoneCorners, GridCounts,   HaloMpiTag::GridCells, HaloMpiTag::GridDimensions, HaloMpiTag::AtomIndices }
enum	HaloType { Coordinates, Forces }
	Whether the halo exchange is of coordinates or forces.
enum	DdRankOrder {   DdRankOrder::select, DdRankOrder::interleave, DdRankOrder::pp_pme, DdRankOrder::cartesian,   DdRankOrder::Count }
	The options for the domain decomposition MPI task ordering. More...
enum	DlbOption {   DlbOption::select, DlbOption::turnOnWhenUseful, DlbOption::no, DlbOption::yes,   DlbOption::Count }
	The options for the dynamic load balancing. More...
enum	DDBondedChecking : bool { DDBondedChecking::ExcludeZeroLimit = false, DDBondedChecking::All = true }
	Options for checking bonded interactions. More...
enum	DirectionX : int { Up = 0, Down, Center, Count }
	Direction of neighbouring rank in X-dimension relative to current rank. Used in GPU implementation of PME halo exchange.
enum	DirectionY : int { Left = 0, Right, Center, Count }
	Direction of neighbouring rank in Y-dimension relative to current rank. Used in GPU implementation of PME halo exchange.
enum	PmeLoadBalancingLimit : int {   No, Box, DD, PmeGrid,   MaxScaling, Count }
	Enumeration whose values describe the effect limiting the load balancing.
enum	FftBackend {   FftBackend::Cufft, FftBackend::OclVkfft, FftBackend::Ocl, FftBackend::CuFFTMp,   FftBackend::HeFFTe_CUDA, FftBackend::HeFFTe_Sycl_OneMkl, FftBackend::HeFFTe_Sycl_Rocfft, FftBackend::HeFFTe_Sycl_cuFFT,   FftBackend::HeFFTe_HIP, FftBackend::SyclMkl, FftBackend::SyclOneMath, FftBackend::SyclRocfft,   FftBackend::SyclVkfft, FftBackend::SyclBbfft, FftBackend::Sycl, FftBackend::HipVkfft,   FftBackend::HipRocfft, Count }
enum	FftDirection : int { RealToComplex, ComplexToReal, Count }
	Model the kinds of 3D FFT implemented.
enum	CheckPointVersion : int {   CheckPointVersion::UnknownVersion0, CheckPointVersion::UnknownVersion1, CheckPointVersion::AddMagicNumber, CheckPointVersion::SafeSimulationPart,   CheckPointVersion::EkinDataAndFlags, CheckPointVersion::SafeSteps, CheckPointVersion::Version45, CheckPointVersion::UnknownVersion7,   CheckPointVersion::FileChecksumAndSize, CheckPointVersion::UnknownVersion9, CheckPointVersion::NoseHooverThermostat, CheckPointVersion::NoseHooverBarostat,   CheckPointVersion::HostInformation, CheckPointVersion::DoublePrecisionBuild, CheckPointVersion::LambdaStateAndHistory, CheckPointVersion::EssentialDynamics,   CheckPointVersion::SwapState, CheckPointVersion::AwhHistoryFlags, CheckPointVersion::RemoveBuildMachineInformation, CheckPointVersion::ComPrevStepAsPullGroupReference,   CheckPointVersion::PullAverage, CheckPointVersion::MDModules, CheckPointVersion::ModularSimulator, CheckPointVersion::AwhLocalWeightSum,   CheckPointVersion::Count, CheckPointVersion::CurrentVersion = Count - 1 }
	Enum of values that describe the contents of a cpt file whose format matches a version number. More...
enum	H5mdFileMode : char { Read = 'r', H5mdFileMode::Write = 'w', H5mdFileMode::Append = 'a' }
enum	H5mdCompression : int { H5mdCompression::Uncompressed, H5mdCompression::LosslessNoShuffle, H5mdCompression::LosslessShuffle }
	Data set compression options. More...
enum	SpaceGroup : int32_t { SpaceGroup::P1 = 1 }
	Space group in three dimensions. More...
enum	MrcDataMode : int32_t {   MrcDataMode::uInt8 = 0, MrcDataMode::int16 = 1, MrcDataMode::float32 = 2, MrcDataMode::complexInt32 = 3,   MrcDataMode::complexFloat64 = 4 }
	The type of density data stored in an mrc file. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" Modes 0-4 are defined by the standard. NOTE only mode 2 is currently implemented and used. More...
enum	YesNoType { Yes, No, Count, Default = Yes }
	Enum class for boolean that should be true by default.
enum	FmmDirectProvider { FmmDirectProvider::Gromacs, FmmDirectProvider::Fmm, Count }
	Enumeration of possible direct interaction providers. More...
enum	ActiveFmmBackend { ActiveFmmBackend::Inactive, ActiveFmmBackend::ExaFmm, ActiveFmmBackend::FMSolvr, Count }
	Indicates which FMM backend is active based on MDP configuration. More...
enum	ExaFmmTreeType { Uniform, Adaptive, Count }
	Tree type options for ExaFMM.
enum	{   DDB_CH3, DDB_NH3, DDB_NH2, DDB_PHE,   DDB_TYR, DDB_TRP, DDB_HISA, DDB_HISB,   DDB_HISH, DDB_DIR_NR }
enum	{ eifTRUE, eifFALSE, eifIGNORE, eifNR }
enum	{   eCPP_OK, eCPP_FILE_NOT_FOUND, eCPP_EOF, eCPP_SYNTAX,   eCPP_INTERRUPT, eCPP_INVALID_HANDLE, eCPP_INVALID_INCLUDE_DELIMITER, eCPP_FILE_NOT_OPEN,   eCPP_UNKNOWN, eCPP_NR }
enum	BondedTypes : int {   Bonds, Angles, ProperDihedrals, ImproperDihedrals,   Exclusions, Cmap, Count }
	Used for reading .rtp/.tdb BondedTypes::Bonds must be the first, new types can be added to the end these MUST correspond to the arrays in hackblock.cpp.
enum	MoleculePatchType { MoleculePatchType::Add, MoleculePatchType::Delete, MoleculePatchType::Replace }
	Declare different types of hacks for later check. More...
enum	RotationType : int { XYZ, Z, None, Count }
enum	{   ematchNone, ematchWild, ematchElem, ematchExact,   ematchNR }
enum	HistidineStates : int {   A, B, H, One,   Count }
enum	ReplaceType : int { Repl, Add, Del, Count }
enum	DeprecatedDirectives : int {   d_dummies1, d_dummies2, d_dummies3, d_dummies4,   d_dummiesn, Count }
enum	Directive : int {   d_defaults, d_atomtypes, d_bondtypes, d_constrainttypes,   d_pairtypes, d_angletypes, d_dihedraltypes, d_nonbond_params,   d_implicit_genborn_params, d_implicit_surface_params, d_cmaptypes, d_moleculetype,   d_atoms, d_vsites1, d_vsites2, d_vsites3,   d_vsites4, d_vsitesn, d_bonds, d_exclusions,   d_pairs, d_pairs_nb, d_angles, d_dihedrals,   d_constraints, d_settles, d_polarization, d_water_polarization,   d_thole_polarization, d_system, d_molecules, d_position_restraints,   d_angle_restraints, d_angle_restraints_z, d_distance_restraints, d_orientation_restraints,   d_dihedral_restraints, d_cmap, d_intermolecular_interactions, d_maxdir,   d_invalid, d_none, Count }
enum	DeviceStreamType : int {   DeviceStreamType::NonBondedLocal, DeviceStreamType::NonBondedNonLocal, DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer,   DeviceStreamType::UpdateAndConstraints, DeviceStreamType::HaloExchange, DeviceStreamType::Count }
	Class enum to describe the different logical streams used for GPU work. More...
enum	PinningPolicy : int { CannotBePinned, PinnedIfSupported }
	Helper enum for pinning policy of the allocation of HostAllocationPolicy. More...
enum	Architecture {   Architecture::Unknown, Architecture::X86, Architecture::Arm, Architecture::PowerPC,   Architecture::RiscV32, Architecture::RiscV64, Architecture::Loongarch64 }
	Enum for GROMACS CPU hardware detection support. More...
enum	SimdType {   SimdType::None, SimdType::Reference, SimdType::Generic, SimdType::X86_Sse2,   SimdType::X86_Sse4_1, SimdType::X86_Avx128Fma, SimdType::X86_Avx, SimdType::X86_Avx2,   SimdType::X86_Avx2_128, SimdType::X86_Avx512, SimdType::Arm_NeonAsimd, SimdType::Arm_Sve,   SimdType::Ibm_Vsx }
	Enumerated options for SIMD architectures. More...
enum	IMDMessageType : int {   IMDMessageType::Disconnect, IMDMessageType::Energies, IMDMessageType::FCoords, IMDMessageType::Go,   IMDMessageType::Handshake, IMDMessageType::Kill, IMDMessageType::Mdcomm, IMDMessageType::Pause,   IMDMessageType::TRate, IMDMessageType::IOerror, IMDMessageType::Count }
	Enum for types of IMD messages. More...
enum	DensitySimilarityMeasureMethod : int { DensitySimilarityMeasureMethod::innerProduct, DensitySimilarityMeasureMethod::relativeEntropy, DensitySimilarityMeasureMethod::crossCorrelation, Count }
	The methods that determine how two densities are compared to one another. More...
enum	CheckpointSignal { noSignal = 0, doCheckpoint = 1 }
	Checkpoint signals. More...
enum	ConstraintVariable : int {   Positions, Velocities, Derivative, Deriv_FlexCon,   Force, ForceDispl }
	Describes supported flavours of constrained updates.
enum	FlexibleConstraintTreatment { FlexibleConstraintTreatment::Include, FlexibleConstraintTreatment::Exclude }
	Tells make_at2con how to treat flexible constraints. More...
enum	NumTempScaleValues {   NumTempScaleValues::None = 0, NumTempScaleValues::Single = 1, NumTempScaleValues::Multiple = 2, NumTempScaleValues::Count = 3,   NumTempScaleValues::None, NumTempScaleValues::Single, NumTempScaleValues::Multiple, Count }
	Sets the number of different temperature coupling values. More...
enum	GraphState : int {   GraphState::Invalid, GraphState::Recording, GraphState::Recorded, GraphState::Instantiated,   GraphState::Count }
	State of graph. More...
enum	ResetSignal { noSignal = 0, doResetCounters = 1 }
	Reset signals. More...
enum	StopSignal : int { noSignal = 0, stopAtNextNSStep = 1, stopImmediately = -1 }
	Stop signals. More...
enum	AccelerationType {   None, Group, Cosine, BoxDeformation,   Count }
	Sets the NEMD acceleration type.
enum	StoreUpdatedVelocities { StoreUpdatedVelocities::Yes, StoreUpdatedVelocities::No, Count }
	Sets whether we store the updated velocities. More...
enum	NumTempScaleValues {   NumTempScaleValues::None = 0, NumTempScaleValues::Single = 1, NumTempScaleValues::Multiple = 2, NumTempScaleValues::Count = 3,   NumTempScaleValues::None, NumTempScaleValues::Single, NumTempScaleValues::Multiple, Count }
	Sets the number of different temperature coupling values. More...
enum	ParrinelloRahmanVelocityScaling {   ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Anisotropic, Count,   ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Anisotropic, Count }
	Describes the properties of the Parrinello-Rahman pressure scaling matrix. More...
enum	IncompatibilityReasons {   FlexibleConstraint, IncompatibleVsite, VsiteConstructingAtomsSplit, ConstrainedAtomOrder,   NoCentralConstraintAtom, Count }
	Reasons why the system can be incompatible with update groups.
enum	VSiteCalculatePosition { Yes, No }
	Whether we're calculating the virtual site position.
enum	VSiteCalculateVelocity { Yes, No }
	Whether we're calculating the virtual site velocity.
enum	PbcMode { PbcMode::all, PbcMode::none }
	PBC modes for vsite construction and spreading. More...
enum	VSiteOperation { VSiteOperation::Positions, VSiteOperation::Velocities, VSiteOperation::PositionsAndVelocities, VSiteOperation::Count }
	Whether we calculate vsite positions, velocities, or both. More...
enum	VirtualSiteVirialHandling : int { VirtualSiteVirialHandling::None, VirtualSiteVirialHandling::Pbc, VirtualSiteVirialHandling::NonLinear }
	Tells how to handle virial contributions due to virtual sites. More...
enum	StartingBehavior : int { StartingBehavior::RestartWithAppending, StartingBehavior::RestartWithoutAppending, StartingBehavior::NewSimulation, StartingBehavior::Count }
	Enumeration for describing how mdrun is (re)starting. More...
enum	: std::ptrdiff_t { dynamic_extent = -1 }
	Define constant that signals dynamic extent.
enum	AwhTargetType : int {   Constant, Cutoff, Boltzmann, LocalBoltzmann,   Count, Default = Constant }
	Target distribution enum.
enum	AwhHistogramGrowthType : int { ExponentialLinear, Linear, Count, Default = ExponentialLinear }
	Weight histogram growth enum.
enum	AwhPotentialType : int { Convolved, Umbrella, Count, Default = Convolved }
	AWH potential type enum.
enum	AwhCoordinateProviderType : int { Pull, FreeEnergyLambda, Count, Default = Pull }
	AWH bias reaction coordinate provider.
enum	CheckpointDataOperation { Read, Write, Count }
	The operations on CheckpointData. More...
enum	AtomLocality : int { AtomLocality::Local = 0, AtomLocality::NonLocal = 1, AtomLocality::All = 2, AtomLocality::Count = 3 }
	Atom locality indicator: local, non-local, all. More...
enum	InteractionLocality : int { InteractionLocality::Local = 0, InteractionLocality::NonLocal = 1, InteractionLocality::Count = 2 }
	Interaction locality indicator: local, non-local, all. More...
enum	AppendingBehavior { AppendingBehavior::Auto, AppendingBehavior::Appending, AppendingBehavior::NoAppending }
	Enumeration for mdrun appending behavior. More...
enum	MtsForceGroups : int {   MtsForceGroups::LongrangeNonbonded, MtsForceGroups::Nonbonded, MtsForceGroups::Pair, MtsForceGroups::Dihedral,   MtsForceGroups::Angle, MtsForceGroups::Pull, MtsForceGroups::Awh, MtsForceGroups::Count }
	Force group available for selection for multiple time step integration. More...
enum	ReductionRequirement : int { ReductionRequirement::Soon, ReductionRequirement::Eventually }
	Control whether reduction is required soon. More...
enum	ObservablesReducerStatus : int { ObservablesReducerStatus::ReadyToReduce, ObservablesReducerStatus::AlreadyReducedThisStep }
	Report whether the reduction has happened this step. More...
enum	ComputeGlobalsAlgorithm { LeapFrog, VelocityVerlet }
	The different global reduction schemes we know about.
enum	EnergySignallerEvent { EnergyCalculationStep, VirialCalculationStep, FreeEnergyCalculationStep }
	The energy events signalled by the EnergySignaller.
enum	TrajectoryEvent { StateWritingStep, EnergyWritingStep }
	The trajectory writing events.
enum	ModularSimulatorBuilderState { AcceptingClientRegistrations, NotAcceptingClientRegistrations }
	Enum allowing builders to store whether they can accept client registrations.
enum	ReportPreviousStepConservedEnergy { Yes, No, Count }
	Enum describing whether an element is reporting conserved energy from the previous step.
enum	ScheduleOnInitStep { ScheduleOnInitStep::Yes, ScheduleOnInitStep::No, ScheduleOnInitStep::Count }
	Whether the element does schedule on the initial step. More...
enum	NhcUsage { NhcUsage::System, NhcUsage::Barostat, NhcUsage::Count }
	The usages of Nose-Hoover chains. More...
enum	ScaleVelocities { PreStepOnly, PreStepAndPostStep }
	Which velocities the thermostat scales.
enum	IntegrationStage {   IntegrationStage::PositionsOnly, IntegrationStage::VelocitiesOnly, IntegrationStage::LeapFrog, IntegrationStage::VelocityVerletPositionsAndVelocities,   IntegrationStage::ScaleVelocities, IntegrationStage::ScalePositions, IntegrationStage::Count }
	The different integration types we know about. More...
enum	NumPositionScalingValues { NumPositionScalingValues::None, NumPositionScalingValues::Single, NumPositionScalingValues::Multiple, NumPositionScalingValues::Count }
	Sets the number of different position scaling values. More...
enum	NumVelocityScalingValues { NumVelocityScalingValues::None, NumVelocityScalingValues::Single, NumVelocityScalingValues::Multiple, Count }
	Sets the number of different velocity scaling values. More...
enum	ParrinelloRahmanVelocityScaling {   ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Anisotropic, Count,   ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Anisotropic, Count }
	Describes the properties of the Parrinello-Rahman pressure scaling matrix. More...
enum	ReferenceTemperatureChangeAlgorithm
enum	EnergySignallerVirialMode { EnergySignallerVirialMode::Off, EnergySignallerVirialMode::OnStep, EnergySignallerVirialMode::OnStepAndNext, EnergySignallerVirialMode::Count }
	When we calculate virial. More...
enum	UseFullStepKE { Yes, No, Count }
	Enum describing whether the thermostat is using full or half step kinetic energy.
enum	{ nbatXYZ, nbatXYZQ, nbatX4, nbatX8 }
enum	LJCombinationRule : int { LJCombinationRule::Geometric, LJCombinationRule::LorentzBerthelot, LJCombinationRule::None, LJCombinationRule::Count }
	LJ combination rules. More...
enum	NbnxmBenchMarkKernels : int {   SimdAuto, SimdNo, Simd4XM, Simd2XMM,   Count }
	Enum for selecting the SIMD kernel type for benchmarks.
enum	NbnxmBenchMarkCombRule : int { RuleGeom, RuleLB, RuleNone, Count }
	Enum for selecting the combination rule for kernel benchmarks.
enum	NbnxmBenchMarkCoulomb : int { Pme, ReactionField, Count }
	Enum for selecting coulomb type for kernel benchmarks.
enum	NbnxmBenchMarkInteractionModifiers : int { PotShift, PotSwitch, ForceSwitch, Count }
enum	ClusterDistanceKernelType : int {   ClusterDistanceKernelType::CpuPlainC_4x4, ClusterDistanceKernelType::CpuSimd_4xM, ClusterDistanceKernelType::CpuSimd_2xMM, ClusterDistanceKernelType::Gpu,   ClusterDistanceKernelType::CpuPlainC_1x1 }
	The types of kernel for calculating the distance between pairs of atom clusters. More...
enum	LJKernelType { LJKernelType::Cutoff, LJKernelType::ForceSwitch, LJKernelType::PotentialSwitch, LJKernelType::Ewald }
	The free-energy kernel Lennard-Jones functional shape. More...
enum	{   vdwktLJCUT_COMBGEOM, vdwktLJCUT_COMBLB, vdwktLJCUT_COMBNONE, vdwktLJFORCESWITCH,   vdwktLJPOTSWITCH, vdwktLJEWALDCOMBGEOM, vdwktLJEWALDCOMBLB, vdwktNR = vdwktLJEWALDCOMBLB,   vdwktNR_ref }
	Kinds of Van der Waals treatments in NBNxM SIMD kernels. More...
enum	{ enbvClearFNo, enbvClearFYes }
	Flag to tell the nonbonded kernels whether to clear the force output buffers.
enum	ElecType : int {   ElecType::Cut, ElecType::RF, ElecType::EwaldTab, ElecType::EwaldTabTwin,   ElecType::EwaldAna, ElecType::EwaldAnaTwin, ElecType::None, ElecType::Fmm,   ElecType::Count }
	Nbnxm electrostatic GPU kernel flavors. More...
enum	VdwType : int {   VdwType::Cut, VdwType::CutCombGeom, VdwType::CutCombLB, VdwType::FSwitch,   VdwType::PSwitch, VdwType::EwaldGeom, VdwType::EwaldLB, VdwType::Count }
	Nbnxm VdW GPU kernel flavors. More...
enum	NbnxmKernelType : int {   NotSet = 0, Cpu4x4_PlainC, Cpu4xN_Simd_4xN, Cpu4xN_Simd_2xNN,   Gpu8x8x8, Cpu8x8x8_PlainC, Cpu1x1_PlainC, Count }
	Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation.
enum	EwaldExclusionType : int { NotSet = 0, Table, Analytical, DecidedByGpuModule }
	Ewald exclusion types.
enum	PairlistType : int {   Simple4x2, Simple4x4, Simple4x8, Hierarchical8x8x8,   Simple1x1, Count }
	The available pair list types.
enum	CoulombKernelType : int {   ReactionField, Table, TableTwin, Ewald,   EwaldTwin, None, Fmm, Count }
	Kinds of electrostatic treatments in SIMD Verlet kernels.
enum	NonbondedResource : int { Cpu, Gpu, EmulateGpu }
	Resources that can be used to execute non-bonded kernels on.
enum	{ enbsCCgrid, enbsCCsearch, enbsCCcombine, enbsCCnr }
	Local cycle count enum for profiling different parts of search.
enum	KernelCoulombType { KernelCoulombType::RF, KernelCoulombType::EwaldAnalytical, KernelCoulombType::EwaldTabulated, KernelCoulombType::None }
	List of type of Nbnxm kernel coulomb type implementations. More...
enum	ILJInteractions { ILJInteractions::All, ILJInteractions::Half, ILJInteractions::None }
	The fraction of i-particles for which LJ interactions need to be computed. More...
enum	HelpOutputFormat { eHelpOutputFormat_Console, eHelpOutputFormat_Rst, eHelpOutputFormat_Other, eHelpOutputFormat_NR }
	Output format for help writing. More...
enum	COMShiftType : int { Residue, Molecule, Count }
	How COM shifting should be applied.
enum	CenteringType : int { Triclinic, Rectangular, Zero, Count }
	Helper enum class to define centering types.
enum	UnitCellType : int { Triclinic, Rectangular, Compact, Count }
	Helper enum class to define Unit cell representation types.
enum	RandomDomain {   RandomDomain::Other = 0x00000000, RandomDomain::MaxwellVelocities = 0x00001000, RandomDomain::TestParticleInsertion = 0x00002000, RandomDomain::UpdateCoordinates = 0x00003000,   RandomDomain::UpdateConstraints = 0x00004000, RandomDomain::Thermostat = 0x00005000, RandomDomain::Barostat = 0x00006000, RandomDomain::ReplicaExchange = 0x00007000,   RandomDomain::ExpandedEnsemble = 0x00008000, RandomDomain::AwhBiasing = 0x00009000 }
	Enumerated values for fixed part of random seed (domain) More...
enum	EndianSwapBehavior : int {   EndianSwapBehavior::DoNotSwap, EndianSwapBehavior::Swap, EndianSwapBehavior::SwapIfHostIsBigEndian, EndianSwapBehavior::SwapIfHostIsLittleEndian,   EndianSwapBehavior::Count }
	Specify endian swapping behavoir. More...
enum	{   elsqWEIGHT_NONE, elsqWEIGHT_X, elsqWEIGHT_Y, elsqWEIGHT_XY,   elsqWEIGHT_NR }
	Enum for statistical weights.
enum	ChannelHistory : int { None, Ch0, Ch1, Count }
	Keep track of through which channel the ions have passed.
enum	Domain : int { Notset, A, B, Count }
	Domain identifier. More...
enum	{   etabLJ6, etabLJ12, etabLJ6Shift, etabLJ12Shift,   etabShift, etabRF, etabRF_ZERO, etabCOUL,   etabEwald, etabEwaldSwitch, etabEwaldUser, etabEwaldUserSwitch,   etabLJ6Ewald, etabLJ6Switch, etabLJ12Switch, etabCOULSwitch,   etabEXPMIN, etabUSER, etabNR }
enum	TableInteraction : int { VdwRepulsionVdwDispersion, ElectrostaticVdwRepulsionVdwDispersion, Count }
	The types of interactions contained in the table.
enum	TableFormat : int { CubicsplineYfgh, Count }
enum	{ etiCOUL, etiLJ6, etiLJ12, etiNR }
	Enumerated type to describe the interaction types in a table. More...
enum	TaskTarget : int { Auto, Cpu, Gpu }
	Record where a compute task is targetted.
enum	EmulateGpuNonbonded : bool { EmulateGpuNonbonded::No, EmulateGpuNonbonded::Yes }
	Help pass GPU-emulation parameters with type safety. More...
enum	GpuTask : int { GpuTask::Nonbonded, GpuTask::Pme, GpuTask::Count }
	Types of compute tasks that can be run on a GPU. More...
enum	Isotope {   H, D, He, Li,   Be, B, C, N,   O, F, Ne, Na,   Mg, Al, Si, P,   S, Cl, Ar, K,   Ca, Sc, Ti, V,   Cr, Mn, Fe, Co,   Ni, Cu, Zn, Ga,   Ge, As, Se, Br,   Kr, Rb, Sr, Y,   Zr, Nb, Mo, Tc,   Ru, Rh, Pd, Ag,   Cd, In, Sn, Sb,   Te, I, Xe, Cs,   Ba, La, Ce, Pr,   Nd, Pm, Sm, Eu,   Gd, Tb, Dy, Ho,   Er, Tm, Yb, Lu,   Hf, Ta, W, Re,   Os, Ir, Pt, Au,   Hg, Tl, Pb, Bi,   Po, At, Rn, Fr,   Ra, Ac, Th, Pa,   U, Np, Pu, Am,   Cm, Bk, Cf, Es,   Fm, Md, No, Lr,   Rf, Db, Sg, Bh,   Hs, Mt, Count }
	isotopes
enum	ErrorCode {   eeOK, eeOutOfMemory, eeFileNotFound, eeFileIO,   eeInvalidInput, eeInconsistentInput, eeTolerance, eeInstability,   eeNotImplemented, eeInvalidValue, eeInvalidCall, eeInternalError,   eeAPIError, eeRange, eeParallelConsistency, eeModularSimulator,   eeMDModuleSetup, eeUnknownError }
	Possible error return codes from Gromacs functions. More...
enum	GpuAwareMpiStatus : int { GpuAwareMpiStatus::NotSupported = 0, GpuAwareMpiStatus::Forced, GpuAwareMpiStatus::Supported, GpuAwareMpiStatus::Count }
	Enum describing GPU-aware support in underlying MPI library. More...
enum	StringCompareType { StringCompareType::Exact, StringCompareType::CaseInsensitive, StringCompareType::CaseAndDashInsensitive }
	Specifies how strings should be compared in various contexts. More...
enum	StripStrings : int { StripStrings::No, StripStrings::Yes }
	Enum class for whether StringToEnumValueConverter will strip strings of leading and trailing whitespace before comparison. More...
enum	TimeUnit : int {   Femtoseconds, Picoseconds, Nanoseconds, Microseconds,   Milliseconds, Seconds, Count, Default = Picoseconds }
	Time values for TimeUnitManager and legacy oenv module.
enum	OptionFileType : int {   Topology, RunInput, Trajectory, Energy,   PDB, AtomIndex, Plot, GenericData,   Csv, QMInput, Count }
	Purpose of file(s) provided through an option.
enum	OptionFlag : uint64_t {   efOption_Set = 1 << 0, efOption_HasDefaultValue = 1 << 1, efOption_ExplicitDefaultValue = 1 << 2, efOption_ClearOnNextSet = 1 << 3,   efOption_Required = 1 << 4, efOption_MultipleTimes = 1 << 5, efOption_Hidden = 1 << 6, efOption_Vector = 1 << 8,   efOption_DefaultValueIfSetExists = 1 << 11, efOption_NoDefaultValue = 1 << 9, efOption_DontCheckMinimumCount = 1 << 10 }
	Flags for options. More...

Functions
static bool	anyDimUsesProvider (const AwhBiasParams &awhBiasParams, const AwhCoordinateProviderType awhCoordProvider)
	Checks whether any dimension uses the given coordinate provider type. More...
static bool	anyDimUsesProvider (const AwhParams &awhParams, const AwhCoordinateProviderType awhCoordProvider)
	Checks whether any dimension uses the given coordinate provider type. More...
static bool	anyBiasIsScaledByMetric (const AwhParams &awhParams)
	Checks whether any bias scales the target distribution based on the AWH friction metric. More...
std::unique_ptr< Awh >	prepareAwhModule (FILE *fplog, const t_inputrec &inputRecord, t_state *stateGlobal, const MpiComm &mpiComm, const gmx_multisim_t *multiSimRecord, bool startingFromCheckpoint, bool usingShellParticles, const std::string &biasInitFilename, pull_t *pull_work)
	Makes an Awh and prepares to use it if the user input requests that. More...
static int64_t	countSamples (ArrayRef< const PointState > pointState)
	Count the total number of samples / sample weight over all grid points. More...
static void	ensureStateAndRunConsistency (const BiasParams &params, const BiasState &state)
	Check if the state (loaded from checkpoint) and the run are consistent. More...
double	getDeviationFromPointAlongGridAxis (const BiasGrid &grid, int dimIndex, int pointIndex, double value)
	Get the deviation along one dimension from the given value to a point in the grid. More...
double	getDeviationFromPointAlongGridAxis (const BiasGrid &grid, int dimIndex, int pointIndex1, int pointIndex2)
	Get the deviation from one point to another along one dimension in the grid. More...
bool	pointsAlongLambdaAxis (const BiasGrid &grid, int pointIndex1, int pointIndex2)
	Checks whether two points are along a free energy lambda state axis. More...
bool	pointsHaveDifferentLambda (const BiasGrid &grid, int pointIndex1, int pointIndex2)
	Checks whether two points are different in the free energy lambda state dimension (if any). More...
void	linearArrayIndexToMultiDim (int indexLinear, int ndim, const awh_ivec numPointsDim, awh_ivec indexMulti)
	Convert a linear array index to a multidimensional one. More...
void	linearGridindexToMultiDim (const BiasGrid &grid, int indexLinear, awh_ivec indexMulti)
	Convert a linear grid point index to a multidimensional one. More...
int	multiDimArrayIndexToLinear (const awh_ivec indexMulti, int numDim, const awh_ivec numPointsDim)
	Convert multidimensional array index to a linear one. More...
int	multiDimGridIndexToLinear (const BiasGrid &grid, const awh_ivec indexMulti)
	Convert a multidimensional grid point index to a linear one. More...
bool	advancePointInSubgrid (const BiasGrid &grid, const awh_ivec subgridOrigin, const awh_ivec subgridNpoints, int *gridPointIndex)
	Find the next grid point in the sub-part of the grid given a starting point. More...
static int	pointDistanceAlongAxis (const GridAxis &axis, double x, double x0)
	Returns the point distance between from value x to value x0 along the given axis. More...
static bool	valueIsInGrid (const awh_dvec value, ArrayRef< const GridAxis > axis)
	Query if a value is in range of the grid. More...
static int	getNearestIndexInGrid (const awh_dvec value, ArrayRef< const GridAxis > axis)
	Map a value to the nearest point in the grid. More...
void	mapGridToDataGrid (std::vector< int > *gridpointToDatapoint, const MultiDimArray< std::vector< double >, dynamicExtents2D > &data, int numDataPoints, const std::string &dataFilename, const BiasGrid &grid, const std::string &correctFormatMessage)
	Maps each point in the grid to a point in the data grid. More...
template<typename T >
void	sumOverSimulations (ArrayRef< T > data, MPI_Comm multiSimComm, const bool broadcastWithinSimulation, const MpiComm &mpiComm)
	Sum an array over all simulations on main ranks or all ranks of each simulation. More...
bool	haveBiasSharingWithinSimulation (const AwhParams &awhParams)
	Returns if any bias is sharing within a simulation. More...
void	biasesAreCompatibleForSharingBetweenSimulations (const AwhParams &awhParams, ArrayRef< const size_t > pointSize, const BiasSharing &biasSharing)
	Checks whether biases are compatible for sharing between simulations, throws when not. More...
static void	normalizeFreeEnergyAndPmfSum (std::vector< PointState > *pointState)
	Normalizes the free energy and PMF sum. More...
static int	countTrailingZeroRows (const MultiDimArray< std::vector< double >, dynamicExtents2D > &data, int numRows, int numColumns)
	Count trailing data rows containing only zeros. More...
static void	readUserPmfAndTargetDistribution (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const std::string &filename, int numBias, int biasIndex, std::vector< PointState > *pointState)
	Initializes the PMF and target with data read from an input table. More...
static void	normalizeBlock (AwhEnergyBlock *block, const Bias &bias)
	Normalizes block data for output. More...
void	initCorrelationGridHistory (CorrelationGridHistory *correlationGridHistory, int numCorrelationTensors, int tensorSize, int blockDataListSize)
	Initialize correlation grid history, sets all sizes. More...
CorrelationGridHistory	initCorrelationGridHistoryFromState (const CorrelationGrid &corrGrid)
	Allocate a correlation grid history with the same structure as the given correlation grid. More...
void	updateCorrelationGridHistory (CorrelationGridHistory *corrGridHist, const CorrelationGrid &corrGrid)
	Update the correlation grid history for checkpointing. More...
void	restoreCorrelationGridStateFromHistory (const CorrelationGridHistory &corrGridHist, CorrelationGrid *corrGrid)
	Restores the correlation grid state from the correlation grid history. More...
double	getSqrtDeterminant (gmx::ArrayRef< const double > correlationIntegral)
	Returns the volume element of the correlation metric. More...
const char *	enumValueToString (AwhTargetType enumValue)
	String for target distribution.
const char *	enumValueToString (AwhHistogramGrowthType enumValue)
	String for weight histogram growth.
const char *	enumValueToString (AwhPotentialType enumValue)
	String for AWH potential type.
const char *	enumValueToString (AwhCoordinateProviderType enumValue)
	String for AWH bias reaction coordinate provider.
static double	get_pull_coord_period (const t_pull_coord &pullCoordParams, const t_pbc &pbc, const real intervalLength)
	Gets the period of a pull coordinate. More...
static bool	intervalIsInPeriodicInterval (double origin, double end, double period)
	Checks if the given interval is defined in the correct periodic interval. More...
static bool	valueIsInInterval (double origin, double end, double period, double value)
	Checks if a value is within an interval. More...
static void	checkInputConsistencyInterval (const AwhParams &awhParams, WarningHandler *wi)
	Check if the starting configuration is consistent with the given interval. More...
static void	setStateDependentAwhPullDimParams (AwhDimParams *dimParams, const int biasIndex, const int dimIndex, const pull_params_t &pull_params, pull_t *pull_work, const t_pbc &pbc, const tensor &compressibility, WarningHandler *wi)
	Sets AWH parameters, for one AWH pull dimension. More...
void	setStateDependentAwhParams (AwhParams *awhParams, const pull_params_t &pull_params, pull_t *pull_work, const matrix box, PbcType pbcType, const tensor &compressibility, const t_inputrec &inputrec, real initLambda, const gmx_mtop_t &mtop, WarningHandler *wi)
	Sets AWH parameters that need state parameters such as the box vectors. More...
void	checkAwhParams (const AwhParams &awhParams, const t_inputrec &inputrec, WarningHandler *wi)
	Check the AWH parameters. More...
bool	awhHasFepLambdaDimension (const AwhParams &awhParams)
	Returns true when AWH has a bias with a free energy lambda state dimension.
std::string	colvarsDescription ()
	Returns information for describing the colvars support.
bool	operator== (const DensityFittingParameters &lhs, const DensityFittingParameters &rhs)
	Check if two structs holding density fitting parameters are equal. More...
bool	operator!= (const DensityFittingParameters &lhs, const DensityFittingParameters &rhs)
	Check if two structs holding density fitting parameters are not equal. More...
std::string	torchDescription ()
	Returns information for describing the Torch support.
static std::tuple< std::vector < RVec >, std::vector< real > >	getMMPositionsAndCharges (const std::unique_ptr< LocalAtomSet > &mmAtoms, ArrayRef< const RVec > positions, ArrayRef< const real > charges)
	Helper function to gather the positions of the NNP atoms from the input. More...
static void	centerAtomPositions (ArrayRef< RVec > nnPositions, ArrayRef< RVec > mmPositions, const matrix &box, const PbcType &pbcType)
static std::string	recordToString (std::tuple< at::DataPtr, size_t > data)
static void	loadModelExtensions (const std::string &ext_libs, const MDLogger &logger)
	load custom extensions used to compile the TorchScript model from extra_files
static std::tuple< std::string, std::optional< int > >	getMdrunActiveDevice ()
static torch::Device	determineDevice (const MDLogger &logger, const MpiComm &mpiComm)
	Determine which device to use depending on GMX_NN_DEVICE environment variable. More...
std::string	plumedDescription ()
	Returns information for describing the PLUMED support.
std::string	qmmmDescription ()
	Returns information for describing the CP2K QM/MM support.
RVec	computeQMBoxVec (const RVec &a, const RVec &b, const RVec &c, real h, real minNorm, real maxNorm)
	Transforms vector a such as distance from it to the plane defined by vectors b and c will be h minimum length will be milL and maximum length maxL. More...
CommandLineProgramContext &	initForCommandLine (int *argc, char ***argv)
	Initializes the GROMACS library for command-line use. More...
void	finalizeForCommandLine ()
	Deinitializes the GROMACS library after initForCommandLine(). More...
int	processExceptionAtExitForCommandLine (const std::exception &ex)
	Handles an exception and deinitializes after initForCommandLine. More...
int	runCommandLineModule (int argc, char *argv[], ICommandLineModule *module)
	Implements a main() method that runs a single module. More...
int	runCommandLineModule (int argc, char *argv[], const char *name, const char *description, std::function< std::unique_ptr< ICommandLineOptionsModule >()> factory)
	Implements a main() method that runs a single module. More...
void	writeCommandLineHelpCMain (const CommandLineHelpContext &context, const char *name, int(*mainFunction)(int argc, char *argv[]))
	Helper to implement ICommandLineModule::writeHelp() with a C-like main() function that calls parse_common_args(). More...
static int	getFileType (const std::filesystem::path &filename)
	Get the internal file type from the filename. More...
static unsigned long	getSupportedOutputAdapters (int filetype)
	Get the flag representing the requirements for a given file output. More...
static OutputAdapterContainer	addOutputAdapters (const OutputRequirements &requirements, AtomsDataPtr atoms, const Selection &sel, unsigned long abilities)
	Creates a new container object with the user requested IOutputAdapter derived methods attached to it. More...
std::unique_ptr < TrajectoryFrameWriter >	createTrajectoryFrameWriter (const gmx_mtop_t *top, const Selection &sel, const std::filesystem::path &filename, AtomsDataPtr atoms, OutputRequirements requirements)
	Factory function for TrajectoryFrameWriter. More...
static void	deepCopy_t_trxframe (const t_trxframe &input, t_trxframe *copy, RVec *xvec, RVec *vvec, RVec *fvec, int *indexvec)
	Create a deep copy of a t_trxframe input into copy. More...
static t_trxstatus *	openTNG (const std::filesystem::path &name, const Selection &sel, const gmx_mtop_t *mtop)
	Method to open TNG file. More...
unsigned long	convertFlag (CoordinateFileFlags flag)
	Conversion of flag to its corresponding unsigned long value.
unsigned long	convertFlag (FrameConverterFlags flag)
	Conversion of flag to its corresponding unsigned long value.
static void	adjustAtomInformation (t_atoms *atoms, t_atoms *selectionAtoms, const Selection &sel)
	Modify atoms information in coordinate frame to fit output selection. More...
static CommSetup	split_communicator (const MDLogger &mdlog, const MpiComm &mpiCommSimulation, const DdRankOrder ddRankOrder, const bool gmx_unused reorder, const DDRankSetup &ddRankSetup)
static CommSetup	makeGroupCommunicators (const MDLogger &mdlog, const DDSettings &ddSettings, const DdRankOrder ddRankOrder, const DDRankSetup &ddRankSetup, const MpiComm &mpiCommSimulation)
	Makes the PP communicator and the PME communicator, when needed. More...
static void	setupGroupCommunication (const MDLogger &mdlog, const DDSettings &ddSettings, const int numAtomsInSystem, gmx_domdec_t *dd)
	For PP ranks, sets or makes the communicator. More...
static std::vector< real >	get_slb_frac (const gmx::MDLogger &mdlog, const char *dir, int nc, const char *size_string)
HaloPlan	computeHaloPlan (const gmx_domdec_comm_t &comm, int dimIndex, int pulse, const MpiComm &mpiCommGroup, int sendRankX, int recvRankX)
template<bool usePbc>
static auto	packSendBufKernel (Float3 *__restrict__ gm_dataPacked, const Float3 *__restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift)
template<bool accumulate>
static auto	unpackRecvBufKernel (Float3 *__restrict__ gm_data, const Float3 *__restrict__ gm_dataPacked, const int *__restrict__ gm_map, int mapSize)
	unpack non-local force data buffer on the GPU using pre-populated "map" containing index information. More...
template<bool usePbc, class... Args>
static void	launchPackSendBufKernel (const DeviceStream &deviceStream, int xSendSize, Args &&...args)
template<bool accumulateForces, class... Args>
static void	launchUnpackRecvBufKernel (const DeviceStream &deviceStream, int fRecvSize, Args &&...args)
static void	flagInteractionsForType (const InteractionFunction ftype, const InteractionList &il, const reverse_ilist_t &ril, const Range< int > &atomRange, const int numAtomsPerMolecule, ArrayRef< const int > globalAtomIndices, ArrayRef< int > isAssigned)
	Checks whether interactions have been assigned for one function type. More...
static std::string	printMissingInteractionsMolblock (const MpiComm &mpiComm, const gmx_domdec_t &dd, const gmx_reverse_top_t &rt, const char *moltypename, const reverse_ilist_t &ril, const Range< int > &atomRange, const int numAtomsPerMolecule, const int numMolecules, const InteractionDefinitions &idef)
	Help print error output when interactions are missing in a molblock. More...
static void	printMissingInteractionsAtoms (const MDLogger &mdlog, const MpiComm &mpiComm, const gmx_domdec_t &dd, const gmx_mtop_t &mtop, const InteractionDefinitions &idef)
	Help print error output when interactions are missing.
static void	dd_print_missing_interactions (const MDLogger &mdlog, const MpiComm &mpiComm, const gmx_domdec_t &dd, const int numBondedInteractionsOverAllDomains, const int expectedNumGlobalBondedInteractions, const gmx_mtop_t &top_global, const gmx_localtop_t &top_local, ArrayRef< const RVec > x, const matrix box)
	Print error output when interactions are missing.
static int	computeExpectedNumGlobalBondedInteractions (const gmx_mtop_t &mtop, const DDBondedChecking ddBondedChecking, const bool useUpdateGroups)
	Compute the total bonded interaction count. More...
void	mdAlgorithmsSetupAtomData (const SimulationWorkload &simulationWork, gmx_domdec_t *dd, const t_inputrec &inputrec, const gmx_mtop_t &top_global, gmx_localtop_t *top, t_forcerec *fr, ForceBuffers *force, MDAtoms *mdAtoms, Constraints *constr, VirtualSitesHandler *vsite, shellfc_t *shellfc, StatePropagatorDataGpu *stateGpu, gmx_wallcycle *wcycle)
	Sets atom data for several MD algorithms. More...
void	make_local_shells (const gmx_domdec_t *dd, const t_mdatoms &md, shellfc_t *shfc)
	Gets the local shell with domain decomposition. More...
bool	check_grid_jump (int64_t step, const gmx_domdec_t *dd, real cutoff, const gmx_ddbox_t *ddbox, bool bFatal)
	Check whether the DD grid has moved too far for correctness.
void	print_dd_statistics (gmx_domdec_t *dd, const t_inputrec &inputrec, FILE *fplog)
	Print statistics for domain decomposition communication.
void	dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, const SimulationWorkload &simulationWork, int64_t step, gmx_domdec_t *dd, bool bMainState, t_state *state_global, const gmx_mtop_t &top_global, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, gmx::ImdSession *imdSession, pull_t *pull_work, t_state *state_local, StatePropagatorDataGpu *stateGpu, gmx::ForceBuffers *f, gmx::MDAtoms *mdAtoms, gmx_localtop_t *top_local, t_forcerec *fr, gmx::VirtualSitesHandler *vsite, gmx::Constraints *constr, t_nrnb *nrnb, gmx_wallcycle *wcycle, bool bVerbose)
	TODO Remove fplog when group scheme and charge groups are gone. More...
static void	fit_to_reference (rvec *xcoll, rvec transvec, matrix rotmat, t_edpar *edi)
static void	translate_and_rotate (rvec *x, int nat, rvec transvec, matrix rotmat)
static real	rmsd_from_structure (rvec *x, struct gmx_edx *s)
static void	crosscheck_edi_file_vs_checkpoint (const edsam &ed, edsamhistory_t *EDstate)
static void	init_edsamstate (const edsam &ed, edsamhistory_t *EDstate)
static void	write_edo_legend (edsam *ed, int nED, const gmx_output_env_t *oenv)
static char	get_EDgroupChar (int nr_edi, int nED)
static void	project (rvec *x, t_edpar *edi)
static void	do_edfit (int natoms, rvec *xp, rvec *x, matrix R, t_edpar *edi)
static void	rmfit (int nat, rvec *xcoll, const rvec transvec, matrix rotmat)
static real	flood_energy (t_edpar *edi, int64_t step)
static void	flood_forces (t_edpar *edi)
static void	update_adaption (t_edpar *edi)
static void	do_single_flood (FILE *edo, gmx::ArrayRef< const gmx::RVec > coords, gmx::ArrayRef< gmx::RVec > force, t_edpar *edi, int64_t step, const matrix box, const gmx::MpiComm &mpiComm, gmx_bool bNS)
void	do_flood (const MpiComm &mpiComm, const t_inputrec &ir, ArrayRef< const RVec > coords, ArrayRef< RVec > force, edsam *ed, const matrix box, int64_t step, bool bNS)
	Evaluate the flooding potential(s) and forces as requested in the .edi input file. More...
static void	init_flood (t_edpar *edi, edsam *ed, real dt)
static std::unique_ptr < gmx::EssentialDynamics >	ed_open (int natoms, ObservablesHistory *oh, const char *ediFileName, const char *edoFileName, const gmx::StartingBehavior startingBehavior, const gmx_output_env_t *oenv, const gmx::MpiComm &mpiComm)
static void	bc_ed_positions (const gmx::MpiComm &mpiComm, struct gmx_edx *s, EssentialDynamicsStructure stype)
static void	bc_ed_vecs (const gmx::MpiComm &mpiComm, t_eigvec *ev, int length)
static void	broadcast_ed_data (const gmx::MpiComm &mpiComm, edsam *ed)
static void	init_edi (const gmx_mtop_t &mtop, t_edpar *edi)
static void	check (const char *line, const char *label)
static int	read_checked_edint (FILE *file, const char *label)
static bool	read_checked_edbool (FILE *file, const char *label)
static int	read_edint (FILE *file, bool *bEOF)
static real	read_checked_edreal (FILE *file, const char *label)
static void	read_edx (FILE *file, int number, int *anrs, rvec *x)
static gmx_bool	check_if_same (struct gmx_edx sref, struct gmx_edx sav)
void	dd_make_local_ed_indices (gmx_domdec_t *dd, edsam *ed)
	Make a selection of the home atoms for the ED groups. More...
static void	ed_unshift_single_coord (const matrix box, const rvec x, const ivec is, rvec xu)
static void	do_radfix (rvec *xcoll, t_edpar *edi)
static void	do_radacc (rvec *xcoll, t_edpar *edi)
static void	do_radcon (rvec *xcoll, t_edpar *edi)
static void	ed_apply_constraints (rvec *xcoll, t_edpar *edi, int64_t step)
static bool	ed_constraints (EssentialDynamicsType edtype, const t_edpar &edi)
static void	copyEvecReference (t_eigvec *floodvecs, real *initialReferenceProjection)
static void	nice_legend (std::vector< std::string > *setname, std::string *LegendStr, const std::string &value, const std::string &unit, char EDgroupchar)
static void	nice_legend_evec (std::vector< std::string > *setname, std::string *LegendStr, t_eigvec *evec, char EDgroupChar, const std::string &EDtype)
std::unique_ptr < gmx::EssentialDynamics >	init_edsam (const MDLogger &mdlog, const char *ediFileName, const char *edoFileName, const gmx_mtop_t &mtop, const t_inputrec &ir, const MpiComm &mpiComm, const gmx_domdec_t *dd, Constraints *constr, const t_state *globalState, ObservablesHistory *oh, const gmx_output_env_t *oenv, StartingBehavior startingBehavior)
	Initializes the essential dynamics and flooding module. More...
void	do_edsam (const t_inputrec *ir, int64_t step, const MpiComm &mpiComm, ArrayRef< RVec > coords, ArrayRef< RVec > velocities, const matrix box, edsam *ed)
	Applies essential dynamics constrains as defined in the .edi input file. More...
static const char *	enumValueToString (PmeLoadBalancingLimit enumValue)
	Descriptive strings for PmeLoadBalancingLimit enumValue.
bool	pmeTuningIsSupported (CoulombInteractionType coulombInteractionType, bool reproducibilityRequested, const SimulationWorkload &simulationWork)
	Returns whether PME tuning is supported.
static Cutoffs	getCutoffs (const t_inputrec &ir, const matrix box, const interaction_const_t &ic, const nonbonded_verlet_t &nbv)
	Computes and returns initially set cutoffs and box.
static int	numPmeGridPoints (const pme_setup_t &setup)
	Return product of the number of PME grid points in each dimension.
static void	printGrid (FILE *fp_err, const MDLogger &mdlog, const char *pre, const char *desc, const pme_setup_t &set, double cycles)
	Print the PME grid.
static void	printLoadBalLimited (FILE *fp_err, const MDLogger &mdlog, int64_t step, const PmeLoadBalancingLimit limited, const pme_setup_t &setup)
	Print descriptive string about what limits PME load balancing.
static void	applySetup (pme_setup_t *setup, gmx_pme_t *oldPmedata, const t_inputrec &ir, interaction_const_t *ic, nonbonded_verlet_t *nbv, gmx_domdec_t *dd, const PmePpComm *pmePpComm)
	Updates all the mdrun machinery for setup. More...
static bool	processCycles (FILE *fp_err, const MDLogger &mdlog, const double cycles, const int64_t step, const bool isInLastStage, pme_setup_t *set)
	Checks the cycles and adds them to *set. More...
static void	printLoadBalSetup (const MDLogger &mdlog, const char *name, const pme_setup_t &setup)
	Print one load-balancing setting.
static void	printLoadBalSettings (const PmeLoadBalancingLimit limited, const bool currentSetupIsLastSetup, const pme_setup_t &currentSetup, const pme_setup_t &originalSetup, const bool useGpuForNonbondeds, const MDLogger &mdlog)
	Print all load-balancing settings.
static void	waitForSentData (std::vector< MPI_Request > *requests)
	Wait for the pending data send requests to PME ranks to complete.
std::string	cpuFftDescription ()
	Construct a string that describes the library that provides CPU FFT support to this build. More...
std::string	gpuFftDescription ()
	Construct a string that describes the library that provides GPU FFT support to this build. More...
std::string	multiGpuFftDescription ()
	Construct a string that describes the library (if any) that provides multi-GPU FFT support to this build. More...
static void	handleCufftError (cufftResult_t status, const char *msg)
	makePlan ("complex-to-real", rocfft_transform_type_real_inverse, PlanSetupData{rocfft_array_type_hermitian_interleaved, makeComplexStrides(complexGridSizePadded), computeTotalSize(complexGridSizePadded)}, PlanSetupData{rocfft_array_type_real, makeRealStrides(realGridSizePadded), computeTotalSize(realGridSizePadded)}, std::vector< size_t >{size_t(realGridSize[ZZ]), size_t(realGridSize[YY]), size_t(realGridSize[XX])})}
realGrid_	pmeStream_ (pmeStream)
static void	handleClfftError (clfftStatus status, const char *msg)
	Throws the exception on clFFT error.
	makePlan ("complex-to-real", rocfft_transform_type_real_inverse, PlanSetupData{rocfft_array_type_hermitian_interleaved, makeComplexStrides(complexGridSizePadded), computeTotalSize(complexGridSizePadded)}, PlanSetupData{rocfft_array_type_real, makeRealStrides(realGridSizePadded), computeTotalSize(realGridSizePadded)}, std::vector< size_t >{size_t(realGridSize[ZZ]), size_t(realGridSize[YY]), size_t(realGridSize[XX])}, pmeStream)
realGrid_ *	realGrid ()),{GMX_RELEASE_ASSERT(performOutOfPlaceFFT,"Only out-of-place FFT is implemented"
	GMX_RELEASE_ASSERT (allocateRealGrid==false,"Grids need to be pre-allocated")
	GMX_RELEASE_ASSERT (gridSizesInXForEachRank.size()==1 &&gridSizesInYForEachRank.size()==1,"FFT decomposition not implemented with the SYCL rocFFT backend")
template<typename NativeQueue >
static void	launchVkFft (const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication *application, VkFFTLaunchParams *launchParams)
void	handleRocFftError (rocfft_status result, const char *msg)
	Helper for consistent error handling.
void	handleRocFftError (rocfft_status result, const char *direction, const char *msg)
	Helper for consistent error handling.
std::array< size_t, DIM >	makeRealStrides (ivec realGridSizePadded)
	Compute the stride through the real 1D array.
std::array< size_t, DIM >	makeComplexStrides (ivec complexGridSizePadded)
	Compute the stride through the complex 1D array.
size_t	computeTotalSize (ivec gridSize)
	Compute total grid size.
template<typename ValueType >
void	readKvtCheckpointValue (compat::not_null< ValueType * > value, std::string_view name, std::string_view identifier, const KeyValueTreeObject &kvt)
	Read to a key-value-tree value used for checkpointing. More...
template void	readKvtCheckpointValue (compat::not_null< std::int64_t * > value, std::string_view name, std::string_view identifier, const KeyValueTreeObject &kvt)
	Read to a key-value-tree value used for checkpointing. More...
template void	readKvtCheckpointValue (compat::not_null< real * > value, std::string_view name, std::string_view identifier, const KeyValueTreeObject &kvt)
	Read to a key-value-tree value used for checkpointing. More...
template<typename ValueType >
void	writeKvtCheckpointValue (const ValueType &value, std::string_view name, std::string_view identifier, KeyValueTreeObjectBuilder kvtBuilder)
	Write to a key-value-tree used for checkpointing. More...
template void	writeKvtCheckpointValue (const std::int64_t &value, std::string_view name, std::string_view identifier, KeyValueTreeObjectBuilder kvtBuilder)
	Write to a key-value-tree used for checkpointing. More...
template void	writeKvtCheckpointValue (const real &value, std::string_view name, std::string_view identifier, KeyValueTreeObjectBuilder kvtBuilder)
	Write to a key-value-tree used for checkpointing. More...
void	write_checkpoint_data (const std::filesystem::path &filename, CheckpointHeaderContents headerContents, gmx_bool bExpanded, LambdaWeightCalculation elamstats, t_state *state, ObservablesHistory *observablesHistory, const MDModulesNotifiers &mdModulesNotifiers, std::vector< gmx_file_position_t > *outputfiles, WriteCheckpointDataHolder *modularSimulatorCheckpointData)
	Low-level checkpoint writing function.
static void	check_int (FILE *fplog, const char *type, int p, int f, gmx_bool *mm)
static void	check_string (FILE *fplog, const char *type, const char *p, const char *f, gmx_bool *mm)
static void	check_match (FILE *fplog, const CheckpointHeaderContents &headerContents, gmx_bool reproducibilityRequested)
static void	read_checkpoint (const std::filesystem::path &fn, t_fileio *logfio, const MpiComm &mpiCommSimulation, IntegrationAlgorithm eIntegrator, int *init_fep_state, CheckpointHeaderContents *headerContents, t_state *state, ObservablesHistory *observablesHistory, gmx_bool reproducibilityRequested, const MDModulesNotifiers &mdModulesNotifiers, ReadCheckpointDataHolder *modularSimulatorCheckpointData, bool useModularSimulator)
void	load_checkpoint (const std::filesystem::path &fn, t_fileio *logfio, const MpiComm &mpiCommSimulation, t_inputrec *ir, t_state *state, ObservablesHistory *observablesHistory, gmx_bool reproducibilityRequested, const MDModulesNotifiers &mdModulesNotifiers, ReadCheckpointDataHolder *modularSimulatorCheckpointData, bool useModularSimulator)
void	read_checkpoint_part_and_step (const std::filesystem::path &filename, int *simulation_part, int64_t *step)
	Read simulation step and part from a checkpoint file. More...
static CheckpointHeaderContents	read_checkpoint_data (XdrSerializer *serializer, t_state *state, std::vector< gmx_file_position_t > *outputfiles, ReadCheckpointDataHolder *modularSimulatorCheckpointData)
void	read_checkpoint_trxframe (const std::filesystem::path &filename, t_trxframe *fr)
	Read everything that can be stored in t_trxframe from a checkpoint file. More...
void	list_checkpoint (const std::filesystem::path &fn, FILE *out)
CheckpointHeaderContents	read_checkpoint_simulation_part_and_filenames (const std::filesystem::path &filename, std::vector< gmx_file_position_t > *outputfiles)
	Return header information from an open checkpoint file. More...
H5md *	makeH5md (const std::filesystem::path &fileName, H5mdFileMode mode)
	Builder method to isolate creation from callers. More...
void	setupFileFromInput (H5md *h5md, const gmx_mtop_t &topology, const t_inputrec &inputRecord)
	Set up the file from input data. More...
void	setupFromExistingFileForAppending (H5md *h5md, int64_t restartingFromStep, int64_t numParticles)
	Set up from an existing h5md file for restarting with appending. More...
void	writeNextFrame (H5md *h5md, ArrayRef< const RVec > positions, ArrayRef< const RVec > velocities, ArrayRef< const RVec > forces, const matrix box, int64_t step, double time)
	Write input data as the next frame of the trajectory. More...
void	destroyH5md (H5md *h5md)
	Deallocate h5md.
void	flushH5md (H5md *h5md)
	Flush h5md file.
void	setStringAttributeByBuffer (hid_t container, const char *attributeName, size_t numberOfStrings, int maxStrLength, ArrayRef< const char > buffer)
	Low-level utility function to write a string-vector attribute via a character buffer. More...
template<typename ValueType >
std::optional< ValueType >	getAttribute (hid_t container, const char *attributeName)
	Read an attribute of a given data type. More...
template<>
std::optional< std::string >	getAttribute< std::string > (hid_t container, const char *attributeName)
	Read an attribute of a given data type. More...
template<typename ValueType >
std::optional< std::vector < ValueType > >	getAttributeVector (hid_t container, const char *attributeName)
	Read a vector-like attribute of a given data type. More...
template<>
std::optional< std::vector < std::string > >	getAttributeVector< std::string > (hid_t container, const char *attributeName)
	Read a vector-like attribute of a given data type. More...
template<typename ValueType >
void	setAttribute (hid_t container, const char *attributeName, const ValueType &value)
	Write a scalar attribute of a given data type. More...
void	setAttribute (hid_t container, const char *attributeName, const char *value)
	Write a scalar attribute of a given data type. More...
void	setAttribute (hid_t container, const char *attributeName, const std::string &value)
	Write a scalar attribute of a given data type. More...
template<typename ValueType >
void	setAttributeVector (hid_t container, const char *attributeName, ArrayRef< const ValueType > value)
	Write a vector-like attribute of a given data type. More...
void	setAttributeVector (hid_t container, const char *attributeName, ArrayRef< const std::string > values)
	Write a vector-like attribute of strings. More...
void	setAttributeVector (hid_t container, const char *attributeName, ArrayRef< const char *const > values)
	Write a vector-like attribute of C-strings. More...
template<typename Iterator >
std::vector< char >	setAttributeStringVector (hid_t container, const char *attributeName, std::vector< char > &&buffer, Iterator begin, Iterator end)
	Write a vector-like string attribute via iterators String data type is treated specially because of the HDF5 requirements for contiguous memory storage for fixed-length strings. A reusable character buffer is needed to avoid frequent memory allocations for multiple writing of different string attributes. More...
template<typename ValueType >
static DataSetDims	primitiveDimsToValueTypeDims (const DataSetDims &dims)
	Return the dimensions of the templated ValueType for the primitive type data set dimensions.
static hsize_t	numValuesInDataSet (const DataSetDims &dims)
	Return the number of values in a data set with templated type dimensions dims.
static DataSetDims	getFullDims (const DataSetDims &dataSetDims)
static hsize_t	getNumValues (const DataSetDims &dims)
hid_t	createGroup (hid_t container, const char *name)
	Create an H5MD group, and intermediate groups if they do not exist. More...
hid_t	openGroup (hid_t container, const char *name)
	Open an existing HDF5 group. More...
hid_t	openOrCreateGroup (hid_t container, const char *name)
	Open an existing HDF5 group or create it if it did not exist already. More...
std::pair< hid_t, H5mdGuard >	makeH5mdGuard (hid_t object, H5mdCloseType unboundCloser)
	Helper function for guarding an HDF5 object with a closing function (H5Gclose, etc.). More...
std::pair< hid_t, H5mdGuard >	makeH5mdGroupGuard (hid_t object)
	Helper function for guarding an HDF5 group with H5Gclose. More...
std::pair< hid_t, H5mdGuard >	makeH5mdDataSetGuard (hid_t object)
	Helper function for guarding an HDF5 data set with H5Dclose. More...
std::pair< hid_t, H5mdGuard >	makeH5mdDataSpaceGuard (hid_t object)
	Helper function for guarding an HDF5 data space with H5Sclose. More...
std::pair< hid_t, H5mdGuard >	makeH5mdPropertyListGuard (hid_t object)
	Helper function for guarding an HDF5 property list with H5Pclose. More...
std::pair< hid_t, H5mdGuard >	makeH5mdAttributeGuard (hid_t object)
	Helper function for guarding an HDF5 attribute with H5Aclose. More...
std::pair< hid_t, H5mdGuard >	makeH5mdTypeGuard (hid_t object)
	Helper function for guarding an HDF5 type with H5Tclose. More...
IndexMap	mapSelectionToInternalIndices (ArrayRef< const int32_t > selectedIndices)
	Map the selected atoms to local internal indices. More...
void	writeAtomicProperties (AtomRange &atomRange, hid_t baseContainer, const std::optional< IndexMap > &selectedAtomsIndexMap=std::nullopt)
	Write atomic properties to the H5MD file. More...
void	writeResidueInfo (AtomRange &atomRange, hid_t baseContainer, const std::optional< IndexMap > &selectedAtomsIndexMap=std::nullopt)
	Write residue and sequence information to the H5MD file. More...
void	writeBonds (const gmx_mtop_t &topology, hid_t baseContainer, const std::optional< IndexMap > &selectedAtomsIndexMap=std::nullopt)
	Write the covalent connectivity to the H5MD file. More...
void	writeDisulfideBonds (const gmx_mtop_t &topology, hid_t baseContainer, const std::optional< IndexMap > &selectedAtomsIndexMap=std::nullopt)
	Write the additional annotation of disulfide bonds to the H5MD file. More...
void	labelInternalTopologyVersion (hid_t baseContainer)
	Label the version of the internal topology module. More...
void	labelTopologyName (hid_t baseContainer, const char *topName)
	Label the name of the simulation system. More...
void	writeMoleculeTypes (hid_t baseContainer, ArrayRef< const gmx_moltype_t > molTypes)
	Write the internal representation of molecules molTypes to the HDF5 container baseContainer of GROMACS topology. More...
void	writeMoleculeBlocks (hid_t baseContainer, ArrayRef< const gmx_molblock_t > molBlocks, ArrayRef< const gmx_moltype_t > molTypes)
	Write the molecule block information to the HDF5 container of GROMACS topology. More...
template<typename ValueType >
hid_t	hdf5DataTypeFor () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
template<>
hid_t	hdf5DataTypeFor< int32_t > () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
template<>
hid_t	hdf5DataTypeFor< int64_t > () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
template<>
hid_t	hdf5DataTypeFor< float > () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
template<>
hid_t	hdf5DataTypeFor< double > () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
template<>
hid_t	hdf5DataTypeFor< uint32_t > () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
template<>
hid_t	hdf5DataTypeFor< uint64_t > () noexcept
	Return a handle to a native HDF5 type corresponding to the templated value type. More...
hid_t	hdf5DataTypeForFixedLengthString (const hsize_t maxStringLength)
	Return a handle to a HDF5 data type for fixed-length strings. More...
hid_t	hdf5DataTypeForVariableLengthString ()
	Return a handle to a HDF5 data type for variable-length strings.
template<typename ValueType >
bool	valueTypeIsDataType (const hid_t dataType) noexcept
	Return true if the template value type matches the HDF5 data type. More...
template<>
bool	valueTypeIsDataType< char * > (const hid_t dataType) noexcept
	Return true if the template value type matches the HDF5 data type. More...
template<>
bool	valueTypeIsDataType< const char * > (const hid_t dataType) noexcept
	Return true if the template value type matches the HDF5 data type. More...
template<>
bool	valueTypeIsDataType< std::string > (const hid_t dataType) noexcept
	Return true if the template value type matches the HDF5 data type. More...
template<typename ValueType >
bool	valueTypeIsDataType (const hid_t dataType, const ArrayRef< const ValueType > gmx_unused valueBuffer) noexcept
	Return true if the template value type matches the HDF5 data type. More...
bool	objectExists (const hid_t container, const char *name) noexcept
	Return whether object name exists in the given HDF5 container. More...
bool	handleIsValid (const hid_t handle) noexcept
	Return whether HDF5 handle is valid. More...
std::optional< std::string >	getHandlePath (const hid_t handle)
	Return the full name (HDF-path) of an HDF5 handle. More...
std::optional< std::string >	getHandleBaseName (const hid_t handle)
	Return the base name (last component of the HDF-path) of an HDF5 handle. More...
template<typename Iterator , typename Callback >
std::pair< size_t, size_t >	estimateBufferSize (Iterator begin, Iterator end, Callback cStringFromIterator)
	Iterate over a list of objects and calculate the maximum string length via a callback function. More...
template<typename Iterator , typename Callback >
std::vector< char >	packBufferViaIterator (Iterator begin, Iterator end, std::vector< char > &&packingBuffer, const size_t maxStrLength, Callback cStringFromIterator)
	Pack a string buffer from a range of iterators and a callback function. More...
size_t	numberOfExpectedDataItems (const MrcDensityMapHeader &header)
	Return the number of density data items that are expected to follow this header. More...
TranslateAndScale	getCoordinateTransformationToLattice (const MrcDensityMapHeader &header)
	Extract the transformation into lattice coordinates. More...
dynamicExtents3D	getDynamicExtents3D (const MrcDensityMapHeader &header)
	Extract the extents of the density data. More...
bool	mrcHeaderIsSane (const MrcDensityMapHeader &header)
	Checks if the values in the header are sane. More...
void	serializeMrcDensityMapHeader (ISerializer *serializer, const MrcDensityMapHeader &mrcHeader)
	Serializes an MrcDensityMapHeader from a given serializer. More...
MrcDensityMapHeader	deserializeMrcDensityMapHeader (ISerializer *serializer)
	Deserializes an MrcDensityMapHeader from a given serializer. More...
const char *	enumValueToString (YesNoType enumValue)
	Strings for YesNoType.
std::string	tngDescription ()
	Returns information for describing the TNG support.
std::string	fmmBackendName (ActiveFmmBackend backend)
	Returns the string name for a given FMM backend. More...
std::string	fmmDirectProviderName (FmmDirectProvider directProvider)
	Returns the string name for a given FMM direct provider. More...
std::string	exaFmmTreeTypeName (ExaFmmTreeType treeType)
	Returns the string name for a given ExaFmm Tree Type. More...
void	add_param (InteractionsOfType *ps, int ai, int aj, ArrayRef< const real > c, const char *s)
	Adds an interaction to the list of interactions. More...
void	add_cmap_param (InteractionsOfType *ps, int ai, int aj, int ak, int al, int am, ArrayRef< const real > c, const char *s)
	Adds a CMAP interaction to the list of interactions. More...
void	add_vsite2_param (InteractionsOfType *ps, int ai, int aj, int ak, real c0)
void	add_vsite3_param (InteractionsOfType *ps, int ai, int aj, int ak, int al, real c0, real c1)
void	add_vsite3_atoms (InteractionsOfType *ps, int ai, int aj, int ak, int al, bool bSwapParity)
void	add_vsite4_atoms (InteractionsOfType *ps, int ai, int aj, int ak, int al, int am)
int	search_jtype (const PreprocessResidue &localPpResidue, const char *name, bool bNterm)
static void	gen_waterhydrogen (int nh, rvec xa[], rvec xh[], int *l)
void	calc_h_pos (int nht, rvec xa[], rvec xh[], int *l)
static int	div_nsteps (int nsteps, int nst)
double	compute_io (const t_inputrec *ir, int natoms, const SimulationGroups &groups, int nrener, int nrepl)
	Return an estimate of the total output in MiB to be written from this simulation.
static int	round_check (real r, int limit, InteractionFunction ftype, const char *name)
static void	set_ljparams (CombinationRule comb, double reppow, double v, double w, real *c6, real *c12)
static int	assign_param (InteractionFunction ftype, t_iparams *newparam, ArrayRef< const real > old, CombinationRule comb, double reppow)
static int	enter_params (gmx_ffparams_t *ffparams, InteractionFunction ftype, ArrayRef< const real > forceparams, CombinationRule comb, real reppow, int start, bool bAppend)
static void	append_interaction (InteractionList *ilist, int type, ArrayRef< const int > a)
static void	enter_function (const InteractionsOfType *p, InteractionFunction ftype, CombinationRule comb, real reppow, gmx_ffparams_t *ffparams, InteractionList *il, bool bNB, bool bAppend)
bool	shouldConvertInteractionType (InteractionFunction ftype)
	Whether interactions of type ftype should have parameters converted.
void	convertInteractionsOfType (int atnr, const EnumerationArray< InteractionFunction, InteractionsOfType > &nbtypes, ArrayRef< const MoleculeInformation > mi, const MoleculeInformation *intermolecular_interactions, CombinationRule comb, double reppow, real fudgeQQ, gmx_mtop_t *mtop)
	Convert the raw arrays of parameters read from the topology file to those which match the interaction type and fill into mtop. More...
static real	calc_mass (t_atoms *atoms, gmx_bool bGetMass, AtomProperties *aps)
static real	calc_geom (int isize, const int *index, rvec *x, rvec geom_center, rvec minval, rvec maxval, gmx_bool bDiam)
static void	center_conf (int natom, rvec *x, rvec center, rvec geom_cent)
static void	scale_conf (int natom, rvec x[], matrix box, const rvec scale)
static void	read_bfac (const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
static void	set_pdb_conf_bfac (int natoms, int nres, t_atoms *atoms, int n_bfac, double *bfac, int *bfac_nr, gmx_bool peratom)
static void	pdb_legend (FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
static void	visualize_images (const char *fn, PbcType pbcType, matrix box)
static void	visualize_box (FILE *out, int a0, int r0, matrix box, const rvec gridsize)
static void	calc_rotmatrix (rvec principal_axis, rvec targetvec, matrix rotmatrix)
static void	renum_resnr (t_atoms *atoms, int isize, const int *index, int resnr_start)
int	gmx_editconf (int argc, char *argv[])
std::filesystem::path	fflib_forcefield_dir_ext ()
std::filesystem::path	fflib_forcefield_itp ()
std::filesystem::path	fflib_forcefield_doc ()
std::filesystem::path	fflib_filename_base (const std::filesystem::path &filename)
std::vector < std::filesystem::path >	fflib_search_file_end (const std::filesystem::path &ffdir, const char *file_end, bool bFatalError)
std::vector< DataFileInfo >	fflib_enumerate_forcefields ()
	Enumerates forcefields in the data directories.
bool	fflib_fexist (const std::filesystem::path &file)
FILE *	fflib_open (const std::filesystem::path &file)
static bool	was_dihedral_set_in_rtp (const InteractionOfType &dih)
static bool	acomp (const InteractionOfType &a1, const InteractionOfType &a2)
static bool	pcomp (const InteractionOfType &a1, const InteractionOfType &a2)
static bool	dcomp (const InteractionOfType &d1, const InteractionOfType &d2)
static bool	is_dihedral_on_same_bond (const InteractionOfType &p1, const InteractionOfType &p2)
static bool	preq (const InteractionOfType &p1, const InteractionOfType &p2)
static void	rm2par (std::vector< InteractionOfType > *p, peq eq)
static void	cppar (ArrayRef< const InteractionOfType > types, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, InteractionFunction ftype)
static bool	idcomp (const InteractionOfType &a, const InteractionOfType &b)
static void	sort_id (ArrayRef< InteractionOfType > ps)
static int	n_hydro (ArrayRef< const int > a, char ***atomname)
static bool	dihedralIsOnSameBondAsImproper (const InteractionOfType &dihedral, ArrayRef< const InteractionOfType > improperDihedrals)
static std::vector < InteractionOfType >	clean_dih (ArrayRef< const InteractionOfType > originalDihedrals, ArrayRef< const InteractionOfType > improperDihedrals, t_atoms *atoms, bool bKeepAllGeneratedDihedrals, bool bRemoveDihedralIfWithImproper)
static std::vector < InteractionOfType >	get_impropers (t_atoms *atoms, ArrayRef< MoleculePatchDatabase > globalPatches, bool bAllowMissing, ArrayRef< const int > cyclicBondsIndex, ArrayRef< const DisulfideBond > ssbonds)
static int	nb_dist (t_nextnb *nnb, int ai, int aj)
static bool	is_hydro (t_atoms *atoms, int ai)
static void	get_atomnames_min (int n, ArrayRef< std::string > anm, int resind, t_atoms *atoms, ArrayRef< const int > a)
static void	gen_excls (t_atoms *atoms, t_excls *excls, ArrayRef< MoleculePatchDatabase > globalPatches, bool bAllowMissing, ArrayRef< const int > cyclicBondsIndex)
static void	remove_excl (t_excls *excls, int remove)
static void	clean_excls (t_nextnb *nnb, int nrexcl, t_excls excls[])
void	gen_pad (t_atoms *atoms, ArrayRef< const PreprocessResidue > rtpFFDB, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, t_excls excls[], ArrayRef< MoleculePatchDatabase > globalPatches, bool bAllowMissing, ArrayRef< const int > cyclicBondsIndex, ArrayRef< const DisulfideBond > ssbonds)
	Generate pairs, angles and dihedrals from .rtp settings. More...
static void	low_mspeed (real tempi, gmx_mtop_t *mtop, rvec v[], ThreeFry2x64<> *rng, const MDLogger &logger)
void	maxwell_speed (real tempi, int seed, gmx_mtop_t *mtop, rvec v[], const MDLogger &logger)
	Generate Maxwellian velocities. More...
static real	calc_cm (int natoms, const real mass[], rvec x[], rvec v[], rvec xcm, rvec vcm, rvec acm, matrix L)
void	stop_cm (const MDLogger gmx_unused &logger, int natoms, real mass[], rvec x[], rvec v[])
void	stop_cm (const MDLogger &logger, int natoms, real mass[], rvec x[], rvec v[])
	Remove the center of mass motion in a set of coordinates. More...
static int	ddb_name2dir (char *name)
static void	read_vsite_database (const std::filesystem::path &ddbname, std::vector< VirtualSiteConfiguration > *vsiteconflist, std::vector< VirtualSiteTopology > *vsitetoplist)
static int	nitrogen_is_planar (ArrayRef< const VirtualSiteConfiguration > vsiteconflist, const std::string &atomtype)
static std::string	get_dummymass_name (ArrayRef< const VirtualSiteConfiguration > vsiteconflist, const std::string &atom, const std::string &nextheavy)
static real	get_ddb_bond (ArrayRef< const VirtualSiteTopology > vsitetop, const std::string &res, const std::string &atom1, const std::string &atom2)
static real	get_ddb_angle (ArrayRef< const VirtualSiteTopology > vsitetop, const std::string &res, const std::string &atom1, const std::string &atom2, const std::string &atom3)
static void	count_bonds (int atom, InteractionsOfType *psb, char ***atomname, int *nrbonds, int *nrHatoms, int Hatoms[], int *Heavy, int *nrheavies, int heavies[])
static void	print_bonds (FILE *fp, int o2n[], int nrHatoms, const int Hatoms[], int Heavy, int nrheavies, const int heavies[])
static int	get_atype (int atom, t_atoms *at, ArrayRef< const PreprocessResidue > rtpFFDB, const ResidueTypeMap &residueTypeMap)
static int	vsite_nm2type (const char *name, PreprocessingAtomTypes *atype)
static real	get_amass (int atom, t_atoms *at, ArrayRef< const PreprocessResidue > rtpFFDB, const ResidueTypeMap &residueTypeMap)
static void	my_add_param (InteractionsOfType *plist, int ai, int aj, real b)
static void	add_vsites (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, ArrayRef< const VsiteTypeAndSign > vsite_type, int Heavy, int nrHatoms, int Hatoms[], int nrheavies, int heavies[])
static int	gen_vsites_6ring (t_atoms *at, ArrayRef< VsiteTypeAndSign > vsite_type, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, int nrfound, int *ats, real bond_cc, real bond_ch, real xcom, bool bDoZ)
static int	gen_vsites_phe (t_atoms *at, ArrayRef< VsiteTypeAndSign > vsite_type, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, int nrfound, int *ats, ArrayRef< const VirtualSiteTopology > vsitetop)
static void	calc_vsite3_param (real xd, real yd, real xi, real yi, real xj, real yj, real xk, real yk, real *a, real *b)
static int	gen_vsites_trp (PreprocessingAtomTypes *atype, std::vector< RVec > *newx, t_atom *newatom[], char ***newatomname[], int *o2n[], std::vector< VsiteTypeAndSign > *newvsite_type, t_symtab *symtab, int *nadd, ArrayRef< const RVec > x, t_atoms *at, ArrayRef< VsiteTypeAndSign > vsite_type, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, int nrfound, int *ats, int add_shift, ArrayRef< const VirtualSiteTopology > vsitetop)
static int	gen_vsites_tyr (PreprocessingAtomTypes *atype, std::vector< RVec > *newx, t_atom *newatom[], char ***newatomname[], int *o2n[], std::vector< VsiteTypeAndSign > *newvsite_type, t_symtab *symtab, int *nadd, ArrayRef< const RVec > x, t_atoms *at, ArrayRef< VsiteTypeAndSign > vsite_type, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, int nrfound, int *ats, int add_shift, ArrayRef< const VirtualSiteTopology > vsitetop)
static int	gen_vsites_his (t_atoms *at, ArrayRef< VsiteTypeAndSign > vsite_type, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, int nrfound, int *ats, ArrayRef< const VirtualSiteTopology > vsitetop)
static bool	is_vsite (const std::optional< InteractionFunction > &vsiteType)
	Returns true when vsiteType is set and the value is an interaction type that is a vsite.
void	do_vsites (ArrayRef< const PreprocessResidue > rtpFFDB, PreprocessingAtomTypes *atype, t_atoms *at, t_symtab *symtab, std::vector< RVec > *x, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, std::vector< VsiteTypeAndSign > *vsiteTypeAndSign, real mHmult, bool bVSiteAromatics, const std::filesystem::path &ffdir)
	Turn all hydrogens that can be turned into virtual sites into virtual sites.
void	do_h_mass (const InteractionsOfType &psb, ArrayRef< const VsiteTypeAndSign > vsiteType, t_atoms *at, real mHmult, bool deuterate)
	Optionally, change masses of hydrogens. More...
static void	rand_rot (int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[], DefaultRandomEngine *rng, const rvec max_rot)
int	gmx_genconf (int argc, char *argv[])
static void	copy_atom (const t_atoms *atoms1, int a1, t_atoms *atoms2, int a2, t_symtab *symtab)
static std::optional< int >	pdbasearch_atom (const char *name, int resind, const t_atoms *pdba, const char *searchtype, bool bAllowMissing, ArrayRef< const int > cyclicBondsIndex)
static bool	hasNumericSuffixAfterStem (const std::string &atomName, const std::string &stem)
static int	numericSuffixAfterStem (const std::string &atomName, const std::string &stem)
static bool	shouldLookupHydrogenNameFromResidueTopology (const MoleculePatch &patch)
static std::optional< const char * >	bondedAtomNameIfBondedToAttachmentAtom (const BondedInteraction &bond, const MoleculePatch &patch)
static bool	matchesHydrogenNameFromResidueTopology (const char *bondedAtomName, const MoleculePatch &patch)
static void	sortHydrogenNamesByNumericSuffix (std::vector< std::string > *names, const MoleculePatch &patch)
static std::vector< std::string >	findHydrogenAtomNamesInResidue (const PreprocessResidue &residueTopology, const MoleculePatch &patch)
static bool	patchAppliesToLocalAtom (const MoleculePatch &patch, const std::string &localAtomName)
static void	hacksearch_atom (int *ii, int *jj, const char *name, ArrayRef< const std::vector< MoleculePatch >> patches, int resind, const t_atoms *pdba)
	Return the index of the first atom whose residue index matches and which has a patch with the given name. More...
static std::vector < MoleculePatchDatabase >	getMoleculePatchDatabases (const t_atoms *pdba, ArrayRef< const MoleculePatchDatabase > globalPatches, int nterpairs, ArrayRef< MoleculePatchDatabase *const > ntdb, ArrayRef< MoleculePatchDatabase *const > ctdb, ArrayRef< const int > rN, ArrayRef< const int > rC)
static void	expand_hackblocks_one (const MoleculePatchDatabase &newPatch, const std::string localAtomName, const PreprocessResidue &residueTopology, std::vector< MoleculePatch > *globalPatches, bool bN, bool bC)
static void	expand_hackblocks (const t_atoms *pdba, ArrayRef< const MoleculePatchDatabase > hb, ArrayRef< const PreprocessResidue > residueTopology, ArrayRef< std::vector< MoleculePatch >> patches, int nterpairs, ArrayRef< const int > rN, ArrayRef< const int > rC)
static int	check_atoms_present (const t_atoms *pdba, ArrayRef< std::vector< MoleculePatch >> patches, ArrayRef< const int > cyclicBondsIndex)
static void	calc_all_pos (const t_atoms *pdba, ArrayRef< const RVec > x, ArrayRef< std::vector< MoleculePatch >> patches, bool bCheckMissing, ArrayRef< const int > cyclicBondsIndex)
static int	add_h_low (t_atoms **initialAtoms, t_atoms **modifiedAtoms, std::vector< RVec > *xptr, ArrayRef< const MoleculePatchDatabase > globalPatches, ArrayRef< const PreprocessResidue > residueTopology, t_symtab *symtab, const int nterpairs, ArrayRef< MoleculePatchDatabase *const > ntdb, ArrayRef< MoleculePatchDatabase *const > ctdb, ArrayRef< const int > rN, ArrayRef< const int > rC, const bool bCheckMissing, ArrayRef< const int > cyclicBondsIndex)
int	add_h (t_atoms **initialAtoms, t_atoms **localAtoms, std::vector< gmx::RVec > *xptr, gmx::ArrayRef< const MoleculePatchDatabase > globalPatches, gmx::ArrayRef< const PreprocessResidue > residueTopology, t_symtab *symtab, int nterpairs, gmx::ArrayRef< MoleculePatchDatabase *const > ntdb, gmx::ArrayRef< MoleculePatchDatabase *const > ctdb, gmx::ArrayRef< const int > rN, gmx::ArrayRef< const int > rC, bool bMissing, gmx::ArrayRef< const int > cyclicBondsIndex)
	Generate hydrogen atoms and N and C terminal patches. More...
static bool	groupsCloserThanCutoffWithPbc (t_pbc *pbc, rvec x[], ArrayRef< const int > smallerGroupIndices, ArrayRef< const int > largerGroupIndices, real minimumDistance)
	Return whether any atoms of two groups are below minimum distance. More...
static std::vector< int >	solventMoleculeIndices (int solventMoleculeNumber, int numberAtomsPerSolventMolecule, ArrayRef< const int > solventGroupIndex)
	Calculate the solvent molecule atom indices from molecule number. More...
static void	insert_ion (int nsa, std::vector< int > *solventMoleculesForReplacement, int repl[], ArrayRef< const int > index, rvec x[], t_pbc *pbc, int sign, int q, const char *ionname, t_atoms *atoms, real rmin, std::vector< int > *notSolventGroup)
static char *	aname (const char *mname)
static void	sort_ions (int nsa, int nw, const int repl[], ArrayRef< const int > index, t_atoms *atoms, rvec x[], char **pptr, char **nptr, char **paptr, char **naptr)
static void	update_topol (const char *topinout, int p_num, int n_num, const char *p_name, const char *n_name, char *grpname)
static std::vector< int >	invertIndexGroup (int nrAtoms, std::vector< int > indexGroup)
	Return all atom indices that do not belong to an index group. More...
int	gmx_genion (int argc, char *argv[])
int	gmx_genrestr (int argc, char *argv[])
static bool	is_word_end (char c)
static const char *	strstrw (const char *buf, const char *word)
static bool	find_directive (const char *buf, std::string *name, std::string *val)
static bool	is_ifdeffed_out (ArrayRef< const int > ifdefs)
static void	add_include (std::vector< std::filesystem::path > *includes, const std::filesystem::path &includePath)
static void	add_define (std::vector< t_define > *defines, const std::string &name, const char *value)
static int	cpp_open_file (const std::filesystem::path &filenm, CPreProcessor_t *handle, char **cppopts, std::shared_ptr< std::vector< t_define >> *definesFromParent, std::shared_ptr< std::vector< std::filesystem::path >> *includesFromParent)
int	cpp_open_file (const std::filesystem::path &filenm, CPreProcessor_t *handle, char **cppopts)
static int	process_directive (CPreProcessor_t *handlep, const std::string &dname, const std::string &dval)
int	cpp_read_line (CPreProcessor_t *handlep, int n, char buf[])
std::filesystem::path	cpp_cur_file (const CPreProcessor_t *handlep)
int	cpp_cur_linenr (const CPreProcessor_t *handlep)
int	cpp_close_file (CPreProcessor_t *handlep)
const std::string *	cpp_find_define (const CPreProcessor_t *handlep, const std::string &defineName)
void	cpp_done (CPreProcessor_t handle)
char *	cpp_error (CPreProcessor_t *handlep, int status)
std::string	checkAndWarnForUnusedDefines (const CPreProcessor &handle)
static int	search_atomtypes (const PreprocessingAtomTypes *ga, int *n, ArrayRef< int > typelist, int thistype, ArrayRef< const InteractionOfType > interactionTypes, InteractionFunction ftype)
static int	bond_sort (const void *a, const void *b)
static int	compare_int (const void *a, const void *b)
void	init_nnb (t_nextnb *nnb, int nr, int nrex)
static void	add_nnb (t_nextnb *nnb, int nre, int i, int j)
void	done_nnb (t_nextnb *nnb)
static void	nnb2excl (t_nextnb *nnb, ListOfLists< int > *excls)
static bool	atom_is_present_in_nnb (const t_nextnb *nnb, int atom, int highest_order, int query)
	Return true of neighbor is already present in some exclusion level. More...
static void	do_gen (int nrbonds, sortable *s, t_nextnb *nnb)
static void	add_b (InteractionsOfType *bonds, int *nrf, sortable *s)
void	gen_nnb (t_nextnb *nnb, EnumerationArray< InteractionFunction, InteractionsOfType > &plist)
static void	sort_and_purge_nnb (t_nextnb *nnb)
void	generate_excl (int nrexcl, int nratoms, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, ListOfLists< int > *excls)
int	gmx_grompp (int argc, char *argv[])
bool	is_int (double x)
void	print_ab (FILE *out, const MoleculePatch &hack, const char *nname)
void	read_ab (char *line, const std::filesystem::path &fn, MoleculePatch *hack)
static void	read_h_db_file (const std::filesystem::path &hfn, std::vector< MoleculePatchDatabase > *globalPatches)
int	read_h_db (const std::filesystem::path &ffdir, std::vector< MoleculePatchDatabase > *globalPatches)
	Read the databse from hdb file(s). More...
ArrayRef< const MoleculePatchDatabase > ::iterator	search_h_db (ArrayRef< const MoleculePatchDatabase > globalPatches, const char *key)
	Search for an entry. More...
const char *	enumValueToString (BondedTypes enumValue)
	Names for interaction type entries.
int	enumValueToNumIAtoms (BondedTypes enumValue)
	Numbers for atoms in the interactions.
void	clearModificationBlock (MoleculePatchDatabase *globalPatches)
	Reset modification block. More...
static bool	contains_char (const BondedInteraction &s, char c)
static int	rbonded_find_atoms_in_list (const BondedInteraction &b, ArrayRef< const BondedInteraction > blist, int natoms)
bool	mergeBondedInteractionList (ArrayRef< const BondedInteractionList > s, ArrayRef< BondedInteractionList > d, bool bMin, bool bPlus)
	Add bond information in s to d. More...
void	copyPreprocessResidues (const PreprocessResidue &s, PreprocessResidue *d, t_symtab *symtab)
	Copy residue information. More...
void	mergeAtomModifications (const MoleculePatchDatabase &s, MoleculePatchDatabase *d)
	Add the individual modifications in s to d. More...
void	mergeAtomAndBondModifications (const MoleculePatchDatabase &s, MoleculePatchDatabase *d)
	Add the individual modifications in s to d. More...
void	copyModificationBlocks (const MoleculePatchDatabase &s, MoleculePatchDatabase *d)
	Copy all information from datastructure. More...
static int	in_strings (char *key, int nstr, const char **str)
static bool	hbond (rvec x[], int i, int j, real distance)
static void	chk_allhb (t_atoms *pdba, rvec x[], t_blocka *hb, const bool donor[], const bool accept[], real dist)
static bool	chk_hbonds (int i, t_atoms *pdba, rvec x[], const bool ad[], bool hbond[], rvec xh, real angle, real dist)
static void	calc_ringh (rvec xattach, rvec xb, rvec xc, rvec xh)
void	set_histp (t_atoms *pdba, rvec *x, t_symtab *symtab, real angle, real dist)
static void	center_molecule (ArrayRef< RVec > x)
static void	generate_trial_conf (ArrayRef< RVec > xin, const rvec offset, RotationType enum_rot, DefaultRandomEngine *rng, std::vector< RVec > *xout)
static bool	isInsertionAllowed (AnalysisNeighborhoodSearch *search, const std::vector< real > &exclusionDistances, const std::vector< RVec > &x, const std::vector< real > &exclusionDistances_insrt, const t_atoms &atoms, const std::set< int > &removableAtoms, AtomsRemover *remover)
static void	insert_mols (int nmol_insrt, int ntry, int seed, real defaultDistance, real scaleFactor, t_atoms *atoms, t_symtab *symtab, std::vector< RVec > *x, const std::set< int > &removableAtoms, const t_atoms &atoms_insrt, ArrayRef< RVec > x_insrt, PbcType pbcType, matrix box, const std::string &posfn, const rvec deltaR, RotationType enum_rot)
std::vector< real >	makeExclusionDistances (const t_atoms *a, AtomProperties *aps, real defaultDistance, real scaleFactor)
	Allocate and fill an array of inter-atomic half distances. More...
static real	smallestAtomMass (const gmx_mtop_t &mtop)
void	repartitionAtomMasses (gmx_mtop_t *mtop, bool useFep, real massFactor, WarningHandler *wi)
	Scales the smallest masses in the system by up to massFactor. More...
static void	rd_nm2type_file (const std::filesystem::path &filename, int *nnm, t_nm2type **nmp)
t_nm2type *	rd_nm2type (const std::filesystem::path &ffdir, int *nnm)
void	dump_nm2type (FILE *fp, int nnm, t_nm2type nm2t[])
static int	match_str (const char *atom, const char *template_string)
int	nm2type (int nnm, t_nm2type nm2t[], t_atoms *atoms, PreprocessingAtomTypes *atype, int *nbonds, InteractionsOfType *bonds)
const char *	enumValueToString (HistidineStates enumValue)
static int	missing_atoms (const PreprocessResidue *rp, int resind, t_atoms *at, int i0, int i, const MDLogger &logger)
static std::filesystem::path	choose_ff_impl (const char *ffsel, char *forcefield, int ff_maxlen, const MDLogger &logger)
std::filesystem::path	choose_ff (const char *ffsel, char *forcefield, int ff_maxlen, const MDLogger &logger)
void	choose_watermodel (const char *wmsel, const std::filesystem::path &ffdir, char **watermodel, const MDLogger &logger)
static int	name2type (t_atoms *at, ArrayRef< const PreprocessResidue > usedPpResidues, const ResidueTypeMap &residueTypeMap, const MDLogger &logger)
static void	print_top_heavy_H (FILE *out, real mHmult)
void	print_top_comment (FILE *out, const std::filesystem::path &filename, const std::filesystem::path &ffdir, bool bITP)
void	print_top_header (FILE *out, const std::filesystem::path &filename, bool bITP, const std::filesystem::path &ffdir, real mHmult)
static void	print_top_posre (FILE *out, const std::filesystem::path &pr)
static void	print_top_water (FILE *out, const std::filesystem::path &ffdir, const char *water)
static void	print_top_system (FILE *out, const char *title)
void	print_top_mols (FILE *out, const char *title, const std::filesystem::path &ffdir, const char *water, ArrayRef< const std::filesystem::path > incls, ArrayRef< const t_mols > mols)
void	write_top (FILE *out, const std::filesystem::path &pr, const char *molname, t_atoms *at, bool bRTPresname, ArrayRef< const int > bts, const EnumerationArray< InteractionFunction, InteractionsOfType > &plist, t_excls excls[], PreprocessingAtomTypes *atype, int nrexcl)
static void	do_ssbonds (InteractionsOfType *ps, t_atoms *atoms, ArrayRef< const DisulfideBond > ssbonds, bool bAllowMissing)
static void	at2bonds (InteractionsOfType *psb, ArrayRef< MoleculePatchDatabase > globalPatches, t_atoms *atoms, ArrayRef< const RVec > x, real long_bond_dist, real short_bond_dist, ArrayRef< const int > cyclicBondsIndex, const MDLogger &logger)
static bool	pcompar (const InteractionOfType &a, const InteractionOfType &b)
static void	clean_bonds (InteractionsOfType *ps, const MDLogger &logger)
void	print_sums (const t_atoms *atoms, bool bSystem, const MDLogger &logger)
static void	check_restp_type (const char *name, int t1, int t2)
static void	check_restp_types (const PreprocessResidue &r0, const PreprocessResidue &r1)
static void	add_atom_to_restp (PreprocessResidue *usedPpResidues, t_symtab *symtab, int at_start, const MoleculePatch *patch)
void	get_hackblocks_rtp (std::vector< MoleculePatchDatabase > *globalPatches, std::vector< PreprocessResidue > *usedPpResidues, ArrayRef< const PreprocessResidue > rtpFFDB, int nres, t_resinfo *resinfo, int nterpairs, t_symtab *symtab, ArrayRef< MoleculePatchDatabase * > ntdb, ArrayRef< MoleculePatchDatabase * > ctdb, ArrayRef< const int > rn, ArrayRef< const int > rc, bool bAllowMissing, const MDLogger &logger)
static bool	atomname_cmp_nr (const char *anm, const MoleculePatch *patch, int *nr)
static bool	match_atomnames_with_rtp_atom (t_atoms *pdba, ArrayRef< RVec > x, t_symtab *symtab, int atind, PreprocessResidue *localPpResidue, const MoleculePatchDatabase &singlePatch, bool bVerbose, const MDLogger &logger)
void	match_atomnames_with_rtp (ArrayRef< PreprocessResidue > usedPpResidues, ArrayRef< MoleculePatchDatabase > globalPatches, t_atoms *pdba, t_symtab *symtab, ArrayRef< RVec > x, bool bVerbose, const MDLogger &logger)
static void	gen_cmap (InteractionsOfType *psb, ArrayRef< const PreprocessResidue > usedPpResidues, t_atoms *atoms, ArrayRef< const int > cyclicBondsIndex, const MDLogger &logger)
void	pdb2top (FILE *top_file, const std::filesystem::path &posre_fn, const char *molname, t_atoms *atoms, std::vector< RVec > *x, PreprocessingAtomTypes *atype, t_symtab *tab, ArrayRef< const PreprocessResidue > rtpFFDB, ArrayRef< PreprocessResidue > usedPpResidues, ArrayRef< MoleculePatchDatabase > globalPatches, bool bAllowMissing, bool bVsites, bool bVsiteAromatics, const std::filesystem::path &ffdir, real mHmult, ArrayRef< const DisulfideBond > ssbonds, real long_bond_dist, real short_bond_dist, bool bDeuterate, bool bCmap, bool bRenumRes, bool bRTPresname, ArrayRef< const int > cyclicBondsIndex, const MDLogger &logger)
static void	atom_not_found (int fatal_errno, const char *file, int line, const char *atomname, int resind, const char *resname, const char *bondtype, bool bAllowMissing)
std::optional< int >	search_atom (const char *atomName, int start, const t_atoms *atoms, const char *bondtype, bool bAllowMissing, ArrayRef< const int > cyclicBondsIndex)
	Search for an atom named atomName in atoms. More...
std::optional< int >	search_res_atom (const char *atomName, int resind, const t_atoms *atoms, const char *bondtype, bool bAllowMissing)
void	init_inputrec_strings ()
	Initialise object to hold strings parsed from an .mdp file.
void	done_inputrec_strings ()
	Clean up object that holds strings parsed from an .mdp file.
void	check_ir (const char *mdparin, MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts, WarningHandler *wi)
	Performs all validation on ir that can be done without index groups and topology. More...
void	get_ir (const char *mdparin, const char *mdparout, MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts, WriteMdpHeader writeMdpHeader, WarningHandler *wi)
	Parse input, apply defaults, prepare mdp output. More...
int	getGroupIndex (const std::string &s, ArrayRef< const IndexGroup > indexGroups)
	Returns the index of string s in indexGroups or exit with a verbose fatal error when not found.
void	do_index (const char *mdparin, const std::optional< std::filesystem::path > &ndx, gmx_mtop_t *mtop, bool bVerbose, const MDModulesNotifiers &mdModulesNotifiers, t_inputrec *ir, WarningHandler *wi)
void	processConstantAcceleration (t_inputrec *ir, const gmx_mtop_t &sys)
	Processes constant acceleration options.
void	triple_check (const char *mdparin, const t_inputrec &ir, const gmx_mtop_t &sys, WarningHandler *wi)
	Do checks that can only be done when a complete topology is available.
void	double_check (t_inputrec *ir, matrix box, bool bHasNormalConstraints, bool bHasAnyConstraints, WarningHandler *wi)
	Do checks that are relevant when constraints are present.
std::vector< std::string >	read_pullparams (std::vector< t_inpfile > *inp, pull_params_t *pull, WarningHandler *wi)
void	process_pull_groups (ArrayRef< t_pull_group > pullGroups, ArrayRef< const std::string > pullGroupNames, ArrayRef< const IndexGroup > indexGroups)
void	checkPullCoords (ArrayRef< const t_pull_group > pullGroups, ArrayRef< const t_pull_coord > pullCoords)
pull_t *	set_pull_init (t_inputrec *ir, const gmx_mtop_t &mtop, ArrayRef< const RVec > x, matrix box, real lambda, WarningHandler *wi)
std::vector< std::string >	read_rotparams (std::vector< t_inpfile > *inp, t_rot *rot, WarningHandler *wi)
void	make_rotation_groups (t_rot *rot, ArrayRef< const std::string > rotateGroupNames, ArrayRef< const IndexGroup > indexGroups)
void	set_reference_positions (t_rot *rot, rvec *x, matrix box, const char *fn, bool bSet, WarningHandler *wi)
PreprocessingAtomTypes	read_atype (const std::filesystem::path &ffdir)
	Read atom types into database. More...
static void	print_resatoms (FILE *out, const PreprocessingAtomTypes &atype, const PreprocessResidue &rtpDBEntry)
static bool	read_atoms (FILE *in, char *line, PreprocessResidue *r0, t_symtab *tab, PreprocessingAtomTypes *atype)
static bool	read_bondeds (BondedTypes bt, FILE *in, char *line, PreprocessResidue *rtpDBEntry)
static void	print_resbondeds (FILE *out, BondedTypes bt, const PreprocessResidue &rtpDBEntry)
static void	check_rtp (ArrayRef< const PreprocessResidue > rtpDBEntry, const std::filesystem::path &libfn, const MDLogger &logger)
static std::optional< BondedTypes >	get_bt (const char *header)
static void	print_resall_header (FILE *out, ArrayRef< const PreprocessResidue > rtpDBEntry)
static void	print_resall_log (const MDLogger &logger, ArrayRef< const PreprocessResidue > rtpDBEntry)
void	print_resall (FILE *out, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry, const PreprocessingAtomTypes &atype)
	Print out database. More...
void	readResidueDatabase (const std::filesystem::path &resdb, std::vector< PreprocessResidue > *rtpDBEntry, PreprocessingAtomTypes *atype, t_symtab *tab, const gmx::MDLogger &logger, bool bAllowOverrideRTP)
	Read in database, append to exisiting. More...
static bool	is_sign (char c)
static int	neq_str_sign (const char *a1, const char *a2)
std::string	searchResidueDatabase (const std::string &key, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry, const gmx::MDLogger &logger)
	Search for an entry in the rtp database. More...
ArrayRef< const PreprocessResidue > ::const_iterator	getDatabaseEntry (const std::string &rtpname, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry)
	Returns matching entry in database. More...
static void	sort_molecule (t_atoms **atoms_solvt, t_atoms **newatoms, std::vector< RVec > *x, std::vector< RVec > *v)
static void	rm_res_pbc (const t_atoms *atoms, std::vector< RVec > *x, matrix box)
static void	replicateSolventBox (t_atoms *atoms, std::vector< RVec > *x, std::vector< RVec > *v, std::vector< real > *r, const matrix box, const matrix boxTarget)
	Generates a solvent configuration of desired size by stacking solvent boxes. More...
static void	removeSolventBoxOverlap (t_atoms *atoms, std::vector< RVec > *x, std::vector< RVec > *v, std::vector< real > *r, const t_pbc &pbc)
	Removes overlap of solvent atoms across the edges. More...
static void	removeSolventOutsideShell (t_atoms *atoms, std::vector< RVec > *x_solvent, std::vector< RVec > *v_solvent, std::vector< real > *r, const t_pbc &pbc, const std::vector< RVec > &x_solute, real rshell)
	Remove all solvent molecules outside a give radius from the solute. More...
static void	removeSolventOverlappingWithSolute (t_atoms *atoms, std::vector< RVec > *x, std::vector< RVec > *v, std::vector< real > *r, const t_pbc &pbc, const std::vector< RVec > &x_solute, const std::vector< real > &r_solute)
	Removes solvent molecules that overlap with the solute. More...
static void	removeExtraSolventMolecules (t_atoms *atoms, std::vector< RVec > *x, std::vector< RVec > *v, int numberToRemove)
	Removes a given number of solvent residues. More...
static void	add_solv (const char *filename, t_atoms *atoms, t_symtab *symtab, std::vector< RVec > *x, std::vector< RVec > *v, PbcType pbcType, matrix box, AtomProperties *aps, real defaultDistance, real scaleFactor, real rshell, int max_sol)
static void	update_top (t_atoms *atoms, int firstSolventResidueIndex, matrix box, int NFILE, t_filenm fnm[], AtomProperties *aps)
int	gmx_solvate (int argc, char *argv[])
static bool	yesno ()
std::vector< SpecialBond >	generateSpecialBonds ()
static bool	is_special (ArrayRef< const SpecialBond > sb, const char *res, const char *atom)
static bool	is_bond (ArrayRef< const SpecialBond > sb, t_atoms *pdba, int a1, int a2, real d, int *index_sb, bool *bSwap)
static void	rename_1res (t_atoms *pdba, t_symtab *symtab, int resind, const char *newres, bool bVerbose)
std::vector< DisulfideBond >	makeDisulfideBonds (t_atoms *pdba, t_symtab *symtab, rvec x[], bool bInteractive, bool bVerbose)
static const char *	enumValueToString (ReplaceType enumValue)
template<typename EnumType >
static std::optional< EnumType >	findTypeFromKeyword (char *keyw)
static void	read_atom (char *line, bool bAdd, std::string *nname, t_atom *a, PreprocessingAtomTypes *atype, int *cgnr)
static void	print_atom (FILE *out, const t_atom &a, PreprocessingAtomTypes *atype)
static void	print_ter_db (const char *ff, char C, ArrayRef< const MoleculePatchDatabase > tb, PreprocessingAtomTypes *atype)
static void	read_ter_db_file (const std::filesystem::path &fn, std::vector< MoleculePatchDatabase > *tbptr, PreprocessingAtomTypes *atype)
int	read_ter_db (const std::filesystem::path &ffdir, char ter, std::vector< MoleculePatchDatabase > *tbptr, PreprocessingAtomTypes *atype)
	Read database for N&C terminal modifications. More...
std::vector < MoleculePatchDatabase * >	filter_ter (gmx::ArrayRef< MoleculePatchDatabase > tb, const char *resname)
	Return entries for modification blocks that match a residue name. More...
MoleculePatchDatabase *	choose_ter (gmx::ArrayRef< MoleculePatchDatabase * > tb, const char *title)
	Interactively select one terminus. More...
static t_2morse *	read_dissociation_energies (int *n2morse)
static int	nequal (const char *a1, const char *a2)
static real	search_e_diss (int n2m, t_2morse t2m[], const char *ai, const char *aj)
void	convert_harmonics (ArrayRef< MoleculeInformation > mols, PreprocessingAtomTypes *atype)
const char *	enumValueToString (Directive d)
InteractionFunction	ifunc_index (Directive d, int type)
static const char *	enumValueToString (DeprecatedDirectives d)
Directive	str2dir (const char *dstr)
static void	set_nec (Directive **n,...)
void	DS_Init (DirStack **DS)
void	DS_Done (DirStack **DS)
void	DS_Push (DirStack **DS, Directive d)
int	DS_Search (DirStack *DS, Directive d)
int	DS_Check_Order (DirStack *DS, Directive d)
static void	gen_pairs (const InteractionsOfType &nbs, InteractionsOfType *pairs, real fudge, CombinationRule comb)
double	check_mol (const gmx_mtop_t *mtop, WarningHandler *wi)
static std::string	describeAtomsForRBDihedralOfGivenType (const gmx_mtop_t &mtop, int interactionType)
	Describe molecule and involved atoms for a dihedral interaction of a given type. More...
void	checkRBDihedralSum (const gmx_mtop_t &mtop, const t_inputrec &ir, WarningHandler *wi)
	Check that RB/Fourier style dihedral sums to zero in free-energy computation. More...
static double	roundedMoleculeCharge (double qMol, double sumAbsQ)
	Returns the rounded charge of a molecule, when close to integer, otherwise returns the original charge. More...
static void	sum_q (const t_atoms *atoms, int numMols, double *qTotA, double *qTotB)
static void	get_nbparm (char *nb_str, char *comb_str, VanDerWaalsPotential *nb, CombinationRule *comb, WarningHandler *wi)
static std::vector< char * >	cpp_opts (const char *define, const char *include, WarningHandler *wi)
	Parses define and include flags. More...
static void	make_atoms_sys (ArrayRef< const gmx_molblock_t > molblock, ArrayRef< const MoleculeInformation > molinfo, t_atoms *atoms)
static char **	read_topol (const char *infile, const std::optional< std::filesystem::path > &outfile, const char *define, const char *include, t_symtab *symtab, PreprocessingAtomTypes *atypes, std::vector< MoleculeInformation > *molinfo, std::unique_ptr< MoleculeInformation > *intermolecular_interactions, EnumerationArray< InteractionFunction, InteractionsOfType > &interactions, CombinationRule *combination_rule, double *reppow, t_gromppopts *opts, real *fudgeQQ, std::vector< gmx_molblock_t > *molblock, bool *ffParametrizedWithHBondConstraints, bool bFEP, bool bZero, bool usingFullRangeElectrostatics, WarningHandler *wi, const MDLogger &logger)
char **	do_top (bool bVerbose, const char *topfile, const std::optional< std::filesystem::path > &topppfile, t_gromppopts *opts, bool bZero, t_symtab *symtab, EnumerationArray< InteractionFunction, InteractionsOfType > &interactions, CombinationRule *combination_rule, double *repulsion_power, real *fudgeQQ, PreprocessingAtomTypes *atypes, std::vector< MoleculeInformation > *molinfo, std::unique_ptr< MoleculeInformation > *intermolecular_interactions, const t_inputrec *ir, std::vector< gmx_molblock_t > *molblock, bool *ffParametrizedWithHBondConstraints, WarningHandler *wi, const MDLogger &logger)
static void	generate_qmexcl_moltype (gmx_moltype_t *molt, const unsigned char *grpnr, t_inputrec *ir, const MDLogger &logger)
	Exclude molecular interactions for QM atoms handled by MiMic. More...
void	generate_qmexcl (gmx_mtop_t *sys, t_inputrec *ir, const MDLogger &logger)
void	generate_nbparams (CombinationRule comb, int ftype, InteractionsOfType *interactions, PreprocessingAtomTypes *atypes, WarningHandler *wi)
static void	realloc_nb_params (PreprocessingAtomTypes *atypes, t_nbparam ***nbparam, t_nbparam ***pair)
int	copy_nbparams (t_nbparam **param, int ftype, InteractionsOfType *interactions, int nr)
void	free_nbparam (t_nbparam **param, int nr)
static void	copy_B_from_A (InteractionFunction ftype, double *c)
static const char *	enumValueToLetterAsString (ParticleType enumValue)
	Local definition that supersedes the central one, as we only want the leading letter.
void	push_at (PreprocessingAtomTypes *at, PreprocessingBondAtomType *bondAtomType, char *line, int nb_funct, t_nbparam ***nbparam, t_nbparam ***pair, WarningHandler *wi)
template<typename T >
static bool	equalEitherForwardOrBackward (ArrayRef< const T > a, ArrayRef< const T > b)
	Return whether the contents of a and b are the same, considering also reversed order.
static void	push_bondtype (InteractionsOfType *bt, const InteractionOfType &b, int nral, InteractionFunction ftype, bool bAllowRepeat, const char *line, WarningHandler *wi)
template<typename T >
static std::vector< int >	atomTypesFromAtomNames (const PreprocessingAtomTypes *atomTypes, const PreprocessingBondAtomType *bondAtomTypes, ArrayRef< T > atomNames, WarningHandler *wi)
void	push_bt (Directive d, EnumerationArray< InteractionFunction, InteractionsOfType > &bt, int nral, PreprocessingAtomTypes *at, PreprocessingBondAtomType *bondAtomType, char *line, WarningHandler *wi)
void	push_dihedraltype (Directive d, EnumerationArray< InteractionFunction, InteractionsOfType > &bt, PreprocessingBondAtomType *bondAtomType, char *line, WarningHandler *wi)
void	push_nbt (Directive d, t_nbparam **nbt, PreprocessingAtomTypes *atypes, char *pline, int nb_funct, WarningHandler *wi)
void	push_cmaptype (Directive d, EnumerationArray< InteractionFunction, InteractionsOfType > &bt, int nral, const PreprocessingBondAtomType &bondAtomType, char *line, WarningHandler *wi)
static void	push_atom_now (t_symtab *symtab, t_atoms *at, int atomnr, int atomicnumber, int type, char *ctype, ParticleType ptype, char *resnumberic, char *resname, char *name, real m0, real q0, int typeB, char *ctypeB, real mB, real qB, WarningHandler *wi)
void	push_atom (t_symtab *symtab, t_atoms *at, PreprocessingAtomTypes *atypes, char *line, WarningHandler *wi)
void	push_molt (t_symtab *symtab, std::vector< MoleculeInformation > *mol, char *line, WarningHandler *wi)
static bool	findIfAllNBAtomsMatch (ArrayRef< const int > atomsFromParameterArray, ArrayRef< const int > atomsFromCurrentParameter, const t_atoms *at, bool bB)
static bool	default_nb_params (InteractionFunction ftype, EnumerationArray< InteractionFunction, InteractionsOfType > &bt, t_atoms *at, InteractionOfType *p, int c_start, bool bB, bool bGenPairs)
static int	findCmapType (EnumerationArray< InteractionFunction, InteractionsOfType > &bondtype, const t_atoms &at, const PreprocessingAtomTypes &atypes, const InteractionOfType &p, WarningHandler *wi)
	Find the appropriate type for the current CMAP p interaction. More...
static int	findNumberOfDihedralAtomMatches (const InteractionOfType &bondType, const ArrayRef< const int > atomTypes)
static std::vector < InteractionOfType > ::iterator	defaultInteractionsOfType (InteractionFunction ftype, EnumerationArray< InteractionFunction, InteractionsOfType > &bondType, const PreprocessingAtomTypes &atypes, const ArrayRef< int > atomIndices, const ArrayRef< const int > atomTypes, const bool atomReorderingLEaP, int *nparam_def)
void	push_bond (Directive d, EnumerationArray< InteractionFunction, InteractionsOfType > &bondtype, EnumerationArray< InteractionFunction, InteractionsOfType > &bond, t_atoms *at, PreprocessingAtomTypes *atypes, char *line, bool bBonded, bool bGenPairs, real fudgeQQ, bool bZero, const bool atomReorderingLEaP, bool *bWarn_copy_A_B, WarningHandler *wi)
void	push_cmap (Directive d, EnumerationArray< InteractionFunction, InteractionsOfType > &bondtype, EnumerationArray< InteractionFunction, InteractionsOfType > &bond, t_atoms *at, PreprocessingAtomTypes *atypes, char *line, WarningHandler *wi)
void	push_vsitesn (Directive d, EnumerationArray< InteractionFunction, InteractionsOfType > &bond, t_atoms *at, char *line, WarningHandler *wi)
void	push_mol (ArrayRef< MoleculeInformation > mols, char *pline, int *whichmol, int *nrcopies, WarningHandler *wi)
void	push_excl (char *line, ArrayRef< ExclusionBlock > b2, WarningHandler *wi)
int	add_atomtype_decoupled (PreprocessingAtomTypes *at, t_nbparam ***nbparam, t_nbparam ***pair)
static void	convert_pairs_to_pairsQ (EnumerationArray< InteractionFunction, InteractionsOfType > &interactions, real fudgeQQ, t_atoms *atoms)
static void	generate_LJCpairsNB (MoleculeInformation *mol, int nb_funct, InteractionsOfType *nbp, WarningHandler *wi)
static void	set_excl_all (ListOfLists< int > *excl)
static void	decouple_atoms (t_atoms *atoms, int atomtype_decouple, int couple_lam0, int couple_lam1, const char *mol_name, WarningHandler *wi)
void	convert_moltype_couple (MoleculeInformation *mol, int atomtype_decouple, real fudgeQQ, int couple_lam0, int couple_lam1, bool bCoupleIntra, int nb_funct, InteractionsOfType *nbp, WarningHandler *wi)
static int	count_hydrogens (char ***atomname, int nra, ArrayRef< const int > a)
void	make_shake (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, t_atoms *atoms, int nshake, const MDLogger &logger)
void	add_param_to_list (InteractionsOfType *list, const InteractionOfType &b)
static void	print_bt (FILE *out, Directive d, PreprocessingAtomTypes *at, InteractionFunction ftype, int fsubtype, const EnumerationArray< InteractionFunction, InteractionsOfType > &plist, bool bFullDih)
void	print_excl (FILE *out, int natoms, t_excls excls[])
static double	get_residue_charge (const t_atoms *atoms, int at)
void	print_atoms (FILE *out, PreprocessingAtomTypes *atype, t_atoms *at, bool bRTPresname)
void	print_bondeds (FILE *out, int natoms, Directive d, InteractionFunction ftype, int fsubtype, const EnumerationArray< InteractionFunction, InteractionsOfType > &plist)
static int	vsite_bond_nrcheck (InteractionFunction ftype)
static void	enter_bonded (int nratoms, std::vector< VsiteBondedInteraction > *bondeds, const InteractionOfType &type)
static AllVsiteBondedInteractions	createVsiteBondedInformation (int nrat, ArrayRef< const int > atoms, ArrayRef< const Atom2VsiteBond > at2vb)
static std::vector < Atom2VsiteBond >	make_at2vsitebond (int natoms, EnumerationArray< InteractionFunction, InteractionsOfType > &plist)
static std::vector < Atom2VsiteConnection >	make_at2vsitecon (int natoms, EnumerationArray< InteractionFunction, InteractionsOfType > &plist)
static void	print_bad (FILE *fp, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles, ArrayRef< const VsiteBondedInteraction > idihs)
static void	printInteractionOfType (FILE *fp, InteractionFunction ftype, int i, const InteractionOfType &type)
static real	get_bond_length (ArrayRef< const VsiteBondedInteraction > bonds, t_iatom ai, t_iatom aj)
static real	get_angle (ArrayRef< const VsiteBondedInteraction > angles, t_iatom ai, t_iatom aj, t_iatom ak)
static bool	cmp_atomtype_name_AB (t_atom *atom, PreprocessingAtomTypes *atypes, const std::string &compare, int compareLength)
static bool	calc_vsite3_param (PreprocessingAtomTypes *atypes, InteractionOfType *vsite, t_atoms *at, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles)
static bool	calc_vsite3fd_param (InteractionOfType *vsite, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles)
static bool	calc_vsite3fad_param (InteractionOfType *vsite, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles)
static bool	calc_vsite3out_param (PreprocessingAtomTypes *atypes, InteractionOfType *vsite, t_atoms *at, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles)
static bool	calc_vsite4fd_param (InteractionOfType *vsite, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles, const MDLogger &logger)
static bool	calc_vsite4fdn_param (InteractionOfType *vsite, ArrayRef< const VsiteBondedInteraction > bonds, ArrayRef< const VsiteBondedInteraction > angles, const MDLogger &logger)
int	set_vsites (bool bVerbose, t_atoms *atoms, PreprocessingAtomTypes *atypes, EnumerationArray< InteractionFunction, InteractionsOfType > &plist, const MDLogger &logger)
void	set_vsites_ptype (bool bVerbose, gmx_moltype_t *molt, const MDLogger &logger)
static void	check_vsite_constraints (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, InteractionFunction cftype, ArrayRef< const std::optional< InteractionFunction >> vsite_type, const MDLogger &logger)
static void	clean_vsite_bonds (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, ArrayRef< const std::optional< VsiteAtomMapping >> pindex, InteractionFunction cftype, ArrayRef< const std::optional< InteractionFunction >> vsite_type, const MDLogger &logger)
static void	clean_vsite_angles (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, ArrayRef< std::optional< VsiteAtomMapping >> pindex, InteractionFunction cftype, ArrayRef< const std::optional< InteractionFunction >> vsite_type, ArrayRef< const Atom2VsiteConnection > at2vc, const MDLogger &logger)
static void	clean_vsite_dihs (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, ArrayRef< std::optional< VsiteAtomMapping >> pindex, InteractionFunction cftype, ArrayRef< const std::optional< InteractionFunction >> vsite_type, const MDLogger &logger)
void	clean_vsite_bondeds (EnumerationArray< InteractionFunction, InteractionsOfType > &ps, int natoms, bool bRmVSiteBds, const MDLogger &logger)
	Clean up the bonded interactions. More...
static bool	is_bond (int nnm, t_nm2type nmt[], const char *ai, const char *aj, real blen)
static void	mk_bonds (int nnm, t_nm2type nmt[], t_atoms *atoms, const rvec x[], InteractionsOfType *bond, int nbond[], bool bPBC, matrix box)
static int *	set_cgnr (t_atoms *atoms, bool bUsePDBcharge, real *qtot, real *mtot)
static void	set_atom_type (PreprocessingAtomTypes *atypes, t_atoms *atoms, InteractionsOfType *bonds, int *nbonds, int nnm, t_nm2type nm2t[], const MDLogger &logger)
static void	lo_set_force_const (InteractionsOfType *plist, real c[], int nrfp, bool bRound, bool bDih, bool bParam)
static void	set_force_const (EnumerationArray< InteractionFunction, InteractionsOfType > &plist, real kb, real kt, real kp, bool bRound, bool bParam)
static void	calc_angles_dihs (InteractionsOfType *ang, InteractionsOfType *dih, const rvec x[], bool bPBC, matrix box)
static void	dump_hybridization (FILE *fp, t_atoms *atoms, int nbonds[])
static void	print_pl (FILE *fp, const EnumerationArray< InteractionFunction, InteractionsOfType > &plist, InteractionFunction ftp, const char *name, char ***atomname)
static void	print_rtp (const char *filenm, const char *title, t_atoms *atoms, const EnumerationArray< InteractionFunction, InteractionsOfType > &plist, PreprocessingAtomTypes *atypes, int cgnr[])
int	gmx_x2top (int argc, char *argv[])
static void	get_xlatoms (const std::filesystem::path &filename, FILE *fp, int *nptr, t_xlate_atom **xlptr)
static void	done_xlatom (int nxlate, t_xlate_atom *xlatom)
void	rename_atoms (const std::filesystem::path &xlfile, const std::filesystem::path &ffdir, t_atoms *atoms, t_symtab *symtab, ArrayRef< const PreprocessResidue > localPpResidue, bool bResname, const ResidueTypeMap &rt, bool bReorderNum, bool bVerbose)
std::unordered_map < std::string, std::string >	gpuDescriptions ()
	Returns information for describing the GPU support.
template<typename Queue , typename CommandGroupFunction >
static void	syclSubmitWithCghWithoutEvent (Queue &&queue, CommandGroupFunction &&commandGroupFunction)
	Helper function to submit to a queue via a handler, avoiding returning an event (if possible).
template<typename KernelNameType , typename KernelFunctionBuilder , typename Queue , typename Range , class... Args>
static void	syclSubmitWithoutEvent (Queue &&queue, KernelFunctionBuilder kernelFunctionBuilder, Range &&range, Args &&...args)
	Helper function to submit a SYCL operation without returning an event (if possible). More...
template<typename KernelNameType , typename KernelFunctionBuilder , typename Queue , typename Range , class... Args>
static void	syclSubmitWithoutCghOrEvent (Queue &&queue, KernelFunctionBuilder kernelFunctionBuilder, Range &&range, Args &&...args)
	Helper function to submit a SYCL operation without returning an event. More...
template<typename Queue >
static void	syclMemcpyWithoutEvent (Queue &&queue, void *destination, const void *source, size_t numBytes)
	Helper function to submit a SYCL async memcpy without returning an event (if possible). More...
static void	syclMemsetWithoutEvent (sycl::queue &&queue, void *pointer, int value, size_t numBytes)
	Helper function to submit a SYCL async memset without returning an event (if possible). More...
template<typename CommandGroupFunc >
static void	syclEnqueueCustomOp (sycl::handler &cgh, CommandGroupFunc &&cgf)
	Helper function to add a custom operation to the SYCL handler. More...
template<typename T >
static Float3 *	asGenericFloat3Pointer (T *in)
	Reinterpret-cast any pointer in to Float3, checking the type compatibility.
template<typename T >
static const Float3 *	asGenericFloat3Pointer (const T *in)
	Reinterpret-cast any const pointer in to Float3, checking the type compatibility.
template<typename C >
static Float3 *	asGenericFloat3Pointer (C &in)
	Reinterpret-cast any container in to Float3, checking the type compatibility.
template<typename C >
static const Float3 *	asGenericFloat3Pointer (const C &in)
	Reinterpret-cast any const container in to Float3, checking the type compatibility.
std::string	getDeviceErrorString (const hipError_t deviceError)
	Add the API information on the specific error to the error message. More...
void	checkDeviceError (const hipError_t deviceError, const std::string_view errorMessage)
	Check if API returned an error and throw an exception with information on it. More...
void	ensureNoPendingDeviceError (const std::string_view errorMessage)
	Helper function to ensure no pending error silently disrupts error handling. More...
HostAllocationPolicy	makeHostAllocationPolicy (bool pinBuffers, const DeviceStreamManager *deviceStreamManager, bool propagateDuringContainerCopyConstruction=false)
	Helper function to make a suitable HostAllocationPolicy. More...
template<typename PinnableVector >
void	changePinningPolicy (PinnableVector *v, PinningPolicy pinningPolicy)
	Helper function for changing the pinning policy of a pinnable vector. More...
bool	isNvshmemInitialized ()
	Return whether NVSHMEM is initialized and ready for API use.
void	doDeviceTransfers (const DeviceContext &deviceContext, ArrayRef< const char > input, ArrayRef< char > output)
	Helper function for GPU test code to be platform agnostic. More...
bool	cpuIsX86Nehalem (const CpuInfo &cpuInfo)
	Return true if the CPU is an Intel x86 Nehalem. More...
bool	cpuIsAmdZen1 (const CpuInfo &cpuInfo)
	Return true if the CPU is a first generation AMD Zen (produced by AMD or Hygon) More...
bool	cpuIsNeoverseV2 (const CpuInfo &cpuInfo)
	Return true if the CPU has Neoverse V2 cores (including Grace and Graviton 4) More...
static DeviceDetectionResult	detectAllDeviceInformation (const PhysicalNodeCommunicator &physicalNodeComm)
	Detect GPUs when that makes sense to attempt. More...
static void	gmx_collect_hardware_mpi (const gmx::CpuInfo &cpuInfo, const PhysicalNodeCommunicator &physicalNodeComm, gmx_hw_info_t *hardwareInfo, [[maybe_unused]] MPI_Comm world)
	Reduce the locally collected hardwareInfo over MPI ranks.
std::unique_ptr< gmx_hw_info_t >	gmx_detect_hardware (const PhysicalNodeCommunicator &physicalNodeComm, MPI_Comm libraryCommWorld)
	Run detection and make correct and consistent hardware information available on all ranks. More...
void	logHardwareDetectionWarnings (const gmx::MDLogger &mdlog, const gmx_hw_info_t &hardwareInformation)
	Issue warnings to mdlog that were decided during detection. More...
static bool	runningOnCompatibleOSForAmd ()
	Return true if executing on compatible OS for AMD OpenCL. More...
static bool	runningOnCompatibleHWForNvidia (const DeviceInformation &deviceInfo)
	Return true if executing on compatible GPU for NVIDIA OpenCL. More...
static FixedCapacityVector < int, 12 >	fillSupportedSubGroupSizes (const cl_device_id devId, const DeviceVendor deviceVendor)
	Return the list of sub-group sizes supported by the device. More...
static bool	runningOnCompatibleHWForAmd (const DeviceInformation &deviceInfo)
	Return true if executing on compatible GPU for AMD OpenCL. More...
static DeviceStatus	isDeviceFunctional (const DeviceInformation &deviceInfo)
	Checks that device deviceInfo is compatible with GROMACS. More...
std::string	makeOpenClInternalErrorString (const char *message, cl_int status)
	Make an error string following an OpenCL API call. More...
static bool	isDeviceFunctional (const DeviceInformation &deviceInfo, std::string *errorMessage)
	Checks that device deviceInfo is sane (ie can run a kernel). More...
static DeviceStatus	checkGpu (size_t deviceId, const DeviceInformation &deviceInfo)
	Check whether the ocl_gpu_device is suitable for use by mdrun. More...
std::string	hwlocDescription ()
	Returns information for describing the hwloc support.
int	identifyAvx512FmaUnits ()
	Test whether machine has dual AVX512 FMA units. More...
static const std::string &	simdString (SimdType s)
SimdType	simdSuggested (const CpuInfo &c)
	Return the SIMD type that would fit this hardware best.
static SimdType	simdCompiled ()
bool	simdCheck (const CpuInfo &cpuInfo, SimdType wanted, FILE *log, bool warnToStdErr)
	Check if binary was compiled with the provided SIMD type. More...
std::string	simdDescription ()
	Return a string describing the SIMD support.
static const char *	enumValueToString (IMDMessageType enumValue)
	Names of the IMDType for error messages.
static void	fill_header (IMDHeader *header, IMDMessageType type, int32_t length)
	Fills the header with message and the length argument.
static void	swap_header (IMDHeader *header)
	Swaps the endianess of the header.
static int32_t	imd_read_multiple (IMDSocket *socket, char *datptr, int32_t toread)
	Reads multiple bytes from socket.
static int32_t	imd_write_multiple (IMDSocket *socket, const char *datptr, int32_t towrite)
	Writes multiple bytes to socket in analogy to imd_read_multiple.
static int	imd_handshake (IMDSocket *socket)
	Handshake with IMD client.
static int	imd_send_energies (IMDSocket *socket, const IMDEnergyBlock *energies, char *buffer)
	Send energies using the energy block and the send buffer.
static IMDMessageType	imd_recv_header (IMDSocket *socket, int32_t *length)
	Receive IMD header from socket, sets the length and returns the IMD message.
static bool	imd_recv_mdcomm (IMDSocket *socket, int32_t nforces, int32_t *forcendx, float *forces)
	Receive force indices and forces. More...
void	write_IMDgroup_to_file (bool bIMD, t_inputrec *ir, const t_state *state, const gmx_mtop_t &sys, int nfile, const t_filenm fnm[])
	Writes out the group of atoms selected for interactive manipulation. More...
static int	imd_send_rvecs (IMDSocket *socket, int nat, rvec *x, char *buffer)
	Send positions from rvec. More...
static bool	rvecs_differ (const rvec v1, const rvec v2)
	Returns true if any component of the two rvecs differs.
static void	shift_positions (const matrix box, rvec x[], const ivec is, int nr)
	Copied and modified from groupcoord.c shift_positions_group().
static void	imd_check_integrator_parallel (const t_inputrec *ir, const MpiComm &mpiComm)
	Check for non-working integrator / parallel options.
std::unique_ptr< ImdSession >	makeImdSession (const t_inputrec *ir, const MpiComm &mpiComm, const gmx_domdec_t *dd, gmx_wallcycle *wcycle, gmx_enerdata_t *enerd, const gmx_multisim_t *ms, const gmx_mtop_t &top_global, const MDLogger &mdlog, gmx::ArrayRef< const gmx::RVec > coords, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const ImdOptions &options, StartingBehavior startingBehavior)
	Makes and returns an initialized IMD session, which may be inactive. More...
int	imdsock_winsockinit ()
	Define a function to initialize winsock.
static void	print_IMD_error (const char *file, int line, char *msg)
	Print a nice error message on UNIX systems, using errno.h.
IMDSocket *	imdsock_create ()
	Create an IMD main socket. More...
void	imd_sleep (unsigned int seconds)
	Portability wrapper around sleep function.
int	imdsock_bind (IMDSocket *sock, int port)
	Bind the IMD socket to address and port. More...
int	imd_sock_listen (IMDSocket *sock)
	Set socket to listening state. More...
IMDSocket *	imdsock_accept (IMDSocket *sock)
	Accept incoming connection and redirect to client socket. More...
int	imdsock_getport (IMDSocket *sock, int *port)
	Get the port number used for IMD connection. More...
int	imd_htonl (int src)
	Portability wrapper around system htonl function.
int	imd_ntohl (int src)
	Portability wrapper around system ntohl function.
int	imdsock_write (IMDSocket *sock, const char *buffer, int length)
	Write to socket. More...
int	imdsock_read (IMDSocket *sock, char *buffer, int length)
	Read from socket. More...
void	imdsock_shutdown (IMDSocket *sock)
	Shutdown the socket. More...
int	imdsock_destroy (IMDSocket *sock)
	Close the socket and free the sock struct memory. More...
int	imdsock_tryread (IMDSocket *sock, int timeoutsec, int timeoutusec)
	Try to read from the socket. More...
std::string	blasDescription ()
	Returns information for describing the BLAS libary.
std::string	lapackDescription ()
	Returns information for describing the LAPACK libary.
bool	buildSupportsListedForcesGpu (std::string *error)
	Checks whether the GROMACS build allows to compute bonded interactions on a GPU. More...
bool	inputSupportsListedForcesGpu (const t_inputrec &ir, const gmx_mtop_t &mtop, std::string *error)
	Checks whether the input system allows to compute bonded interactions on a GPU. More...
static bool	someInteractionsCanRunOnGpu (const InteractionLists &ilists)
	Returns whether there are any interactions in ilists suitable for a GPU.
static bool	bondedInteractionsCanRunOnGpu (const gmx_mtop_t &mtop)
	Returns whether there are any bonded interactions in the global topology suitable for a GPU.
static int	chooseSubGroupSizeForDevice (const DeviceInformation &deviceInfo)
static bool	fTypeHasPerturbedEntries (const InteractionDefinitions &idef, int fType)
	Return whether function type fType in idef has perturbed interactions.
static void	convertIlistToNbnxmOrder (const InteractionList &src, HostInteractionList *dest, int numAtomsPerInteraction, ArrayRef< const int > nbnxmAtomOrder)
	Converts src with atom indices in state order to dest in nbnxm order.
static int	roundUpToFactor (const int input, const int factor)
	Returns input rounded up to the closest multiple of factor.
template<bool calcVir, bool calcEner>
	__launch_bounds__ (c_threadsBondedPerBlock) __global__ void bonded_kernel_gpu(BondedGpuKernelParameters kernelParams
if	constexpr (calcVir)
	for (int j=0;j< numFTypesOnGpu;j++)
	if (threadComputedPotential)
template<bool calcVir, bool calcEner, typename CommandGroupHandler >
auto	bondedKernel (CommandGroupHandler cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float *__restrict__ gm_vTot, const t_iparams *__restrict__ gm_forceParams_, const sycl::float4 *__restrict__ gm_xq_in_, Float3 *__restrict__ gm_f_, Float3 *__restrict__ gm_fShift_)
static void	PrintTo (const RVec &value, std::ostream *os)
	Print an RVec to os.
static void	PrintTo (const PaddedVector< RVec > &vector, std::ostream *os)
	Print a padded vector of RVec to os.
void	normalizeSumPositiveValuesToUnity (ArrayRef< float > data)
	Divide all values of a view by a constant so that the sum of all its positive values is one. More...
void	exponentialMovingAverageStateAsKeyValueTree (KeyValueTreeObjectBuilder builder, const ExponentialMovingAverageState &state)
	Convert the exponential moving average state as key-value-tree object.
ExponentialMovingAverageState	exponentialMovingAverageStateFromKeyValueTree (const KeyValueTreeObject &object)
	Sets the exponential moving average state from a key-value-tree object. More...
unsigned int	log2I (std::uint32_t x)
	Compute floor of logarithm to base 2, 32 bit unsigned argument. More...
unsigned int	log2I (std::uint64_t x)
	Compute floor of logarithm to base 2, 64 bit unsigned argument. More...
unsigned int	log2I (std::int32_t x)
	Compute floor of logarithm to base 2, 32 bit signed argument. More...
unsigned int	log2I (std::int64_t x)
	Compute floor of logarithm to base 2, 64 bit signed argument. More...
std::int64_t	greatestCommonDivisor (std::int64_t p, std::int64_t q)
	Find greatest common divisor of two numbers. More...
double	erfinv (double x)
	Inverse error function, double precision. More...
float	erfinv (float x)
	Inverse error function, single precision. More...
IntegerBox	spreadRangeWithinLattice (const IVec &center, dynamicExtents3D extent, IVec range)
	Construct a box that holds all indices that are not more than a given range remote from center coordinates and still within a given lattice extent. More...
static void	assertMatrixIsBoxMatrix (const Matrix3x3 gmx_used_in_debug &m)
	Assert that the matrix m describes a simulation box. More...
static void	assertMatrixIsBoxMatrix (const matrix gmx_used_in_debug m)
	Assert that the matrix m describes a simulation box. More...
static void	multiplyVectorByTransposeOfBoxMatrix (const Matrix3x3 &m, const rvec v, rvec result)
	Multiply vector v by the transpose of the box matrix m, relying on the fact that the upper triangle of the matrix is zero.
static RVec	multiplyVectorByTransposeOfBoxMatrix (const Matrix3x3 &m, const RVec &v)
	Multiply vector v by the transpose of the box matrix m, relying on the fact that the upper triangle of the matrix is zero.
static Matrix3x3	multiplyBoxMatrices (const Matrix3x3 &a, const Matrix3x3 &b)
	Multiply box matrices, relying on the fact that their upper triangle is zero.
static Matrix3x3	multiplyBoxMatrices (const Matrix3x3 &a, const matrix b)
	Multiply box matrices, relying on the fact that their upper triangle is zero.
static Matrix3x3	invertBoxMatrix (const Matrix3x3 &src)
	Invert a simulation-box matrix. More...
static void	invertBoxMatrix (const matrix src, matrix dest)
	Invert a simulation-box matrix in src, return in dest. More...
void	invertMatrix (const matrix src, matrix dest)
	Invert a general 3x3 matrix in src, return in dest. More...
template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::const_iterator	begin (const MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray begin function addressing its contiguous memory.
template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::iterator	begin (MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray begin function addressing its contiguous memory.
template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::const_iterator	end (const MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray end function addressing its contiguous memory.
template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::iterator	end (MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray end function addressing its contiguous memory.
template<class TContainer , class Extents >
void	swap (MultiDimArray< TContainer, Extents > &a, MultiDimArray< TContainer, Extents > &b) noexcept
	Swap function.
OptimisationResult	nelderMead (const std::function< real(ArrayRef< const real >)> &functionToMinimize, ArrayRef< const real > initialGuess, real minimumRelativeSimplexLength=1e-8, int maxSteps=10'000)
	Derivative-free downhill simplex optimisation. More...
std::unique_ptr< BoxDeformation >	buildBoxDeformation (const Matrix3x3 &initialBox, DDRole ddRole, NumRanks numRanks, MPI_Comm communicator, const t_inputrec &inputrec)
	Factory function for box deformation module. More...
void	setBoxDeformationFlowMatrix (const matrix boxDeformationVelocity, const matrix box, matrix flowMatrix)
	Set a matrix for computing the flow velocity at coordinates. More...
static CheckpointSignal	convertToCheckpointSignal (signed char sig)
	Convert signed char (as used by SimulationSignal) to CheckpointSignal enum. More...
static void	clear_constraint_quantity_nonlocal (const gmx_domdec_t &dd, ArrayRef< RVec > q)
	Clears constraint quantities for atoms in nonlocal region.
void	too_many_constraint_warnings (ConstraintAlgorithm eConstrAlg, int warncount)
	Generate a fatal error because of too many LINCS/SETTLE warnings.
static void	write_constr_pdb (const char *fn, const char *title, const gmx_mtop_t &mtop, int start, int homenr, const MpiComm &mpiComm, const gmx_domdec_t *dd, ArrayRef< const RVec > x, const matrix box)
	Writes out coordinates.
static void	dump_confs (FILE *log, int64_t step, const gmx_mtop_t &mtop, int start, int homenr, const MpiComm &mpiComm, const gmx_domdec_t *dd, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, const matrix box)
	Writes out domain contents to help diagnose crashes.
FlexibleConstraintTreatment	flexibleConstraintTreatment (bool haveDynamicsIntegrator)
	Returns the flexible constraint treatment depending on whether the integrator is dynamic.
static ListOfLists< int >	makeAtomsToConstraintsList (int numAtoms, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a block struct to go from atoms to constraints. More...
ListOfLists< int >	make_at2con (int numAtoms, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilist, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
ListOfLists< int >	make_at2con (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
static std::vector< int >	make_at2settle (int natoms, const InteractionList &ilist)
	Returns the index of the settle to which each atom belongs.
static std::vector < ListOfLists< int > >	makeAtomToConstraintMappings (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Makes a per-moleculetype container of mappings from atom indices to constraint indices. More...
bool	hasTriangleConstraints (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns True if there is at least one triangular constraint.
void	do_constrain_first (FILE *log, gmx::Constraints *constr, const t_inputrec &inputrec, int numHomeAtoms, ArrayRefWithPadding< RVec > x, ArrayRefWithPadding< RVec > v, const matrix box, real lambda)
	Constrain the initial coordinates and velocities.
void	constrain_velocities (gmx::Constraints *constr, bool computeRmsd, int64_t step, t_state *state, real *dhdlambda, bool computeVirial, tensor constraintsVirial)
	Constrain the velocities only. More...
void	constrain_coordinates (gmx::Constraints *constr, bool computeRmsd, int64_t step, t_state *state, ArrayRefWithPadding< RVec > xp, real *dhdlambda, bool computeVirial, tensor constraintsVirial)
	Constrain the coordinates. More...
static bool	isConstraintFlexible (ArrayRef< const t_iparams > iparams, int iparamsIndex)
	Returns whether constraint with parameter iparamsIndex is a flexible constraint.
const int *	constr_iatomptr (gmx::ArrayRef< const int > iatom_constr, gmx::ArrayRef< const int > iatom_constrnc, int con)
	Returns the constraint iatoms for a constraint number con which comes from a list where InteractionFunction::Constraints and InteractionFunction::ConstraintsNoCoupling constraints are concatenated.
static void	constr_recur (const ListOfLists< int > &at2con, const InteractionLists &ilist, gmx::ArrayRef< const t_iparams > iparams, gmx_bool bTopB, int at, int depth, int nc, ArrayRef< int > path, real r0, real r1, real *r2max, int *count)
	Recursing function to help find all adjacent constraints.
static real	constr_r_max_moltype (const gmx_moltype_t *molt, gmx::ArrayRef< const t_iparams > iparams, const t_inputrec *ir)
	Find the interaction radius needed for constraints for this molecule type.
real	constr_r_max (const MDLogger &mdlog, const gmx_mtop_t *mtop, const t_inputrec *ir)
	Returns an estimate of the maximum distance between atoms required for LINCS.
void	update_tcouple (int64_t step, const t_inputrec *inputrec, t_state *state, gmx_ekindata_t *ekind, const t_extmass *MassQ, int homenr, ArrayRef< const unsigned short > cTC)
void	update_pcouple_before_coordinates (const MDLogger &mdlog, int64_t step, const PressureCouplingOptions &pressureCouplingOptions, const tensor deform, const real delta_t, t_state *state, Matrix3x3 *parrinellorahmanMu, Matrix3x3 *M)
void	update_pcouple_after_coordinates (FILE *fplog, int64_t step, const PressureCouplingOptions &pressureCoupling, int64_t ld_seed, real ensembleTemperature, const ivec *nFreeze, const tensor deform, real delta_t, int homenr, ArrayRef< const unsigned short > cFREEZE, const matrix pressure, const matrix forceVirial, const matrix constraintVirial, Matrix3x3 *pressureCouplingMu, t_state *state, t_nrnb *nrnb, BoxDeformation *boxDeformation, bool scaleCoordinates)
	Implement aspects of pressure coupling. More...
bool	update_randomize_velocities (const t_inputrec *ir, int64_t step, const gmx_domdec_t *dd, int homenr, ArrayRef< const unsigned short > cTC, ArrayRef< const real > invMass, ArrayRef< RVec > v, const Update *upd, const Constraints *constr)
real	calc_pres (PbcType pbcType, int nwall, const matrix box, const Matrix3x3 &ekin, const Matrix3x3 &vir, Matrix3x3 *pres)
real	calc_temp (real ekin, real nrdf)
void	init_parrinellorahman (const PressureCouplingOptions &pressureCouplingOptions, const tensor deform, real couplingTimePeriod, const tensor box, tensor box_rel, tensor boxv, Matrix3x3 *M, Matrix3x3 *mu)
	Initialize the Parrinello-Rahman mu and M tensors. More...
void	parrinellorahman_pcoupl (const MDLogger &mdlog, int64_t step, const PressureCouplingOptions &pressureCouplingOptions, const tensor deform, real couplingTimePeriod, const tensor pres, const tensor box, tensor box_rel, tensor boxv, Matrix3x3 *M, Matrix3x3 *mu)
	Calculate the change in box vectors due to Parrinello-Rahman pressure coupling. More...
template<PressureCoupling pressureCouplingType>
void	pressureCouplingCalculateScalingMatrix (FILE *fplog, int64_t step, const PressureCouplingOptions &pressureCoupling, int64_t ld_seed, real ensembleTemperature, real delta_t, const tensor pres, const matrix box, const matrix force_vir, const matrix constraint_vir, Matrix3x3 *mu, double *baros_integral)
	Calculate the pressure coupling scaling matrix. More...
template void	pressureCouplingCalculateScalingMatrix< PressureCoupling::CRescale > (FILE *, int64_t, const PressureCouplingOptions &, int64_t, real, real, const tensor, const matrix, const matrix, const matrix, Matrix3x3 *, double *)
template void	pressureCouplingCalculateScalingMatrix< PressureCoupling::Berendsen > (FILE *, int64_t, const PressureCouplingOptions &, int64_t, real, real, const tensor, const matrix, const matrix, const matrix, Matrix3x3 *, double *)
template<PressureCoupling pressureCouplingType>
void	pressureCouplingScaleBoxAndCoordinates (const PressureCouplingOptions &pressureCoupling, const tensor deform, const ivec *nFreeze, const Matrix3x3 &mu, matrix box, matrix box_rel, int start, int nr_atoms, ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const unsigned short > cFREEZE, t_nrnb *nrnb, bool scaleCoordinates)
	Scale the box and coordinates. More...
template void	pressureCouplingScaleBoxAndCoordinates< PressureCoupling::Berendsen > (const PressureCouplingOptions &, const tensor, const ivec *, const Matrix3x3 &, matrix, matrix, int, int, ArrayRef< RVec >, ArrayRef< RVec >, ArrayRef< const unsigned short >, t_nrnb *, const bool)
template void	pressureCouplingScaleBoxAndCoordinates< PressureCoupling::CRescale > (const PressureCouplingOptions &, const tensor, const ivec *, const Matrix3x3 &, matrix, matrix, int, int, ArrayRef< RVec >, ArrayRef< RVec >, ArrayRef< const unsigned short >, t_nrnb *, const bool)
void	berendsen_tcoupl (const t_inputrec *ir, gmx_ekindata_t *ekind, real dt, std::vector< double > &therm_integral)
void	andersen_tcoupl (const t_inputrec *ir, int64_t step, const gmx_domdec_t *dd, const int homenr, ArrayRef< const unsigned short > cTC, ArrayRef< const real > invMass, ArrayRef< RVec > v, real rate, const std::vector< bool > &randomize, ArrayRef< const real > boltzfac)
void	trotter_update (const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind, t_state *state, const tensor vir, int homenr, ArrayRef< const unsigned short > cTC, ArrayRef< const real > invMass, const t_extmass *MassQ, ArrayRef< std::vector< int >> trotter_seqlist, TrotterSequence trotter_seqno)
void	init_npt_masses (const t_inputrec &ir, const gmx_ekindata_t &ekind, t_state *state, t_extmass *MassQ, bool bInit)
EnumerationArray < TrotterSequence, std::vector < int > >	init_npt_vars (const t_inputrec *ir, const gmx_ekindata_t &ekind, t_state *state, t_extmass *MassQ, bool bTrotter)
real	NPT_energy (const PressureCouplingOptions &pressureCouplingOptions, const TemperatureCoupling etc, const ArrayRef< const real > degreesOfFreedom, const gmx_ekindata_t &ekind, const bool isTrotterWithConstantTemperature, const t_state *state, const t_extmass *MassQ)
real	vrescale_resamplekin (real kk, real sigma, real ndeg, real taut, int64_t step, int64_t seed)
	Generate a new kinetic energy for the v-rescale thermostat. More...
void	vrescale_tcoupl (const t_inputrec *ir, int64_t step, gmx_ekindata_t *ekind, real dt, ArrayRef< double > therm_integral)
void	rescale_velocities (const gmx_ekindata_t *ekind, ArrayRef< const unsigned short > cTC, int start, int end, ArrayRef< RVec > v)
bool	initSimulatedAnnealing (const t_inputrec &ir, gmx_ekindata_t *ekind, Update *upd)
	Initialize simulated annealing.
void	update_annealing_target_temp (const t_inputrec &ir, real t, gmx_ekindata_t *ekind, Update *upd)
	Set reference temperature for simulated annealing.
void	pleaseCiteCouplingAlgorithms (FILE *fplog, const t_inputrec &ir)
real	calculateAcceptanceWeight (LambdaWeightCalculation calculationMode, real lambdaEnergyDifference)
	Calculates the acceptance weight for a lambda state transition. More...
void	do_force (FILE *log, const t_commrec *cr, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t *top, const matrix box, ArrayRefWithPadding< RVec > coordinates, ArrayRef< RVec > velocities, const history_t *hist, ForceBuffersView *force, tensor vir_force, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, ArrayRef< const real > lambda, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, VirtualSitesHandler *vsite, rvec mu_tot, double t, edsam *ed, CpuPpLongRangeNonbondeds *longRangeNonbondeds, const DDBalanceRegionHandler &ddBalanceRegionHandler)
gmx::EnumerationArray < FreeEnergyPerturbationCouplingType, real >	currentLambdas (int64_t step, const t_lambda &fepvals, int currentLambdaState)
	Evaluate the current lambdas. More...
void	launchForceReductionKernel (int numAtoms, int atomStart, bool addRvecForce, bool accumulate, const DeviceBuffer< Float3 > d_nbnxmForceToAdd, const DeviceBuffer< Float3 > d_rvecForceToAdd, DeviceBuffer< Float3 > d_baseForce, DeviceBuffer< int > d_cell, const DeviceStream &deviceStream, DeviceBuffer< uint64_t > d_forcesReadyNvshmemFlags, const uint64_t forcesReadyNvshmemFlagsCounter)
	Backend-specific function to launch GPU Force Reduction kernel. More...
template<bool addRvecForce, bool accumulateForce, typename CommandGroupHandler >
static auto	reduceKernel (CommandGroupHandler, const Float3 *__restrict__ gm_nbnxmForce, const Float3 *__restrict__ gm_rvecForceToAdd, Float3 *__restrict__ gm_forceTotal, const int *__restrict__ gm_cell, const int atomStart)
	Function returning the force reduction kernel lambda.
template<bool addRvecForce, bool accumulateForce>
static void	launchReductionKernel_ (const int numAtoms, const int atomStart, const DeviceBuffer< Float3 > &d_nbnxmForce, const DeviceBuffer< Float3 > &d_rvecForceToAdd, DeviceBuffer< Float3 > &d_forceTotal, const DeviceBuffer< int > &d_cell, const DeviceStream &deviceStream)
	Force reduction SYCL kernel launch code.
NumTempScaleValues	getTempScalingType (bool doTemperatureScaling, int numTempScaleValues)
	Convert doTemperatureScaling and numTempScaleValues to NumTempScaleValues.
void	launchLeapFrogKernel (int numAtoms, DeviceBuffer< Float3 > d_x, DeviceBuffer< Float3 > d_x0, DeviceBuffer< Float3 > d_v, DeviceBuffer< Float3 > d_f, DeviceBuffer< float > d_inverseMasses, float dt, bool doTemperatureScaling, int numTempScaleValues, DeviceBuffer< unsigned short > d_tempScaleGroups, DeviceBuffer< float > d_lambdas, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, Float3 prVelocityScalingMatrixDiagonal, const DeviceStream &deviceStream)
	Backend-specific function to launch GPU Leap Frog kernel. More...
template<NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
auto	leapFrogKernel (Float3 *__restrict__ gm_x, Float3 *__restrict__ gm_x0, Float3 *__restrict__ gm_v, const Float3 *__restrict__ gm_f, const float *__restrict__ gm_inverseMasses, float dt, const float *__restrict__ gm_lambdas, const unsigned short *__restrict__ gm_tempScaleGroups, Float3 prVelocityScalingMatrixDiagonal)
	Main kernel for the Leap-Frog integrator. More...
template<NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, class... Args>
static void	launchLeapFrogKernel (const DeviceStream &deviceStream, int numAtoms, Args &&...args)
	Leap Frog SYCL kernel launch code.
template<class... Args>
static void	launchLeapFrogKernel (NumTempScaleValues tempScalingType, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, Args &&...args)
	Select templated kernel and launch it.
real	lincs_rmsd (const Lincs *lincsd)
	Return the RMSD of the constraint.
static void	lincs_matrix_expand (const Lincs &lincsd, const Task &li_task, gmx::ArrayRef< const real > blcc, gmx::ArrayRef< real > rhs1, gmx::ArrayRef< real > rhs2, gmx::ArrayRef< real > sol)
	Do a set of nrec LINCS matrix multiplications. More...
static void	lincs_update_atoms_noind (int ncons, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update atomic coordinates when an index is not required.
static void	lincs_update_atoms_ind (gmx::ArrayRef< const int > ind, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update atomic coordinates when an index is required.
static void	lincs_update_atoms (Lincs *li, int th, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update coordinates for atoms.
static void	do_lincsp (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > fPadded, ArrayRef< RVec > fp, t_pbc *pbc, Lincs *lincsd, int th, ArrayRef< const real > invmass, ConstraintVariable econq, bool bCalcDHDL, bool bCalcVir, tensor rmdf)
	LINCS projection, works on derivatives of the coordinates.
static gmx_unused void	calc_dist_iter (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict xp, const real *gmx_restrict bllen, const real *gmx_restrict blc, const t_pbc *pbc, real wfac, real *gmx_restrict rhs, real *gmx_restrict sol, bool *bWarn)
	Determine the distances and right-hand side for the next iteration.
static void	do_lincs (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > xpPadded, const matrix box, t_pbc *pbc, Lincs *lincsd, int th, ArrayRef< const real > invmass, gmx_domdec_t *dd, bool bCalcDHDL, real wangle, bool *bWarn, real invdt, ArrayRef< RVec > vRef, bool bCalcVir, tensor vir_r_m_dr, gmx_wallcycle *wcycle)
	Implements LINCS constraining.
static void	set_lincs_matrix_task (Lincs *li, Task *li_task, ArrayRef< const real > invmass, int *ncc_triangle, int *nCrossTaskTriangles)
	Sets the elements in the LINCS matrix for task task.
static void	set_lincs_matrix (Lincs *li, ArrayRef< const real > invmass, real lambda)
	Sets the elements in the LINCS matrix.
int	count_triangle_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Counts the number of constraint triangles, i.e. triplets of atoms connected by three constraints. More...
static bool	more_than_two_sequential_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Finds sequences of sequential constraints.
Lincs *	init_lincs (FILE *fplog, const gmx_mtop_t &mtop, int nflexcon_global, ArrayRef< const ListOfLists< int >> atomsToConstraintsPerMolType, bool bPLINCS, int nIter, int nProjOrder, ObservablesReducerBuilder *observablesReducerBuilder)
	Initializes and returns the lincs data struct.
void	done_lincs (Lincs *li)
	Destructs the lincs object when it is not nullptr.
static void	lincs_thread_setup (Lincs *li, int natoms)
	Sets up the work division over the threads.
static void	assign_constraint (Lincs *li, int constraint_index, int a1, int a2, real lenA, real lenB, const ListOfLists< int > &at2con)
	Assign a constraint.
static void	check_assign_connected (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is connected to other constraints, and if so add those connected constraints to our task.
static void	check_assign_triangle (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int constraint_index, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is involved in a constraint triangle, and if so add the other two constraints in the triangle to our task.
static void	set_matrix_indices (Lincs *li, const Task &li_task, const ListOfLists< int > &at2con, bool bSortMatrix)
	Sets matrix indices.
void	set_lincs (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass, real lambda, bool bDynamics, const gmx_domdec_t *dd, Lincs *li)
	Initialize lincs stuff.
static void	lincs_warning (gmx_domdec_t *dd, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, t_pbc *pbc, int ncons, gmx::ArrayRef< const AtomPair > atoms, gmx::ArrayRef< const real > bllen, real wangle, int maxwarn, int *warncount)
	Issues a warning when LINCS constraints cannot be satisfied.
static LincsDeviations	makeLincsDeviations (const Lincs &lincsd, ArrayRef< const RVec > x, const t_pbc *pbc)
	Determine how well the constraints have been satisfied.
bool	constrain_lincs (bool computeRmsd, const t_inputrec &ir, int64_t step, Lincs *lincsd, ArrayRef< const real > invmass, gmx_domdec_t *dd, const gmx_multisim_t *ms, ArrayRefWithPadding< const RVec > x, ArrayRefWithPadding< RVec > xprime, ArrayRef< RVec > min_proj, const matrix box, t_pbc *pbc, bool hasMassPerturbed, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq, t_nrnb *nrnb, int maxwarn, int *warncount, gmx_wallcycle *wcycle)
	Applies LINCS constraints. More...
void	findConstraintGroupSizes (int numConstraints, ArrayRef< const AtomPair > constraintsHost, ArrayRef< int > constraintGroupSize)
	Calculate constraint group sizes. More...
void	addWithCoupled (ArrayRef< const int > iatoms, const int stride, const gmx::ListOfLists< AtomsAdjacencyListElement > &atomsAdjacencyList, ArrayRef< int > splitMap, const int c, int *currentMapIndex)
	Add constraint to splitMap with all constraints coupled to it. More...
void	launchLincsGpuKernel (LincsGpuKernelParameters *kernelParams, const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, const DeviceStream &deviceStream)
	Backend-specific function to launch LINCS kernel. More...
template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, typename CommandGroupHandler >
auto	lincsKernel (CommandGroupHandler &cgh, const int numConstraintsThreads, const AtomPair *__restrict__ gm_constraints, const float *__restrict__ gm_constraintsTargetLengths, const int *__restrict__ gm_coupledConstraintsCounts, const int *__restrict__ gm_coupledConstraintsIndices, const float *__restrict__ gm_massFactors, float *__restrict__ gm_matrixA, const float *__restrict__ gm_inverseMasses, const int numIterations, const int expansionOrder, const Float3 *__restrict__ gm_x, Float3 *__restrict__ gm_xp, const float invdt, Float3 *__restrict__ gm_v, float *__restrict__ gm_virialScaled, PbcAiuc pbcAiuc)
	Main kernel for LINCS constraints. More...
template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, class... Args>
static void	launchLincsKernel (const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&...args)
template<class... Args>
static void	launchLincsKernel (bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, Args &&...args)
	Select templated kernel and launch it.
template<typename... Args>
std::unique_ptr< Constraints >	makeConstraints (const gmx_mtop_t &mtop, const t_inputrec &ir, pull_t *pull_work, bool havePullConstraintsWork, bool doEssentialDynamics, Args &&...args)
	Factory function for Constraints. More...
std::unique_ptr< MDAtoms >	makeMDAtoms (FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir, bool useGpuForPme, const DeviceStreamManager *deviceStreamManager)
	Builder function for MdAtomsWrapper. More...
static ResetSignal	convertToResetSignal (signed char sig)
	Convert signed char (as used by SimulationSignal) to ResetSignal enum. More...
static void	initializeProjectionMatrix (const real invmO, const real invmH, const real dOH, const real dHH, matrix inverseCouplingMatrix)
	Initializes a projection matrix. More...
SettleParameters	settleParameters (real mO, real mH, real invmO, real invmH, real dOH, real dHH)
	Computes and returns settle parameters. More...
SettleWaterTopology	getSettleTopologyData (const gmx_mtop_t &mtop)
	Validates that settle can run and returns setup data.
void	settle_proj (const SettleData &settled, ConstraintVariable econq, int nsettle, const int iatoms[], const t_pbc *pbc,ArrayRef< const RVec > x, ArrayRef< RVec > der, ArrayRef< RVec > derp, int CalcVirAtomEnd, tensor vir_r_m_dder)
	Analytical algorithm to subtract the components of derivatives of coordinates working on settle type constraint.
template<typename T , typename TypeBool , int packSize, typename TypePbc , bool bCorrectVelocity, bool bCalcVirial>
static void	settleTemplate (const SettleData &settled, int settleStart, int settleEnd, const TypePbc pbc, const real *x, real *xprime, real invdt, real *gmx_restrict v, tensor vir_r_m_dr, bool *bErrorHasOccurred)
	The actual settle code, templated for real/SimdReal and for optimization.
template<typename T , typename TypeBool , int packSize, typename TypePbc >
static void	settleTemplateWrapper (const SettleData &settled, int nthread, int thread, TypePbc pbc, const real x[], real xprime[], real invdt, real *v, bool bCalcVirial, tensor vir_r_m_dr, bool *bErrorHasOccurred)
	Wrapper template function that divides the settles over threads and instantiates the core template with instantiated booleans.
void	csettle (const SettleData &settled,int nthread,int thread,const t_pbc *pbc,ArrayRefWithPadding< const RVec > x,ArrayRefWithPadding< RVec > xprime,real invdt,ArrayRefWithPadding< RVec > v,bool bCalcVirial,tensor vir_r_m_dr,bool *bErrorHasOccurred)
	Constrain coordinates using SETTLE. Can be called on any number of threads.
void	launchSettleGpuKernel (int numSettles, const DeviceBuffer< WaterMolecule > &d_atomIds, const SettleParameters &settleParameters, const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, DeviceBuffer< float > d_virialScaled, const PbcAiuc &pbcAiuc, const DeviceStream &deviceStream)
	Apply SETTLE. More...
template<bool updateVelocities, bool computeVirial, typename CommandGroupHandler >
auto	settleKernel (CommandGroupHandler cgh, const int numSettles, const WaterMolecule *__restrict__ gm_settles, SettleParameters pars, const Float3 *__restrict__ gm_x, Float3 *__restrict__ gm_xp, float invdt, Float3 *__restrict__ gm_v, float *__restrict__ gm_virialScaled, PbcAiuc pbcAiuc)
	Function returning the SETTLE kernel lambda.
template<bool updateVelocities, bool computeVirial, class... Args>
static void	launchSettleKernel (const DeviceStream &deviceStream, int numSettles, Args &&...args)
	SETTLE SYCL kernel launch code.
template<class... Args>
static void	launchSettleKernel (bool updateVelocities, bool computeVirial, Args &&...args)
	Select templated kernel and launch it.
static int	pcomp (const void *p1, const void *p2)
	Compares sort blocks.
static void	pr_sortblock (FILE *fp, const char *title, gmx::ArrayRef< const t_sortblock > sb)
	Prints sortblocks.
static void	resizeLagrangianData (shakedata *shaked, int ncons)
	Reallocates a vector.
void	make_shake_sblock_serial (shakedata *shaked, InteractionDefinitions *idef, int numAtoms)
	Make SHAKE blocks when not using DD.
void	make_shake_sblock_dd (shakedata *shaked, const InteractionList &ilcon)
	Make SHAKE blocks when using DD.
void	cshake (const int iatom[], int ncon, int *nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > positions, const t_pbc *pbc, ArrayRef< const RVec > initial_displacements, ArrayRef< const real > half_of_reduced_mass, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int *nerror)
	Inner kernel for SHAKE constraints. More...
static void	crattle (const int iatom[], int ncon, int *nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > vp, ArrayRef< const RVec > rij, ArrayRef< const real > m2, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int *nerror, real invdt)
	Implements RATTLE (ie. SHAKE for velocity verlet integrators)
static int	vec_shakef (FILE *fplog, shakedata *shaked, ArrayRef< const real > invmass, int ncon, ArrayRef< const t_iparams > ip, const int *iatom, real tol, ArrayRef< const RVec > x, ArrayRef< RVec > prime, const t_pbc *pbc, real omega, bool bFEP, real lambda, ArrayRef< real > scaled_lagrange_multiplier, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq)
	Applies SHAKE.
static void	check_cons (FILE *log, int nc, ArrayRef< const RVec > x, ArrayRef< const RVec > prime, ArrayRef< const RVec > v, const t_pbc *pbc, ArrayRef< const t_iparams > ip, const int *iatom, ArrayRef< const real > invmass, ConstraintVariable econq)
	Check that constraints are satisfied.
static bool	bshakef (FILE *log, shakedata *shaked, ArrayRef< const real > invmass, const InteractionDefinitions &idef, const t_inputrec &ir, ArrayRef< const RVec > x_s, ArrayRef< RVec > prime, const t_pbc *pbc, t_nrnb *nrnb, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, bool bDumpOnError, ConstraintVariable econq)
	Applies SHAKE.
bool	constrain_shake (FILE *log,shakedata *shaked,gmx::ArrayRef< const real > invmass,const InteractionDefinitions &idef,const t_inputrec &ir,ArrayRef< const RVec > x_s,ArrayRef< RVec > xprime,ArrayRef< RVec > vprime,const t_pbc *pbc,t_nrnb *nrnb,real lambda,real *dvdlambda,real invdt,ArrayRef< RVec > v,bool bCalcVir,tensor vir_r_m_dr,bool bDumpOnError,ConstraintVariable econq)
	Shake all the atoms blockwise. It is assumed that all the constraints in the idef->shakes field are sorted, to ascending block nr. The sblock array points into the idef->shakes.iatoms field, with block 0 starting at sblock[0] and running to ( < ) sblock[1], block n running from sblock[n] to sblock[n+1]. Array sblock should be large enough. Return TRUE when OK, FALSE when shake-error.
static void	sum_forces (ArrayRef< RVec > f, ArrayRef< const RVec > forceToAdd)
static void	calc_virial (int start, int homenr, const rvec x[], const ForceWithShiftForces &forceWithShiftForces, tensor vir_part, const matrix box, t_nrnb *nrnb, const t_forcerec *fr, PbcType pbcType)
static void	pull_potential_wrapper (const MpiComm &mpiComm, const t_inputrec &ir, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, gmx_enerdata_t *enerd, pull_t *pull_work, const real *lambda, double t, gmx_wallcycle *wcycle)
static void	pme_receive_force_ener (t_forcerec *fr, gmx_domdec_t *dd, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, bool receivePmeForceToGpu, bool isVirialOrEnergyStep, gmx_wallcycle *wcycle)
static void	print_large_forces (FILE *fp, const t_mdatoms *md, const gmx_domdec_t *dd, int64_t step, real forceTolerance, ArrayRef< const RVec > x, ArrayRef< const RVec > f)
static void	postProcessForceWithShiftForces (t_nrnb *nrnb, gmx_wallcycle *wcycle, const matrix box, ArrayRef< const RVec > x, ForceOutputs *forceOutputs, tensor vir_force, const t_mdatoms &mdatoms, const t_forcerec &fr, VirtualSitesHandler *vsite, const StepWorkload &stepWork)
	When necessary, spreads forces on vsites and computes the virial for forceOutputs->forceWithShiftForces()
static void	postProcessForces (const gmx_domdec_t *dd, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const matrix box, ArrayRef< const RVec > x, ForceOutputs *forceOutputs, tensor vir_force, const t_mdatoms *mdatoms, const t_forcerec *fr, VirtualSitesHandler *vsite, const StepWorkload &stepWork)
	Spread, compute virial for and sum forces, when necessary.
static void	do_nb_verlet (t_forcerec *fr, const interaction_const_t *ic, gmx_enerdata_t *enerd, const StepWorkload &stepWork, const InteractionLocality ilocality, const int clearF, const int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle)
static void	clearRVecs (ArrayRef< RVec > v, const bool useOpenmpThreading)
static real	averageKineticEnergyEstimate (const t_grpopts &groupOptions)
	Return an estimate of the average kinetic energy or 0 when unreliable. More...
static void	checkPotentialEnergyValidity (int64_t step, const gmx_enerdata_t &enerd, const t_inputrec &inputrec)
	This routine checks that the potential energy is finite. More...
static void	computeSpecialForces (FILE *fplog, const MpiComm &mpiComm, const gmx_domdec_t *dd, const t_inputrec &inputrec, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, double t, gmx_wallcycle *wcycle, ForceProviders *forceProviders, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, ArrayRef< const real > lambda, const StepWorkload &stepWork, ForceWithVirial *forceWithVirialMtsLevel0, ForceWithVirial *forceWithVirialMtsLevel1, gmx_enerdata_t *enerd, edsam *ed, bool didNeighborSearch)
	Compute forces and/or energies for special algorithms. More...
static void	launchPmeGpuSpread (gmx_pme_t *pmedata, const matrix box, const SimulationWorkload &simulationWork, const PmeStepWorkload &stepWork, GpuEventSynchronizer *xReadyOnDevice, const real lambdaQ, gmx_wallcycle *wcycle)
	Launch the prepare_step and spread stages of PME GPU. More...
static void	launchPmeGpuFftAndGather (gmx_pme_t *pmedata, const real lambdaQ, gmx_wallcycle *wcycle, const PmeStepWorkload &stepWork)
	Launch the FFT and gather stages of PME GPU. More...
static void	pmeGpuWaitAndReduce (gmx_pme_t *pme, const PmeStepWorkload &stepWork, gmx_wallcycle *wcycle, ForceWithVirial *forceWithVirial, gmx_enerdata_t *enerd, const real lambdaQ)
	Blocks until PME GPU tasks are completed, and gets the output forces and virial/energy (if they were to be computed). More...
static void	alternatePmeNbGpuWaitReduce (nonbonded_verlet_t *nbv, gmx_pme_t *pmedata, ForceOutputs *forceOutputsNonbonded, ForceOutputs *forceOutputsPme, gmx_enerdata_t *enerd, const real lambdaQ, const StepWorkload &stepWork, const SimulationWorkload &simulationWork, gmx_wallcycle *wcycle)
	Polling wait for either of the PME or nonbonded GPU tasks. More...
static ForceOutputs	setupForceOutputs (ForceHelperBuffers *forceHelperBuffers, ArrayRefWithPadding< RVec > force, const DomainLifetimeWorkload &domainWork, const StepWorkload &stepWork, const bool havePpDomainDecomposition, gmx_wallcycle *wcycle)
	Set up the different force buffers; also does clearing. More...
static void	launchGpuEndOfStepTasks (nonbonded_verlet_t *nbv, ListedForcesGpu *listedForcesGpu, gmx_pme_t *pmedata, gmx_enerdata_t *enerd, const MdrunScheduleWorkload &runScheduleWork, int64_t step, gmx_wallcycle *wcycle)
static int	getExpectedLocalXReadyOnDeviceConsumptionCount (const SimulationWorkload &simulationWork, const StepWorkload &stepWork, const DomainLifetimeWorkload &domainWork, const bool pmeSendCoordinatesFromGpu)
	Compute the number of times the "local coordinates ready on device" GPU event will be used as a synchronization point. More...
static int	getExpectedLocalFReadyOnDeviceConsumptionCount (const SimulationWorkload &simulationWork, const DomainLifetimeWorkload &domainWork, const StepWorkload &stepWork, bool useOrEmulateGpuNb, bool alternateGpuWait)
	Compute the number of times the "local forces ready on device" GPU event will be used as a synchronization point. More...
static void	reduceAndUpdateMuTot (DipoleData *dipoleData, const MpiComm &mpiComm, const bool haveFreeEnergy, ArrayRef< const real > lambda, rvec muTotal, const DDBalanceRegionHandler &ddBalanceRegionHandler)
static void	combineMtsForces (const int numAtoms, ArrayRef< RVec > forceMtsLevel0, ArrayRef< RVec > forceMts, const real mtsFactor)
	Combines MTS level0 and level1 force buffers into a full and MTS-combined force buffer. More...
static void	setupLocalGpuForceReduction (const MdrunScheduleWorkload &runScheduleWork, nonbonded_verlet_t *nbv, StatePropagatorDataGpu *stateGpu, GpuForceReduction *gpuForceReduction, PmePpCommGpu *pmePpCommGpu, const gmx_pme_t *pmedata, const gmx_domdec_t *dd)
	Setup for the local GPU force reduction: reinitialization plus the registration of forces and dependencies. More...
static void	setupNonLocalGpuForceReduction (const MdrunScheduleWorkload &runScheduleWork, nonbonded_verlet_t *nbv, StatePropagatorDataGpu *stateGpu, GpuForceReduction *gpuForceReduction, const gmx_domdec_t *dd)
	Setup for the non-local GPU force reduction: reinitialization plus the registration of forces and dependencies. More...
static int	getLocalAtomCount (const gmx_domdec_t *dd, const t_mdatoms &mdatoms, bool havePPDomainDecomposition)
	Return the number of local atoms.
static void	doPairSearch (const t_commrec *cr, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, int64_t step, t_nrnb *nrnb, gmx_wallcycle *wcycle, const gmx_localtop_t &top, const matrix box, ArrayRefWithPadding< RVec > x, ArrayRef< RVec > v, const t_mdatoms &mdatoms, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork)
	Does pair search and closely related activities required on search steps.
static StopSignal	convertToStopSignal (signed char sig)
	Convert signed char (as used by SimulationSignal) to StopSignal enum. More...
template<StoreUpdatedVelocities storeUpdatedVelocities, NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, typename VelocityType >
std::enable_if_t < std::is_same_v< VelocityType, RVec >||std::is_same_v < VelocityType, const RVec > , void >	updateMDLeapfrogSimple (int start, int nrend, real dt, real dtPressureCouple, const RVec *gmx_restrict invMassPerDim, ArrayRef< const t_grp_tcstat > tcstat, ArrayRef< const unsigned short > cTC, const RVec pRVScaleMatrixDiagonal, const RVec *gmx_restrict x, RVec *gmx_restrict xprime, VelocityType *gmx_restrict v, const RVec *gmx_restrict f)
	Integrate using leap-frog with T-scaling and optionally diagonal Parrinello-Rahman p-coupling. More...
void	init_ekinstate (ekinstate_t *ekinstate, const t_inputrec *ir)
void	update_ekinstate (ekinstate_t *ekinstate, const gmx_ekindata_t &ekind, const MpiComm &mpiComm, const gmx_domdec_t *dd)
	Updates ekinstate. More...
void	restore_ekinstate_from_state (const MpiComm &mpiComm, gmx_ekindata_t *ekind, const ekinstate_t *ekinstate)
	Restores data from ekinstate to ekind, then broadcasts it to the rest of the simulation.
void	getThreadAtomRange (int numThreads, int threadIndex, int numAtoms, int *startAtom, int *endAtom)
	Computes the atom range for a thread to operate on, ensuring SIMD aligned ranges. More...
void	launchScaleCoordinatesKernel (int numAtoms, DeviceBuffer< Float3 > d_coordinates, const ScalingMatrix &mu, const DeviceStream &deviceStream)
	Launches positions of velocities scaling kernel. More...
static auto	scaleKernel (Float3 *gm_x, const ScalingMatrix &scalingMatrix)
	Function returning the scaling kernel lambda.
static bool	hasFlexibleConstraints (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns whether moltype contains flexible constraints.
static bool	hasIncompatibleVsites (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns whether moltype has incompatible vsites. More...
static InteractionList	jointConstraintList (const gmx_moltype_t &moltype)
	Returns a merged list with constraints of all types.
static AtomIndexExtremes	vsiteConstructRange (int a, const gmx_moltype_t &moltype)
	Returns the range of constructing atom for vsite with atom index a.
static AtomIndexExtremes	constraintAtomRange (int a, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
	Returns the range of atoms constrained to atom a (including a itself)
static std::vector< bool >	buildIsParticleVsite (const gmx_moltype_t &moltype)
	Returns a list that tells whether atoms in moltype are vsites.
static std::variant< int, IncompatibilityReasons >	detectGroup (int firstAtom, const gmx_moltype_t &moltype, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
	Returns the size of the update group starting at firstAtom or an incompatibility reason.
static std::variant < RangePartitioning, IncompatibilityReasons >	makeUpdateGroupingsPerMoleculeType (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns a list of update groups for moltype or an incompatibility reason.
std::variant< std::vector < RangePartitioning > , std::string >	makeUpdateGroupingsPerMoleculeType (const gmx_mtop_t &mtop)
	Returns a vector with update groups for each moleculetype in mtop or an error string when the criteria (see below) are not satisfied. More...
static std::unordered_multimap < int, int >	getAngleIndices (const gmx_moltype_t &moltype)
	Returns a map of angles ilist.iatoms indices with the middle atom as key.
template<int numPartnerAtoms>
static real	constraintGroupRadius (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, const int centralAtom, const ListOfLists< int > &at2con, const std::unordered_multimap< int, int > &angleIndices, const real constraintLength, const real temperature)
	When possible, computes the maximum radius of constrained atom in an update group. More...
static real	computeMaxUpdateGroupRadius (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, const RangePartitioning &updateGrouping, real temperature)
	Returns the maximum update group radius for moltype.
real	computeMaxUpdateGroupRadius (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType, real temperature)
	Returns the maximum update group radius. More...
bool	systemHasConstraintsOrVsites (const gmx_mtop_t &mtop)
	Returns whether mtop contains any constraints and/or vsites. More...
UpdateGroups	makeUpdateGroups (const gmx::MDLogger &mdlog, std::vector< RangePartitioning > &&updateGroupingPerMoleculeType, real maxUpdateGroupRadius, bool doRerun, bool useDomainDecomposition, bool systemHasConstraintsOrVsites, real cutoffMargin)
	Builder for update groups. More...
static int	vsiteIlistNrCount (const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists)
	Returns the sum of the vsite ilist sizes over all vsite types. More...
static int	pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
	Computes the distance between xi and xj, pbc is used when pbc!=nullptr.
static real	inverseNorm (const rvec x)
	Returns the 1/norm(x)
static PbcMode	getPbcMode (const t_pbc *pbcPtr)
	Returns the PBC mode based on the system PBC and vsite properties. More...
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void	construct_vsites_thread (ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, const t_pbc *pbc_null)
	Executes the vsite construction task for a single thread. More...
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void	construct_vsites (const ThreadingInfo *threadingInfo, ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, const DomainInfo &domainInfo, const matrix box)
	Dispatch the vsite construction tasks for all threads. More...
void	constructVirtualSites (ArrayRef< RVec > x, ArrayRef< const t_iparams > ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists)
	Create positions of vsite atoms based for the local system. More...
static int	vsite_count (const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, InteractionFunction ftype)
	Returns the number of virtual sites in the interaction list, for VSITEN the number of atoms.
template<VirialHandling virialHandling>
static void	spreadForceForThread (ArrayRef< const RVec > x, ArrayRef< RVec > f, ArrayRef< RVec > fshift, matrix dxdf, ArrayRef< const t_iparams > ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, const t_pbc *pbc_null)
	Executes the force spreading task for a single thread.
static void	spreadForceWrapper (ArrayRef< const RVec > x, ArrayRef< RVec > f, const VirialHandling virialHandling, ArrayRef< RVec > fshift, matrix dxdf, const bool clearDxdf, ArrayRef< const t_iparams > ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, const t_pbc *pbc_null)
	Wrapper function for calling the templated thread-local spread function.
static void	clearTaskForceBufferUsedElements (InterdependentTask *idTask)
	Clears the task force buffer elements that are written by task idTask.
static std::vector< int >	makeAtomToGroupMapping (const gmx::RangePartitioning &grouping)
	Returns the an array with group indices for each atom. More...
int	countNonlinearVsites (const gmx_mtop_t &mtop)
	Return the number of non-linear virtual site constructions in the system.
int	countInterUpdategroupVsites (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingsPerMoleculeType)
	Return the number of virtual sites that cross update groups. More...
std::optional< std::string >	checkVsiteHierarchy (const gmx_mtop_t &mtop)
	Checks whether constructing atom are vsites with the same or higher function type. More...
std::unique_ptr < VirtualSitesHandler >	makeVirtualSitesHandler (const gmx_mtop_t &mtop, gmx_domdec_t *domdec, PbcType pbcType, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType)
	Create the virtual site handler. More...
	iparams_ (mtop.ffparams.iparams)
static void	flagAtom (InterdependentTask *idTask, const int atom, const int numThreads, const int numAtomsPerThread)
	Flag that atom atom which is home in another task, if it has not already been added before.
static void	assignVsitesToThread (VsiteThread *tData, const int thread, const int numThreads, const int numAtomsPerThread, gmx::ArrayRef< int > taskIndex, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilist, ArrayRef< const t_iparams > ip, ArrayRef< const ParticleType > ptype)
	Here we try to assign all vsites that are in our local range. More...
static void	assignVsitesToSingleTask (VsiteThread *tData, int task, gmx::ArrayRef< const int > taskIndex, const gmx::EnumerationArray< InteractionFunction, InteractionList > &ilists, ArrayRef< const t_iparams > ip)
	Assign all vsites with taskIndex[]==task to task tData.
void	constructVirtualSitesGlobal (const gmx_mtop_t &mtop, ArrayRef< RVec > x)
	Create positions of vsite atoms for the whole system assuming all molecules are wholex. More...
void	printBinaryInformation (FILE *fp, const IProgramContext &programContext, const BinaryInformationSettings &settings)
	Print basic information about the executable with custom settings. More...
void	printBinaryInformation (TextWriter *writer, const IProgramContext &programContext, const BinaryInformationSettings &settings)
	Print basic information about the executable with custom settings. More...
static bool	is_multisim_option_set (int argc, const char *const argv[])
	Return whether the command-line parameter that will trigger a multi-simulation is set.
static void	print_em_start (FILE *fplog, const t_commrec *cr, gmx_walltime_accounting_t walltime_accounting, gmx_wallcycle *wcycle, const char *name)
	Print the EM starting conditions.
static void	em_time_end (gmx_walltime_accounting_t walltime_accounting)
	Stop counting time for EM.
static void	sp_header (FILE *out, const char *minimizer, real ftol, int nsteps)
	Printing a log file and console header.
static void	warn_step (FILE *fp, real ftol, real fmax, gmx_bool bLastStep, gmx_bool bConstrain)
	Print warning message.
static void	print_converged (FILE *fp, const char *alg, real ftol, int64_t count, gmx_bool bDone, int64_t nsteps, const em_state_t *ems, double sqrtNumAtoms)
	Print message about convergence of the EM.
static void	get_f_norm_max (const t_commrec *cr, const t_grpopts *opts, t_mdatoms *mdatoms, const RVec *gmx_restrict f, real *fnorm, real *fmax, int *a_fmax)
	Compute the norm and max of the force array in parallel.
static void	get_state_f_norm_max (const t_commrec *cr, const t_grpopts *opts, t_mdatoms *mdatoms, em_state_t *ems)
	Compute the norm of the force.
static void	copyCGP (t_state *dest, const t_state &src)
	Copies the p vector contents from one t_state to another.
static void	init_em (FILE *fplog, const MDLogger &mdlog, const char *title, const t_commrec *cr, const t_inputrec *ir, const MDModulesNotifiers &mdModulesNotifiers, ImdSession *imdSession, pull_t *pull_work, t_state *state_global, const gmx_mtop_t &top_global, em_state_t *ems, gmx_localtop_t *top, t_nrnb *nrnb, t_forcerec *fr, MDAtoms *mdAtoms, gmx_global_stat_t *gstat, VirtualSitesHandler *vsite, Constraints *constr, const MdrunScheduleWorkload &runScheduleWork, shellfc_t **shellfc, gmx_wallcycle *wcycle)
	Initialize the energy minimization.
static void	finish_em (const PmePpComm *pmePpComm, gmx_mdoutf_t outf, gmx_walltime_accounting_t walltime_accounting)
	Finalize the minimization.
static void	write_em_traj (FILE *fplog, const t_commrec *cr, gmx_mdoutf_t outf, gmx_bool bX, gmx_bool bF, const char *confout, const gmx_mtop_t &top_global, const t_inputrec *ir, int64_t step, em_state_t *state, t_state *state_global, ObservablesHistory *observablesHistory)
	Save the EM trajectory.
static bool	do_em_step (const t_commrec *cr, const t_inputrec *ir, const t_mdatoms *md, t_state *s1, const real stepSize, ArrayRef< const RVec > force, em_state_t *ems2, Constraints *constr, const int64_t count)
	Do one minimization step. More...
static void	em_dd_partition_system (FILE *fplog, const MDLogger &mdlog, const SimulationWorkload &simulationWork, int step, const t_commrec *cr, const gmx_mtop_t &top_global, const t_inputrec *ir, const MDModulesNotifiers &mdModulesNotifiers, ImdSession *imdSession, pull_t *pull_work, em_state_t *ems, gmx_localtop_t *top, MDAtoms *mdAtoms, t_forcerec *fr, VirtualSitesHandler *vsite, Constraints *constr, t_nrnb *nrnb, gmx_wallcycle *wcycle)
	Prepare EM for using domain decomposition parallellization.
static double	reorder_partsum (const t_commrec *cr, const t_grpopts *opts, const gmx_mtop_t &top_global, const em_state_t *s_min, const em_state_t *s_b)
	Parallel utility summing energies and forces.
static real	pr_beta (const t_commrec *cr, const t_grpopts *opts, t_mdatoms *mdatoms, const gmx_mtop_t &top_global, const em_state_t *s_min, const em_state_t *s_b)
	Print some stuff, like beta, whatever that means.
gmx_repl_ex_t	init_replica_exchange (FILE *fplog, const gmx_multisim_t *ms, int numAtomsInSystem, const t_inputrec *ir, const ReplicaExchangeParameters &replExParams)
	Setup function. More...
gmx_bool	replica_exchange (FILE *fplog, const t_commrec *cr, const gmx_multisim_t *ms, gmx_repl_ex_t re, t_state *state, const gmx_enerdata_t *enerd, t_state *state_local, int64_t step, real time)
	Attempts replica exchange. More...
void	print_replica_exchange_statistics (FILE *fplog, gmx_repl_ex_t re)
	Prints replica exchange statistics to the log file. More...
static void	prepareRerunState (const t_trxframe &rerunFrame, t_state *globalState, bool constructVsites, const VirtualSitesHandler *vsite)
	Copy the state from rerunFrame to globalState and, if requested, construct vsites. More...
static DevelopmentFeatureFlags	manageDevelopmentFeatures (const MDLogger &mdlog, const PmeRunMode pmeRunMode, const int numRanksPerSimulation, const int numPmeRanksPerSimulation, const bool canUseGpuAwareMpi)
	Manage any development feature flag variables encountered. More...
static void	threadMpiMdrunnerAccessBarrier ()
	Barrier for safe simultaneous thread access to mdrunner data. More...
static void	mdrunner_start_fn (const void *arg)
	The callback used for running on spawned threads. More...
static LoggerOwner	buildLogger (FILE *fplog, const bool isSimulationMainRank)
	Initializes the logger for mdrun.
static TaskTarget	findTaskTarget (const std::string_view optionString)
	Make a TaskTarget from an mdrun argument string.
static void	finish_run (FILE *fplog, const MDLogger &mdlog, const t_commrec *cr, const t_inputrec &inputrec, t_nrnb nrnb[], gmx_wallcycle *wcycle, gmx_walltime_accounting_t walltime_accounting, nonbonded_verlet_t *nbv, const std::optional< gmx_wallclock_gpu_pme_t > &pmeGpuTimings, const int nratoms, gmx_bool bWriteStat)
	Finish run, aggregate data to print performance info.
static bool	localStateHasFillerParticles (const gmx_mtop_t &mtop, const t_inputrec &inputrec, const bool useDomainDecomposition, const bool haveSinglePPRank, const bool useGpuDirectHalo)
	Returns whether the run conditions permit the local state to have filler particles.
static void	pr_shell (FILE *fplog, ArrayRef< const t_shell > shells)
static void	predict_shells (FILE *fplog, ArrayRef< RVec > x, ArrayRef< RVec > v, real dt, ArrayRef< const t_shell > shells, ArrayRef< const real > mass, gmx_bool bInit)
shellfc_t *	init_shell_flexcon (FILE *fplog, const gmx_mtop_t &mtop, int nflexcon, int nstcalcenergy, bool usingDomainDecomposition, const DeviceStreamManager *deviceStreamManager, const SimulationWorkload &simulationWork)
	Initialization function, also predicts the initial shell positions. More...
static void	do_1pos (rvec xnew, const rvec xold, const rvec f, real step)
static void	do_1pos3 (rvec xnew, const rvec xold, const rvec f, const rvec step)
static void	directional_sd (ArrayRef< const RVec > xold, ArrayRef< RVec > xnew, ArrayRef< const RVec > acc_dir, int homenr, real step)
static void	shell_pos_sd (ArrayRef< const RVec > xcur, ArrayRef< RVec > xnew, ArrayRef< const RVec > f, ArrayRef< t_shell > shells, int count)
static void	decrease_step_size (ArrayRef< t_shell > shells)
static void	print_epot (FILE *fp, int64_t mdstep, int count, real epot, real df, int ndir, real sf_dir)
static real	rms_force (const t_commrec *cr, ArrayRef< const RVec > force, ArrayRef< const t_shell > shells, int ndir, real *sf_dir, real *Epot)
static void	dump_shells (FILE *fp, ArrayRef< RVec > f, real ftol, ArrayRef< const t_shell > shells)
static void	init_adir (shellfc_t *shfc, Constraints *constr, const t_inputrec *ir, const t_commrec *cr, int dd_ac1, int64_t step, const t_mdatoms &md, int end, ArrayRefWithPadding< RVec > xOld, ArrayRef< RVec > x_init, ArrayRefWithPadding< RVec > xCurrent, ArrayRef< RVec > f, ArrayRef< RVec > acc_dir, const matrix box, ArrayRef< const real > lambda, real *dvdlambda)
void	relax_shell_flexcon (FILE *fplog, const t_commrec *cr, gmx_bool bVerbose, gmx_enfrot *enforcedRotation, int64_t mdstep, const t_inputrec *inputrec, const MDModulesNotifiers &mdModulesNotifiers, ImdSession *imdSession, pull_t *pull_work, gmx_bool bDoNS, const gmx_localtop_t *top, Constraints *constr, gmx_enerdata_t *enerd, int natoms, ArrayRefWithPadding< RVec > xPadded, ArrayRefWithPadding< RVec > vPadded, const matrix box, ArrayRef< real > lambda, const history_t *hist, ForceBuffersView *f, tensor force_vir, const t_mdatoms &md, CpuPpLongRangeNonbondeds *longRangeNonbondeds, t_nrnb *nrnb, gmx_wallcycle *wcycle, shellfc_t *shfc, t_forcerec *fr, const MdrunScheduleWorkload &runScheduleWork, double t, rvec mu_tot, VirtualSitesHandler *vsite, const DDBalanceRegionHandler &ddBalanceRegionHandler)
void	done_shellfc (FILE *fplog, shellfc_t *shfc, int64_t numSteps)
void	applyLocalState (const SimulationInput &simulationInput, t_fileio *logfio, const MpiComm &mpiCommSimulation, t_inputrec *ir, t_state *state, ObservablesHistory *observablesHistory, bool reproducibilityRequested, const MDModulesNotifiers &notifiers, ReadCheckpointDataHolder *modularSimulatorCheckpointData, bool useModularSimulator)
	Initialize local stateful simulation data. More...
SimulationInputHandle	makeSimulationInput (const LegacyMdrunOptions &options)
static void	global_max (const MpiComm &mpiComm, int *n)
	Global max algorithm.
static real	reactionFieldExclusionCorrection (ArrayRef< const RVec > x, const t_mdatoms &mdatoms, const interaction_const_t &ic, const int beginAtom)
	Computes and returns the RF exclusion energy for the last molecule starting at beginAtom.
int	computeFepPeriod (const t_inputrec &inputrec, const ReplicaExchangeParameters &replExParams)
	Compute the period at which FEP calculation is performed. More...
std::tuple< StartingBehavior, LogFilePtr >	handleRestart (bool isSimulationMain, MPI_Comm communicator, const gmx_multisim_t *ms, AppendingBehavior appendingBehavior, int nfile, t_filenm fnm[])
	Handle startup of mdrun, particularly regarding -cpi and -append. More...
static void	prepareLogFile (BinaryInformationSettings settings, FILE *fplog)
	Implements aspects of logfile handling common to opening either for writing or appending.
LogFilePtr	openLogFile (const char *lognm, bool appendFiles)
	Open the log file for writing/appending. More...
void	prepareLogAppending (FILE *fplog)
	Prepare to use the open log file when appending. More...
void	closeLogFile (t_fileio *logfio)
	Close the log file.
void	logValidationMessages (const MDLogger &mdlog, const SimulationWorkload &simulationWorkload, bool haveFillerParticlesInLocalState, bool useH5mdOutputFile, bool useModularSimulator, IntegrationAlgorithm integrationAlgorithm, const DeviceInformation *deviceInfo)
	Write a messages for lists of features with status "experimental" and "validation pending" to the log. More...
template<class BasicMdspan >
constexpr std::enable_if_t < BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer >	begin (const BasicMdspan &basicMdspan)
	Free begin function addressing memory of a contiguously laid out basic_mdspan. More...
template<class BasicMdspan >
constexpr std::enable_if_t < BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer >	end (const BasicMdspan &basicMdspan)
	Free end function addressing memory of a contiguously laid out basic_mdspan. More...
template<class BasicMdspan >
constexpr BasicMdspan	addElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise addition.
template<class BasicMdspan >
constexpr BasicMdspan	subtractElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise subtraction - left minus right.
template<class BasicMdspan >
constexpr BasicMdspan	multiplyElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise multiplication.
template<class BasicMdspan >
constexpr BasicMdspan	divideElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise division - left / right.
template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool	operator== (const extents< LHS...> &lhs, const extents< RHS...> &rhs) noexcept
	Comparison operator. More...
template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool	operator!= (const extents< LHS...> &lhs, const extents< RHS...> &rhs) noexcept
	Check for non-equality. More...
template<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t < operation==CheckpointDataOperation::Write||std::is_const_v < std::remove_reference_t< T > >, const typename std::remove_reference_t< T > ::value_type, typename std::remove_reference_t< T > ::value_type > >	makeCheckpointArrayRef (T &&container)
template<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t < operation==CheckpointDataOperation::Write||std::is_const_v < T >, const T, T > >	makeCheckpointArrayRefFromArray (T *begin, size_t size)
template<typename VersionEnum >
VersionEnum	checkpointVersion (const ReadCheckpointData *checkpointData, const std::string &key, const VersionEnum programVersion)
	Read a checkpoint version enum variable. More...
template<typename VersionEnum >
VersionEnum	checkpointVersion (WriteCheckpointData *checkpointData, const std::string &key, const VersionEnum programVersion)
	Write the current code checkpoint version enum variable. More...
	forceMtsCombined_ ({})
	view_ ({},{}, false)
	useForceMtsCombined_ (false)
template<class T >
T &	makeRefFromPointer (T *ptr)
	Take pointer, check if valid, return reference.
template<class ToType , class TransformWithFunctionType >
void	addMdpTransformFromString (IKeyValueTreeTransformRules *rules, TransformWithFunctionType transformationFunction, std::string_view moduleName, std::string_view optionName)
	Helper to declare mdp transform rules. More...
template<class ValueType >
void	addMdpOutputValue (KeyValueTreeObjectBuilder *builder, std::string_view moduleName, std::string_view optionName, const ValueType &optionValue)
	Add an mdp value to output KVT with a module-prefixed name. More...
void	addMdpOutputComment (KeyValueTreeObjectBuilder *builder, std::string_view moduleName, std::string_view optionName, const std::string &comment)
	Add a comment for an mdp value with a module-prefixed name. More...
static const char *	enumValueToString (AtomLocality enumValue)
	Get the human-friendly name for atom localities. More...
static const char *	enumValueToString (InteractionLocality enumValue)
	Get the human-friendly name for interaction localities. More...
static InteractionLocality	atomToInteractionLocality (const AtomLocality atomLocality)
	Convert atom locality to interaction locality. More...
int	nonbondedMtsFactor (const t_inputrec &ir)
	Returns the interval in steps at which the non-bonded pair forces are calculated. More...
std::vector< MtsLevel >	setupMtsLevels (const GromppMtsOpts &mtsOpts, std::vector< std::string > *errorMessages)
	Sets up and returns the MTS levels and checks requirements of MTS. More...
bool	haveValidMtsSetup (const t_inputrec &ir)
	Returns whether we use MTS and the MTS setup is internally valid. More...
std::vector< std::string >	checkMtsRequirements (const t_inputrec &ir)
	Checks whether the MTS requirements on other algorithms and output frequencies are met. More...
static int	forceGroupMtsLevel (ArrayRef< const MtsLevel > mtsLevels, const MtsForceGroups mtsForceGroup)
	Returns the MTS level at which a force group is to be computed. More...
void	setOutputControlTarget (IMDModule *module, OutputControl *outputControl)
	Set the target OutputControl for an OutputControlModule. More...
void	setOutputControlWriteToMdpOutput (IMDModule *module, bool enable)
	Enable MDP output writing for OutputControl module (for testing only) More...
void	setOutputControlPreprocessingStrings (IMDModule *module, inputrec_strings *preprocessingStrings)
	Set preprocessing-only string storage for an OutputControlModule. More...
bool	needStateGpu (SimulationWorkload simulationWorkload)
	If StatePropagatorDataGpu object is needed. More...
std::vector< int >	genQmmmIndices (const gmx_mtop_t &mtop)
	Generates the list of QM atoms. More...
	conservedEnergyContribution_ (0)
	previousStepConservedEnergyContribution_ (0)
	conservedEnergyContributionStep_ (-1)
	reportPreviousStepConservedEnergy_ (reportPreviousStepConservedEnergy)
	statePropagatorData_ (statePropagatorData)
	energyData_ (energyData)
	fplog_ (fplog)
	inputrec_ (inputrec)
	mdAtoms_ (mdAtoms)
	nrnb_ (nrnb)
	identifier_ ("FirstOrderPressureCoupling-"+std::string(enumValueToString(pressureCouplingType_)))
	numDegreesOfFreedom_ (numDegreesOfFreedom)
	simulationTimeStep_ (simulationTimeStep)
	ensembleTemperature_ (ensembleTemperature)
	mttkPropagatorConnection_ (mttkPropagatorConnection)
	nextEnergyCalculationStep_ (-1)
	mdlog_ (mdlog)
template<NumVelocityScalingValues numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, NumVelocityScalingValues numEndVelocityScalingValues>
static void	updateVelocities (int a, real dt, real lambdaStart, real lambdaEnd, const RVec *gmx_restrict invMassPerDim, RVec *gmx_restrict v, const RVec *gmx_restrict f, const RVec &diagPR, const Matrix3x3 &matrixPR)
	Update velocities. More...
static void	updatePositions (int a, real dt, const RVec *gmx_restrict x, RVec *gmx_restrict xprime, const RVec *gmx_restrict v)
	Update positions. More...
template<NumVelocityScalingValues numStartVelocityScalingValues>
static void	scaleVelocities (int a, real lambda, RVec *gmx_restrict v)
	Scale velocities. More...
template<NumPositionScalingValues numPositionScalingValues>
static void	scalePositions (int a, real lambda, RVec *gmx_restrict x)
	Scale positions. More...
template<ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
static bool	canTreatPRScalingMatrixAsDiagonal (const Matrix3x3 &matrixPR)
	Is the PR matrix diagonal?
template<IntegrationStage integrationStage>
constexpr bool	hasStartVelocityScaling ()
template<IntegrationStage integrationStage>
constexpr bool	hasEndVelocityScaling ()
template<IntegrationStage integrationStage>
constexpr bool	hasPositionScaling ()
template<IntegrationStage integrationStage>
constexpr bool	hasParrinelloRahmanScaling ()
template<IntegrationStage integrationStage>
static PropagatorConnection	getConnection (Propagator< integrationStage > *propagator, const PropagatorTag &propagatorTag)
template<CheckpointDataOperation operation>
static void	doCheckpointData (CheckpointData< operation > *checkpointData, ArrayRef< DVec > previousStepCom)
static void	runAllCallbacks (const std::vector< SignallerCallback > &callbacks, Step step, Time time)
	Helper function to call all callbacks in a list.
template<typename Element , typename... Args>
ISimulatorElement *	getElementPointer (LegacySimulatorData *legacySimulatorData, ModularSimulatorAlgorithmBuilderHelper *builderHelper, StatePropagatorData *statePropagatorData, EnergyData *energyData, FreeEnergyPerturbationData *freeEnergyPerturbationData, GlobalCommunicationHelper *globalCommunicationHelper, ObservablesReducer *observablesReducer, const DeviceStreamManager *deviceStreamManager, Args &&...args)
template<typename Base , typename Element >
static std::enable_if_t < std::is_base_of_v< Base, Element >, Base * >	castOrNull (Element *element)
	Returns a pointer casted to type Base if the Element is derived from Base.
template<typename Base , typename Element >
static std::enable_if_t <!std::is_base_of_v< Base, Element >, Base * >	castOrNull (Element gmx_unused *element)
	Returns a nullptr of type Base if Element is not derived from Base.
	ddpCount_ (0)
	element_ (std::make_unique< Element >(this, fplog, cr, inputrec->outputControl.nstxout, inputrec->outputControl.nstvout, inputrec->outputControl.nstfout, inputrec->outputControl.nstxout_compressed, canMoleculesBeDistributedOverPBC, writeFinalConfiguration, finalConfigurationFilename, inputrec, globalTop))
	referenceTemperatureHelper_ (std::make_unique< ReferenceTemperatureHelper >(inputrec, this, mdatoms))
	vvResetVelocities_ (false)
	isRegularSimulationEnd_ (false)
	lastStep_ (-1)
	globalState_ (globalState)
static void	updateGlobalState (t_state *globalState, const PaddedHostVector< RVec > &x, const PaddedHostVector< RVec > &v, const tensor box, int ddpCount, int ddpCountCgGl, const std::vector< int > &cgGl)
	Update the legacy global state. More...
bool	timesClose (Time time, Time referenceTime)
	Check whether two times are nearly equal. More...
const char *	enumValueToString (LJCombinationRule enumValue)
	String corresponding to LJ combination rule.
static void	copy_int_to_nbat_int (const int *a, int na, int na_round, const int *in, int fill, int *innb)
void	copy_rvec_to_nbat_real (const int *a, int na, int na_round, const rvec *x, int nbatFormat, real *xnb, int a0)
	Copy na rvec elements from x to xnb using nbatFormat, start dest a0, and fills up to na_round with coordinates that are far away.
template<int coordinateStride>
static void	copyRVecToNbatXYZReal (int numAtoms, const rvec *x, real *xnb, int a0)
template<int packSize>
static void	copyRVecToNbatPackedReal (int numAtoms, const rvec *x, real *xnb, int a0)
	Copies coordinates with RVec layout to SIMD layout with X/Y/Z packs. More...
static void	set_lj_parameter_data (nbnxm_atomdata_t::Params *params, gmx_bool bSIMD)
template<typename T >
static gmx_unused void	setExclusionFilters (AlignedVector< T > *exclusionFilters, const NbnxmKernelType kernelType)
	Allocates and sets the SIMD exclusion filters.
template<int packSize>
static void	copy_lj_to_nbat_lj_comb (ArrayRef< const real > ljparam_type, const int *type, int na, real *ljparam_at)
static void	nbnxm_atomdata_set_atomtypes (nbnxm_atomdata_t::Params *params, const GridSet &gridSet, ArrayRef< const int > atomTypesA, ArrayRef< const int > atomTypesB, const bool useGpuNonbondedFE)
static void	nbnxm_atomdata_set_ljcombparams (nbnxm_atomdata_t::Params *params, const int XFormat, const GridSet &gridSet, const bool useGpuNonbondedFE)
static void	nbnxm_atomdata_set_charges (nbnxm_atomdata_t *nbat, const GridSet &gridSet, ArrayRef< const real > chargesA, ArrayRef< const real > chargesB, const bool useGpuNonbondedFE)
static void	nbnxm_atomdata_mask_fep (nbnxm_atomdata_t *nbat, const GridSet &gridSet)
static void	nbnxm_atomdata_set_energygroups (const GridSet &gridSet, ArrayRef< const int32_t > atomInfo, EnergyGroupsPerCluster *energyGroupsPerCluster)
void	nbnxm_atomdata_set (nbnxm_atomdata_t gmx_unused *nbat, const GridSet gmx_unused &gridSet, ArrayRef< const int > gmx_unused atomTypesA, ArrayRef< const int > gmx_unused atomTypesB, ArrayRef< const real > gmx_unused atomChargesA, ArrayRef< const real > gmx_unused atomChargesB, ArrayRef< const int32_t > gmx_unused atomInfo, bool gmx_unused useGpuNonbondedFE)
	Sets the atomdata after pair search.
void	nbnxm_atomdata_copy_shiftvec (std::optional< bool > haveDynamicBox, ArrayRef< const RVec > shiftVectors, nbnxm_atomdata_t *nbat)
	Copy the shift vectors to nbat.
static Range< int >	getGridRange (const GridSet &gridSet, const AtomLocality locality)
static void	copyXToNbatXForGridPart (const Grid &grid, const Range< int > &cellRange, const rvec *coordinates, nbnxm_atomdata_t *nbat)
static void	copyXToNbatXForGridPartIndexed (const Grid &grid, const Range< int > &cellRange, ArrayRef< const int > atomIndices, const rvec *coordinates, nbnxm_atomdata_t *nbat)
void	nbnxm_atomdata_copy_x_to_nbat_x (const GridSet &gridSet, AtomLocality locality, const rvec *coordinates, nbnxm_atomdata_t *nbat)
	Transform coordinates to xbat layout. More...
static void	nbnxm_atomdata_clear_reals (ArrayRef< real > dest, int i0, int i1)
static gmx_unused void	nbnxm_atomdata_reduce_reals (real *gmx_restrict dest, gmx_bool bDestSet, const real **gmx_restrict src, int nsrc, int i0, int i1)
static gmx_unused void	nbnxm_atomdata_reduce_reals_simd (real gmx_unused *gmx_restrict dest, gmx_bool gmx_unused bDestSet, const gmx_unused real **gmx_restrict src, int gmx_unused nsrc, int gmx_unused i0, int gmx_unused i1)
template<int forceStride>
static void	addNbatFXYZToFPart (const nbnxm_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces)
template<int packSize>
static void	addNbatFPackedToFPart (const nbnxm_atomdata_output_t &out, const int a0, const int a1, const int *cellIndices, ArrayRef< RVec > forces)
	Adds forces in SIMD packed layout to an RVec array. More...
static Range< int >	getAtomRange (const AtomLocality locality, const GridSet &gridSet)
void	nbnxm_atomdata_add_nbat_fshift_to_fshift (const nbnxm_atomdata_t &nbat, ArrayRef< RVec > fshift)
	Add the fshift force stored in nbat to fshift.
static void	clearBufferAll (ArrayRef< real > buffer)
	Clears all elements of buffer.
template<int numComponentsPerElement>
static void	clearBufferFlagged (const int outputIndex, ArrayRef< const gmx_bitmask_t > flags, ArrayRef< real > buffer)
	Clears elements of size and stride numComponentsPerElement. More...
template<int packSize>
static int	atom_to_x_index (int a)
	Returns the index in a coordinate array corresponding to atom a.
static RVec	getCoordinate (const nbnxm_atomdata_t &nbat, const int a)
	Returns the coordinates of atoms a.
static std::optional< std::string >	checkKernelSetup (const NbnxmKernelBenchOptions &options)
	Checks the kernel setup. More...
static NbnxmKernelType	translateBenchmarkEnum (const NbnxmBenchMarkKernels &kernel)
	Helper to translate between the different enumeration values.
static NbnxmKernelSetup	getKernelSetup (const NbnxmKernelBenchOptions &options)
	Returns the kernel setup.
static InteractionModifiers	convertInteractionModifiers (const NbnxmBenchMarkInteractionModifiers interactionModifier)
	Converts the benchmark interaction modifier enum to the corresponding NBNxM enum.
static interaction_const_t	setupInteractionConst (const NbnxmKernelBenchOptions &options)
	Return an interaction constants struct with members used in the benchmark set appropriately.
static LJCombinationRule	convertLJCombinationRule (const NbnxmBenchMarkCombRule combRule)
	Converts the benchmark LJ comb.rule. enum to the corresponding NBNxM enum.
static std::unique_ptr < nonbonded_verlet_t >	setupNbnxmForBenchInstance (const NbnxmKernelBenchOptions &options, const BenchmarkSystem &system)
	Sets up and returns a Nbnxm object for the given benchmark options and system.
static void	expandSimdOptionAndPushBack (const NbnxmKernelBenchOptions &options, std::vector< NbnxmKernelBenchOptions > *optionsList)
	Add the options instance to the list for all requested kernel SIMD types.
static void	setupAndRunInstance (const BenchmarkSystem &system, const NbnxmKernelBenchOptions &options, const bool doWarmup)
	Sets up and runs the requested benchmark instance and prints the results.
void	bench (int sizeFactor, const NbnxmKernelBenchOptions &options)
	Sets up and runs one or more Nbnxm kernel benchmarks. More...
static void	generateCoordinates (int multiplicationFactor, std::vector< gmx::RVec > *coordinates, matrix box)
	Generates coordinates and a box for the base system scaled by multiplicationFactor.
template<typename T >
static std::enable_if_t < std::is_same_v< T, gmx::BasicVector< float > >, gmx::BasicVector< float > >	loadBoundingBoxCorner (const BoundingBox::Corner &corner)
	Loads a corner of a bounding box into a float vector.
static gmx::BasicVector< float >	max (const gmx::BasicVector< float > &v1, const gmx::BasicVector< float > &v2)
	Return the element-wise max of two 3-float vectors, needed to share code with SIMD.
static float	dotProduct (const gmx::BasicVector< float > &v1, const gmx::BasicVector< float > &v2)
	Return the dot product of two 3-float vectors, needed to share code with SIMD.
static float	clusterBoundingBoxDistance2 (const BoundingBox &bb_i, const BoundingBox &bb_j)
	Returns the distance^2 between two bounding boxes. More...
static gmx_unused void	clusterBoundingBoxDistance2_xxxx_simd4 (const float *, const int, const float *, float *)
	4-wide SIMD code for nsi bb distances for bb format xxxxyyyyzzzz
static ClusterDistanceKernelType	getClusterDistanceKernelType (const PairlistType pairlistType, const nbnxm_atomdata_t &atomdata)
	Return the cluster distance kernel type given the pairlist type and atomdata.
void	cuda_set_cacheconfig ()
	Set up the cache configuration for the non-bonded kernels.
static int	computeNumGlobalPerturbedExclusions (const gmx_mtop_t &mtop)
	Compute the number of exclusions involving perturbed atoms. More...
template<bool computeScalarForce, class RealType >
static void	pmeCoulombCorrectionVF (const RealType rSq, const real beta, RealType *pot, RealType gmx_unused *force)
template<bool computeScalarForce, class RealType , class BoolType >
static void	pmeLJCorrectionVF (const RealType rInv, const RealType rSq, const real ewaldLJCoeffSq, const real ewaldLJCoeffSixDivSix, RealType *pot, RealType gmx_unused *force, const BoolType mask, const BoolType bIiEqJnr)
template<class RealType >
static void	sixthRoot (const RealType r, RealType *sixthRoot, RealType *invSixthRoot)
	Computes r^(1/6) and 1/r^(1/6)
template<class RealType >
static RealType	calculateRinv6 (const RealType rInvV)
template<class RealType >
static RealType	calculateVdw6 (const RealType c6, const RealType rInv6)
template<class RealType >
static RealType	calculateVdw12 (const RealType c12, const RealType rInv6)
template<class RealType >
static RealType	reactionFieldScalarForce (const RealType qq, const RealType rInv, const RealType r, const real reactionFieldCoefficient, const real two)
template<class RealType >
static RealType	reactionFieldPotential (const RealType qq, const RealType rInv, const RealType r, const real reactionFieldCoefficient, const real potentialShift)
template<class RealType >
static RealType	ewaldScalarForce (const RealType coulomb, const RealType rInv)
template<class RealType >
static RealType	ewaldPotential (const RealType coulomb, const RealType rInv, const real potentialShift)
template<class RealType >
static RealType	lennardJonesScalarForce (const RealType v6, const RealType v12)
template<class RealType >
static RealType	lennardJonesPotential (const RealType v6, const RealType v12, const RealType c6, const RealType c12, const real repulsionShift, const real dispersionShift, const real oneSixth, const real oneTwelfth)
template<class RealType >
static RealType	ewaldLennardJonesGridSubtract (const RealType c6grid, const real potentialShift, const real oneSixth)
template<class RealType >
static void	computeForceSwitchVariables (const RealType r, const real rSwitch, RealType *rSwitched, RealType *rSwitchedSquared, RealType *rSwitchedSquaredTimesR)
	Generates intermediate quantities for force switch interactions.
template<class RealType , class BoolType >
static RealType	forceSwitchScalarForceMod (const RealType fScalarInp, const RealType rSwitched, const RealType rSwitchedSquaredTimesR, const real c2, const real c3, const BoolType mask)
	Return the force for force-switch interactions.
template<class RealType , class BoolType >
static RealType	forceSwitchPotentialMod (const RealType rSwitched, const RealType rSwitchedSquaredTimesR, const real c3, const real c4, const BoolType mask)
	Return the modification of the potential for force-switch interactions.
template<class RealType , class BoolType >
static RealType	potSwitchScalarForceMod (const RealType fScalarInp, const RealType potential, const RealType sw, const RealType r, const RealType dsw, const BoolType mask)
template<class RealType , class BoolType >
static RealType	potSwitchPotentialMod (const RealType potentialInp, const RealType sw, const BoolType mask)
template<typename DataTypes , KernelSoftcoreType softcoreType, bool scLambdasOrAlphasDiffer, bool elecInteractionTypeIsEwald, LJKernelType ljKernelType, bool computeForces>
static void	nb_free_energy_kernel (const AtomPairlist &nlist, const ArrayRefWithPadding< const RVec > &coords, const int ntype, const interaction_const_t &ic, ArrayRef< const RVec > shiftvec, ArrayRef< const real > nbfp, ArrayRef< const real > gmx_unused nbfp_grid, ArrayRef< const real > chargeA, ArrayRef< const real > chargeB, ArrayRef< const int > typeA, ArrayRef< const int > typeB, const bool computeForeignLambda, const StepWorkload *stepWork, ArrayRef< const real > lambda, t_nrnb *gmx_restrict nrnb, ArrayRefWithPadding< RVec > threadForceBuffer, rvec gmx_unused *threadForceShiftBuffer, ArrayRef< real > threadVCoul, ArrayRef< real > threadVVdw, ArrayRef< real > threadDvdl)
	Templated free-energy non-bonded kernel.
template<KernelSoftcoreType softcoreType, bool scLambdasOrAlphasDiffer, bool elecInteractionTypeIsEwald, LJKernelType ljKernelType, bool computeForces>
static KernelFunction	dispatchKernelOnUseSimd (const bool useSimd)
template<KernelSoftcoreType softcoreType, bool scLambdasOrAlphasDiffer, bool elecInteractionTypeIsEwald, LJKernelType ljKernelType>
static KernelFunction	dispatchKernelOnComputeForces (const bool computeForces, const bool useSimd)
template<KernelSoftcoreType softcoreType, bool scLambdasOrAlphasDiffer, bool elecInteractionTypeIsEwald>
static KernelFunction	dispatchKernelOnLJType (const LJKernelType ljKernelType, const bool computeForces, const bool useSimd)
template<KernelSoftcoreType softcoreType, bool scLambdasOrAlphasDiffer>
static KernelFunction	dispatchKernelOnElecInteractionType (const bool elecInteractionTypeIsEwald, const LJKernelType ljKernelType, const bool computeForces, const bool useSimd)
template<KernelSoftcoreType softcoreType>
static KernelFunction	dispatchKernelOnScLambdasOrAlphasDifference (const bool scLambdasOrAlphasDiffer, const bool elecInteractionTypeIsEwald, const LJKernelType ljKernelType, const bool computeForces, const bool useSimd)
static KernelFunction	dispatchKernel (const bool scLambdasOrAlphasDiffer, const bool elecInteractionTypeIsEwald, const LJKernelType ljKernelType, const bool computeForces, const bool useSimd, const interaction_const_t &interactionParameters)
void	gmx_nb_free_energy_kernel (const AtomPairlist &nlist, const ArrayRefWithPadding< const RVec > &coords, const bool useSimd, const int ntype, const interaction_const_t &interactionParameters, ArrayRef< const RVec > shiftvec, ArrayRef< const real > nbfp, ArrayRef< const real > nbfp_grid, ArrayRef< const real > chargeA, ArrayRef< const real > chargeB, ArrayRef< const int > typeA, ArrayRef< const int > typeB, const bool computeForeignLambda, const StepWorkload *stepWork, ArrayRef< const real > lambda, t_nrnb *nrnb, ArrayRefWithPadding< RVec > threadForceBuffer, rvec *threadForceShiftBuffer, ArrayRef< real > threadVCoul, ArrayRef< real > threadVVdw, ArrayRef< real > threadDvdl)
void	gmx_nb_free_energy_kernel (const AtomPairlist &nlist, const ArrayRefWithPadding< const RVec > &coords, bool useSimd, int ntype, const interaction_const_t &ic, ArrayRef< const RVec > shiftvec, ArrayRef< const real > nbfp, ArrayRef< const real > nbfp_grid, ArrayRef< const real > chargeA, ArrayRef< const real > chargeB, ArrayRef< const int > typeA, ArrayRef< const int > typeB, bool computeForeignLambda, const StepWorkload *stepWork, ArrayRef< const real > lambda, t_nrnb *gmx_restrict nrnb, ArrayRefWithPadding< RVec > threadForceBuffer, rvec *threadForceShiftBuffer, ArrayRef< real > threadVc, ArrayRef< real > threadVv, ArrayRef< real > threadDvdl)
	The non-bonded free-energy kernel. More...
static void	countPruneKernelTime (GpuTimers *timers, gmx_wallclock_gpu_nbnxm_t *timings, const InteractionLocality iloc)
	Count pruning kernel time if either kernel has been triggered. More...
static void	gpu_reduce_staged_outputs (const NBStagingData &nbst, const InteractionLocality iLocality, const bool reduceEnergies, const bool reduceFshift, real *e_lj, real *e_el, double *dvdl_lj, double *dvdl_el, rvec *fshift)
	Reduce data staged internally in the nbnxm module. More...
static void	gpu_reduce_staged_foreign_term (const NBStagingData &nbst, const InteractionLocality iLocality, const int nLambda, ForeignLambdaTerms *foreign_term)
	Reduce free energy lambda data staged internally in the nbnxm module. More...
template<typename GpuPairlist >
static void	gpu_accumulate_timings (gmx_wallclock_gpu_nbnxm_t *timings, GpuTimers *timers, const GpuPairlist *plist, AtomLocality atomLocality, const StepWorkload &stepWork, bool doTiming)
	Do the per-step timing accounting of the nonbonded tasks. More...
bool	gpu_try_finish_task (NbnxmGpu *nb, const StepWorkload &stepWork, const AtomLocality aloc, real *e_lj, real *e_el, double *dvdl_lj, double *dvdl_el, ArrayRef< RVec > shiftForces, ForeignLambdaTerms *foreign_term, GpuTaskCompletion completionKind)
	Attempts to complete nonbonded GPU task. More...
float	gpu_wait_finish_task (NbnxmGpu *nb, const StepWorkload &stepWork, AtomLocality aloc, const bool haveSoftCore, gmx_enerdata_t *enerd, ArrayRef< RVec > shiftForces, gmx_wallcycle *wcycle)
	Wait for the asynchronously launched nonbonded tasks and data transfers to finish. More...
static bool	canSkipNonbondedWork (const NbnxmGpu &nb, InteractionLocality iloc)
	An early return condition for empty NB GPU workloads. More...
static Range< int >	getGpuAtomRange (const NBAtomDataGpu *atomData, const AtomLocality atomLocality)
	Calculate atom range and return start index and length. More...
void	copy_gpu_fepparams (NbnxmGpu gmx_unused *nb, bool gmx_unused bFepGpuNonBonded, float gmx_unused alphaCoul, float gmx_unused alphaVdw, int gmx_unused lambdaPower, float gmx_unused sigma6WithInvalidSigma, float gmx_unused sigma6Minimum, float gmx_unused lambdaCoul, float gmx_unused lambdaVdw, int gmx_unused nLambda, const EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double >> gmx_unused &all_lambda)
	Copy FEP parameters to GPU. More...
NbnxmGpu *	gpu_init (const DeviceStreamManager gmx_unused &deviceStreamManager, const interaction_const_t gmx_unused *ic, const PairlistParams gmx_unused &listParams, const nbnxm_atomdata_t gmx_unused *nbat, bool gmx_unused bLocalAndNonlocal, const std::optional< size_t > gmx_unused nLambda)
	Initializes the data structures related to GPU nonbonded calculations. More...
void	gpu_init_pairlist (NbnxmGpu gmx_unused *nb, const struct NbnxmPairlistGpu gmx_unused *h_nblist, InteractionLocality gmx_unused iloc)
	Initializes pair-list data for GPU, called at every pair search step. More...
void	gpu_init_feppairlist (NbnxmGpu gmx_unused *nb, const AtomPairlist gmx_unused &h_feplist, InteractionLocality gmx_unused iloc, ArrayRef< const int > gmx_unused atomIndices)
	Initializes fep pair-list data for GPU, called at every pair search step. More...
void	gpu_init_atomdata (NbnxmGpu gmx_unused *nb, const nbnxm_atomdata_t gmx_unused *nbat)
	Initializes atom-data on the GPU, called at every pair search step. More...
void	gpu_pme_loadbal_update_param (struct nonbonded_verlet_t gmx_unused *nbv, const interaction_const_t gmx_unused &ic)
	Re-generate the GPU Ewald force table, resets rlist, and update the electrostatic type switching to twin cut-off (or back) if needed.
void	gpu_upload_shiftvec (NbnxmGpu gmx_unused *nb, const nbnxm_atomdata_t gmx_unused *nbatom)
	Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). More...
void	gpu_clear_outputs (NbnxmGpu gmx_unused *nb, bool gmx_unused computeVirial)
	Clears GPU outputs: nonbonded force, shift force and energy. More...
void	gpu_free (NbnxmGpu gmx_unused *nb)
	Frees all GPU resources used for the nonbonded calculations. More...
struct gmx_wallclock_gpu_nbnxm_t *	gpu_get_timings (NbnxmGpu gmx_unused *nb)
	Returns the GPU timings structure or NULL if GPU is not used or timing is off. More...
void	gpu_reset_timings (struct nonbonded_verlet_t gmx_unused *nbv)
	Resets nonbonded GPU timings. More...
int	gpu_min_ci_balanced (NbnxmGpu gmx_unused *nb)
	Calculates the minimum size of proximity lists to improve SM load balance with GPU non-bonded kernels. More...
bool	gpu_is_kernel_ewald_analytical (const NbnxmGpu gmx_unused *nb)
	Returns if analytical Ewald GPU kernels are used. More...
NBAtomDataGpu *	gpuGetNBAtomData (NbnxmGpu gmx_unused *nb)
	Returns an opaque pointer to the GPU NBNXM atom data.
DeviceBuffer< RVec >	gpu_get_f (NbnxmGpu gmx_unused *nb)
	Returns forces device buffer.
size_t	getExclusiveScanWorkingArraySize (GpuPairlist *plist, const DeviceStream &deviceStream)
	Calculates working memory required for exclusive sum, used in neighbour list sorting on GPU. More...
void	performExclusiveScan (size_t temporaryBufferSize, char *temporaryBuffer, GpuPairlist *plist, const DeviceStream &deviceStream)
	Perform exclusive scan to obtain input for sci sorting.
void	nbnxm_gpu_compile_kernels (NbnxmGpu gmx_unused *nb)
	Handles any JIT compilation of nbnxm kernels for the selected device.
static real	gridAtomDensity (int numAtoms, const RVec &gridBoundingBoxSize)
	Returns the atom density (> 0) of a rectangular grid.
static RVec	getTargetCellLength (const Grid::Geometry &geometry, const real atomDensity)
	Get approximate dimensions of the grid cells. More...
static int	getMaxNumCells (const Grid::Geometry &geometry, const int numAtoms, const int numCells)
static bool	isHomeZone (const int ddZone)
	Returns whether ddZone is the home zone.
static void	sort_atoms (int dim, gmx_bool Backwards, int gmx_unused dd_zone, bool gmx_unused relevantAtomsAreWithinGridBounds, int *a, int n, ArrayRef< const RVec > x, real h0, real invh, int n_per_h, ArrayRef< int > sort)
	Sorts particle index a on coordinates x along dim. More...
static float	R2F_D (const float x)
	Returns x.
static float	R2F_U (const float x)
	Returns x.
static void	calc_bounding_box (const int numAtoms, const int stride, const real *x, BoundingBox *bb)
	Computes the bounding box for na coordinates in order x,y,z, bb order xyz0.
template<int packSize>
static void	calcBoundingBoxXPacked (const int numAtoms, const real *x, BoundingBox *bb)
	Computes the bounding box for packed coordinates. More...
template<int packSize>
static gmx_unused void	calcBoundingBoxHalves (const int numAtoms, const real *x, BoundingBox *bb, BoundingBox *bbj)
	Computes the whole plus half bounding boxes for packed coordinates. More...
static void	calc_bounding_box_xxxx (int na, int stride, const real *x, float *bb)
	Computes the bounding box for na coordinates in order xyz, bb order xxxxyyyyzzzz.
static void	combine_bounding_box_pairs (const Grid &grid, ArrayRef< const BoundingBox > bb, ArrayRef< BoundingBox > bbj)
	Combines pairs of consecutive bounding boxes.
static void	print_bbsizes_simple (FILE *fp, const Grid &grid)
	Prints the average bb size, used for debug output.
static void	print_bbsizes_supersub (FILE *fp, const Grid &grid)
	Prints the average bb size, used for debug output.
static void	sort_cluster_on_flag (int numAtomsInCluster, int atomStart, int atomEnd, ArrayRef< const int32_t > atomInfo, ArrayRef< int > order, int *flags)
	Set non-bonded interaction flags for the current cluster. More...
static void	setCellAndAtomCount (ArrayRef< int > cells, const int cellIndexXY, const int cellIndexZ, const int numCellsZ, ArrayRef< int > numAtomsPerCell, const int atomIndex)
	Sets the cell index in the cell array for atom atomIndex and increments the atom count for the grid cell.
static void	resizeForNumberOfBins (const int numNbnxmAtoms, const int numAtomsMoved, const int ddZone, GridSetData *gridSetData, nbnxm_atomdata_t *nbat)
	Resizes grid and atom data which depend on the number of bins.
static int	numGrids (const GridSet::DomainSetup &domainSetup)
	Returns the number of search grids.
static int	getGridOffset (ArrayRef< const Grid > grids, int gridIndex)
void	launchNbnxmKernelTransformXToXq (const FusedXToXqLaunchParams &launchParams, NbnxmGpu *nb, DeviceBuffer< Float3 > d_x, const DeviceStream &deviceStream)
	Launch the fused coordinate layout conversion kernel. More...
void	gpu_launch_kernel_pruneonly (NbnxmGpu *nb, const InteractionLocality iloc, const int numParts)
	Launch the pairlist prune only kernel for the given locality. numParts tells in how many parts, i.e. calls the list will be pruned.
void	gpu_launch_kernel (NbnxmGpu *nb, const gmx::StepWorkload &stepWork, const InteractionLocality iloc)
	Launch GPU kernel. More...
void	gpu_launch_free_energy_kernel (NbnxmGpu gmx_unused *nb, const SimulationWorkload gmx_unused &simulationWork, const StepWorkload gmx_unused &stepWork, InteractionLocality gmx_unused iloc)
	Launch asynchronously the nonbonded free energy calculations. More...
void	gpu_init_platform_specific (NbnxmGpu *nb)
	Initializes the NBNXM GPU data structures.
void	gpu_free_platform_specific (NbnxmGpu *nb)
	Releases the NBNXM GPU data structures. More...
int	gpu_min_ci_balanced (NbnxmGpu *nb)
	This function is documented in the header file.
template<bool hasLargeRegisterPool, bool doPruneNBL, bool doCalcEnergies>
void	launchNbnxmKernelHelper (NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc)
template void	launchNbnxmKernelHelper< false, false, false > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< false, false, true > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< false, true, true > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< false, true, false > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< true, false, false > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< true, false, true > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< true, true, true > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
template void	launchNbnxmKernelHelper< true, true, false > (NbnxmGpu *nb, const StepWorkload &stepWork, const InteractionLocality iloc)
void	launchNbnxmKernel (NbnxmGpu *nb, const StepWorkload &stepWork, InteractionLocality iloc, bool doPrune)
	Launch HIP NBNXM kernel. More...
template<ElecType elecType, VdwType vdwType, bool doPrune, bool doCalcEnergies, PairlistType pairlistType>
static const std::string	getKernelName ()
	Lookup kernel name based on launch configuration.
template<bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType, int nthreadZ, int minBlocksPerMp, PairlistType pairlistType>
	__launch_bounds__ (c_clSizeSq< pairlistType > *nthreadZ, minBlocksPerMp) __global__ static void nbnxmKernel(NBAtomDataGpu atdat
	Main kernel for NBNXM. More...
template<PairlistType pairlistType, bool haveFreshList, int threadZ, int minBlocksPp>
	__launch_bounds__ (c_clSizeSq< pairlistType > *threadZ, minBlocksPp) __global__ static void nbnxmKernelPruneOnly(NBAtomDataGpu atdat
	Prune-only kernel for NBNXM. More...
void	launchNbnxmKernelPruneOnly (NbnxmGpu *nb, const InteractionLocality iloc, const int *numParts, const int numSciInPart)
	Launch HIP NBNXM prune-only kernel. More...
template<int threadsPerBlock>
	__launch_bounds__ (threadsPerBlock) __global__ void nbnxmKernelBucketSciSort(GpuPairlist plist)
	HIP bucket sci sort kernel. More...
void	launchNbnxmKernelHelperSciSort (const DeviceStream &deviceStream, GpuPairlist *plist)
	NBNXM kernel launch code.
void	launchNbnxmKernelSciSort (NbnxmGpu *nb, InteractionLocality iloc)
	Launch kernel to sum up energies and shifts.
template<PairlistType pairlistType>
__device__ __forceinline__ int	nb_any_internal (int predicate, int widx)
template<PairlistType pairlistType, typename T >
__device__ size_t	incrementSharedMemorySlotPtr ()
	Increment the pointer into shared memory. More...
size_t	numberOfKernelBlocksSanityCheck (int numSci, const DeviceInformation &deviceInfo)
template<bool isPruneKernel, int numThreadZ, VdwType vdwType, PairlistType pairlistType>
constexpr size_t	requiredSharedMemorySize ()
bool	targetHasLargeRegisterPool (const DeviceInformation &deviceInfo)
	Find out if the target device has a large enough register pool (MI2xx and later)
static __device__ float2	fetchNbfpC6C12 (const float2 *nbfpComb, int type)
template<PairlistType pairlistType>
static __device__ float	reduceForceJWarpShuffle (AmdPackedFloat3 f, const int tidxi)
	Reduce c_clSize j-force components using AMD DPP instruction. More...
template<PairlistType pairlistType>
static __device__ float	reduceForceIWarpShuffle (AmdPackedFloat3 f, const int tidxi, const int tidxj)
	Lowest level i force reduction. More...
template<PairlistType pairlistType, bool calculateShift>
static __device__ float3	reduceForceIAtomics (AmdPackedFloat3 input, float3 *result, const int tidxj, const int aidx)
	Lowest level i force reduction. More...
template<bool calculateShift, PairlistType pairlistType>
static __device__ void	reduceForceI (AmdPackedFloat3 *input, float3 *result, const int tidxi, const int tidxj, const int tidx, const int sci, float3 *fShift, const int shiftBase)
	Reduce i forces. More...
template<PairlistType pairlistType>
static __device__ void	reduceEnergyWarpShuffle (float localLJ, float localEl, float *gm_LJ, float *gm_El, int tidx)
	Energy reduction kernel for regular nbnxm kernels. More...
void	clear_fshift (real *fshift)
	Clears the shift forces.
void	reduce_energies_over_lists (const nbnxm_atomdata_t *nbat, int nlist, real *Vvdw, real *Vc)
	Reduces the collected energy terms over the pair-lists/threads.
enum EwaldExclusionType int typedef void()	NbnxmKernelFunc (const NbnxmPairlistCpu &nbl, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
	Pair-interaction kernel type that also calculates energies.
CoulombKernelType	getCoulombKernelType (EwaldExclusionType ewaldExclusionType, CoulombInteractionType coulombInteractionType, bool haveEqualCoulombVwdRadii, bool nbnxmIsDirectCoulombProvider)
	Lookup function for Coulomb kernel type.
int	getVdwKernelType (NbnxmKernelType kernelType, LJCombinationRule ljCombinationRule, VanDerWaalsType vanDerWaalsType, InteractionModifiers interactionModifiers, LongRangeVdW longRangeVdW)
	Lookup function for Vdw kernel type.
static void	nbnxm_kernel_cpu (const PairlistSet &pairlistSet, const NbnxmKernelSetup &kernelSetup, nbnxm_atomdata_t *nbat, const interaction_const_t &ic, gmx::ArrayRef< const gmx::RVec > shiftVectors, const gmx::StepWorkload &stepWork, int clearF, real *vCoulomb, real *vVdw, gmx_wallcycle *wcycle)
	Dispatches the non-bonded N versus M atom cluster CPU kernels. More...
static void	accountFlops (t_nrnb *nrnb, const PairlistSet &pairlistSet, const nonbonded_verlet_t &nbv, const interaction_const_t &ic, const gmx::StepWorkload &stepWork)
void	nbnxm_kernel_gpu_ref (const NbnxmPairlistGpu *nbl, const nbnxm_atomdata_t *nbat, const interaction_const_t &iconst, ArrayRef< const RVec > shiftvec, const StepWorkload &stepWork, int clearF, ArrayRef< real > f, real *fshift, real *Vc, real *Vvdw)
	Reference (slow) kernel for nb n vs n GPU type pair lists.
void	nbnxm_kernel_1x1_ElecRF_VdwLJ_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJ_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJFsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJFsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJPsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJPsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJ_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJ_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJ_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJ_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJFsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJFsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJPsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJPsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJ_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJ_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
void	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template<NbnxmKernelType kernelType>
void	nbnxmRefPruneKernel (NbnxmPairlistCpu *nbl, const nbnxm_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner)
	Prune a single NbnxmPairlistCpu entry with distance rlistInner. More...
template void	nbnxmRefPruneKernel< NbnxmKernelType::Cpu4x4_PlainC > (NbnxmPairlistCpu *nbl, const nbnxm_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner)
template void	nbnxmRefPruneKernel< NbnxmKernelType::Cpu1x1_PlainC > (NbnxmPairlistCpu *nbl, const nbnxm_atomdata_t *nbat, ArrayRef< const RVec > shiftvec, real rlistInner)
template<KernelLayout kernelLayout, KernelCoulombType coulombType, VdwCutoffCheck vdwCutoffCheck, LJCombinationRule ljCombinationRule, InteractionModifiers vdwModifier, LJEwald ljEwald, EnergyOutput energyOutput>
void	nbnxmKernelSimd (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
	The actual NBNxM SIMD kernel. More...
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
template void	nbnxmKernelSimd< KernelLayout::r4xM, KernelCoulombType::None, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxmPairlistCpu &pairlist, const nbnxm_atomdata_t &nbat, const interaction_const_t &ic, const rvec *shift_vec, nbnxm_atomdata_output_t *out)
std::unique_ptr < nonbonded_verlet_t >	init_nb_verlet (const MDLogger &mdlog, const t_inputrec &inputrec, const t_forcerec &forcerec, const MpiComm &mpiComm, const gmx_domdec_t *dd, const gmx_hw_info_t &hardwareInfo, bool useGpuForNonbonded, bool useGpuForNonbondedFE, const DeviceStreamManager *deviceStreamManager, const gmx_mtop_t &mtop, bool localAtomOrderMatchesNbnxmOrder, ObservablesReducerBuilder *observablesReducerBuilder, ArrayRef< const RVec > coordinates, matrix box, gmx_wallcycle *wcycle)
	Creates an Nbnxm object.
void	nbnxm_put_on_grid_nonlocal (nonbonded_verlet_t *nb_verlet, const gmx::DomdecZones &zones, ArrayRef< const int32_t > atomInfo, ArrayRef< const RVec > x)
	As nbnxm_put_on_grid, but for the non-local atoms. More...
std::optional< std::string >	nbnxmGpuClusteringDescription ()
	Returns information for describing the NBNXM GPU clustering support, if applicable to the build.
static constexpr bool	isGpuKernelType (const NbnxmKernelType kernelType)
const char *	nbnxmKernelTypeToName (NbnxmKernelType kernelType)
static constexpr bool	sc_isGpuSpecificPairlist (const PairlistType pairlistType)
static constexpr int	sc_gpuClusterSize (const PairlistType pairlistType)
	The NBNxM GPU i-cluster size in atoms for the given NBNxM GPU kernel layout.
static constexpr int	sc_gpuNumClusterPerBinX (const PairlistType pairlistType)
	The number of super clusters in the X dimension.
static constexpr int	sc_gpuNumClusterPerBinY (const PairlistType pairlistType)
	The number of super clusters in the X dimension.
static constexpr int	sc_gpuNumClusterPerBinZ (const PairlistType pairlistType)
	The number of super clusters in the X dimension.
static constexpr int	sc_gpuClusterPerSuperCluster (const PairlistType pairlistType)
	The NBNxM GPU super cluster size according to the kernel layout.
static constexpr int	sc_gpuNumClusterPerBin (const PairlistType pairlistType)
	The NBNxM GPU super cluster size according to the kernel layout.
static constexpr int	sc_gpuClusterPairSplit (const PairlistType pairlistType)
	The number of sub-parts used for data storage for a GPU cluster pair. More...
static constexpr bool	sc_gpuPairlistHasSplitJCluster (const PairlistType pairlistType)
static constexpr int	sc_gpuSplitJClusterSize (const PairlistType pairlistType)
	The size of the J clusters on the GPU, after taking pair splitting into account.
constexpr int	sc_gpuJgroupSize (const PairlistType pairlistType)
	With GPU kernels we group cluster pairs in 4 to optimize memory usage of integers containing 32 bits.
static constexpr int	sc_gpuParallelExecutionWidth (const PairlistType pairlistType)
	Parallel execution width corresponding to the current kernel layout.
static constexpr int	sc_gpuExclSize (const PairlistType pairlistType)
	The fixed size of the exclusion mask array for a half GPU cluster pair.
real	nbnxmPairlistVolumeRadiusIncrease (bool useGpu, real atomDensity)
	Returns the increase in pairlist radius when including volume of pairs beyond rlist. More...
real	nbnxm_get_rlist_effective_inc (int clusterSize, const RVec &averageClusterBoundingBox)
	Returns the effective list radius of the pair-list. More...
static int	get_2log (int n)
	Returns the base-2 log of n. Generates a fatal error when n is not an integer power of 2.
static constexpr int	sc_iClusterSize (const NbnxmKernelType kernelType)
	The nbnxm i-cluster size in atoms for the given NBNxM kernel type.
static constexpr int	sc_jClusterSize (const NbnxmKernelType kernelType)
	The nbnxm j-cluster size in atoms for the given NBNxM kernel type. More...
static constexpr bool	kernelTypeIsSimd (const NbnxmKernelType kernelType)
	Returns whether a SIMD kernel is in use.
static constexpr bool	kernelTypeIsPlainC (const NbnxmKernelType kernelType)
	Returns whether a plain-C kernel is in use.
static constexpr bool	kernelTypeUsesSimplePairlist (const NbnxmKernelType kernelType)
	Returns whether the pair-list corresponding to kernelType is simple.
static bool	useLjCombRule (const enum VdwType vdwType)
	Returns true if LJ combination rules are used in the non-bonded kernels. More...
void	gpu_copy_xq_to_gpu (NbnxmGpu gmx_unused *nb, const struct nbnxm_atomdata_t gmx_unused *nbdata, AtomLocality gmx_unused aloc)
	Launch asynchronously the xq buffer host to device copy. More...
void	gpu_launch_kernel (NbnxmGpu gmx_unused *nb, const StepWorkload gmx_unused &stepWork, InteractionLocality gmx_unused iloc)
	Launch asynchronously the nonbonded force calculations. More...
void	gpu_launch_kernel_pruneonly (NbnxmGpu gmx_unused *nb, InteractionLocality gmx_unused iloc, int gmx_unused numParts)
	Launch asynchronously the nonbonded prune-only kernel. More...
void	gpu_launch_cpyback (NbnxmGpu gmx_unused *nb, nbnxm_atomdata_t gmx_unused *nbatom, const StepWorkload gmx_unused &stepWork, AtomLocality gmx_unused aloc)
	Launch asynchronously the download of short-range forces from the GPU (and energies/shift forces if required).
bool	gpu_try_finish_task (NbnxmGpu gmx_unused *nb, const StepWorkload gmx_unused &stepWork, AtomLocality gmx_unused aloc, real gmx_unused *e_lj, real gmx_unused *e_el, double gmx_unused *dvdl_lj, double gmx_unused *dvdl_el, ArrayRef< RVec > gmx_unused shiftForces, ForeignLambdaTerms gmx_unused *foreign_term, GpuTaskCompletion gmx_unused completionKind)
	Attempts to complete nonbonded GPU task. More...
float	gpu_wait_finish_task (NbnxmGpu gmx_unused *nb, const StepWorkload gmx_unused &stepWork, AtomLocality gmx_unused aloc, const bool gmx_unused haveSoftCore, gmx_enerdata_t gmx_unused *enerd, ArrayRef< RVec > gmx_unused shiftForces, gmx_wallcycle gmx_unused *wcycle)
	Completes the nonbonded GPU task blocking until GPU tasks and data transfers to finish. More...
void	nbnxm_gpu_init_x_to_nbat_x (const GridSet gmx_unused &gridSet, NbnxmGpu gmx_unused *gpu_nbv)
	Initialization for X buffer operations on GPU. Called on the NS step and performs (re-)allocations and memory copies. !
void	nbnxm_gpu_x_to_nbat_x (NbnxmGpu gmx_unused *gpu_nbv, DeviceBuffer< RVec > gmx_unused d_x, GpuEventSynchronizer gmx_unused *xReadyOnDevice, AtomLocality gmx_unused locality)
	X buffer operations on GPU: performs conversion from rvec to nb format. More...
void	nbnxmInsertNonlocalGpuDependency (NbnxmGpu gmx_unused *nb, InteractionLocality gmx_unused interactionLocality)
	Sync the nonlocal stream with dependent tasks in the local queue. More...
void	setupGpuShortRangeWorkLow (NbnxmGpu gmx_unused *nb, const ListedForcesGpu gmx_unused *listedForcesGpu, InteractionLocality gmx_unused iLocality)
	Set up internal flags that indicate what type of short-range work there is. More...
bool	haveGpuShortRangeWork (const NbnxmGpu gmx_unused *nb, InteractionLocality gmx_unused interactionLocality)
	Returns true if there is GPU short-range work for the given interaction locality. More...
void	nbnxm_gpu_x_to_nbat_x (NbnxmGpu *nb, DeviceBuffer< RVec > d_x, GpuEventSynchronizer *xReadyOnDevice, const AtomLocality locality)
static void	init_ewald_coulomb_force_table (const EwaldCorrectionTables &tables, NBParamGpu *nbp, const DeviceContext &deviceContext, const DeviceStream &deviceStream)
static bool	useTabulatedEwaldByDefault (InteractionModifiers vdwModifier, const DeviceInformation &deviceInfo)
static ElecType	nbnxm_gpu_pick_ewald_kernel_type (const interaction_const_t &ic, const DeviceInformation &deviceInfo)
static void	set_cutoff_parameters (NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams)
static void	init_timings (gmx_wallclock_gpu_nbnxm_t *t)
static void	initAtomdataFirst (NBAtomDataGpu *atomdata, int numTypes, const DeviceContext &deviceContext, const DeviceStream &localStream, const std::optional< size_t > nLambda)
	Initialize atomdata first time; it only gets filled at pair-search.
static VdwType	nbnxmGpuPickVdwKernelType (const interaction_const_t &ic, LJCombinationRule ljCombinationRule)
static ElecType	nbnxmGpuPickElectrostaticsKernelType (const interaction_const_t &ic, const DeviceInformation &deviceInfo)
static void	initNbparam (NBParamGpu *nbp, const interaction_const_t &ic, const PairlistParams &listParams, const nbnxm_atomdata_t::Params &nbatParams, const DeviceContext &deviceContext, const DeviceStream &localStream, const std::optional< size_t > nLambda)
	Initialize the nonbonded parameter data structure.
static GpuPairlistByLocality	initializeGpuLists (bool localAndNonLocal)
static gmx_unused GpuFeplistByLocality	initializeGpuFepLists (bool localAndNonLocal)
void	copy_gpu_fepparams (NbnxmGpu *nb, const bool bFepGpuNonBonded, const float alphaCoul, const float alphaVdw, const int lambdaPower, const float sigma6WithInvalidSigma, const float sigma6Minimum, const float lambdaCoul, const float lambdaVdw, const int nLambda, const EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double >> &all_lambda)
	nbst (hostAllocationPolicy, nLambda)
NbnxmGpu *	gpu_init (const DeviceStreamManager &deviceStreamManager, const interaction_const_t *ic, const PairlistParams &listParams, const nbnxm_atomdata_t *nbat, const bool bLocalAndNonlocal, const std::optional< size_t > nLambda)
void	gpu_pme_loadbal_update_param (nonbonded_verlet_t *nbv, const interaction_const_t &ic)
void	gpu_upload_shiftvec (NbnxmGpu *nb, const nbnxm_atomdata_t *nbatom)
void	gpu_init_pairlist (NbnxmGpu *nb, const NbnxmPairlistGpu *h_plist, const InteractionLocality iloc)
	This function is documented in the header file.
void	gpu_init_feppairlist (NbnxmGpu *nb, const AtomPairlist &h_feplist, const InteractionLocality iloc, ArrayRef< const int > atomIndices)
void	gpu_init_atomdata (NbnxmGpu *nb, const nbnxm_atomdata_t *nbat)
void	gpu_clear_outputs (NbnxmGpu *nb, bool computeVirial)
gmx_wallclock_gpu_nbnxm_t *	gpu_get_timings (NbnxmGpu *nb)
	This function is documented in the header file.
void	gpu_reset_timings (nonbonded_verlet_t *nbv)
	This function is documented in the header file.
bool	gpu_is_kernel_ewald_analytical (const NbnxmGpu *nb)
void	setupGpuShortRangeWorkLow (NbnxmGpu *nb, const ListedForcesGpu *listedForcesGpu, const InteractionLocality iLocality)
bool	haveGpuShortRangeWork (const NbnxmGpu *nb, const InteractionLocality interactionLocality)
void	gpu_launch_cpyback (NbnxmGpu *nb, struct nbnxm_atomdata_t *nbatom, const StepWorkload &stepWork, const AtomLocality atomLocality)
	Launch asynchronously the download of nonbonded forces from the GPU (and energies/shift forces if required).
void	nbnxmInsertNonlocalGpuDependency (NbnxmGpu *nb, const InteractionLocality interactionLocality)
void	gpu_copy_xq_to_gpu (NbnxmGpu *nb, const nbnxm_atomdata_t *nbatom, const AtomLocality atomLocality)
	Launch asynchronously the xq buffer host to device copy.
static FusedXToXqLaunchParams	setupFusedXToXqLaunchParams (ArrayRef< const Grid > grids, int gridBegin, int numCellsMax)
	Compute all kernel launch parameters for a given set of grids. More...
void	nbnxm_gpu_init_x_to_nbat_x (const GridSet &gridSet, NbnxmGpu *gpu_nbv)
void	gpu_free (NbnxmGpu *nb)
	This function is documented in the header file.
NBAtomDataGpu *	gpuGetNBAtomData (NbnxmGpu *nb)
DeviceBuffer< RVec >	gpu_get_f (NbnxmGpu *nb)
static	__attribute__ ((always_inline)) Float2 convertSigmaEpsilonToC6C12(const float sigma
	Convert sigma and epsilon VdW parameters to c6,c12 pair. More...
if	constexpr (calcFr)
if	constexpr (doCalcEnergies)
static bool	nbnxmSimdSupported (const MDLogger &mdlog, const t_inputrec &inputrec)
	Returns whether CPU SIMD support exists for the given inputrec. More...
static NbnxmKernelType	pickNbnxmKernelCpuSimdType (const t_inputrec &inputrec, const gmx_hw_info_t gmx_unused &hardwareInfo)
	Returns the most suitable CPU SIMD kernel type. More...
static EwaldExclusionType	pickNbnxmKernelCpuSimdExclusion (const gmx_hw_info_t gmx_unused &hardwareInfo)
	Returns the most suitable CPU SIMD kernel exclusion type. More...
static NbnxmKernelSetup	pickNbnxmKernelCpu (const t_inputrec &inputrec, const gmx_hw_info_t &hardwareInfo, bool useSimd, const MDLogger &mdlog)
	Returns the most suitable CPU kernel type and Ewald handling.
static NbnxmKernelSetup	pick_nbnxm_kernel (const gmx::MDLogger &mdlog, gmx_bool use_simd_kernels, const gmx_hw_info_t &hardwareInfo, const PairlistType gpuPairlistType, const NonbondedResource &nonbondedResource, const t_inputrec &inputrec)
	Returns the most suitable kernel type and Ewald handling.
static int	getMinimumIlistCountForGpuBalancing (NbnxmGpu *nbnxmGpu)
	Gets and returns the minimum i-list count for balancing based on the GPU used or env.var. when set.
static std::optional < LJCombinationRule >	chooseLJCombinationRule (const t_forcerec &forcerec)
	Returns the LJ combination rule choices for the LJ pair parameters.
static LJCombinationRule	chooseLJPmeCombinationRule (const t_forcerec &forcerec)
	Returns the LJ combination rule choices for the LJ PME-grid parameters.
static void	validate_global_work_size (const KernelLaunchConfig &config, int work_dim, const DeviceInformation *dinfo)
	Validates the input global work size parameter.
static cl_kernel	selectPruneKernel (cl_kernel kernel_pruneonly[], bool firstPrunePass)
	Return a pointer to the prune kernel version to be executed at the current invocation. More...
static cl_kernel	select_nbnxm_kernel (NbnxmGpu *nb, enum ElecType elecType, enum VdwType vdwType, bool bDoEne, bool bDoPrune)
	Return a pointer to the kernel version to be executed at the current step. OpenCL kernel objects are cached in nb. If the requested kernel is not found in the cache, it will be created and the cache will be updated.
static int	calc_shmem_required_nonbonded (enum VdwType vdwType, bool bPrefetchLjParam)
	Calculates the amount of shared memory required by the nonbonded kernel in use.
static void	fillin_ocl_structures (NBParamGpu *nbp, cl_nbparam_params_t *nbparams_params)
	Initializes data structures that are going to be sent to the OpenCL device. More...
static int	calc_shmem_required_prune (const int num_threads_z)
	Calculates the amount of shared memory required by the prune kernel. More...
static cl_kernel	nbnxm_gpu_create_kernel (NbnxmGpu *nb, const char *kernel_name)
	Initializes the OpenCL kernel pointers of the nbnxm_ocl_ptr_t input data structure.
static void	nbnxm_gpu_init_kernels (NbnxmGpu *nb)
	Initializes the OpenCL kernel pointers of the nbnxm_ocl_ptr_t input data structure.
static void	free_kernel (cl_kernel *kernel_ptr)
	Releases an OpenCL kernel pointer.
static void	free_kernels (cl_kernel *kernels, int count)
	Releases a list of OpenCL kernel pointers.
static void	freeGpuProgram (cl_program program)
	Free the OpenCL program. More...
static std::string	makeDefinesForKernelTypes (bool bFastGen, enum ElecType elecType, enum VdwType vdwType)
	Returns a string with the compiler defines required to avoid all flavour generation. More...
void	nbnxm_gpu_compile_kernels (NbnxmGpu *nb)
	Compiles nbnxm kernels for OpenCL GPU given by mygpu. More...
static constexpr bool	c_useSimdGpuClusterPairDistance (const PairlistType layoutType)
static constexpr int	sizeNeededForBufferFlags (const int numAtoms)
static void	resizeAndZeroBufferFlags (std::vector< gmx_bitmask_t > *flags, const int numAtoms)
static real	listRangeForBoundingBoxToGridBin (real rlist, const GridDimensions &gridDims)
static real	listRangeForGridBinToGridBin (real rlist, const GridDimensions &iGridDims, const GridDimensions &jGridDims)
template<int dim>
static void	get_cell_range (real b0, real b1, const GridDimensions &jGridDims, real d2, real rlist, int *cf, int *cl)
template<PairlistType layoutType>
static bool gmx_unused	clusterpairInRangePlainC (const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2)
template<PairlistType layoutType>
static bool	clusterpairInRange (const NbnxmPairlistGpuWork &work, const int si, const int csj, const int jCoordStride, const real *x_j, const real rlist2)
template<typename JClusterListType >
static int	findJClusterInJList (int jCluster, const JListRanges &ranges, const JClusterListType &cjList)
template<PairlistType layoutType>
static void	setExclusionsForIEntry (const GridSet &gridSet, NbnxmPairlistCpu *nbl, bool diagRemoved, int na_cj_2log, const ListOfLists< int > &exclusions)
static KernelLayoutClusterRatio	layoutClusterRatio (const Grid::Geometry &geometry)
	Returns the j/i cluster size ratio for the geometry of a grid.
static void	fep_list_new_nri_copy (AtomPairlist *nlist, int energyGroupPair=-1)
	Add a new entry to the i-list as a copy of the last entry. More...
template<PairlistType layoutType>
static void	make_fep_list (ArrayRef< const int > atomIndices, const nbnxm_atomdata_t *nbat, NbnxmPairlistCpu *nbl, bool bDiagRemoved, const real shx, const real shy, const real shz, const real gmx_unused rlist_fep2, const Grid &iGrid, const Grid &jGrid, AtomPairlist *nlist)
template<PairlistType layoutType>
static int	cj_mod_cjPacked (int cj)
template<PairlistType layoutType>
static int	cj_to_cjPacked (int cj)
template<PairlistType layoutType>
static void	make_fep_list (ArrayRef< const int > atomIndices, const nbnxm_atomdata_t *nbat, NbnxmPairlistGpu *nbl, bool bDiagRemoved, real shx, real shy, real shz, real rlist_fep2, const Grid &iGrid, const Grid &jGrid, AtomPairlist *nlist)
template<PairlistType layoutType>
static void	setExclusionsForIEntry (const GridSet &gridSet, NbnxmPairlistGpu *nbl, bool diagRemoved, int gmx_unused na_cj_2log, const ListOfLists< int > &exclusions)
template<PairlistType layoutType>
static void	addNewIEntry (NbnxmPairlistCpu *nbl, int ci, int shift, int flags)
template<PairlistType layoutType>
static void	addNewIEntry (NbnxmPairlistGpu *nbl, int sci, int shift, int gmx_unused flags)
static void	sort_cj_excl (nbnxm_cj_t *cj, int ncj, NbnxmPairlistCpuWork *work)
template<PairlistType layoutType>
static void	closeIEntry (NbnxmPairlistCpu *nbl, int gmx_unused sp_max_av, bool gmx_unused progBal, float gmx_unused nsp_tot_est, int gmx_unused thread, int gmx_unused nthread)
template<PairlistType layoutType>
static void	split_sci_entry (NbnxmPairlistGpu *nbl, int nsp_target_av, bool progBal, float nsp_tot_est, int thread, int nthread)
template<PairlistType layoutType>
static void	closeIEntry (NbnxmPairlistGpu *nbl, int nsp_max_av, bool progBal, float nsp_tot_est, int thread, int nthread)
template<PairlistType layoutType>
static void	sync_work (NbnxmPairlistCpu gmx_unused *nbl)
template<PairlistType layoutType>
static void	sync_work (NbnxmPairlistGpu *nbl)
static void	clear_pairlist (NbnxmPairlistCpu *nbl)
static void	clear_pairlist (NbnxmPairlistGpu *nbl)
static void	set_icell_bb_simple (ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci)
template<PairlistType layoutType>
static void	set_icell_bb (const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistCpuWork *work)
template<PairlistType layoutType>
static gmx_unused void	set_icell_bbxxxx_supersub (ArrayRef< const float > bb, int ci, const RVec &shift, float *bb_ci)
template<PairlistType layoutType>
static gmx_unused void	set_icell_bb_supersub (ArrayRef< const BoundingBox > bb, int ci, const RVec &shift, BoundingBox *bb_ci)
template<PairlistType layoutType>
static gmx_unused void	set_icell_bb (const Grid &iGrid, int ci, const RVec &shift, NbnxmPairlistGpuWork *work)
template<ClusterDistanceKernelType kernelType>
static void	icellSetXSimple (int ci, const RVec &shift, int stride, const real *x, NbnxmPairlistCpuWork::IClusterData *iClusterData)
template<PairlistType >
static void	icell_set_x (int ci, const RVec &shift, int stride, const real *x, const ClusterDistanceKernelType kernelType, NbnxmPairlistCpuWork *work)
template<PairlistType layoutType>
static void	icell_set_x (int ci, const RVec &shift, int stride, const real *x, ClusterDistanceKernelType, NbnxmPairlistGpuWork *work)
template<PairlistType layoutType>
static real	minimum_subgrid_size_xy (const Grid &grid)
template<PairlistType layoutType>
static real	effective_buffer_1x1_vs_MxN (const Grid &iGrid, const Grid &jGrid)
static real	nonlocal_vol2 (const gmx::DomdecZones &zones, const rvec ls, real r)
static void	get_nsubpair_target (const GridSet &gridSet, const InteractionLocality iloc, const real rlist, const int min_ci_balanced, int *nsubpair_target, float *nsubpair_tot_est)
static void	print_nblist_ci_cj (FILE *fp, const NbnxmPairlistCpu &nbl)
template<PairlistType layoutType>
static void	print_nblist_sci_cj (FILE *fp, const NbnxmPairlistGpu &nbl)
template<PairlistType layoutType>
static void	combine_nblists (ArrayRef< const NbnxmPairlistGpu > nbls, NbnxmPairlistGpu *nblc)
static void	balance_fep_lists (ArrayRef< std::unique_ptr< AtomPairlist >> fepLists, ArrayRef< PairsearchWork > work)
static void	combine_fep_lists (ArrayRef< std::unique_ptr< AtomPairlist >> fepLists)
static float	boundingbox_only_distance2 (const GridDimensions &iGridDims, const GridDimensions &jGridDims, real rlist, bool simple, const PairlistType layoutType)
static int	get_ci_block_size (const Grid &iGrid, const bool haveMultipleDomains, const int numLists)
	Returns a suitable block size, in cells, per thread that will generate reasonably balanced lists.
static int	getBufferFlagShift (int numAtomsPerCluster)
static void	makeClusterListWrapper (NbnxmPairlistCpu *nbl, const Grid gmx_unused &iGrid, const int ci, const Grid &jGrid, const int firstBin, const int lastBin, const bool excludeSubDiagonal, const nbnxm_atomdata_t *nbat, const real rlist2, const real rbb2, const ClusterDistanceKernelType kernelType, int *numDistanceChecks)
static void	makeClusterListWrapper (NbnxmPairlistGpu *nbl, const Grid &gmx_unused iGrid, const int ci, const Grid &jGrid, const int firstBin, const int lastBin, const bool excludeSubDiagonal, const nbnxm_atomdata_t *nbat, const real rlist2, const real rbb2, ClusterDistanceKernelType gmx_unused kernelType, int *numDistanceChecks)
static int	getNumSimpleJClustersInList (const NbnxmPairlistCpu &nbl)
static int	getNumSimpleJClustersInList (const gmx_unused NbnxmPairlistGpu &nbl)
static void	incrementNumSimpleJClustersInList (NbnxmPairlistCpu *nbl, int ncj_old_j)
static void	incrementNumSimpleJClustersInList (NbnxmPairlistGpu gmx_unused *nbl, int gmx_unused ncj_old_j)
static void	checkListSizeConsistency (const NbnxmPairlistCpu &nbl, const bool haveFreeEnergy)
static void	checkListSizeConsistency (const NbnxmPairlistGpu gmx_unused &nbl, bool gmx_unused haveFreeEnergy)
static void	setBufferFlags (const NbnxmPairlistCpu &nbl, const int ncj_old_j, const int gridj_flag_shift, gmx_bitmask_t *gridj_flag, const int th)
static void	setBufferFlags (const NbnxmPairlistGpu gmx_unused &nbl, int gmx_unused ncj_old_j, int gmx_unused gridj_flag_shift, gmx_bitmask_t gmx_unused *gridj_flag, int gmx_unused th)
template<typename T >
static void	nbnxm_make_pairlist_part (const GridSet &gridSet, const Grid &iGrid, const Grid &jGrid, PairsearchWork *work, const nbnxm_atomdata_t *nbat, const ListOfLists< int > &exclusions, const bool includeAllPairs, real rlist, const PairlistType pairlistType, bool bFBufferFlag, int nsubpair_max, bool progBal, float nsubpair_tot_est, int th, int nth, T *nbl, AtomPairlist *nbl_fep)
static void	reduce_buffer_flags (ArrayRef< PairsearchWork > searchWork, int nsrc, ArrayRef< gmx_bitmask_t > dest)
static void	print_reduction_cost (ArrayRef< const gmx_bitmask_t > flags, int nout)
template<bool setFlags>
static void	copySelectedListRange (const nbnxm_ci_t *gmx_restrict srcCi, const NbnxmPairlistCpu *gmx_restrict src, NbnxmPairlistCpu *gmx_restrict dest, gmx_bitmask_t *flag, int iFlagShift, int jFlagShift, int t)
static int	countClusterpairs (ArrayRef< const NbnxmPairlistCpu > pairlists)
static void	rebalanceSimpleLists (ArrayRef< const NbnxmPairlistCpu > srcSet, ArrayRef< NbnxmPairlistCpu > destSet, ArrayRef< PairsearchWork > searchWork)
static bool	checkRebalanceSimpleLists (ArrayRef< const NbnxmPairlistCpu > lists)
static void	sort_sci (NbnxmPairlistGpu *nbl)
static Range< int >	getIZoneRange (const GridSet::DomainSetup &domainSetup, const InteractionLocality locality)
static Range< int >	getJZoneRange (const gmx::DomdecZones *ddZones, const InteractionLocality locality, const int iZone)
static ArrayRef< const Grid >	getGridList (ArrayRef< const Grid > grids, const Range< int > &ddZoneRange)
static void	prepareListsForDynamicPruning (ArrayRef< NbnxmPairlistCpu > lists)
	Prepares CPU lists produced by the search for dynamic pruning.
static bool	isLastLocality (const PairSearch &pairSearch, const InteractionLocality iLocality)
	Returns whether iLocality is the last locality to construct pairlists for.
template<PairlistType layoutType>
static int	atomIndexInClusterpairSplit (const int atomIndex)
	Returns the index of atom with index atomIndex within a split (or whole when not split) cluster-pair.
constexpr bool	nbnxmSortListsOnGpu ()
	Whether we want to use GPU for neighbour list sorting.
template<typename T , int iClusterSize, int jClusterSize>
constexpr std::array< T, iClusterSize/jClusterSize >	diagonalMaskJSmallerI ()
	Returns a diagonal interaction mask with atoms j<i masked out. More...
template<typename T , int iClusterSize, int jClusterSize>
constexpr std::array< T, jClusterSize/iClusterSize >	diagonalMaskJLargerI ()
	Returns a diagonal interaction mask with atoms j>i masked out. More...
template<int iClusterSize, int jClusterSize>
static gmx_unused uint32_t	getImask (const bool maskOutSubDiagonal, const int ci, const int cj)
	Returns a diagonal or off-diagonal interaction mask. More...
template<ClusterDistanceKernelType kernelType>
static gmx_unused constexpr int	sc_iClusterSizeSimd ()
template<ClusterDistanceKernelType kernelType>
static gmx_unused constexpr int	sc_jClusterSizeSimd ()
template<ClusterDistanceKernelType kernelType>
static gmx_unused constexpr int	sc_xStride ()
	Stride of the packed x coordinate array.
template<ClusterDistanceKernelType kernelType>
static gmx_unused int	xIndexFromCi (int ci)
	Returns the nbnxm coordinate data index given the i-cluster index.
template<ClusterDistanceKernelType kernelType>
static gmx_unused int	xIndexFromCj (int cj)
	Returns the nbnxm coordinate data index given the j-cluster index.
template<ClusterDistanceKernelType kernelType, int jSubClusterIndex>
static gmx_unused int	cjFromCi (int ci)
	Returns the j-cluster index given the i-cluster index. More...
void	setICellCoordinatesSimd4xM (int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work)
void	setICellCoordinatesSimd2xMM (int gmx_unused ci, const RVec gmx_unused &shift, int gmx_unused stride, const real gmx_unused *x, NbnxmPairlistCpuWork gmx_unused *work)
void	makeClusterListSimd4xM (const Grid gmx_unused &jGrid, NbnxmPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstBin, int gmx_unused lastBin, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks)
void	makeClusterListSimd2xMM (const Grid gmx_unused &jGrid, NbnxmPairlistCpu gmx_unused *nbl, int gmx_unused icluster, int gmx_unused firstBin, int gmx_unused lastBin, bool gmx_unused excludeSubDiagonal, const real gmx_unused *gmx_restrict x_j, real gmx_unused rlist2, float gmx_unused rbb2, int gmx_unused *gmx_restrict numDistanceChecks)
void	setICellCoordinatesSimd4xM (int ci, const RVec &shift, int gmx_unused stride, const real *x, NbnxmPairlistCpuWork *work)
	Copies PBC shifted i-cell packed atom coordinates to working array for the 4xM layout.
void	setICellCoordinatesSimd2xMM (int ci, const RVec &shift, int gmx_unused stride, const real *x, NbnxmPairlistCpuWork *work)
	Copies PBC shifted i-cell packed atom coordinates to working array for the 2xMM layout.
void	makeClusterListSimd4xM (const Grid &jGrid, NbnxmPairlistCpu *nbl, int icluster, int firstCell, int lastCell, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks)
	SIMD code for checking and adding cluster-pairs to the list using the 4xM layout. More...
void	makeClusterListSimd2xMM (const Grid &jGrid, NbnxmPairlistCpu *nbl, int icluster, int firstCell, int lastCell, bool excludeSubDiagonal, const real *gmx_restrict x_j, real rlist2, float rbb2, int *gmx_restrict numDistanceChecks)
	SIMD code for checking and adding cluster-pairs to the list using the 2xMM layout. More...
static bool	supportsDynamicPairlistGenerationInterval (const t_inputrec &ir)
	Returns if we can (heuristically) change nstlist and rlist. More...
static real	getPressureTolerance (const real inputrecVerletBufferPressureTolerance)
	Returns the Verlet buffer pressure tolerance set by an env.var. or from input.
void	increaseNstlist (FILE *fplog, const MpiComm &mpiCommSimulation, t_inputrec *ir, int nstlistOnCmdline, const gmx_mtop_t *mtop, const matrix box, real effectiveAtomDensity, bool useOrEmulateGpuForNonbondeds)
	Try to increase nstlist when using the Verlet cut-off scheme. More...
static real	calcPruneVerletBufferSize (const CalcVerletBufferParameters &params, const int nstlist)
	Wrapper for calcVerletBufferSize() for determining the pruning cut-off. More...
static void	setDynamicPairlistPruningParameters (const t_inputrec &inputrec, const gmx_mtop_t &mtop, const real effectiveAtomDensity, const bool useGpuList, const VerletbufListSetup &listSetup, const bool userSetNstlistPrune, const interaction_const_t &interactionConst, PairlistParams *listParams)
	Set the dynamic pairlist pruning parameters in ic. More...
static std::string	formatListSetup (const std::string &listName, int nstList, int nstListForSpacing, real rList, real interactionCutoff)
	Returns a string describing the setup of a single pair-list. More...
void	setupDynamicPairlistPruning (const MDLogger &mdlog, const t_inputrec &inputrec, const gmx_mtop_t &mtop, real effectiveAtomDensity, const interaction_const_t &interactionConst, PairlistParams *listParams)
	Set up the dynamic pairlist pruning. More...
void	printNbnxmPressureError (const MDLogger &mdlog, const t_inputrec &inputrec, const gmx_mtop_t &mtop, real effectiveAtomDensity, const PairlistParams &listParams)
	Prints an estimate of the error in the pressure due to missing interactions. More...
template<int nR, KernelLayout kernelLayout>
std::array< std::array < SimdBool, nR > , kernelLayoutClusterRatio < kernelLayout > )==KernelLayoutClusterRatio::JSizeEqualsISize?1:2 >	generateDiagonalMasks (const nbnxm_atomdata_t::SimdMasks &simdMasks)
	Returns the diagonal filter masks.
template<int nR, bool maskInteractions, std::size_t inputSize, std::size_t interactSize>
void	rInvSixAndRInvTwelve (const std::array< SimdReal, inputSize > &rInvSquaredV, const std::array< SimdBool, interactSize > &interactV, std::array< SimdReal, nR > &rInvSixV, std::array< SimdReal, nR > &rInvTwelveV)
	Computes r^-6 and r^-12, masked when requested.
template<int nR, bool maskInteractions, bool haveCutoffCheck, bool calculateEnergies, std::size_t inputSize, std::size_t interactSize, std::size_t vljvSize>
void	lennardJonesInteractionsSigmaEpsilon (const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, const SimdBool *const withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, const SimdReal dispersionShift, const SimdReal repulsionShift, const SimdReal sixth, const SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV)
	Returns F*r and optionally the potential for LJ with (un)shifted potential with sigma/epsilon.
template<int nR, std::size_t inputSize>
void	computeForceSwitchVariables (const std::array< SimdReal, inputSize > &rSquaredV, const std::array< SimdReal, inputSize > &rInvV, SimdReal rSwitch, std::array< SimdReal, nR > &rSwitchedV, std::array< SimdReal, nR > &rSwitchedSquaredV, std::array< SimdReal, nR > &rSwitchedSquaredTimesRV)
	Computes (r - r_switch), (r - r_switch)^2 and (r - r_switch)^2 * r.
SimdReal	addLJForceSwitch (SimdReal force, SimdReal rSwitched, SimdReal rSwitchedSquaredTimesR, SimdReal c2, SimdReal c3)
	Adds the force switch term to force.
SimdReal	ljForceSwitchPotential (SimdReal rSwitched, SimdReal rSwitchedSquaredTimesR, SimdReal c0, SimdReal c3, SimdReal c4)
	Returns the LJ force switch function for the potential.
template<int nR, std::size_t inputSize>
void	computePotentialSwitchVariables (const std::array< SimdReal, inputSize > &rSquaredV, const std::array< SimdReal, inputSize > &rInvV, SimdReal rSwitch, std::array< SimdReal, nR > &rSwitchedV, std::array< SimdReal, nR > &rSwitchedSquaredV)
	Computes (r - r_switch) and (r - r_switch)^2.
SimdReal	potentialSwitchFunction (SimdReal rsw, SimdReal rsw2, SimdReal c3, SimdReal c4, SimdReal c5)
	Returns the potential switch function.
SimdReal	potentialSwitchFunctionDerivative (SimdReal rsw, SimdReal rsw2, SimdReal c2, SimdReal c3, SimdReal c4)
	Returns the derivative of the potential switch function.
template<int nR, bool maskInteractions, bool calculateEnergies, std::size_t inputSize, std::size_t interactSize, std::size_t ljepSize, std::size_t vljvSize>
void	addLennardJonesEwaldCorrections (const std::array< SimdReal, inputSize > &rSquaredV, const std::array< SimdReal, inputSize > &rInvSquaredV, const std::array< SimdBool, interactSize > &interactV, const SimdBool *withinCutoffV, const std::array< SimdReal, nR > &c6GridV, const std::array< SimdReal, ljepSize > &ljEwaldParams, SimdReal sixth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV)
	Adds the Ewald long-range correction for r^-6.
template<KernelLayoutClusterRatio clusterRatio>
static int	cjFromCi (const int iCluster)
	Returns the j-cluster index for the given i-cluster index. More...
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r4xM, SimdReal >	loadIAtomData (const real *ptr, const int offset, const int iRegister)
	Load a single real for an i-atom into iRegister.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r2xMM, SimdReal >	loadIAtomData (const real *ptr, const int offset, const int iRegister)
	Load a pair of consecutive reals for two i-atom into the respective halves of iRegister.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r4xM, SimdReal >	loadJAtomData (const real *ptr, const int offset)
	Returns a SIMD register containing GMX_SIMD_REAL_WIDTH reals loaded from ptr + offset.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r2xMM, SimdReal >	loadJAtomData (const real *ptr, const int offset)
	Returns a SIMD register containing a duplicate sequence of GMX_SIMD_REAL_WIDTH/2 reals loaded from ptr + offset.
template<bool loadMasks, KernelLayout kernelLayout>
std::enable_if_t<!loadMasks, std::array< SimdBool, 0 > >	loadSimdPairInteractionMasks (const int excl, SimdBitMask *filterBitMasksV)
	Loads no interaction masks, returns an empty array.
template<bool loadMasks, KernelLayout kernelLayout>
std::enable_if_t< loadMasks &&kernelLayout==KernelLayout::r4xM, std::array< SimdBool, sc_iClusterSize(kernelLayout)> >	loadSimdPairInteractionMasks (const int excl, SimdBitMask *filterBitMasksV)
	Loads interaction masks for a cluster pair for 4xM kernel layout.
template<bool loadMasks, KernelLayout kernelLayout>
std::enable_if_t< loadMasks &&kernelLayout==KernelLayout::r2xMM, std::array< SimdBool, sc_iClusterSize(kernelLayout)/2 > >	loadSimdPairInteractionMasks (const int excl, SimdBitMask *filterBitMasksV)
	Loads interaction masks for a cluster pair for 2xMM kernel layout.
template<int nR>
int	pairCountWithinCutoff (SimdReal rSquaredV[nR], SimdReal cutoffSquared)
	Return the number of atoms pairs that are within the cut-off distance.
template<KernelLayout kernelLayout>
void	nbnxmSimdPruneKernel (NbnxmPairlistCpu *nbl, const nbnxm_atomdata_t &nbat, ArrayRef< const RVec > shiftvec, real rlistInner)
	Prune a single NbnxmPairlistCpu entry with distance rlistInner.
static auto	nbnxmKernelTransformXToXq (Float4 *__restrict__ gm_xq, const Float3 *__restrict__ gm_x, const int *__restrict__ gm_atomIndex, const int *__restrict__ gm_numAtomsPerCell, const int *__restrict__ gm_cellToBin, int numAtomsPerBin, int gridBegin, int numCellsMax, FusedXToXqGridParams gridParams)
	SYCL kernel for transforming position coordinates from rvec to nbnxm layout. More...
static void	launchSciSortOnGpu (GpuPairlist *plist, const int maxWorkGroupSize, const DeviceStream &deviceStream)
template<int workGroupSize, int nElements>
static auto	nbnxmKernelExclusivePrefixSum (const int *__restrict__ gm_input, int *__restrict__ gm_output)
	SYCL exclusive prefix sum kernel for list sorting. More...
static auto	nbnxmKernelBucketSciSort (const nbnxm_sci_t *__restrict__ gm_sci, const int *__restrict__ gm_sciCount, int *__restrict__ gm_sciOffset, nbnxm_sci_t *__restrict__ gm_sciSorted)
	SYCL bucket sci sort kernel. More...
template<int workGroupSize>
static void	launchPrefixSumKernel (sycl::queue &q, GpuPairlistSorting *sorting)
static void	launchBucketSortKernel (sycl::queue &q, GpuPairlist *plist)
static int	getNbnxmSubGroupSize (const DeviceInformation &deviceInfo, PairlistType layoutType)
constexpr bool	c_avoidFloatingPointAtomics (PairlistType layoutType)
	Should we avoid FP atomics to the same location from the same work-group? More...
static void	reduceForceJShuffle (Float3 f, const sycl::nd_item< 3 > &itemIdx, const int tidxi, const int aidx, sycl::global_ptr< Float3 > a_f)
	Reduce c_clSize j-force components using shifts and atomically accumulate into a_f. More...
template<int subGroupSize, int groupSize>
static float	groupReduce (const sycl::nd_item< 3 > itemIdx, const unsigned int tidxi, sycl::local_ptr< float > sm_buf, float valueToReduce)
	Do workgroup-level reduction of a single float. More...
static void	reduceForceJGeneric (sycl::local_ptr< float > sm_buf, Float3 f, const sycl::nd_item< 3 > &itemIdx, const int tidxi, const int tidxj, const int aidx, sycl::global_ptr< Float3 > a_f)
	Reduce c_clSize j-force components using local memory and atomically accumulate into a_f. More...
template<bool useShuffleReduction>
static void	reduceForceJ (sycl::local_ptr< float > sm_buf, Float3 f, const sycl::nd_item< 3 > itemIdx, const int tidxi, const int tidxj, const int aidx, sycl::global_ptr< Float3 > a_f)
	Reduce c_clSize j-force components using either shifts or local memory and atomically accumulate into a_f.
template<typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >
static void	reduceForceIAndFShiftGeneric (sycl::local_ptr< float > sm_buf, const FCiBufferWrapperX &fCiBufX, const FCiBufferWrapperY &fCiBufY, const FCiBufferWrapperZ &fCiBufZ, const bool calcFShift, const sycl::nd_item< 3 > itemIdx, const int tidxi, const int tidxj, const int sci, const int shift, sycl::global_ptr< Float3 > a_f, sycl::global_ptr< Float3 > a_fShift)
	Local memory-based i-force reduction. More...
template<int numShuffleReductionSteps, typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >
static std::enable_if_t < numShuffleReductionSteps!=1, void >	reduceForceIAndFShiftShuffles (const FCiBufferWrapperX &fCiBufX, const FCiBufferWrapperY &fCiBufY, const FCiBufferWrapperZ &fCiBufZ, const bool calcFShift, const sycl::nd_item< 3 > itemIdx, const int tidxi, const int tidxj, const int sci, const int shift, sycl::global_ptr< Float3 > a_f, sycl::global_ptr< Float3 > a_fShift)
	Shuffle-based i-force reduction. More...
template<int numShuffleReductionSteps, typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >
static std::enable_if_t < numShuffleReductionSteps==1, void >	reduceForceIAndFShiftShuffles (const FCiBufferWrapperX &fCiBufX, const FCiBufferWrapperY &fCiBufY, const FCiBufferWrapperZ &fCiBufZ, const bool calcFShift, const sycl::nd_item< 3 > itemIdx, const int tidxi, const int tidxj, const int sci, const int shift, sycl::global_ptr< Float3 > a_f, sycl::global_ptr< Float3 > a_fShift)
	reduceForceIAndFShiftShuffles specialization for single-step reduction (e.g., Intel iGPUs). More...
template<bool useShuffleReduction, int subGroupSize, typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >
static void	reduceForceIAndFShift (sycl::local_ptr< float > sm_buf, const FCiBufferWrapperX &fCiBufX, const FCiBufferWrapperY &fCiBufY, const FCiBufferWrapperZ &fCiBufZ, const bool calcFShift, const sycl::nd_item< 3 > itemIdx, const int tidxi, const int tidxj, const int sci, const int shift, sycl::global_ptr< Float3 > a_f, sycl::global_ptr< Float3 > a_fShift)
	Final i-force reduction. More...
template<int subGroupSize, bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType, typename CommandGroupHandler >
static auto	nbnxmKernel (CommandGroupHandler cgh, const Float4 *__restrict__ gm_xq, Float3 *__restrict__ gm_f, const Float3 *__restrict__ gm_shiftVec, Float3 *__restrict__ gm_fShift, float *__restrict__ gm_energyElec, float *__restrict__ gm_energyVdw, nbnxm_cj_packed_t *__restrict__ gm_plistCJPacked, const nbnxm_sci_t *__restrict__ gm_plistSci, const nbnxm_excl_t *__restrict__ gm_plistExcl, const Float2 *__restrict__ gm_ljComb, const int *__restrict__ gm_atomTypes, const Float2 *__restrict__ gm_nbfp, const Float2 *__restrict__ gm_nbfpComb, const float *__restrict__ gm_coulombTab, int *__restrict__ gm_sciHistogram, int *__restrict__ gm_sciCount, const int numTypes, const float rCoulombSq, const float rVdwSq, const float twoKRf, const float ewaldBeta, const float rlistOuterSq, const float ewaldShift, const float epsFac, const float ewaldCoeffLJ_2, const float cRF, const shift_consts_t dispersionShift, const shift_consts_t repulsionShift, const switch_consts_t vdwSwitch, const float rVdwSwitch, const float ljEwaldShift, const float coulombTabScale, const bool calcShift)
	Main kernel for NBNXM. More...
template<int subGroupSize, bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType, class... Args>
static void	launchNbnxmKernel (const DeviceStream &deviceStream, const int numSci, Args &&...args)
	NBNXM kernel launch code.
template<int subGroupSize, bool doPruneNBL, bool doCalcEnergies, class... Args>
void	chooseAndLaunchNbnxmKernel (enum ElecType elecType, enum VdwType vdwType, Args &&...args)
	Select templated kernel and launch it.
template<bool haveFreshList, PairlistType layoutType, typename CommandGroupHandler >
auto	nbnxmKernelPruneOnly (CommandGroupHandler cgh, const int numSci, const int numParts, const Float4 *__restrict__ gm_xq, const Float3 *__restrict__ gm_shiftVec, nbnxm_cj_packed_t *__restrict__ gm_plistCJPacked, const nbnxm_sci_t *__restrict__ gm_plistSci, unsigned int *__restrict__ gm_plistIMask, int *__restrict__ gm_rollingPruningPart, int *__restrict__ gm_sciHistogram, int *__restrict__ gm_sciCount, const float rlistOuterSq, const float rlistInnerSq)
	Prune-only kernel for NBNXM. More...
template<bool haveFreshList, PairlistType layoutType, class... Args>
void	launchNbnxmKernelPruneOnly (const DeviceStream &deviceStream, const int numSciInPartMax, Args &&...args)
	Leap Frog SYCL prune-only kernel launch code.
template<PairlistType layoutType, class... Args>
void	chooseAndLaunchNbnxmKernelPruneOnly (bool haveFreshList, Args &&...args)
	Select templated kernel and launch it.
void	launchNbnxmKernelPruneOnly (NbnxmGpu *nb, const InteractionLocality iloc, const int numParts, const int numSciInPartMax)
	Launch SYCL NBNXM prune-only kernel. More...
static constexpr unsigned	sc_superClInteractionMask (const PairlistType layoutType)
void	assignOptionsFromKeyValueTree (Options *options, const KeyValueTreeObject &tree, IKeyValueTreeErrorHandler *errorHandler)
	Assigns option values from a given KeyValueTreeObject. More...
void	checkForUnknownOptionsInKeyValueTree (const KeyValueTreeObject &tree, const Options &options)
	Checks that a given KeyValueTreeObject can be assigned to given Options. More...
KeyValueTreeObject	adjustKeyValueTreeFromOptions (const KeyValueTreeObject &tree, const Options &options)
	Adjusts a KeyValueTreeObject to the structure of given Options. More...
bool	boxesAreEqual (const matrix box1, const matrix box2)
	Returns whether two boxes are of equal size and shape (within reasonable tolerance).
bool	boxIsZero (const matrix box)
	Returns whether a box is only initialised to zero or not.
void	shiftAtoms (const RVec &shift, ArrayRef< RVec > x)
	Shift all coordinates. More...
void	placeCoordinatesWithCOMInBox (const PbcType &pbcType, UnitCellType unitCellType, CenteringType centerType, const matrix box, ArrayRef< RVec > x, const gmx_mtop_t &mtop, COMShiftType comShiftType)
	Moves collection of atoms along the center of mass into a box. More...
static IVec	shiftIndexToXYZ (int shiftIndex)
	Convert shift index to periodic cell shifts.
static int	xyzToShiftIndex (int x, int y, int z)
	Convert grid coordinates to shift index.
static int	ivecToShiftIndex (const gmx::IVec &iv)
	Convert grid coordinates to shift index.
static int	ivecToShiftIndex (ivec iv)
	Convert grid coordinates to shift index.
static int	shiftIndexToXDim (int iv)
	Return the shift in the X dimension of grid space corresponding to iv.
const char *	centerTypeNames (CenteringType type)
	Get names for the different centering types. More...
const char *	unitCellTypeNames (UnitCellType type)
	Get names for the different unit cell representation types. More...
double	getTransformationPullCoordinateValue (pull_coord_work_t *coord, ArrayRef< const pull_coord_work_t > variableCoords, double t)
	Calculates pull->coord[coord_ind].spatialData.value for a transformation pull coordinate. More...
static double	computeDerivativeForTransformationPullCoord (pull_coord_work_t *coord, const int variablePcrdIndex)
	Calculates and returns the derivative of a transformation pull coordinate from a dependent coordinate. More...
void	distributeTransformationPullCoordForce (pull_coord_work_t *pcrd, gmx::ArrayRef< pull_coord_work_t > variableCoords)
	Distributes the force on a transformation pull coordinates to the involved coordinates of lower rank. More...
static bool	checkIfRandomDeviceIsFunctional ()
	Check if the RDRAND random device functioning correctly. More...
template<typename GeneratorType >
static uint64_t	makeRandomSeedInternal (GeneratorType &gen)
	Get the next pure or pseudo-random number. More...
uint64_t	makeRandomSeed ()
	Return 64 random bits from the random device, suitable as seed. More...
template<class RealType = real, unsigned int Bits, class Rng >
RealType	generateCanonical (Rng &g)
	Generate a floating-point value with specified number of random bits. More...
void	compileSelection (SelectionCollection *coll)
void	swap (SelectionCollection &lhs, SelectionCollection &rhs) noexcept
HelpTopicPointer	createSelectionHelpTopic ()
	*/ More...
void	serializeKeyValueTree (const KeyValueTreeObject &root, ISerializer *serializer)
	Serializes a KeyValueTreeObject with given serializer.
KeyValueTreeObject	deserializeKeyValueTree (ISerializer *serializer)
	Deserializes a KeyValueTreeObject from a given serializer.
static void gmx_unused	simdPrefetch (void gmx_unused *m)
	Prefetch memory at address m. More...
static void	store (float *m, float a)
	Store contents of float variable to aligned memory m. More...
static void	storeU (float *m, float a)
	Store contents of float variable to unaligned memory m. More...
static float	fma (float a, float b, float c)
	Float Fused-multiply-add. Result is a*b + c. More...
static float	fms (float a, float b, float c)
	Float Fused-multiply-subtract. Result is a*b - c. More...
static float	fnma (float a, float b, float c)
	Float Fused-negated-multiply-add. Result is -a*b + c. More...
static float	fnms (float a, float b, float c)
	Float Fused-negated-multiply-subtract. Result is -a*b - c. More...
static float	maskAdd (float a, float b, float m)
	Add two float variables, masked version. More...
static float	maskzMul (float a, float b, float m)
	Multiply two float variables, masked version. More...
static float	maskzFma (float a, float b, float c, float m)
	Float fused multiply-add, masked version. More...
static float gmx_simdcall	maskzRcp (float x, float m)
	Float 1.0/x, masked version. More...
static float	abs (float a)
	Float Floating-point abs(). More...
static float	max (float a, float b)
	Set each float element to the largest from two variables. More...
static float	min (float a, float b)
	Set each float element to the smallest from two variables. More...
static float	round (float a)
	Float round to nearest integer value (in floating-point format). More...
static float	trunc (float a)
	Truncate float, i.e. round towards zero - common hardware instruction. More...
static float	reduce (float a)
	Return sum of all elements in float variable (i.e., the variable itself). More...
static float	andNot (float a, float b)
	Bitwise andnot for two scalar float variables. More...
static bool	testBits (float a)
	Return true if any bits are set in the float variable. More...
static bool	anyTrue (bool a)
	Returns if the boolean is true. More...
static float	selectByMask (float a, bool mask)
	Select from single precision variable where boolean is true. More...
static float	selectByNotMask (float a, bool mask)
	Select from single precision variable where boolean is false. More...
static float	blend (float a, float b, bool sel)
	Blend float selection. More...
static std::int32_t	cvtR2I (float a)
	Round single precision floating point to integer. More...
static std::int32_t	cvttR2I (float a)
	Truncate single precision floating point to integer. More...
static std::int32_t	cvtI2R (std::int32_t a)
	Return integer. More...
static void	store (double *m, double a)
	Store contents of double variable to aligned memory m. More...
static void	storeU (double *m, double a)
	Store contents of double variable to unaligned memory m. More...
static double	fma (double a, double b, double c)
	double Fused-multiply-add. Result is a*b + c. More...
static double	fms (double a, double b, double c)
	double Fused-multiply-subtract. Result is a*b - c. More...
static double	fnma (double a, double b, double c)
	double Fused-negated-multiply-add. Result is - a*b + c. More...
static double	fnms (double a, double b, double c)
	double Fused-negated-multiply-subtract. Result is -a*b - c. More...
static double	maskAdd (double a, double b, double m)
	Add two double variables, masked version. More...
static double	maskzMul (double a, double b, double m)
	Multiply two double variables, masked version. More...
static double	maskzFma (double a, double b, double c, double m)
	double fused multiply-add, masked version. More...
static double gmx_simdcall	maskzRcp (double x, double m)
	Double 1.0/x, masked version. More...
static double	abs (double a)
	double doubleing-point abs(). More...
static double	max (double a, double b)
	Set each double element to the largest from two variables. More...
static double	min (double a, double b)
	Set each double element to the smallest from two variables. More...
static double	round (double a)
	double round to nearest integer value (in doubleing-point format). More...
static double	trunc (double a)
	Truncate double, i.e. round towards zero - common hardware instruction. More...
static double	reduce (double a)
	Return sum of all elements in double variable (i.e., the variable itself). More...
static double	andNot (double a, double b)
	Bitwise andnot for two scalar double variables. More...
static bool	testBits (double a)
	Return true if any bits are set in the double variable. More...
static double	selectByMask (double a, bool mask)
	Select from double precision variable where boolean is true. More...
static double	selectByNotMask (double a, bool mask)
	Select from double precision variable where boolean is false. More...
static double	blend (double a, double b, bool sel)
	Blend double selection. More...
static std::int32_t	cvtR2I (double a)
	Round single precision doubleing point to integer. More...
static std::int32_t	cvttR2I (double a)
	Truncate single precision doubleing point to integer. More...
static double	cvtF2D (float a)
	Convert float to double (mimicks SIMD conversion) More...
static float	cvtD2F (double a)
	Convert double to float (mimicks SIMD conversion) More...
static void	store (std::int32_t *m, std::int32_t a)
	Store contents of integer variable to aligned memory m. More...
static void	storeU (std::int32_t *m, std::int32_t a)
	Store contents of integer variable to unaligned memory m. More...
static std::int32_t	andNot (std::int32_t a, std::int32_t b)
	Bitwise andnot for two scalar integer variables. More...
static bool	testBits (std::int32_t a)
	Return true if any bits are set in the integer variable. More...
static std::int32_t	selectByMask (std::int32_t a, bool mask)
	Select from integer variable where boolean is true. More...
static std::int32_t	selectByNotMask (std::int32_t a, bool mask)
	Select from integer variable where boolean is false. More...
static std::int32_t	blend (std::int32_t a, std::int32_t b, bool sel)
	Blend integer selection. More...
static bool	cvtB2IB (bool a)
	Just return a boolean (mimicks SIMD real-to-int bool conversions) More...
static bool	cvtIB2B (bool a)
	Just return a boolean (mimicks SIMD int-to-real bool conversions) More...
static float	copysign (float x, float y)
	Composes single value with the magnitude of x and the sign of y. More...
static void	invsqrtPair (float x0, float x1, float *out0, float *out1)
	Calculate 1/sqrt(x) for two floats. More...
static float	inv (float x)
	Calculate 1/x for float. More...
static float	maskzInvsqrt (float x, bool m)
	Calculate 1/sqrt(x) for masked entry of float. More...
static float	maskzInv (float x, bool m)
	Calculate 1/x for masked entry of float. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	sqrt (float x)
	Float sqrt(x). This is the square root. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	cbrt (float x)
	Float cbrt(x). This is the cubic root. More...
static float	log (float x)
	Float log(x). This is the natural logarithm. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	exp2 (float x)
	Float 2^x. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	exp (float x)
	Float exp(x). More...
static float	erf (float x)
	Float erf(x). More...
static float	erfc (float x)
	Float erfc(x). More...
static void	sincos (float x, float *sinval, float *cosval)
	Float sin & cos. More...
static float	sin (float x)
	Float sin. More...
static float	cos (float x)
	Float cos. More...
static float	tan (float x)
	Float tan. More...
static float	asin (float x)
	float asin. More...
static float	acos (float x)
	Float acos. More...
static float	atan (float x)
	Float atan. More...
static float	atan2 (float y, float x)
	Float atan2(y,x). More...
static float	pmeForceCorrection (float z2)
	Calculate the force correction due to PME analytically in float. More...
static float	pmePotentialCorrection (float z2)
	Calculate the potential correction due to PME analytically in float. More...
static double	copysign (double x, double y)
	Composes double value with the magnitude of x and the sign of y. More...
static void	invsqrtPair (double x0, double x1, double *out0, double *out1)
	Calculate 1/sqrt(x) for two doubles. More...
static double	inv (double x)
	Calculate 1/x for double. More...
static double	maskzInvsqrt (double x, bool m)
	Calculate 1/sqrt(x) for masked entry of double. More...
static double	maskzInv (double x, bool m)
	Calculate 1/x for masked entry of double. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	sqrt (double x)
	Double sqrt(x). This is the square root. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	cbrt (double x)
	Double cbrt(x). This is the cubic root. More...
static double	log (double x)
	Double log(x). This is the natural logarithm. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	exp2 (double x)
	Double 2^x. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	exp (double x)
	Double exp(x). More...
static double	erf (double x)
	Double erf(x). More...
static double	erfc (double x)
	Double erfc(x). More...
static void	sincos (double x, double *sinval, double *cosval)
	Double sin & cos. More...
static double	sin (double x)
	Double sin. More...
static double	cos (double x)
	Double cos. More...
static double	tan (double x)
	Double tan. More...
static double	asin (double x)
	Double asin. More...
static double	acos (double x)
	Double acos. More...
static double	atan (double x)
	Double atan. More...
static double	atan2 (double y, double x)
	Double atan2(y,x). More...
static double	pmeForceCorrection (double z2)
	Calculate the force correction due to PME analytically in double. More...
static double	pmePotentialCorrection (double z2)
	Calculate the potential correction due to PME analytically in double. More...
static double	invsqrtSingleAccuracy (double x)
	Calculate 1/sqrt(x) for double, but with single accuracy. More...
static void	invsqrtPairSingleAccuracy (double x0, double x1, double *out0, double *out1)
	Calculate 1/sqrt(x) for two doubles, but with single accuracy. More...
static double	invSingleAccuracy (double x)
	Calculate 1/x for double, but with single accuracy. More...
static double	maskzInvsqrtSingleAccuracy (double x, bool m)
	Calculate 1/sqrt(x) for masked entry of double, but with single accuracy. More...
static double	maskzInvSingleAccuracy (double x, bool m)
	Calculate 1/x for masked entry of double, but with single accuracy. More...
static double	sqrtSingleAccuracy (double x)
	Calculate sqrt(x) for double, but with single accuracy. More...
static double	logSingleAccuracy (double x)
	Double log(x), but with single accuracy. This is the natural logarithm. More...
static double	exp2SingleAccuracy (double x)
	Double 2^x, but with single accuracy. More...
static double	expSingleAccuracy (double x)
	Double exp(x), but with single accuracy. More...
static double	erfSingleAccuracy (double x)
	Double erf(x), but with single accuracy. More...
static double	erfcSingleAccuracy (double x)
	Double erfc(x), but with single accuracy. More...
static void	sincosSingleAccuracy (double x, double *sinval, double *cosval)
	Double sin & cos, but with single accuracy. More...
static double	sinSingleAccuracy (double x)
	Double sin, but with single accuracy. More...
static double	cosSingleAccuracy (double x)
	Double cos, but with single accuracy. More...
static double	tanSingleAccuracy (double x)
	Double tan, but with single accuracy. More...
static double	asinSingleAccuracy (double x)
	Double asin, but with single accuracy. More...
static double	acosSingleAccuracy (double x)
	Double acos, but with single accuracy. More...
static double	atanSingleAccuracy (double x)
	Double atan, but with single accuracy. More...
static double	atan2SingleAccuracy (double y, double x)
	Double atan2(y,x), but with single accuracy. More...
static double	pmeForceCorrectionSingleAccuracy (double z2)
	Force correction due to PME in double, but with single accuracy. More...
static double	pmePotentialCorrectionSingleAccuracy (double z2)
	Potential correction due to PME in double, but with single accuracy. More...
template<int align>
static void	gatherLoadTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1, float *v2, float *v3)
	Load 4 consecutive floats from base/offset into four variables. More...
template<int align>
static void	gatherLoadTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1)
	Load 2 consecutive floats from base/offset into four variables. More...
template<int align>
static void	gatherLoadUTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1, float *v2)
	Load 3 consecutive floats from base/offsets, store into three vars. More...
template<int align>
static void	transposeScatterStoreU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Store 3 floats to 3 to base/offset. More...
template<int align>
static void	transposeScatterIncrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Add 3 floats to base/offset. More...
template<int align>
static void	transposeScatterDecrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Subtract 3 floats from base/offset. More...
static void	expandScalarsToTriplets (float scalar, float *triplets0, float *triplets1, float *triplets2)
	Copy single float to three variables. More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1, float *v2, float *v3)
	Load 4 floats from base/offsets and store into variables. More...
template<int align>
static void	gatherLoadUBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1)
	Load 2 floats from base/offsets and store into variables (unaligned). More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1)
	Load 2 floats from base/offsets and store into variables (aligned). More...
static float	reduceIncr4ReturnSum (float *m, float v0, float v1, float v2, float v3)
	Add each float to four consecutive memory locations, return sum. More...
template<int align>
static void	gatherLoadTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1, double *v2, double *v3)
	Load 4 consecutive doubles from base/offset into four variables. More...
template<int align>
static void	gatherLoadTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1)
	Load 2 consecutive doubles from base/offset into four variables. More...
template<int align>
static void	gatherLoadUTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1, double *v2)
	Load 3 consecutive doubles from base/offsets, store into three vars. More...
template<int align>
static void	transposeScatterStoreU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Store 3 doubles to 3 to base/offset. More...
template<int align>
static void	transposeScatterIncrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Add 3 doubles to base/offset. More...
template<int align>
static void	transposeScatterDecrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Subtract 3 doubles from base/offset. More...
static void	expandScalarsToTriplets (double scalar, double *triplets0, double *triplets1, double *triplets2)
	Copy single double to three variables. More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1, double *v2, double *v3)
	Load 4 doubles from base/offsets and store into variables. More...
template<int align>
static void	gatherLoadUBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1)
	Load 2 doubles from base/offsets and store into variables (unaligned). More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1)
	Load 2 doubles from base/offsets and store into variables (aligned). More...
static double	reduceIncr4ReturnSum (double *m, double v0, double v1, double v2, double v3)
	Add each double to four consecutive memory locations, return sum. More...
stats_t	stats_init ()
	Initiate a data structure. More...
void	stats_free (stats_t stats)
	Destroy a data structure. More...
void	stats_add_point (stats_t stats, double x, double y, double dx, double dy)
	Add a point to the data set. More...
static void	stats_compute (stats *s, int weight)
void	stats_get_ab (stats_t stats, int weight, real *a, real *b, real *da, real *db, real *chi2, real *Rfit)
	Fit the data to y = ax + b, possibly weighted, if uncertainties have been input. da and db may be NULL. More...
real	stats_get_average (stats_t stats)
	Computes and returns the average value. More...
std::tuple< real, real, real >	stats_get_ase (stats_t stats)
	Pointers may be null, in which case no assignment will be done. More...
template<typename RealT >
void	low_lsq_y_ax_b (int n, const RealT *xr, real yr[], real *a, real *b, real *r, real *chi2)
void	lsq_y_ax_b (int n, real x[], real y[], real *a, real *b, real *r, real *chi2)
	Fit a straight line y=ax+b thru the n data points x, y. More...
void	lsq_y_ax_b_xdouble (int n, double x[], real y[], real *a, real *b, real *r, real *chi2)
	Fit a straight line y=ax+b thru the n data points x, y. More...
void	lsq_y_ax_b_error (int n, real x[], real y[], real dy[], real *a, real *b, real *da, real *db, real *r, real *chi2)
	Fit a straight line y=ax+b thru the n data points x, y. More...
static gmx_bool	is_in_channel (const gmx::RVec point, const gmx::RVec center, real d_up, real d_down, real r_cyl2, t_pbc *pbc, int normal)
	Check whether point is in channel. More...
static void	print_ionlist (SwapCoords::Impl *s, double time, const char comment[])
	Prints output to CompEL output file. More...
static gmx::RVec	get_molecule_center (gmx::ArrayRef< const gmx::RVec > x, gmx::ArrayRef< const real > weights, t_pbc *pbc)
	Get the center of a group of nat atoms. More...
static gmx_bool	compartment_contains_atom (real w1, real w2, real x, real l, real bulkOffset, real *distance_from_b)
	Return TRUE if position x of ion (or water) is found in the compartment, i.e. between w1 and w2. More...
static void	update_time_window (t_compartment *comp, int values, int replace)
	Updates the time-averaged number of ions in a compartment.
static void	add_to_list (int ci, t_compartment *comp, real distance)
	Add the atom with collective index ci to the atom list in compartment 'comp'. More...
static void	get_compartment_boundaries (Compartment c, SwapCoords::Impl *s, const matrix box, real *left, real *right)
	Determine the compartment boundaries from the channel centers.
static void	detect_flux_per_channel (t_swapgrp *group, int iAtom, Compartment comp, const gmx::RVec atomPosition, Domain *comp_now, Domain *comp_from, ChannelHistory *channel_label, const t_swapcoords &sc, SwapCoords::Impl *s, real cyl0_r2, real cyl1_r2, int64_t step, gmx_bool bRerun, FILE *fpout)
	Determine the per-channel ion flux. More...
static void	sortMoleculesIntoCompartments (t_swapgrp *group, const gmx::MpiComm &mpiComm, const t_swapcoords &sc, SwapCoords::Impl *s, const matrix box, int64_t step, FILE *fpout, gmx_bool bRerun, gmx_bool bIsSolvent)
	Determines which ions or solvent molecules are in compartment A and B.
static void	get_initial_ioncounts (const t_swapcoords &sc, SwapCoords::Impl *s, gmx::ArrayRef< const gmx::RVec > x, const matrix box, const gmx::MpiComm &mpiComm, gmx_bool bRerun)
	Find out how many group atoms are in the compartments initially.
static void	get_initial_ioncounts_from_cpt (const t_swapcoords &sc, SwapCoords::Impl *s, swaphistory_t *swapstate, const gmx::MpiComm &mpiComm, gmx_bool bVerbose)
	Copy history of ion counts from checkpoint file. More...
static void	bc_initial_concentrations (const gmx::MpiComm &mpiComm, t_swapcoords *swap, SwapCoords::Impl *s)
	The main lets all others know about the initial ion counts.
static void	check_swap_groups (SwapCoords::Impl *s, int nat, gmx_bool bVerbose)
	Ensure that each atom belongs to at most one of the swap groups.
static int	get_group_apm_check (const t_swapgrp &group, gmx_bool bVerbose, const gmx_mtop_t &mtop)
	Get the number of atoms per molecule for this group. More...
static void	print_ionlist_legend (const t_inputrec *ir, SwapCoords::Impl *s, const gmx_output_env_t *oenv)
	Print the legend to the swap output file. More...
static void	detect_flux_per_channel_init (SwapCoords::Impl *s, swaphistory_t *swapstate, const bool isRestart)
	Initialize channel ion flux detection routine. More...
static void	outputStartStructureIfWanted (const gmx_mtop_t &mtop, rvec *x, PbcType pbcType, const matrix box)
	Outputs the initial structure to PDB file for debugging reasons. More...
static void	init_swapstate (swaphistory_t *swapstate, SwapCoords::Impl *s, const gmx_mtop_t &mtop, gmx::ArrayRef< const gmx::RVec > x, const matrix box, const t_inputrec *ir)
	Initialize the swapstate structure, used for checkpoint writing. More...
static real	getRequestedChargeImbalance (SwapCoords::Impl *s)
	Determine the total charge imbalance resulting from the swap groups.
static void	copyIndicesToGroup (gmx::ArrayRef< const int > indIons, t_swapGroup *group, const gmx::MpiComm &mpiComm)
	Sorts anions and cations into two separate groups. More...
static void	convertOldToNewGroupFormat (t_swapcoords *sc, const gmx_mtop_t &mtop, gmx_bool bVerbose, const gmx::MpiComm &mpiComm)
	Converts old .tpr file CompEL contents to new data layout. More...
static gmx_bool	bConvertFromOldTpr (t_swapcoords *sc)
	Returns TRUE if we started from an old .tpr. More...
std::unique_ptr< SwapCoords >	init_swapcoords (FILE *fplog, const t_inputrec *ir, const char *fn, const gmx_mtop_t &mtop, const t_state *globalState, ObservablesHistory *oh, const MpiComm &mpiComm, const gmx_domdec_t *dd, LocalAtomSetManager *atomSets, const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, StartingBehavior startingBehavior)
	Initialize ion / water position swapping ("Computational Electrophysiology"). More...
static gmx_bool	need_swap (const t_swapcoords &sc, SwapCoords::Impl *s)
	Do we need to swap a molecule in any of the ion groups with a water molecule at this step? More...
static int	get_index_of_distant_atom (t_compartment *comp, const std::string &molname)
	Return the index of an atom or molecule suitable for swapping. More...
static void	translate_positions (gmx::ArrayRef< gmx::RVec > moleculeX, const gmx::RVec old_com, const gmx::RVec new_com, t_pbc *pbc)
	Swaps centers of mass and makes molecule whole if broken.
static void	apply_modified_positions (const t_swapgrp &group, gmx::ArrayRef< gmx::RVec > x)
	Write back the modified local positions from the collective array to the official positions.
gmx_bool	do_swapcoords (const MpiComm &mpiComm, int64_t step, double t, const t_inputrec *ir, SwapCoords *s, gmx_wallcycle *wcycle, ArrayRef< RVec > x, matrix box, gmx_bool bVerbose, gmx_bool bRerun)
	"Computational Electrophysiology" main routine within MD loop. More...
double	v_q_ewald_lr (double beta, double r)
	Return the real space grid contribution for Ewald. More...
double	v_lj_ewald_lr (double beta, double r)
	Return the real space grid contribution for LJ-Ewald. More...
EwaldCorrectionTables	generateEwaldCorrectionTables (int numPoints, double tableScaling, real beta, real_space_grid_contribution_computer v_lr)
	Construct tables with the Ewald long-range force interaction. More...
static double	spline3_table_scale (double third_deriv_max, double x_scale, double func_tol)
real	ewald_spline3_table_scale (const interaction_const_t &ic, bool generateCoulombTables, bool generateVdwTables)
	Compute scaling for the Ewald quadratic spline tables. More...
static void	copy2table (int n, int offset, int stride, ArrayRef< const double > x, ArrayRef< const double > Vtab, ArrayRef< const double > Ftab, real scalefactor, ArrayRef< real > dest)
static void	spline_forces (int nx, double h, const double v[], gmx_bool bS3, gmx_bool bE3, double f[])
static void	set_forces (FILE *fp, int angle, int nx, double h, double v[], double f[], int table)
static std::vector< t_tabledata >	read_tables (FILE *fp, const char *filename, int ntab, int angle)
static void	fill_table (t_tabledata *td, int tp, const interaction_const_t &ic, gmx_bool b14only)
static void	set_table_type (int tabsel[], const interaction_const_t &ic, gmx_bool b14only)
std::unique_ptr< t_forcetable >	make_tables (FILE *fp, const interaction_const_t &ic, const char *fn, real rtab, int flags)
	Return tables for inner loops. More...
bondedtable_t	make_bonded_table (FILE *fplog, const char *fn, int angle)
	Return a table for bonded interactions,. More...
std::unique_ptr< t_forcetable >	makeDispersionCorrectionTable (FILE *fp, const interaction_const_t &ic, real rtab, const char *tabfn)
	Construct and return tabulated dispersion and repulsion interactions. More...
bool	decideWhetherToUseGpusForNonbondedWithThreadMpi (TaskTarget nonbondedTarget, bool haveAvailableDevices, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool canUseNonbondedOnGpu, bool binaryReproducibilityRequested, int numRanksPerSimulation)
	Decide whether this thread-MPI simulation will run nonbonded tasks on GPUs. More...
static bool	decideWhetherToUseGpusForPmeFft (const TaskTarget pmeFftTarget)
bool	canUseGpusForNonbonded (const t_inputrec &ir, const bool doRerun, std::string *error)
bool	canUseGpusForNonbondedFe (const t_inputrec &ir, std::string *error)
static bool	canUseGpusForPme (const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage)
bool	decideWhetherToUseGpusForPmeWithThreadMpi (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, int numDevicesToUse, const std::vector< int > &userGpuTaskAssignment, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation)
	Decide whether this thread-MPI simulation will run PME tasks on GPUs. More...
bool	decideWhetherToUseGpusForNonbonded (TaskTarget nonbondedTarget, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool canUseNonbondedOnGpu, bool binaryReproducibilityRequested, bool gpusWereDetected)
	Decide whether the simulation will try to run nonbonded tasks on GPUs. More...
bool	decideWhetherToUseGpusForNonbondedFE (bool useGpuForNonbonded, TaskTarget nonBondedFeTarget, const t_inputrec &inputrec)
	Decide whether the simulation will try to run nonbonde FE tasks on GPUs. More...
bool	decideWhetherToUseGpusForPme (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, const std::vector< int > &userGpuTaskAssignment, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation, bool gpusWereDetected)
	Decide whether the simulation will try to run tasks of different types on GPUs. More...
PmeRunMode	determinePmeRunMode (bool useGpuForPme, const TaskTarget &pmeFftTarget, const t_inputrec &inputrec)
	Determine PME run mode. More...
bool	decideWhetherToUseGpusForBonded (bool useGpuForNonbonded, bool useGpuForPme, TaskTarget bondedTarget, const t_inputrec &inputrec, const gmx_mtop_t &mtop, int numPmeRanksPerSimulation, bool gpusWereDetected)
	Decide whether the simulation will try to run bonded tasks on GPUs. More...
bool	decideWhetherToUseGpuForUpdate (bool isDomainDecomposition, bool useUpdateGroups, PmeRunMode pmeRunMode, bool havePmeOnlyRank, bool useGpuForNonbonded, TaskTarget updateTarget, bool gpusWereDetected, const t_inputrec &inputrec, const gmx_mtop_t &mtop, bool useEssentialDynamics, bool doOrientationRestraints, bool haveFrozenAtoms, bool useModularSimulator, bool doRerun, const gmx::MDLogger &mdlog)
	Decide whether to use GPU for update. More...
bool	decideWhetherDirectGpuCommunicationCanBeUsed (gmx::GpuAwareMpiStatus mpiStatus, bool haveMts, bool useReplicaExchange, bool haveSwapCoords, bool gpusWereDetected, const gmx::MDLogger &mdlog)
	Decide whether direct GPU communication can be used. More...
bool	decideWhetherToUseGpuForHalo (bool havePPDomainDecomposition, bool useGpuForNonbonded, bool canUseDirectGpuComm, bool useModularSimulator, bool doRerun, bool haveEnergyMinimization, const gmx::MDLogger &mdlog)
	Decide whether to use GPU for halo exchange. More...
SimulationWorkload	createSimulationWorkload (const gmx::MDLogger &mdlog, const t_inputrec &inputrec, bool haveDynamicBox, bool useReplicaExchange, bool disableNonbondedCalculation, const DevelopmentFeatureFlags &devFlags, bool haveFillerParticlesInLocalState, bool havePpDomainDecomposition, bool haveSeparatePmeRank, bool useGpuForNonbonded, bool useGpuForNonbondedFE, PmeRunMode pmeRunMode, bool useGpuForBonded, bool useGpuForUpdate, bool useGpuDirectHalo, bool canUseDirectGpuComm, bool useGpuPmeDecomposition)
	Build datastructure that contains decisions whether to run different workload task on GPUs. More...
static bool	haveSpecialForces (const t_inputrec &inputrec, const gmx::ForceProviders &forceProviders, const pull_t *pull_work, const edsam *ed)
	Return true if there are special forces computed. More...
DomainLifetimeWorkload	setupDomainLifetimeWorkload (const t_inputrec &inputrec, const t_forcerec &fr, const pull_t *pull_work, const edsam *ed, const t_mdatoms &mdatoms, const SimulationWorkload &simulationWork)
	Set up workload flags that have the lifetime of the PP domain decomposition. More...
StepWorkload	setupStepWorkload (int legacyFlags, ArrayRef< const gmx::MtsLevel > mtsLevels, int64_t step, std::optional< bool > writeCheckpoint, const DomainLifetimeWorkload &domainWork, const SimulationWorkload &simulationWork, const t_inputrec &inputrec)
	Set up force flag struct from the force bitmask. More...
std::vector< GpuTask >	findGpuTasksOnThisRank (bool haveGpusOnThisPhysicalNode, TaskTarget nonbondedTarget, TaskTarget nonbondedFeTarget, TaskTarget pmeTarget, TaskTarget bondedTarget, TaskTarget updateTarget, bool useGpuForNonbonded, bool useGpuForPme, bool rankHasPpTask, bool rankHasPmeTask)
	Returns container of all tasks on this rank that are eligible for GPU execution. More...
GpuTasksOnRanks	findAllGpuTasksOnThisNode (ArrayRef< const GpuTask > gpuTasksOnThisRank, const PhysicalNodeCommunicator &physicalNodeComm)
	Returns container of all tasks on all ranks of this node that are eligible for GPU execution. More...
int	get_nthreads_mpi (const gmx_hw_info_t *hwinfo, gmx_hw_opt_t *hw_opt, int numDevicesToUse, bool nonbondedOnGpu, bool pmeOnGpu, const t_inputrec *inputrec, const gmx_mtop_t &mtop, const MDLogger &mdlog, bool doMembed)
	Return the number of threads to use for thread-MPI based on how many were requested, which algorithms we're using, and how many particles there are. At the point we have already called check_and_update_hw_opt. Thus all options should be internally consistent and consistent with the hardware, except that ntmpi could be larger than number of GPUs. If necessary, this function will modify hw_opt->nthreads_omp.
void	check_resource_division_efficiency (const gmx_hw_info_t *hwinfo, bool willUsePhysicalGpu, const MpiComm *mpiCommMySim, const MDLogger &mdlog)
	Check if the number of OpenMP threads is within reasonable range considering the hardware used. This is a crude check, but mainly intended to catch cases where the user starts 1 MPI rank per hardware thread or 1 rank per physical node. With a sub-optimal setup a note is printed to fplog and stderr. This function should be called after thread-MPI and OpenMP are set up.
void	checkAndUpdateHardwareOptions (const MDLogger &mdlog, gmx_hw_opt_t *hw_opt, bool isSimulationMainRank, int nPmeRanks, const t_inputrec *inputrec)
	Checks what our hardware options are based on how Gromacs was compiled and user-set options. More...
void	checkAndUpdateRequestedNumOpenmpThreads (gmx_hw_opt_t *hw_opt, const gmx_hw_info_t &hwinfo, const MpiComm &mpiCommMySim, const gmx_multisim_t *ms, int numRanksOnThisNode, PmeRunMode pmeRunMode, const gmx_mtop_t &mtop, const t_inputrec &inputrec)
	Check, and if necessary update, the number of OpenMP threads requested. More...
void	checkHardwareOversubscription (int numThreadsOnThisRank, int rank, const HardwareTopology &hwTop, const PhysicalNodeCommunicator &comm, const MDLogger &mdlog)
	Warns for oversubscribing the hardware threads, when that is the case.
void	setThrowForPerformanceProblems (bool newValue)
	Flag for controlling behaviour in cases where performance might be low. More...
std::vector< int >	parseUserGpuIdString (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container describing device IDs exposed to the run. More...
std::vector< int >	makeListOfAvailableDevices (gmx::ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, const std::string &devicesSelectedByUserString)
	Implement GPU ID selection by returning the available GPU IDs on this physical node that are compatible. More...
std::vector< int >	parseUserTaskAssignmentString (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container describing device ID to task mapping. More...
std::vector< int >	makeGpuIds (ArrayRef< const int > compatibleGpus, size_t numGpuTasks)
	Make a vector containing numGpuTasks IDs of the IDs found in compatibleGpus. More...
std::string	makeGpuIdString (const std::vector< int > &gpuIds, int totalNumberOfTasks)
	Convert a container of GPU deviced IDs to a string that can be used by gmx tune_pme as input to mdrun -gputasks. More...
void	checkUserGpuIds (ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, ArrayRef< const int > compatibleGpus, ArrayRef< const int > gpuIds)
	Check that all user-selected GPUs are compatible. More...
void	reportGpuUsage (const MDLogger &mdlog, ArrayRef< const GpuTaskAssignment > gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool printHostName, PmeRunMode pmeRunMode, const SimulationWorkload &simulationWork)
	Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation. More...
static void	print_hw_opt (FILE *fp, const gmx_hw_opt_t *hw_opt)
	Dump a hw_opt to fp.
template<GpuTask TaskType>
static bool	hasTaskType (const GpuTaskMapping &mapping)
	Function for whether the task of mapping has value TaskType. More...
static bool	hasPmeOrNonbondedTask (const GpuTaskMapping &mapping)
	Function for whether the mapping has the GPU PME or Nonbonded task. More...
static std::vector< int >	parseGpuDeviceIdentifierList (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container. More...
void	resumeIttTracingWhenAppropriate ()
	Resume tracing when applicable. More...
std::optional< std::string >	rdtscpDescription ()
	When targeting x86, returns whether RDTSCP support is present.
std::optional< std::string >	instrumentationApiDescription ()
	Returns information for describing a possible profiling/instrumentation API.
static void	comp_tpx (const char *fn1, const char *fn2, gmx_bool bRMSD, real ftol, real abstol)
static void	comp_trx (const gmx_output_env_t *oenv, const char *fn1, const char *fn2, gmx_bool bRMSD, real ftol, real abstol)
static void	chk_coords (int frame, int natoms, rvec *x, matrix box, real fac, real tol)
static void	chk_vels (int frame, int natoms, rvec *v)
static void	chk_forces (int frame, int natoms, rvec *f)
static void	chk_bonds (const InteractionDefinitions *idef, PbcType pbcType, rvec *x, matrix box, real tol)
static void	chk_trj (const gmx_output_env_t *oenv, const char *fn, const char *tpr, real tol)
static void	chk_tps (const char *fn, real vdw_fac, real bon_lo, real bon_hi)
static void	chk_ndx (const char *fn)
static void	chk_enx (const char *fn)
int	gmx_check (int argc, char *argv[])
	Implements gmx check. More...
static int *	select_it (ArrayRef< const gmx_enxnm_t > nm, int *nset)
static void	sort_files (ArrayRef< std::string > files, double *settime)
static int	scan_ene_files (const std::vector< std::string > &files, double *readtime, double *timestep, int *nremax)
static void	edit_files (ArrayRef< std::string > files, double *readtime, double *settime, int *cont_type, gmx_bool bSetTime, gmx_bool bSort)
static void	update_ee_sum (int nre, int64_t *ee_sum_step, int64_t *ee_sum_nsteps, int64_t *ee_sum_nsum, t_energy *ee_sum, t_enxframe *fr, int out_step)
int	gmx_eneconv (int argc, char *argv[])
	Implements gmx eneconv. More...
static int	or_groups (int nr1, const int *at1, int nr2, const int *at2, int *nr, int *at)
static int	and_groups (int nr1, const int *at1, int nr2, const int *at2, int *nr, int *at)
static gmx_bool	is_name_char (char c)
static int	parse_names (char **string, int *n_names, ArrayRef< char * > names)
static gmx_bool	parse_int_char (char **string, int *nr, unsigned char *c)
static gmx_bool	parse_int (char **string, int *nr)
static gmx_bool	isquote (char c)
static gmx_bool	parse_string (char **string, int *nr, ArrayRef< const IndexGroup > indexGroups)
static int	select_atomnumbers (char **string, const t_atoms *atoms, int n1, int *nr, int *index, char *gname)
static int	select_residuenumbers (char **string, const t_atoms *atoms, int n1, unsigned char c, int *nr, int *index, char *gname)
static int	select_residueindices (char **string, const t_atoms *atoms, int n1, unsigned char c, int *nr, int *index, char *gname)
static gmx_bool	atoms_from_residuenumbers (const t_atoms *atoms, const IndexGroup &indexGroup, int *nr, int *index)
static gmx_bool	comp_name (const char *name, const char *search)
static int	select_chainnames (const t_atoms *atoms, int n_names, ArrayRef< char * > names, int *nr, int *index)
static int	select_atomnames (const t_atoms *atoms, int n_names, ArrayRef< char * > names, int *nr, int *index, gmx_bool bType)
static int	select_residuenames (const t_atoms *atoms, int n_names, ArrayRef< char * > names, int *nr, int *index)
static void	make_gname (int n, ArrayRef< char * > names, char *gname)
static void	copy_group (ArrayRef< const int > group, int *nr, int *index)
static void	remove_group (const int first, const int last, std::vector< IndexGroup > *indexGroups)
static void	split_group (const t_atoms *atoms, int sel_nr, std::vector< IndexGroup > *indexGroups, gmx_bool bAtom)
static int	split_chain (const t_atoms *atoms, const rvec *x, int sel_nr, std::vector< IndexGroup > *indexGroups)
static gmx_bool	check_have_atoms (const t_atoms *atoms, char *string)
static gmx_bool	parse_entry (char **string, int natoms, const t_atoms *atoms, std::vector< IndexGroup > *indexGroups, int *nr, int *index, char *gname, ArrayRef< char * > entryNames)
static void	list_residues (const t_atoms *atoms)
static void	edit_index (int natoms, const t_atoms *atoms, const rvec *x, std::vector< IndexGroup > *indexGroups, gmx_bool bVerbose)
static int	impliedNumberOfAtom (ArrayRef< const IndexGroup > indexGroups)
	Find the number of atoms in the system implied by the largest atom index.
int	gmx_make_ndx (int argc, char *argv[])
	Implements gmx make_ndx. More...
static int	calc_ntype (int nft, const InteractionFunction *ft, const t_idef *idef)
static void	fill_ft_ind (int nft, const InteractionFunction *ft, const t_idef *idef, int ft_ind[], char *grpnames[])
static void	fill_ang (int nft, const InteractionFunction *ft, int fac, int nr[], int *index[], const int ft_ind[], const t_topology *top, gmx_bool bNoH, real hq)
static InteractionFunction *	select_ftype (const char *opt, int *nft, int *mult)
int	gmx_mk_angndx (int argc, char *argv[])
	Implements gmx mk_angndx. More...
static gmx_bool	is_charge (real charge)
static void	calc_q2all (const gmx_mtop_t *mtop, real *q2all, real *q2allnr)
static real	estimate_direct (PmeErrorInputs *info)
static real	eps_poly1 (real m, real K, real n)
static real	eps_poly2 (real m, real K, real n)
static real	eps_poly3 (real m, real K, real n)
static real	eps_poly4 (real m, real K, real n)
static real	eps_self (real m, real K, rvec rboxv, real n, rvec x)
static void	calc_recipbox (matrix box, matrix recipbox)
static real	estimate_reciprocal (PmeErrorInputs *info, rvec x[], const real q[], int nr, FILE gmx_unused *fp_out, gmx_bool bVerbose, int seed, int *nsamples, const MpiComm &mpiComm)
static void	create_info (PmeErrorInputs *info)
static int	prepare_x_q (real *q[], rvec *x[], const gmx_mtop_t *mtop, const rvec x_orig[], const MpiComm &mpiComm)
static void	read_tpr_file (const char *fn_sim_tpr, PmeErrorInputs *info, t_state *state, gmx_mtop_t *mtop, t_inputrec *ir, real user_beta, real fracself)
static void	bcast_info (PmeErrorInputs *info, const MpiComm &mpiComm)
static void	estimate_PME_error (PmeErrorInputs *info, const t_state *state, const gmx_mtop_t *mtop, FILE *fp_out, gmx_bool bVerbose, unsigned int seed, const MpiComm &mpiComm)
int	gmx_pme_error (int argc, char *argv[])
	Implements gmx pme_error. More...
void	writeHeader (TextWriter *writer, const std::string &text, const std::string &section, bool writeFormattedText)
	Write appropiate Header to output stream. More...
void	writeSystemInformation (TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
	Write information about the molecules in the system. More...
void	writeParameterInformation (TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
	Write information about system parameters. More...
void	writeInformation (TextOutputFile *outputStream, const t_inputrec &ir, const gmx_mtop_t &top, bool writeFormattedText, bool notStdout)
	Wrapper for writing out information. More...
static void	scan_trj_files (ArrayRef< const std::string > files, real *readtime, real *timestep, int imax, const gmx_output_env_t *oenv)
static void	sort_files (ArrayRef< std::string > files, real *settime)
static void	edit_files (ArrayRef< std::string > files, real *readtime, real *timestep, real *settime, int *cont_type, gmx_bool bSetTime, gmx_bool bSort, const gmx_output_env_t *oenv)
static void	do_demux (ArrayRef< const std::string > inFiles, ArrayRef< const std::string > outFiles, int nval, real **value, real *time, real dt_remd, int isize, int index[], real dt, const gmx_output_env_t *oenv)
int	gmx_trjcat (int argc, char *argv[])
	Implements gmx trjcat. More...
static void	mk_filenm (char *base, const char *ext, int ndigit, int file_nr, char out_file[])
static void	check_trr (const char *fn)
static void	do_trunc (const char *fn, real t0)
static std::unique_ptr < gmx_mtop_t >	read_mtop_for_tng (const char *tps_file, const char *input_file, const char *output_file)
	Read a full molecular topology if useful and available. More...
static void	copyTrxframeDeeply (const t_trxframe &input, t_trxframe *copy)
	Do a deep copy of input and store in (pre-allocated) copy.
static void	swapFrames (t_trxframe *a, t_trxframe *b)
	Swap the contents of a and b.
int	gmx_trjconv (int argc, char *argv[])
	Implements gmx trjconv. More...
static void	sep_line (FILE *fp)
static int	gmx_system_call (const char *command)
static gmx_bool	str_starts (const char *string, const char *substring)
static void	cleandata (t_perf *perfdata, int test_nr)
static void	remove_if_exists (const char *fn)
static void	finalize (const char *fn_out)
static int	parse_logfile (const char *logfile, const char *errfile, t_perf *perfdata, int test_nr, int presteps, int64_t cpt_steps, int nnodes)
static gmx_bool	analyze_data (FILE *fp, const char *fn, t_perf **perfdata, int nnodes, int ntprs, int ntests, int nrepeats, PmeTuneInputs *info, int *index_tpr, int *npme_optimal)
static void	get_program_paths (gmx_bool bThreads, char *cmd_mpirun[], char *cmd_mdrun[])
static void	check_mdrun_works (gmx_bool bThreads, const char *cmd_mpirun, const char *cmd_np, const char *cmd_mdrun, gmx_bool bNeedGpuSupport)
static std::string	make_gpu_id_command_line (const char *eligible_gpu_ids)
static void	launch_simulation (gmx_bool bLaunch, FILE *fp, gmx_bool bThreads, char *cmd_mpirun, char *cmd_np, char *cmd_mdrun, char *args_for_mdrun, const char *simulation_tpr, int nPMEnodes, const char *eligible_gpu_ids)
static void	modify_PMEsettings (int64_t simsteps, int64_t init_step, const char *fn_best_tpr, const char *fn_sim_tpr)
static gmx_bool	can_scale_rvdw (VanDerWaalsType vdwtype)
static void	make_benchmark_tprs (const char *fn_sim_tpr, char *fn_bench_tprs[], int64_t benchsteps, int64_t statesteps, real rmin, real rmax, bool bScaleRvdw, const int *ntprs, PmeTuneInputs *info, FILE *fp)
static void	cleanup (const t_filenm *fnm, int nfile, int k, int nnodes, int nPMEnodes, int nr, gmx_bool bKeepStderr)
static void	make_npme_list (const char *npmevalues_opt, int *nentries, int *nPMEnodes[], int nnodes, int minPMEnodes, int maxPMEnodes)
static void	init_perfdata (t_perf *perfdata[], int ntprs, int datasets, int repeats)
static void	make_sure_it_runs (const char *mdrun_cmd_line, int length, FILE *fp, const t_filenm *fnm, int nfile)
static void	do_the_tests (FILE *fp, char **tpr_names, int maxPMEnodes, int minPMEnodes, int npme_fixed, const char *npmevalues_opt, t_perf **perfdata, int *pmeentries, int repeats, int nnodes, int nr_tprs, gmx_bool bThreads, char *cmd_mpirun, char *cmd_np, char *cmd_mdrun, char *cmd_args_bench, const t_filenm *fnm, int nfile, int presteps, int64_t cpt_steps, gmx_bool bCheck, const char *eligible_gpu_ids)
static void	check_input (int nnodes, int repeats, int *ntprs, real *rmin, real rcoulomb, real *rmax, real maxPMEfraction, real minPMEfraction, int npme_fixed, int64_t bench_nsteps, const t_filenm *fnm, int nfile, int sim_part, int presteps, int npargs, t_pargs *pa)
static gmx_bool	is_launch_file (const char *opt, gmx_bool bSet)
static gmx_bool	is_bench_file (const char *opt, gmx_bool bSet, gmx_bool bOptional, gmx_bool bIsOutput)
static void	add_to_string (char **str, const char *buf)
static void	create_command_line_snippets (gmx_bool bAppendFiles, gmx_bool bKeepAndNumCPT, gmx_bool bResetHWay, int presteps, int nfile, t_filenm fnm[], char *cmd_args_bench[], char *cmd_args_launch[], char extra_args[], char *deffnm)
static void	setopt (const char *opt, int nfile, t_filenm fnm[])
static float	inspect_tpr (int nfile, t_filenm fnm[], real *rcoulomb)
static void	couple_files_options (int nfile, t_filenm fnm[])
int	gmx_tune_pme (int argc, char *argv[])
	Implements gmx tune_pme. More...
static bool	isEmbeddedAtom (Index globalAtomIndex, const std::set< int > &embeddedIndices)
std::vector< bool >	splitEmbeddedBlocks (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices)
	Splits embedded atom containing molecules out of MM blocks in topology. More...
std::vector< real >	removeEmbeddedClassicalCharges (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, real refQ, const MDLogger &logger, WarningHandler *wi)
	Removes classical charges from embedded atoms and virtual sites. More...
void	addEmbeddedNBExclusions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const MDLogger &logger)
	Build exclusion list for non-bonded interactions between embedded atoms. More...
std::vector< int >	buildEmbeddedAtomNumbers (const gmx_mtop_t &mtop)
	Builds and returns a vector of atom numbers for all atoms in mtop. More...
void	modifyEmbeddedTwoCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies pairwise bonded interactions. More...
std::vector< LinkFrontierAtom >	buildLinkFrontier (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Builds link frontier vector with pairs of atoms indicting broken embedded - MM chemical bonds. More...
void	modifyEmbeddedThreeCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies three-centers interactions (i.e. Angles, Settles) More...
void	modifyEmbeddedFourCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies four-centers interactions. More...
void	checkConstrainedBonds (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, WarningHandler *wi)
	Checks for constrained bonds within embedded subsystem. More...
void	blockaToExclusionBlocks (const t_blocka *b, gmx::ArrayRef< ExclusionBlock > b2)
	Convert the exclusions. More...
void	exclusionBlocksToBlocka (gmx::ArrayRef< const ExclusionBlock > b2, t_blocka *b)
	Convert the exclusions expressed in b into t_blocka form.
void	mergeExclusions (ListOfLists< int > *excl, gmx::ArrayRef< ExclusionBlock > b2)
	Merge the contents of b2 into excl. More...
void	comp_frame (FILE *fp, t_trxframe *fr1, t_trxframe *fr2, gmx_bool bRMSD, real ftol, real abstol)
void	done_frame (t_trxframe *frame)
Isotope	getIsotopeFromString (const std::string &isotope)
	Convert isotope name from string to enum.
std::vector< Isotope >	getIsotopes (const t_atoms *atoms)
	Reads element list and returns vector of isotopes.
std::vector < AtomicStructureFactor >	readAtomicStructureFactors ()
	Helper function to read in atomic scattering data from file.
void	registerTrajectoryAnalysisModules (CommandLineModuleManager *manager)
	Registers all trajectory analysis command-line modules. More...
gmx_rmpbc_t	gmx_rmpbc_init (const gmx::TopologyInformation &topInfo)
	Convenience overload useful for implementing legacy tools.
static std::size_t	getPageSize ()
	Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes). More...
std::string	simpleValueToString (const Any &value)
	Converts a Any value to a string. More...
std::unordered_map < std::string, std::string >	versionDescriptions ()
	Returns information for describing the GROMACS version.
ArrayRef< bool >	makeArrayRef (std::vector< BoolType > &boolVector)
	Create ArrayRef to bool from reference to std::vector<BoolType>. More...
ArrayRef< const bool >	makeConstArrayRef (const std::vector< BoolType > &boolVector)
	Create ArrayRef to const bool from reference to std::vector<BoolType>. More...
std::string	bromacs ()
	Return a cool definition for the acronym GROMACS.
std::string	getCoolQuote ()
	Return a string with a cool quote.
const char *	getErrorCodeString (int errorcode)
	Returns a short string description of an error code. More...
void	printFatalErrorMessage (FILE *fp, const std::exception &ex)
	Formats a standard fatal error message for reporting an exception. More...
std::string	formatExceptionMessageToString (const std::exception &ex)
	Formats an error message for reporting an exception. More...
void	formatExceptionMessageToFile (FILE *fp, const std::exception &ex)
	Formats an error message for reporting an exception. More...
void	formatExceptionMessageToWriter (TextWriter *writer, const std::exception &ex)
	Formats an error message for reporting an exception. More...
int	processExceptionAtExit (const std::exception &ex)
	Handles an exception that is causing the program to terminate. More...
void	processExceptionAsFatalError (const std::exception &ex)
	Helper function for terminating the program on an exception. More...
IFileInputRedirector &	defaultFileInputRedirector ()
	Returns default implementation for IFileInputRedirector. More...
IFileOutputRedirector &	defaultFileOutputRedirector ()
	Returns default implementation for IFileOutputRedirector. More...
const DataFileFinder &	getLibraryFileFinder ()
	Gets a finder for locating data files from share/top/. More...
void	setLibraryFileFinder (const DataFileFinder *finder)
	Sets a finder for location data files from share/top/. More...
std::filesystem::path	findLibraryFile (const std::filesystem::path &filename, bool bAddCWD=true, bool bFatal=true)
	Finds full path for a library file. More...
FilePtr	openLibraryFile (const std::filesystem::path &filename, bool bAddCWD=true, bool bFatal=true)
	Opens a library file for reading in an RAII-style FILE handle. More...
std::string	openmpDescription ()
	Returns information for describing the OpenMP support.
IKeyValueTreeErrorHandler *	defaultKeyValueTreeErrorHandler ()
	Returns a default IKeyValueTreeErrorHandler that throws on first exception.
std::size_t	pageSize ()
	Return the memory page size on this system. More...
template<class T1 , class Policy1 , class T2 , class Policy2 >
bool	operator== (const Allocator< T1, Policy1 > &a, const Allocator< T2, Policy2 > &b)
	Return true if two allocators are identical. More...
template<class T1 , class Policy1 , class T2 , class Policy2 >
bool	operator!= (const Allocator< T1, Policy1 > &a, const Allocator< T2, Policy2 > &b)
	Return true if two allocators are different.
template<typename Callable >
auto	coordinateExceptionHandling (MPI_Comm communicator, Callable callable) -> typename std::invoke_result_t< Callable >
	Call the callable and then make sure all MPI ranks of communicator have consistent exception-throwing behaviour. More...
void	init (int *argc, char ***argv)
	Initializes the GROMACS library. More...
void	finalize ()
	Deinitializes the GROMACS library. More...
KeyValueTreePath	operator+ (const KeyValueTreePath &a, const KeyValueTreePath &b)
	Combines two paths as with KeyValueTreePath::append().
KeyValueTreePath	operator+ (const KeyValueTreePath &a, const std::string &b)
	Combines an element to a path as with KeyValueTreePath::append().
void	dumpKeyValueTree (TextWriter *writer, const KeyValueTreeObject &tree)
	Writes a human-readable representation of the tree with given writer. More...
void	compareKeyValueTrees (TextWriter *writer, const KeyValueTreeObject &tree1, const KeyValueTreeObject &tree2, real ftol, real abstol)
	Compares two KeyValueTrees and prints any differences.
static std::string	simpleValueToString (const KeyValueTreeValue &value)
	Helper function to format a simple KeyValueTreeValue.
void	writeKeyValueTreeAsMdp (TextWriter *writer, const KeyValueTreeObject &tree)
	Write a flat key-value tree to writer in mdp style. More...
const char *	enumValueToString (GpuAwareMpiStatus status)
	Helper function to pretty-print GPU-aware status values.
bool	usingIntelMpi ()
	Return whether GROMACS is linked against an MPI library describing itself as Intel MPI.
GpuAwareMpiStatus	checkMpiCudaAwareSupport ()
	Wrapper on top of MPIX_Query_cuda_support() For MPI implementations which don't support this function, it returns NotSupported. Even when an MPI implementation does support this function, MPI library might not be robust enough to detect CUDA-aware support at runtime correctly e.g. when UCX PML is used or CUDA is disabled at runtime. More...
GpuAwareMpiStatus	checkMpiHipAwareSupport ()
	Wrapper on top of MPIX_Query_hip_support() or MPIX_Query_rocm_support(). For MPI implementations which don't support this function, it returns NotSupported. More...
GpuAwareMpiStatus	checkMpiZEAwareSupport ()
	Wrapper on top of MPIX_Query_ze_support() (for MPICH) or custom logic (for IntelMPI). More...
std::unordered_map < std::string, std::string >	mpiDescriptions ()
	Returns information for describing the MPI support.
void	niceHeader (TextWriter *writer, const char *fn, char commentChar)
	Prints creation time stamp and user information into a string as comments, and returns it. More...
std::vector < std::filesystem::path >	splitPathEnvironment (const std::string &pathEnv)
	Split PATH environment variable into search paths. More...
std::vector < std::filesystem::path >	getSystemExecutablePaths ()
	Get collection of possible executable paths.
std::string	stripSourcePrefix (const char *path)
	Strip source prefix from path.
std::filesystem::path	concatenateBeforeExtension (const std::filesystem::path &path, const std::string &addition)
	Concatenate before extension.
std::filesystem::path	stripExtension (const std::filesystem::path &path)
	Remove extension from file path.
bool	extensionMatches (const std::filesystem::path &path, std::string_view extension)
	Check if file extension of path without final '.' matches extension.
void	MPI_Comm_free_wrapper (MPI_Comm *comm)
	Wrapper function for RAII-style cleanup. More...
bool	boolFromString (const char *str)
	Parses a boolean from a string. More...
int	intFromString (const char *str)
	Parses an integer from a string. More...
unsigned int	uintFromString (const char *str)
	Parses an unsigned integer from a string. More...
int64_t	int64FromString (const char *str)
	Parses a 64-bit integer from a string. More...
uint64_t	uint64FromString (const char *str)
	Parses a 64-bit unsigned integer from a string. More...
float	floatFromString (const char *str)
	Parses a float value from a string. More...
double	doubleFromString (const char *str)
	Parses a double value from a string. More...
template<typename T >
static T	fromString (const char *str)
	Parses a value from a string to a given type. More...
template<typename T >
static T	fromString (const std::string &str)
	Parses a value from a string to a given type. More...
template<typename T >
static T	fromStdString (const std::string &str)
	Parses a value from a string to a given type. More...
template<>
bool	fromString< bool > (const char *str)
	Implementation for boolean values.
template<>
int	fromString< int > (const char *str)
	Implementation for integer values.
template<>
unsigned int	fromString< unsigned int > (const char *str)
	Implementation for unsigned integer values.
template<>
int64_t	fromString< int64_t > (const char *str)
	Implementation for 64-bit integer values.
template<>
uint64_t	fromString< uint64_t > (const char *str)
	Implementation for 64-bit unsigned integer values.
template<>
float	fromString< float > (const char *str)
	Implementation for float values.
template<>
double	fromString< double > (const char *str)
	Implementation for double values.
static const char *	boolToString (bool value)
	Converts a boolean to a "true"/"false" string. More...
static std::string	intToString (int t)
	Returns a string containing the value of t. More...
static std::string	uintToString (unsigned int t)
	Returns a string containing the value of t. More...
static std::string	int64ToString (int64_t t)
	Returns a string containing the value of t. More...
static std::string	uint64ToString (uint64_t t)
	Returns a string containing the value of t. More...
static std::string	doubleToString (double t)
	Returns a string containing the value of t. More...
static std::string	unsignedCharToString (unsigned char t)
	Returns a string containing the value of t. More...
template<typename ValueType , int NumExpectedValues>
static std::optional < std::array< ValueType, NumExpectedValues > >	parsedArrayFromInputString (const std::string &str)
	Convert a string into an array of values. More...
template<typename ValueType , int NumExpectedValues>
static std::string	stringIdentityTransformWithArrayCheck (const std::string &toConvert, const std::string &errorContextMessage)
	Returns the input string, throwing an exception if the demanded conversion to an array will not succeed. More...
template<class Function >
auto	dispatchTemplatedFunction (Function &&f)
bool	checkIfAvailable (TextWriter *writer, const char *description, const void *p)
	Returns true if p is non-null, otherwise prints a message to writer and returns false.
void	printTitleAndSize (TextWriter *writer, const char *title, int n)
	Prints a title from the description and number of values n.
const IProgramContext &	getProgramContext ()
	Returns the global IProgramContext instance. More...
void	setProgramContext (const IProgramContext *context)
	Sets the global IProgramContext instance. More...
std::size_t	countWords (const char *s)
	Returns number of space-separated words in zero-terminated char ptr. More...
std::size_t	countWords (const std::string &str)
	Returns the number of space-separated words in a string object. More...
bool	endsWith (const char *str, const char *suffix)
	Tests whether a string ends with another string. More...
std::string	stripSuffixIfPresent (const std::string &str, const char *suffix)
	Removes a suffix from a string. More...
std::string	stripString (const std::string &str)
	Removes leading and trailing whitespace from a string. More...
std::string	formatString (gmx_fmtstr const char *fmt,...)
std::string	formatStringV (const char *fmt, std::va_list ap)
	Formats a string (vsnprintf() wrapper). More...
std::vector< std::string >	splitString (const std::string &str)
	Splits a string to whitespace separated tokens. More...
std::vector< std::string >	splitDelimitedString (const std::string &str, char delim)
	Splits a string to tokens separated by a given delimiter. More...
std::vector< std::string >	splitAndTrimDelimitedString (const std::string &str, char delim)
	Splits str to tokens separated by delimiter delim. Removes leading and trailing whitespace from those strings with std::isspace. More...
std::string	replaceAll (const std::string &input, const char *from, const char *to)
	Replace all occurrences of a string with another string. More...
std::string	replaceAll (const std::string &input, const std::string &from, const std::string &to)
	Replace all occurrences of a string with another string. More...
std::string	replaceAllWords (const std::string &input, const char *from, const char *to)
	Replace whole words with others. More...
std::string	replaceAllWords (const std::string &input, const std::string &from, const std::string &to)
	Replace whole words with others. More...
bool	equalCaseInsensitive (const std::string &source, const std::string &target)
	Return whether two strings are equal, ignoring case. More...
bool	equalIgnoreDash (const std::string &source, const std::string &target)
	Return whether too strings are case sensitive equal, ignoring dashes.
bool	equalCaseInsensitive (const std::string &source, const std::string &target, size_t maxLengthOfComparison)
	Checks if at most maxLengthOfComparison characters of two strings match case insensitive. More...
std::string	toUpperCase (const std::string &text)
	Makes the string uppercase. More...
std::string	toLowerCase (const std::string &text)
	Makes the string lowercase. More...
std::string	prettyPrintListAsRange (ArrayRef< const int > list)
	Formats a range of integers using taskset-style notation when possible. More...
void	registerLegacyModules (CommandLineModuleManager *manager)
int	gmx_mdrun (int argc, char *argv[])
	Implements C-style main function for mdrun. More...
int	gmx_mdrun (MPI_Comm communicator, const gmx_hw_info_t &hwinfo, int argc, char *argv[])
	Implements C-style main function for mdrun. More...
AnalysisHistogramSettingsInitializer	histogramFromRange (real min, real max)
	Initializes a histogram using a range and a bin width. More...
AnalysisHistogramSettingsInitializer	histogramFromBins (real start, size_t nbins, real binwidth)
	Initializes a histogram using bin width and the number of bins. More...
static float	invsqrt (float x)
	Calculate 1.0/sqrt(x) in single precision. More...
static double	invsqrt (double x)
	Calculate 1.0/sqrt(x) in double precision, but single range. More...
static double	invsqrt (int x)
	Calculate 1.0/sqrt(x) for integer x in double precision. More...
static float	invcbrt (float x)
	Calculate inverse cube root of x in single precision. More...
static double	invcbrt (double x)
	Calculate inverse sixth root of x in double precision. More...
static double	invcbrt (int x)
	Calculate inverse sixth root of integer x in double precision. More...
static float	sixthroot (float x)
	Calculate sixth root of x in single precision. More...
static double	sixthroot (double x)
	Calculate sixth root of x in double precision. More...
static double	sixthroot (int x)
	Calculate sixth root of integer x, return double. More...
static float	invsixthroot (float x)
	Calculate inverse sixth root of x in single precision. More...
static double	invsixthroot (double x)
	Calculate inverse sixth root of x in double precision. More...
static double	invsixthroot (int x)
	Calculate inverse sixth root of integer x in double precision. More...
template<typename T >
T	square (T x)
	calculate x^2 More...
template<typename T >
T	power3 (T x)
	calculate x^3 More...
template<typename T >
T	power4 (T x)
	calculate x^4 More...
template<typename T >
T	power5 (T x)
	calculate x^5 More...
template<typename T >
T	power6 (T x)
	calculate x^6 More...
template<typename T >
T	power12 (T x)
	calculate x^12 More...
static real	series_sinhx (real x)
	Maclaurin series for sinh(x)/x. More...
constexpr int32_t	exactDiv (int32_t a, int32_t b)
	Exact integer division, 32bit. More...
constexpr int64_t	exactDiv (int64_t a, int64_t b)
	Exact integer division, 64bit.
static int	roundToInt (float x)
	Round float to int. More...
static int	roundToInt (double x)
	Round double to int.
static int64_t	roundToInt64 (float x)
	Round float to int64_t.
static int64_t	roundToInt64 (double x)
	Round double to int64_t.
template<typename T , typename = std::enable_if_t<std::is_integral_v<T>>>
static constexpr bool	isPowerOfTwo (const T v)
	Check whether v is an integer power of 2.
template<typename T >
constexpr T	divideRoundUp (T numerator, T denominator)
	Return numerator divided by denominator rounded up to the next integer. More...
template<typename T >
T	makePeriodic (const T x, const T period)
	Return x modulo period such that it is within the interval [-0.5*period, 0.5*period]. More...
template<typename T >
ArrayRef< std::conditional_t < std::is_const_v< T >, const typename T::value_type, typename T::value_type > >	makeArrayRef (T &c)
	Create ArrayRef from container with type deduction. More...
template<typename T >
ArrayRef< const typename T::value_type >	makeConstArrayRef (const T &c)
	Create ArrayRef to const T from container with type deduction. More...
template<typename T >
void	swap (ArrayRef< T > &a, ArrayRef< T > &b) noexcept
	Simple swap method for ArrayRef objects. More...
template<typename T >
std::vector< T >	copyOf (const ArrayRef< const T > &arrayRef)
	Return a vector that is a copy of an ArrayRef. More...
template<typename T >
Index	ssize (const T &t)
	Return signed size of container.
template<typename EnumerationArrayType >
EnumerationArrayType::EnumerationWrapperType	keysOf (const EnumerationArrayType &)
	Returns an object that provides iterators over the keys associated with EnumerationArrayType. More...
template<class Exception , class Tag , class T >
std::enable_if_t < std::is_base_of_v < GromacsException, Exception > , Exception >	operator<< (Exception ex, const ExceptionInfo< Tag, T > &item)
	Associates extra information with an exception. More...
void	fclose_wrapper (FILE *fp)
	fclose wrapper to be used as unique_ptr deleter
template<class ElementType >
void	swap (BasicMatrix3x3< ElementType > &mat1, BasicMatrix3x3< ElementType > &mat2) noexcept
	Stand-alone swap function based on https://en.cppreference.com/w/cpp/named_req/Swappable.
template<typename ElementType >
BasicMatrix3x3< ElementType >	operator* (const ElementType scalar, const BasicMatrix3x3< ElementType > &other)
	Return the product of multiplying the 3x3 matrix other by the scalar.
template<typename ElementType >
BasicVector< ElementType >	diagonal (const BasicMatrix3x3< ElementType > &matrix)
	Return a vector that is the diagonal of the 3x3 matrix.
template<typename ElementType >
BasicMatrix3x3< ElementType >	transpose (BasicMatrix3x3< ElementType > matrix)
	Returns the transposition of matrix.
template<typename ElementType >
constexpr ElementType	determinant (BasicMatrix3x3< ElementType > matrix)
	Returns the determinant of matrix.
template<typename ElementType >
constexpr ElementType	trace (BasicMatrix3x3< ElementType > matrix)
	Returns the trace of matrix.
template<typename ElementType >
BasicMatrix3x3< ElementType >	inner (const BasicMatrix3x3< ElementType > &matrixA, const BasicMatrix3x3< ElementType > &matrixB)
	Return the inner product of multiplication of two 3x3 matrices a and b.
template<typename ElementType >
BasicMatrix3x3< ElementType >	diagonalMatrix (const ElementType value)
	Create a diagonal matrix of ElementType. More...
template<typename ElementType >
BasicMatrix3x3< ElementType >	identityMatrix ()
	Create an identity matrix of ElementType. More...
static Matrix3x3	createMatrix3x3FromLegacyMatrix (const matrix legacyMatrix)
	Create new matrix type from legacy type.
static void	fillLegacyMatrix (Matrix3x3 newMatrix, matrix legacyMatrix)
	Fill existing legacy matrix from new matrix type.
static bool	isNullOrEmpty (const char *str)
	Tests whether a string is null or empty. More...
static bool	startsWith (const std::string &str, const std::string &prefix)
	Tests whether a string starts with another string. More...
static bool	startsWith (const char *str, const char *prefix)
	Tests whether a string starts with another string. More...
static bool	endsWith (const std::string &str, const char *suffix)
	Tests whether a string ends with another string. More...
static bool	contains (const std::string &str, const char *substr)
	Tests whether a string contains another as a substring. More...
static bool	contains (const std::string &str, const std::string &substr)
	Tests whether a string contains another as a substring. More...
static bool	endsWith (const std::string &str, const std::string &suffix)
	Tests whether a string ends with another string. More...
std::string	formatString (const char *fmt,...)
	Formats a string (snprintf() wrapper). More...
template<typename InputIterator , typename FormatterType >
std::string	formatAndJoin (InputIterator begin, InputIterator end, const char *separator, const FormatterType &formatter)
	Formats all the range as strings, and then joins them with a separator in between. More...
template<typename ContainerType , typename FormatterType >
std::string	formatAndJoin (const ContainerType &container, const char *separator, const FormatterType &formatter)
	Formats all elements of the container as strings, and then joins them with a separator in between. More...
template<typename InputIterator >
std::string	joinStrings (InputIterator begin, InputIterator end, const char *separator)
	Joins strings from a range with a separator in between. More...
template<typename ContainerType >
std::string	joinStrings (const ContainerType &container, const char *separator)
	Joins strings from a container with a separator in between. More...
template<size_t count>
std::string	joinStrings (const char *const (&array)[count], const char *separator)
	Joins strings from an array with a separator in between. More...
template<class T >
void	free_wrapper (T *p)
	Wrapper of standard library free(), to be used as unique_cptr deleter for memory allocated by malloc, e.g. by an external library such as TNG.
template<class T >
void	sfree_wrapper (T *p)
	sfree wrapper to be used as unique_cptr deleter
template<typename T , typename D >
std::unique_ptr< T, D >	create_unique_with_deleter (T *t, D d)
	Create unique_ptr with any deleter function or lambda.
template<typename ValueType >
constexpr BasicVector< ValueType >	operator* (const BasicVector< ValueType > &basicVector, const ValueType &scalar)
	Allow vector scalar multiplication.
template<typename ValueType >
constexpr BasicVector< ValueType >	operator* (const ValueType &scalar, const BasicVector< ValueType > &basicVector)
	Allow scalar vector multiplication.
template<typename VectorType >
static constexpr VectorType	unitVector (const VectorType &v)
	unitv for gmx::BasicVector
template<typename ValueType >
static constexpr ValueType	norm (BasicVector< ValueType > v)
	norm for gmx::BasicVector
template<typename ValueType >
static constexpr ValueType	norm2 (BasicVector< ValueType > v)
	Square of the vector norm for gmx::BasicVector.
template<typename VectorType >
static constexpr VectorType	cross (const VectorType &a, const VectorType &b)
	cross product for gmx::BasicVector
template<typename ValueType >
static constexpr ValueType	dot (BasicVector< ValueType > a, BasicVector< ValueType > b)
	dot product for gmx::BasicVector
template<typename VectorType >
static constexpr VectorType	scaleByVector (const VectorType &a, const VectorType &b)
	Multiply two vectors element by element and return the result.
template<typename VectorType >
static constexpr VectorType	elementWiseMin (const VectorType &a, const VectorType &b)
	Return the element-wise minimum of two vectors.
template<typename VectorType >
static constexpr VectorType	elementWiseMax (const VectorType &a, const VectorType &b)
	Return the element-wise maximum of two vectors.
template<typename ValueType >
static BasicVector< ValueType > ::RawArray *	as_vec_array (BasicVector< ValueType > *x)
	Casts a gmx::BasicVector array into an equivalent raw C array.
template<typename ValueType >
static const BasicVector < ValueType >::RawArray *	as_vec_array (const BasicVector< ValueType > *x)
	Casts a gmx::BasicVector array into an equivalent raw C array.
static rvec *	as_rvec_array (RVec *x)
	Casts a gmx::RVec array into an rvec array.
static const rvec *	as_rvec_array (const RVec *x)
	Casts a gmx::RVec array into an rvec array.
static dvec *	as_dvec_array (DVec *x)
	Casts a gmx::DVec array into an Dvec array.
static ivec *	as_ivec_array (IVec *x)
	Casts a gmx::IVec array into an ivec array.
static const dvec *	as_dvec_array (const DVec *x)
	Casts a gmx::DVec array into an dvec array.
static const ivec *	as_ivec_array (const IVec *x)
	Casts a gmx::IVec array into an ivec array.
template<typename ValueType , std::enable_if_t< std::is_arithmetic_v< ValueType >, bool > = true>
static DataSetDims	getFrameDims (const DataSetDims &dataSetDims)
	Return the frame dimensions for the data set dimensions.
void	applyGlobalSimulationState (const SimulationInput &simulationInput, PartialDeserializedTprFile *partialDeserializedTpr, t_state *globalState, t_inputrec *inputrec, gmx_mtop_t *globalTopology)
	Get the global simulation input. More...
std::unique_ptr< t_state >	globalSimulationState (const SimulationInput &)
void	applyGlobalInputRecord (const SimulationInput &, t_inputrec *)
void	applyGlobalTopology (const SimulationInput &, gmx_mtop_t *)
Constant width-4 double precision SIMD types and instructions
static Simd4Double gmx_simdcall	load4 (const double *m)
	Load 4 double values from aligned memory into SIMD4 variable. More...
static void gmx_simdcall	store4 (double *m, Simd4Double a)
	Store the contents of SIMD4 double to aligned memory m. More...
static Simd4Double gmx_simdcall	load4U (const double *m)
	Load SIMD4 double from unaligned memory. More...
static void gmx_simdcall	store4U (double *m, Simd4Double a)
	Store SIMD4 double to unaligned memory. More...
static Simd4Double gmx_simdcall	simd4SetZeroD ()
	Set all SIMD4 double elements to 0. More...
static Simd4Double gmx_simdcall	operator& (Simd4Double a, Simd4Double b)
	Bitwise and for two SIMD4 double variables. More...
static Simd4Double gmx_simdcall	andNot (Simd4Double a, Simd4Double b)
	Bitwise andnot for two SIMD4 double variables. c=(~a) & b. More...
static Simd4Double gmx_simdcall	operator| (Simd4Double a, Simd4Double b)
	Bitwise or for two SIMD4 doubles. More...
static Simd4Double gmx_simdcall	operator^ (Simd4Double a, Simd4Double b)
	Bitwise xor for two SIMD4 double variables. More...
static Simd4Double gmx_simdcall	operator+ (Simd4Double a, Simd4Double b)
	Add two double SIMD4 variables. More...
static Simd4Double gmx_simdcall	operator- (Simd4Double a, Simd4Double b)
	Subtract two SIMD4 variables. More...
static Simd4Double gmx_simdcall	operator- (Simd4Double a)
	SIMD4 floating-point negate. More...
static Simd4Double gmx_simdcall	operator* (Simd4Double a, Simd4Double b)
	Multiply two SIMD4 variables. More...
static Simd4Double gmx_simdcall	fma (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-multiply-add. Result is a*b+c. More...
static Simd4Double gmx_simdcall	fms (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-multiply-subtract. Result is a*b-c. More...
static Simd4Double gmx_simdcall	fnma (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-negated-multiply-add. Result is -a*b+c. More...
static Simd4Double gmx_simdcall	fnms (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-negated-multiply-subtract. Result is -a*b-c. More...
static Simd4Double gmx_simdcall	rsqrt (Simd4Double x)
	SIMD4 1.0/sqrt(x) lookup. More...
static Simd4Double gmx_simdcall	abs (Simd4Double a)
	SIMD4 Floating-point abs(). More...
static Simd4Double gmx_simdcall	max (Simd4Double a, Simd4Double b)
	Set each SIMD4 element to the largest from two variables. More...
static Simd4Double gmx_simdcall	min (Simd4Double a, Simd4Double b)
	Set each SIMD4 element to the largest from two variables. More...
static Simd4Double gmx_simdcall	round (Simd4Double a)
	SIMD4 Round to nearest integer value (in floating-point format). More...
static Simd4Double gmx_simdcall	trunc (Simd4Double a)
	Truncate SIMD4, i.e. round towards zero - common hardware instruction. More...
static double gmx_simdcall	dotProduct (Simd4Double a, Simd4Double b)
	Return dot product of two double precision SIMD4 variables. More...
static void gmx_simdcall	transpose (Simd4Double *v0, Simd4Double *v1, Simd4Double *v2, Simd4Double *v3)
	SIMD4 double transpose. More...
static Simd4DBool gmx_simdcall	operator== (Simd4Double a, Simd4Double b)
	a==b for SIMD4 double More...
static Simd4DBool gmx_simdcall	operator!= (Simd4Double a, Simd4Double b)
	a!=b for SIMD4 double More...
static Simd4DBool gmx_simdcall	operator< (Simd4Double a, Simd4Double b)
	a<b for SIMD4 double More...
static Simd4DBool gmx_simdcall	operator<= (Simd4Double a, Simd4Double b)
	a<=b for SIMD4 double. More...
static Simd4DBool gmx_simdcall	operator&& (Simd4DBool a, Simd4DBool b)
	Logical and on single precision SIMD4 booleans. More...
static Simd4DBool gmx_simdcall	operator|| (Simd4DBool a, Simd4DBool b)
	Logical or on single precision SIMD4 booleans. More...
static bool gmx_simdcall	anyTrue (Simd4DBool a)
	Returns non-zero if any of the boolean in SIMD4 a is True, otherwise 0. More...
static Simd4Double gmx_simdcall	selectByMask (Simd4Double a, Simd4DBool mask)
	Select from single precision SIMD4 variable where boolean is true. More...
static Simd4Double gmx_simdcall	selectByNotMask (Simd4Double a, Simd4DBool mask)
	Select from single precision SIMD4 variable where boolean is false. More...
static Simd4Double gmx_simdcall	blend (Simd4Double a, Simd4Double b, Simd4DBool sel)
	Vector-blend SIMD4 selection. More...
static double gmx_simdcall	reduce (Simd4Double a)
	Return sum of all elements in SIMD4 double variable. More...
Constant width-4 single precision SIMD types and instructions
static Simd4Float gmx_simdcall	load4 (const float *m)
	Load 4 float values from aligned memory into SIMD4 variable. More...
static void gmx_simdcall	store4 (float *m, Simd4Float a)
	Store the contents of SIMD4 float to aligned memory m. More...
static Simd4Float gmx_simdcall	load4U (const float *m)
	Load SIMD4 float from unaligned memory. More...
static void gmx_simdcall	store4U (float *m, Simd4Float a)
	Store SIMD4 float to unaligned memory. More...
static Simd4Float gmx_simdcall	simd4SetZeroF ()
	Set all SIMD4 float elements to 0. More...
static Simd4Float gmx_simdcall	operator& (Simd4Float a, Simd4Float b)
	Bitwise and for two SIMD4 float variables. More...
static Simd4Float gmx_simdcall	andNot (Simd4Float a, Simd4Float b)
	Bitwise andnot for two SIMD4 float variables. c=(~a) & b. More...
static Simd4Float gmx_simdcall	operator| (Simd4Float a, Simd4Float b)
	Bitwise or for two SIMD4 floats. More...
static Simd4Float gmx_simdcall	operator^ (Simd4Float a, Simd4Float b)
	Bitwise xor for two SIMD4 float variables. More...
static Simd4Float gmx_simdcall	operator+ (Simd4Float a, Simd4Float b)
	Add two float SIMD4 variables. More...
static Simd4Float gmx_simdcall	operator- (Simd4Float a, Simd4Float b)
	Subtract two SIMD4 variables. More...
static Simd4Float gmx_simdcall	operator- (Simd4Float a)
	SIMD4 floating-point negate. More...
static Simd4Float gmx_simdcall	operator* (Simd4Float a, Simd4Float b)
	Multiply two SIMD4 variables. More...
static Simd4Float gmx_simdcall	fma (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-multiply-add. Result is a*b+c. More...
static Simd4Float gmx_simdcall	fms (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-multiply-subtract. Result is a*b-c. More...
static Simd4Float gmx_simdcall	fnma (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-negated-multiply-add. Result is -a*b+c. More...
static Simd4Float gmx_simdcall	fnms (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-negated-multiply-subtract. Result is -a*b-c. More...
static Simd4Float gmx_simdcall	rsqrt (Simd4Float x)
	SIMD4 1.0/sqrt(x) lookup. More...
static Simd4Float gmx_simdcall	abs (Simd4Float a)
	SIMD4 Floating-point fabs(). More...
static Simd4Float gmx_simdcall	max (Simd4Float a, Simd4Float b)
	Set each SIMD4 element to the largest from two variables. More...
static Simd4Float gmx_simdcall	min (Simd4Float a, Simd4Float b)
	Set each SIMD4 element to the largest from two variables. More...
static Simd4Float gmx_simdcall	round (Simd4Float a)
	SIMD4 Round to nearest integer value (in floating-point format). More...
static Simd4Float gmx_simdcall	trunc (Simd4Float a)
	Truncate SIMD4, i.e. round towards zero - common hardware instruction. More...
static float gmx_simdcall	dotProduct (Simd4Float a, Simd4Float b)
	Return dot product of two single precision SIMD4 variables. More...
static void gmx_simdcall	transpose (Simd4Float *v0, Simd4Float *v1, Simd4Float *v2, Simd4Float *v3)
	SIMD4 float transpose. More...
static Simd4FBool gmx_simdcall	operator== (Simd4Float a, Simd4Float b)
	a==b for SIMD4 float More...
static Simd4FBool gmx_simdcall	operator!= (Simd4Float a, Simd4Float b)
	a!=b for SIMD4 float More...
static Simd4FBool gmx_simdcall	operator< (Simd4Float a, Simd4Float b)
	a<b for SIMD4 float More...
static Simd4FBool gmx_simdcall	operator<= (Simd4Float a, Simd4Float b)
	a<=b for SIMD4 float. More...
static Simd4FBool gmx_simdcall	operator&& (Simd4FBool a, Simd4FBool b)
	Logical and on single precision SIMD4 booleans. More...
static Simd4FBool gmx_simdcall	operator|| (Simd4FBool a, Simd4FBool b)
	Logical or on single precision SIMD4 booleans. More...
static bool gmx_simdcall	anyTrue (Simd4FBool a)
	Returns non-zero if any of the boolean in SIMD4 a is True, otherwise 0. More...
static Simd4Float gmx_simdcall	selectByMask (Simd4Float a, Simd4FBool mask)
	Select from single precision SIMD4 variable where boolean is true. More...
static Simd4Float gmx_simdcall	selectByNotMask (Simd4Float a, Simd4FBool mask)
	Select from single precision SIMD4 variable where boolean is false. More...
static Simd4Float gmx_simdcall	blend (Simd4Float a, Simd4Float b, Simd4FBool sel)
	Vector-blend SIMD4 selection. More...
static float gmx_simdcall	reduce (Simd4Float a)
	Return sum of all elements in SIMD4 float variable. More...
SIMD implementation load/store operations for double precision floating point
static SimdDouble gmx_simdcall	simdLoad (const double *m, SimdDoubleTag={})
	Load GMX_SIMD_DOUBLE_WIDTH numbers from aligned memory. More...
static void gmx_simdcall	store (double *m, SimdDouble a)
	Store the contents of SIMD double variable to aligned memory m. More...
static SimdDouble gmx_simdcall	simdLoadU (const double *m, SimdDoubleTag={})
	Load SIMD double from unaligned memory. More...
static void gmx_simdcall	storeU (double *m, SimdDouble a)
	Store SIMD double to unaligned memory. More...
static SimdDouble gmx_simdcall	setZeroD ()
	Set all SIMD double variable elements to 0.0. More...
SIMD implementation load/store operations for integers (corresponding to double)
static SimdDInt32 gmx_simdcall	simdLoad (const std::int32_t *m, SimdDInt32Tag)
	Load aligned SIMD integer data, width corresponds to gmx::SimdDouble. More...
static void gmx_simdcall	store (std::int32_t *m, SimdDInt32 a)
	Store aligned SIMD integer data, width corresponds to gmx::SimdDouble. More...
static SimdDInt32 gmx_simdcall	simdLoadU (const std::int32_t *m, SimdDInt32Tag)
	Load unaligned integer SIMD data, width corresponds to gmx::SimdDouble. More...
static void gmx_simdcall	storeU (std::int32_t *m, SimdDInt32 a)
	Store unaligned SIMD integer data, width corresponds to gmx::SimdDouble. More...
static SimdDInt32 gmx_simdcall	setZeroDI ()
	Set all SIMD (double) integer variable elements to 0. More...
template<int index>
static std::int32_t gmx_simdcall	extract (SimdDInt32 a)
	Extract element with index i from gmx::SimdDInt32. More...
SIMD implementation double precision floating-point bitwise logical operations
static SimdDouble gmx_simdcall	operator& (SimdDouble a, SimdDouble b)
	Bitwise and for two SIMD double variables. More...
static SimdDouble gmx_simdcall	andNot (SimdDouble a, SimdDouble b)
	Bitwise andnot for SIMD double. More...
static SimdDouble gmx_simdcall	operator| (SimdDouble a, SimdDouble b)
	Bitwise or for SIMD double. More...
static SimdDouble gmx_simdcall	operator^ (SimdDouble a, SimdDouble b)
	Bitwise xor for SIMD double. More...
SIMD implementation double precision floating-point arithmetics
static SimdDouble gmx_simdcall	operator+ (SimdDouble a, SimdDouble b)
	Add two double SIMD variables. More...
static SimdDouble gmx_simdcall	operator- (SimdDouble a, SimdDouble b)
	Subtract two double SIMD variables. More...
static SimdDouble gmx_simdcall	operator- (SimdDouble a)
	SIMD double precision negate. More...
static SimdDouble gmx_simdcall	operator* (SimdDouble a, SimdDouble b)
	Multiply two double SIMD variables. More...
static SimdDouble gmx_simdcall	fma (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-multiply-add. Result is a*b+c. More...
static SimdDouble gmx_simdcall	fms (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-multiply-subtract. Result is a*b-c. More...
static SimdDouble gmx_simdcall	fnma (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-negated-multiply-add. Result is -a*b+c. More...
static SimdDouble gmx_simdcall	fnms (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-negated-multiply-subtract. Result is -a*b-c. More...
static SimdDouble gmx_simdcall	rsqrt (SimdDouble x)
	double SIMD 1.0/sqrt(x) lookup. More...
static SimdDouble gmx_simdcall	rcp (SimdDouble x)
	SIMD double 1.0/x lookup. More...
static SimdDouble gmx_simdcall	maskAdd (SimdDouble a, SimdDouble b, SimdDBool m)
	Add two double SIMD variables, masked version. More...
static SimdDouble gmx_simdcall	maskzMul (SimdDouble a, SimdDouble b, SimdDBool m)
	Multiply two double SIMD variables, masked version. More...
static SimdDouble gmx_simdcall	maskzFma (SimdDouble a, SimdDouble b, SimdDouble c, SimdDBool m)
	SIMD double fused multiply-add, masked version. More...
static SimdDouble gmx_simdcall	maskzRsqrt (SimdDouble x, SimdDBool m)
	SIMD double 1.0/sqrt(x) lookup, masked version. More...
static SimdDouble gmx_simdcall	maskzRcp (SimdDouble x, SimdDBool m)
	SIMD double 1.0/x lookup, masked version. More...
static SimdDouble gmx_simdcall	abs (SimdDouble a)
	SIMD double floating-point fabs(). More...
static SimdDouble gmx_simdcall	max (SimdDouble a, SimdDouble b)
	Set each SIMD double element to the largest from two variables. More...
static SimdDouble gmx_simdcall	min (SimdDouble a, SimdDouble b)
	Set each SIMD double element to the smallest from two variables. More...
static SimdDouble gmx_simdcall	round (SimdDouble a)
	SIMD double round to nearest integer value (in floating-point format). More...
static SimdDouble gmx_simdcall	trunc (SimdDouble a)
	Truncate SIMD double, i.e. round towards zero - common hardware instruction. More...
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall	frexp (SimdDouble value, SimdDInt32 *exponent)
	Extract (integer) exponent and fraction from double precision SIMD. More...
template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall	ldexp (SimdDouble value, SimdDInt32 exponent)
	Multiply a SIMD double value by the number 2 raised to an exp power. More...
static double gmx_simdcall	reduce (SimdDouble a)
	Return sum of all elements in SIMD double variable. More...
SIMD implementation double precision floating-point comparison, boolean, selection.
static SimdDBool gmx_simdcall	operator== (SimdDouble a, SimdDouble b)
	SIMD a==b for double SIMD. More...
static SimdDBool gmx_simdcall	operator!= (SimdDouble a, SimdDouble b)
	SIMD a!=b for double SIMD. More...
static SimdDBool gmx_simdcall	operator< (SimdDouble a, SimdDouble b)
	SIMD a<b for double SIMD. More...
static SimdDBool gmx_simdcall	operator<= (SimdDouble a, SimdDouble b)
	SIMD a<=b for double SIMD. More...
static SimdDBool gmx_simdcall	testBits (SimdDouble a)
	Return true if any bits are set in the single precision SIMD. More...
static SimdDBool gmx_simdcall	operator&& (SimdDBool a, SimdDBool b)
	Logical and on double precision SIMD booleans. More...
static SimdDBool gmx_simdcall	operator|| (SimdDBool a, SimdDBool b)
	Logical or on double precision SIMD booleans. More...
static bool gmx_simdcall	anyTrue (SimdDBool a)
	Returns non-zero if any of the boolean in SIMD a is True, otherwise 0. More...
static SimdDouble gmx_simdcall	selectByMask (SimdDouble a, SimdDBool mask)
	Select from double precision SIMD variable where boolean is true. More...
static SimdDouble gmx_simdcall	selectByNotMask (SimdDouble a, SimdDBool mask)
	Select from double precision SIMD variable where boolean is false. More...
static SimdDouble gmx_simdcall	blend (SimdDouble a, SimdDouble b, SimdDBool sel)
	Vector-blend SIMD double selection. More...
SIMD implementation integer (corresponding to double) bitwise logical operations
static SimdDInt32 gmx_simdcall	operator& (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise and. More...
static SimdDInt32 gmx_simdcall	andNot (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise not/complement. More...
static SimdDInt32 gmx_simdcall	operator| (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise or. More...
static SimdDInt32 gmx_simdcall	operator^ (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise xor. More...
SIMD implementation integer (corresponding to double) arithmetics
static SimdDInt32 gmx_simdcall	operator+ (SimdDInt32 a, SimdDInt32 b)
	Add SIMD integers. More...
static SimdDInt32 gmx_simdcall	operator- (SimdDInt32 a, SimdDInt32 b)
	Subtract SIMD integers. More...
static SimdDInt32 gmx_simdcall	operator* (SimdDInt32 a, SimdDInt32 b)
	Multiply SIMD integers. More...
SIMD implementation integer (corresponding to double) comparisons, boolean selection
static SimdDIBool gmx_simdcall	operator== (SimdDInt32 a, SimdDInt32 b)
	Equality comparison of two integers corresponding to double values. More...
static SimdDIBool gmx_simdcall	operator< (SimdDInt32 a, SimdDInt32 b)
	Less-than comparison of two SIMD integers corresponding to double values. More...
static SimdDIBool gmx_simdcall	testBits (SimdDInt32 a)
	Check if any bit is set in each element. More...
static SimdDIBool gmx_simdcall	operator&& (SimdDIBool a, SimdDIBool b)
	Logical AND on SimdDIBool. More...
static SimdDIBool gmx_simdcall	operator|| (SimdDIBool a, SimdDIBool b)
	Logical OR on SimdDIBool. More...
static bool gmx_simdcall	anyTrue (SimdDIBool a)
	Returns true if any of the boolean in x is True, otherwise 0. More...
static SimdDInt32 gmx_simdcall	selectByMask (SimdDInt32 a, SimdDIBool mask)
	Select from gmx::SimdDInt32 variable where boolean is true. More...
static SimdDInt32 gmx_simdcall	selectByNotMask (SimdDInt32 a, SimdDIBool mask)
	Select from gmx::SimdDInt32 variable where boolean is false. More...
static SimdDInt32 gmx_simdcall	blend (SimdDInt32 a, SimdDInt32 b, SimdDIBool sel)
	Vector-blend SIMD integer selection. More...
SIMD implementation conversion operations
static SimdDInt32 gmx_simdcall	cvtR2I (SimdDouble a)
	Round double precision floating point to integer. More...
static SimdDInt32 gmx_simdcall	cvttR2I (SimdDouble a)
	Truncate double precision floating point to integer. More...
static SimdDouble gmx_simdcall	cvtI2R (SimdDInt32 a)
	Convert integer to double precision floating point. More...
static SimdDIBool gmx_simdcall	cvtB2IB (SimdDBool a)
	Convert from double precision boolean to corresponding integer boolean. More...
static SimdDBool gmx_simdcall	cvtIB2B (SimdDIBool a)
	Convert from integer boolean to corresponding double precision boolean. More...
static SimdDouble gmx_simdcall	cvtF2D (SimdFloat gmx_unused f)
	Convert SIMD float to double. More...
static SimdFloat gmx_simdcall	cvtD2F (SimdDouble gmx_unused d)
	Convert SIMD double to float. More...
static void gmx_simdcall	cvtF2DD (SimdFloat gmx_unused f, SimdDouble gmx_unused *d0, SimdDouble gmx_unused *d1)
	Convert SIMD float to double. More...
static SimdFloat gmx_simdcall	cvtDD2F (SimdDouble gmx_unused d0, SimdDouble gmx_unused d1)
	Convert SIMD double to float. More...
static SimdFInt32 gmx_simdcall	cvtR2I (SimdFloat a)
	Round single precision floating point to integer. More...
static SimdFInt32 gmx_simdcall	cvttR2I (SimdFloat a)
	Truncate single precision floating point to integer. More...
static SimdFloat gmx_simdcall	cvtI2R (SimdFInt32 a)
	Convert integer to single precision floating point. More...
static SimdFIBool gmx_simdcall	cvtB2IB (SimdFBool a)
	Convert from single precision boolean to corresponding integer boolean. More...
static SimdFBool gmx_simdcall	cvtIB2B (SimdFIBool a)
	Convert from integer boolean to corresponding single precision boolean. More...
SIMD implementation load/store operations for single precision floating point
static SimdFloat gmx_simdcall	simdLoad (const float *m, SimdFloatTag={})
	Load GMX_SIMD_FLOAT_WIDTH float numbers from aligned memory. More...
static void gmx_simdcall	store (float *m, SimdFloat a)
	Store the contents of SIMD float variable to aligned memory m. More...
static SimdFloat gmx_simdcall	simdLoadU (const float *m, SimdFloatTag={})
	Load SIMD float from unaligned memory. More...
static void gmx_simdcall	storeU (float *m, SimdFloat a)
	Store SIMD float to unaligned memory. More...
static SimdFloat gmx_simdcall	setZeroF ()
	Set all SIMD float variable elements to 0.0. More...
SIMD implementation load/store operations for integers (corresponding to float)
static SimdFInt32 gmx_simdcall	simdLoad (const std::int32_t *m, SimdFInt32Tag)
	Load aligned SIMD integer data, width corresponds to gmx::SimdFloat. More...
static void gmx_simdcall	store (std::int32_t *m, SimdFInt32 a)
	Store aligned SIMD integer data, width corresponds to gmx::SimdFloat. More...
static SimdFInt32 gmx_simdcall	simdLoadU (const std::int32_t *m, SimdFInt32Tag)
	Load unaligned integer SIMD data, width corresponds to gmx::SimdFloat. More...
static void gmx_simdcall	storeU (std::int32_t *m, SimdFInt32 a)
	Store unaligned SIMD integer data, width corresponds to gmx::SimdFloat. More...
static SimdFInt32 gmx_simdcall	setZeroFI ()
	Set all SIMD (float) integer variable elements to 0. More...
template<int index>
static std::int32_t gmx_simdcall	extract (SimdFInt32 a)
	Extract element with index i from gmx::SimdFInt32. More...
SIMD implementation single precision floating-point bitwise logical operations
static SimdFloat gmx_simdcall	operator& (SimdFloat a, SimdFloat b)
	Bitwise and for two SIMD float variables. More...
static SimdFloat gmx_simdcall	andNot (SimdFloat a, SimdFloat b)
	Bitwise andnot for SIMD float. More...
static SimdFloat gmx_simdcall	operator| (SimdFloat a, SimdFloat b)
	Bitwise or for SIMD float. More...
static SimdFloat gmx_simdcall	operator^ (SimdFloat a, SimdFloat b)
	Bitwise xor for SIMD float. More...
SIMD implementation single precision floating-point arithmetics
static SimdFloat gmx_simdcall	operator+ (SimdFloat a, SimdFloat b)
	Add two float SIMD variables. More...
static SimdFloat gmx_simdcall	operator- (SimdFloat a, SimdFloat b)
	Subtract two float SIMD variables. More...
static SimdFloat gmx_simdcall	operator- (SimdFloat a)
	SIMD single precision negate. More...
static SimdFloat gmx_simdcall	operator* (SimdFloat a, SimdFloat b)
	Multiply two float SIMD variables. More...
static SimdFloat gmx_simdcall	fma (SimdFloat a, SimdFloat b, SimdFloat c)
	SIMD float Fused-multiply-add. Result is a*b+c. More...
static SimdFloat gmx_simdcall	fms (SimdFloat a, SimdFloat b, SimdFloat c)
	SIMD float Fused-multiply-subtract. Result is a*b-c. More...
static SimdFloat gmx_simdcall	fnma (SimdFloat a, SimdFloat b, SimdFloat c)
	SIMD float Fused-negated-multiply-add. Result is -a*b+c. More...
static SimdFloat gmx_simdcall	fnms (SimdFloat a, SimdFloat b, SimdFloat c)
	SIMD float Fused-negated-multiply-subtract. Result is -a*b-c. More...
static SimdFloat gmx_simdcall	rsqrt (SimdFloat x)
	SIMD float 1.0/sqrt(x) lookup. More...
static SimdFloat gmx_simdcall	rcp (SimdFloat x)
	SIMD float 1.0/x lookup. More...
static SimdFloat gmx_simdcall	maskAdd (SimdFloat a, SimdFloat b, SimdFBool m)
	Add two float SIMD variables, masked version. More...
static SimdFloat gmx_simdcall	maskzMul (SimdFloat a, SimdFloat b, SimdFBool m)
	Multiply two float SIMD variables, masked version. More...
static SimdFloat gmx_simdcall	maskzFma (SimdFloat a, SimdFloat b, SimdFloat c, SimdFBool m)
	SIMD float fused multiply-add, masked version. More...
static SimdFloat gmx_simdcall	maskzRsqrt (SimdFloat x, SimdFBool m)
	SIMD float 1.0/sqrt(x) lookup, masked version. More...
static SimdFloat gmx_simdcall	maskzRcp (SimdFloat x, SimdFBool m)
	SIMD float 1.0/x lookup, masked version. More...
static SimdFloat gmx_simdcall	abs (SimdFloat a)
	SIMD float Floating-point abs(). More...
static SimdFloat gmx_simdcall	max (SimdFloat a, SimdFloat b)
	Set each SIMD float element to the largest from two variables. More...
static SimdFloat gmx_simdcall	min (SimdFloat a, SimdFloat b)
	Set each SIMD float element to the smallest from two variables. More...
static SimdFloat gmx_simdcall	round (SimdFloat a)
	SIMD float round to nearest integer value (in floating-point format). More...
static SimdFloat gmx_simdcall	trunc (SimdFloat a)
	Truncate SIMD float, i.e. round towards zero - common hardware instruction. More...
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall	frexp (SimdFloat value, SimdFInt32 *exponent)
	Extract (integer) exponent and fraction from single precision SIMD. More...
template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall	ldexp (SimdFloat value, SimdFInt32 exponent)
	Multiply a SIMD float value by the number 2 raised to an exp power. More...
static float gmx_simdcall	reduce (SimdFloat a)
	Return sum of all elements in SIMD float variable. More...
SIMD implementation single precision floating-point comparisons, boolean, selection.
static SimdFBool gmx_simdcall	operator== (SimdFloat a, SimdFloat b)
	SIMD a==b for single SIMD. More...
static SimdFBool gmx_simdcall	operator!= (SimdFloat a, SimdFloat b)
	SIMD a!=b for single SIMD. More...
static SimdFBool gmx_simdcall	operator< (SimdFloat a, SimdFloat b)
	SIMD a<b for single SIMD. More...
static SimdFBool gmx_simdcall	operator<= (SimdFloat a, SimdFloat b)
	SIMD a<=b for single SIMD. More...
static SimdFBool gmx_simdcall	testBits (SimdFloat a)
	Return true if any bits are set in the single precision SIMD. More...
static SimdFBool gmx_simdcall	operator&& (SimdFBool a, SimdFBool b)
	Logical and on single precision SIMD booleans. More...
static SimdFBool gmx_simdcall	operator|| (SimdFBool a, SimdFBool b)
	Logical or on single precision SIMD booleans. More...
static bool gmx_simdcall	anyTrue (SimdFBool a)
	Returns non-zero if any of the boolean in SIMD a is True, otherwise 0. More...
static SimdFloat gmx_simdcall	selectByMask (SimdFloat a, SimdFBool mask)
	Select from single precision SIMD variable where boolean is true. More...
static SimdFloat gmx_simdcall	selectByNotMask (SimdFloat a, SimdFBool mask)
	Select from single precision SIMD variable where boolean is false. More...
static SimdFloat gmx_simdcall	blend (SimdFloat a, SimdFloat b, SimdFBool sel)
	Vector-blend SIMD float selection. More...
SIMD implementation integer (corresponding to float) bitwise logical operations
static SimdFInt32 gmx_simdcall	operator& (SimdFInt32 a, SimdFInt32 b)
	Integer SIMD bitwise and. More...
static SimdFInt32 gmx_simdcall	andNot (SimdFInt32 a, SimdFInt32 b)
	Integer SIMD bitwise not/complement. More...
static SimdFInt32 gmx_simdcall	operator| (SimdFInt32 a, SimdFInt32 b)
	Integer SIMD bitwise or. More...
static SimdFInt32 gmx_simdcall	operator^ (SimdFInt32 a, SimdFInt32 b)
	Integer SIMD bitwise xor. More...
SIMD implementation integer (corresponding to float) arithmetics
static SimdFInt32 gmx_simdcall	operator+ (SimdFInt32 a, SimdFInt32 b)
	Add SIMD integers. More...
static SimdFInt32 gmx_simdcall	operator- (SimdFInt32 a, SimdFInt32 b)
	Subtract SIMD integers. More...
static SimdFInt32 gmx_simdcall	operator* (SimdFInt32 a, SimdFInt32 b)
	Multiply SIMD integers. More...
SIMD implementation integer (corresponding to float) comparisons, boolean, selection
static SimdFIBool gmx_simdcall	operator== (SimdFInt32 a, SimdFInt32 b)
	Equality comparison of two integers corresponding to float values. More...
static SimdFIBool gmx_simdcall	operator< (SimdFInt32 a, SimdFInt32 b)
	Less-than comparison of two SIMD integers corresponding to float values. More...
static SimdFIBool gmx_simdcall	testBits (SimdFInt32 a)
	Check if any bit is set in each element. More...
static SimdFIBool gmx_simdcall	operator&& (SimdFIBool a, SimdFIBool b)
	Logical AND on SimdFIBool. More...
static SimdFIBool gmx_simdcall	operator|| (SimdFIBool a, SimdFIBool b)
	Logical OR on SimdFIBool. More...
static bool gmx_simdcall	anyTrue (SimdFIBool a)
	Returns true if any of the boolean in x is True, otherwise 0. More...
static SimdFInt32 gmx_simdcall	selectByMask (SimdFInt32 a, SimdFIBool mask)
	Select from gmx::SimdFInt32 variable where boolean is true. More...
static SimdFInt32 gmx_simdcall	selectByNotMask (SimdFInt32 a, SimdFIBool mask)
	Select from gmx::SimdFInt32 variable where boolean is false. More...
static SimdFInt32 gmx_simdcall	blend (SimdFInt32 a, SimdFInt32 b, SimdFIBool sel)
	Vector-blend SIMD integer selection. More...
Higher-level SIMD utilities accessing partial (half-width) SIMD doubles.
See the single-precision versions for documentation. Since double precision is typically half the width of single, this double version is likely only useful with 512-bit and larger implementations.
static SimdDouble gmx_simdcall	loadDualHsimd (const double *m0, const double *m1)
	Load low & high parts of SIMD double from different locations. More...
static SimdDouble gmx_simdcall	loadDuplicateHsimd (const double *m)
	Load half-SIMD-width double data, spread to both halves. More...
static SimdDouble gmx_simdcall	loadU1DualHsimd (const double *m)
	Load two doubles, spread 1st in low half, 2nd in high half. More...
static void gmx_simdcall	storeDualHsimd (double *m0, double *m1, SimdDouble a)
	Store low & high parts of SIMD double to different locations. More...
static void gmx_simdcall	incrDualHsimd (double *m0, double *m1, SimdDouble a)
	Add each half of SIMD variable to separate memory adresses. More...
static void gmx_simdcall	decr3Hsimd (double *m, SimdDouble a0, SimdDouble a1, SimdDouble a2)
	Add the two halves of three SIMD doubles, subtract the sum from three half-SIMD-width consecutive doubles in memory. More...
template<int align>
static void gmx_simdcall	gatherLoadTransposeHsimd (const double *base0, const double *base1, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1)
	Load 2 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH/2 offsets, transpose into SIMD double (low half from base0, high from base1). More...
static double gmx_simdcall	reduceIncr4ReturnSumHsimd (double *m, SimdDouble v0, SimdDouble v1)
	Reduce the 4 half-SIMD-with doubles in 2 SIMD variables (sum halves), increment four consecutive doubles in memory, return sum. More...
static SimdDouble gmx_simdcall	loadUNDuplicate4 (const double *m)
	Load N doubles and duplicate them 4 times each. More...
static SimdDouble gmx_simdcall	load4DuplicateN (const double *m)
	Load 4 doubles and duplicate them N times each. More...
static SimdDouble gmx_simdcall	loadU4NOffset (const double *m, int offset)
	Load doubles in blocks of 4 at fixed offsets. More...
Higher-level SIMD utilities accessing partial (half-width) SIMD floats.
These functions are optional. The are only useful for SIMD implementation where the width is 8 or larger, and where it would be inefficient to process 4*8, 8*8, or more, interactions in parallel. Currently, only Intel provides very wide SIMD implementations, but these also come with excellent support for loading, storing, accessing and shuffling parts of the register in so-called 'lanes' of 4 bytes each. We can use this to load separate parts into the low/high halves of the register in the inner loop of the nonbonded kernel, which e.g. makes it possible to process 4*4 nonbonded interactions as a pattern of 2*8. We can also use implementations with width 16 or greater. To make this more generic, when GMX_SIMD_HAVE_HSIMD_UTIL_REAL is 1, the SIMD implementation provides seven special routines that: Load the low/high parts of a SIMD variable from different pointers Load half the SIMD width from one pointer, and duplicate in low/high parts Load two reals, put 1st one in all low elements, and 2nd in all high ones. Store the low/high parts of a SIMD variable to different pointers Subtract both SIMD halves from a single half-SIMD-width memory location. Load aligned pairs (LJ parameters) from two base pointers, with a common offset list, and put these in the low/high SIMD halves. Reduce each half of two SIMD registers (i.e., 4 parts in total), increment four adjacent memory positions, and return the total sum. Remember: this is ONLY used when the native SIMD width is large. You will just waste time if you implement it for normal 16-byte SIMD architectures. This is part of the new C++ SIMD interface, so these functions are only available when using C++. Since some Gromacs code reliying on the SIMD module is still C (not C++), we have kept the C-style naming for now - this will change once we are entirely C++.
static SimdFloat gmx_simdcall	loadDualHsimd (const float *m0, const float *m1)
	Load low & high parts of SIMD float from different locations. More...
static SimdFloat gmx_simdcall	loadDuplicateHsimd (const float *m)
	Load half-SIMD-width float data, spread to both halves. More...
static SimdFloat gmx_simdcall	loadU1DualHsimd (const float *m)
	Load two floats, spread 1st in low half, 2nd in high half. More...
static void gmx_simdcall	storeDualHsimd (float *m0, float *m1, SimdFloat a)
	Store low & high parts of SIMD float to different locations. More...
static void gmx_simdcall	incrDualHsimd (float *m0, float *m1, SimdFloat a)
	Add each half of SIMD variable to separate memory adresses. More...
static void gmx_simdcall	decr3Hsimd (float *m, SimdFloat a0, SimdFloat a1, SimdFloat a2)
	Add the two halves of three SIMD floats, subtract the sum from three half-SIMD-width consecutive floats in memory. More...
template<int align>
static void gmx_simdcall	gatherLoadTransposeHsimd (const float *base0, const float *base1, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1)
	Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH/2 offsets, transpose into SIMD float (low half from base0, high from base1). More...
static float gmx_simdcall	reduceIncr4ReturnSumHsimd (float *m, SimdFloat v0, SimdFloat v1)
	Reduce the 4 half-SIMD-with floats in 2 SIMD variables (sum halves), increment four consecutive floats in memory, return sum. More...
static SimdFloat gmx_simdcall	loadUNDuplicate4 (const float *m)
	Load N floats and duplicate them 4 times each. More...
static SimdFloat gmx_simdcall	load4DuplicateN (const float *m)
	Load 4 floats and duplicate them N times each. More...
static SimdFloat gmx_simdcall	loadU4NOffset (const float *m, int offset)
	Load floats in blocks of 4 at fixed offsets. More...
Overloads for converting a value of a given type to a string. Exceptions std::bad_alloc if out of memory.
static std::string	toString (bool t)
static std::string	toString (int t)
static std::string	toString (unsigned int t)
static std::string	toString (int64_t t)
static std::string	toString (uint64_t t)
static std::string	toString (float t)
static std::string	toString (double t)
static std::string	toString (unsigned char t)
static std::string	toString (std::string t)
void	dumpIntArrayRef (TextWriter *writer, const char *description, ArrayRef< const int > values, bool showIndices)
	Dump the formatted values to writer along with a description and/or indices.
void	dumpFloatArrayRef (TextWriter *writer, const char *description, ArrayRef< const float > values, bool showIndices)
void	dumpDoubleArrayRef (TextWriter *writer, const char *description, ArrayRef< const double > values, bool showIndices)
void	dumpRealArrayRef (TextWriter *writer, const char *description, ArrayRef< const real > values, bool showIndices)
void	dumpRvecArrayRef (TextWriter *writer, const char *description, ArrayRef< const RVec > values)
template<typename T >
std::remove_const_t< T >	norm (T *v)
	Forward operations on C Array style vectors to C implementations. More...
template<typename T >
std::remove_const_t< T >	norm2 (T *v)

Variables
const gmx::EnumerationArray < XvgFormat, const char * >	c_xvgFormatNames
	Names for XvgFormat. More...
static const int	c_linewidth = 80 - 2
	Linewidth used for warning output.
static const int	c_biasMaxNumDim = 4
	The maximum dimensionality of the AWH coordinate.
static const EnumerationArray < DensitySimilarityMeasureMethod, const char * >	c_densitySimilarityMeasureMethodNames
	Name the methods that may be used to evaluate similarity between densities. More...
static const EnumerationArray < DensityFittingAmplitudeMethod, const char * >	c_densityFittingAmplitudeMethodNames
	The names of the methods to determine the amplitude of the atoms to be spread on a grid. More...
static constexpr auto	sc_torchRealType = GMX_DOUBLE ? torch::kFloat64 : torch::kFloat32
	Define the torch datatype according to GMX_DOUBLE. More...
static const EnumerationArray < QMMMQMMethod, const char * >	c_qmmmQMMethodNames
	The names of the supported QM methods. More...
static const EnumerationArray < QMMMElectrostaticCoupling, const char * >	c_qmmmElectrostaticCouplingNames
	Names of the supported QM/MM electrostatic coupling modes for tight-binding methods in CP2K. More...
const std::vector< std::string >	periodic_system
	symbols of the elements in periodic table More...
static const EnumerationArray < ChangeSettingType, const char * >	c_changeSettingTypeNames
	Mapping for enums from ChangeSettingType. More...
static const EnumerationArray < ChangeAtomsType, const char * >	c_changeAtomsTypeNames
	Mapping for enums from ChangeAtomsType. More...
static const ivec	sc_ddZoneOrder [sc_maxNumZones]
	The DD zone order. More...
static const int	ddNonbondedZonePairRanges [sc_maxNumIZones][3]
	The non-bonded zone-pair setup for domain decomposition. More...
static constexpr int	sc_maxNumZones = 8
	The maximum possible number of zones, 2 along each dimension in the eighth shell method.
static constexpr int	sc_maxNumIZones = sc_maxNumZones / 2
	The maximum possible number of i-zones, half of the zones are needed to cover all pairs.
const char	EDcol_sfmt [] = "%17s"
const char	EDcol_efmt [] = "%17.5e"
const char	EDcol_ffmt [] = "%17f"
const char	max_ev_fmt_d [] = "%7d"
const char	max_ev_fmt_lf [] = "%12lf"
const char	max_ev_fmt_dlf [] = "%7d%12lf"
const char	max_ev_fmt_dlflflf [] = "%7d%12lf%12lf%12lf"
const char	max_ev_fmt_lelele [] = "%12le%12le%12le"
const int	PMETunePeriod = 50
	After 50 nstlist periods of not observing imbalance: never tune PME.
const real	loadBalanceTriggerFactor = 1.05
	Trigger PME load balancing at more than 5% PME overload.
const real	c_maxSpacingScaling = 1.7
	Scale the grid by a most at factor 1.7. More...
const real	gridpointsScaleFactor = 0.8
	In the initial scan, step by grids that are at least a factor 0.8 coarser.
const real	relativeEfficiencyFactor = 1.05
	In the initial scan, try to skip grids with uneven x/y/z spacing, checking if the "efficiency" is more than 5% worse than the previous grid.
const real	maxRelativeSlowdownAccepted = 1.12
	Rerun until a run is 12% slower setups than the fastest run so far.
const real	maxFluctuationAccepted = 1.02
	If setups get more than 2% faster, do another round to avoid choosing a slower setup due to acceleration or fluctuations.
const int	c_numFirstTuningIntervalSkip = 5
	Number of nstlist long tuning intervals to skip before starting.
const int	c_numFirstTuningIntervalSkipWithSepPme = 3
	Number of nstlist long tuning intervals to skip before starting.
const int	c_numPostSwitchTuningIntervalSkip = 1
	Number of nstlist long tuning intervals to skip after switching to a new setting.
const double	c_startupTimeDelay = 5.0
	Number of seconds to delay the tuning at startup to allow processors clocks to ramp up.
static constexpr bool	c_useDelayedWait = false
	Block to wait for communication to PME ranks to complete. More...
realGrid_	realGrid
	pmeStream
static constexpr int64_t	sc_checkpointMaxAtomCount = std::numeric_limits<unsigned int>::max() / 3
	The maximum number of atoms that can be stored in a checkpoint file.
constexpr char	c_unitAttributeKey [] = "unit"
constexpr int	c_h5mdDeflateCompressionLevel = 1
constexpr char	c_valueName [] = "value"
	Name of value data set inside block group per the H5md specification.
constexpr char	c_stepName [] = "step"
	Name of step data set inside block group per the H5md specification.
constexpr char	c_timeName [] = "time"
	Name of time data set inside block group per the H5md specification.
constexpr char	c_timeDataSetUnit [] = "ps"
	Unit for time data for simulations produced by mdrun.
constexpr H5mdCompression	c_stepAndTimeCompression = H5mdCompression::LosslessShuffle
	Compression algorithm used for step and time data sets.
constexpr int	c_h5mdInternalTopologyVersionMajor = 0
	The major version of the GROMACS internal topology.
constexpr int	c_h5mdInternalTopologyVersionMinor = 1
	The minor version of the GROMACS internal topology.
constexpr char	c_massUnit [] = "u"
	Unit for mass data in GROMACS.
constexpr char	c_elementaryChargeUnit [] = "e"
	Unit for electric charge data in GROMACS.
constexpr char	c_particleIdName [] = "id"
	Name of dataset for the identifier for the particles.
constexpr char	c_particleMassName [] = "mass"
	Name of dataset for the mass of the particles.
constexpr char	c_particleChargeName [] = "charge"
	Name of dataset for the charge of the particles.
constexpr char	c_particleSpeciesName [] = "species"
	Name of dataset for the species (atomic number) of the particles.
constexpr char	c_particleNameIndicesName [] = "particle_name"
	Name of dataset for the names of the particles.
constexpr char	c_particleNameTableName [] = "particle_name_table"
	Name of dataset for the particle name lookup table.
constexpr char	c_numParticlesAttributeKey [] = "particle_count"
	Name of attribute for the number of the particles.
constexpr char	c_residueIdName [] = "residue_id"
	Name of dataset for the residue identifier of the particles.
constexpr char	c_residueNameIndicesName [] = "residue_name"
	Name of dataset for the residue names of the particles.
constexpr char	c_residueNameTableName [] = "residue_name_table"
	Name of dataset for the residue name lookup table.
constexpr char	c_residueSequenceName [] = "sequence"
	Name of dataset for the residue sequence.
constexpr char	c_numResiduesAttributeKey [] = "residue_count"
	Name of attribute for the number of the residues.
constexpr char	c_bondsConnectivityName [] = "bonds"
	Name of bond dataset inside connectivity group.
constexpr char	c_numberOfBondsAttributeKey [] = "bond_count"
	Name of the attribute storing number of bonds.
constexpr char	c_disulfideBondsName [] = "disulfide_bonds"
	Name of disulfide bonds within the special bonds group.
constexpr char	c_h5mdInternalTopologyVersionAttributeKey [] = "version"
	Name of attribute for the version of internal topology.
constexpr char	c_h5mdInternalTopologyNameAttributeKey [] = "system_name"
	Name of attribute for topology name.
constexpr char	c_moleculeNamesAttributeKey [] = "molecule_block_names"
	Name of attribute for the names of the molecule types.
constexpr char	c_numMolBlocksAttributeKey [] = "molecule_block_counts"
	Name of attribute for the number of blocks for each molecule types.
static const EnumerationArray < FmmDirectProvider, const char * >	c_fmmDirectProviderNames
	String names corresponding to FmmDirectProvider enum values. More...
const std::string	c_fmmFMSolvrDirectRangeOptionName = "fmsolvr-direct-range"
	MDP option name to configure the direct interaction range for FMSolvr (1 or 2)
const std::string	c_fmmFMSolvrDirectProviderOptionName = "fmsolvr-direct-provider"
	MDP option name to select the direct interaction provider for FMSolvr (GROMACS or FMM).
const std::string	c_fmmFMSolvrDipoleCompensationOptionName = "fmsolvr-dipole-compensation"
	MDP option name to enable dipole compensation for improved accuracy in FMSolvr.
const std::string	c_fmmFMSolvrSparseOptionName = "fmsolvr-sparse"
	MDP option name to enable sparse tree representation in FMSolvr for memory optimization.
static const EnumerationArray < ActiveFmmBackend, const char * >	c_activeFmmBackendNames
	String names corresponding to ActiveFmmBackend enum values. More...
const std::string	c_fmmActiveOptionName = "backend"
	MDP option name to enable one of the FMM backends (e.g., ExaFMM).
static const EnumerationArray < ExaFmmTreeType, const char * >	c_exaFmmTreeTypeNames
	String names corresponding to ExaFmmTreeType enum values. More...
const std::string	c_fmmExaFmmDirectRangeOptionName = "exafmm-direct-range"
	MDP option name to configure the direct interaction range for ExaFMM (1 or 2)
const std::string	c_fmmExaFmmDirectProviderOptionName = "exafmm-direct-provider"
	MDP option name to select the direct interaction provider for ExaFMM (GROMACS or FMM)
const std::string	c_fmmExaFmmOrderOptionName = "exafmm-order"
	MDP option name to set the multipole expansion order for ExaFMM.
const std::string	c_fmmExaFmmTreeTypeOptionName = "exafmm-tree-type"
	MDP option name to choose the tree type for ExaFMM (uniform or adaptive) More...
const std::string	c_fmmExaFmmTreeDepthOptionName = "exafmm-tree-depth"
	MDP option name to set the tree depth for ExaFMM. More...
const std::string	c_fmmExaFmmMaxParticlesPerCellOptionName = "exafmm-max-particles-per-cell"
	MDP option name to set the maximum number of particles per cell for ExaFMM. More...
const std::string	c_fmmFMSolvrOrderOptionName = "fmsolvr-order"
	MDP option name to set the multipole expansion order for FMSolvr.
const std::string	c_fmmFMSolvrTreeDepthOptionName = "fmsolvr-tree-depth"
	MDP option name to set the tree depth for FMSolvr (controls spatial subdivision granularity)
static const t_dirname	ddb_dirnames [DDB_DIR_NR]
static const char	atomnamesuffix [] = "1234"
const int	ncontrol [] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 }
static const EnumerationArray < RotationType, const char * >	c_rotationTypeNames
static const int	NOTSET = -409203
static inputrec_strings *	inputrecStrings = nullptr
static EnumerationArray < Directive, Directive * >	necessary = { { nullptr } }
static constexpr Architecture	c_architecture
	Constant that tells what the architecture is. More...
constexpr int	c_loopWait = 1
	How long shall we wait in seconds until we check for a connection again?
constexpr int	c_connectWait = 1
	How long shall we check for the IMD_GO?
constexpr int	c_headerSize = 8
	IMD Header Size.
constexpr int	c_protocolVersion = 2
	IMD Protocol Version.
static const char	IMDstr [] = "IMD:"
	Tag output from the IMD module with this string. More...
constexpr int	c_maxConnections = 1
	Currently only 1 client connection is supported.
static constexpr int	numFTypesOnGpu = 8
	The number on bonded function types supported on GPUs.
constexpr std::array < InteractionFunction, numFTypesOnGpu >	fTypesOnGpu
	List of all bonded function types supported on GPUs. More...
BondedGpuKernelBuffers	kernelBuffers
BondedGpuKernelBuffers float4 *	gm_xq_in
BondedGpuKernelBuffers float4 float3 *	gm_f
BondedGpuKernelBuffers float4 float3 float3 *	gm_fShift
const int	tid = blockIdx.x * blockDim.x + threadIdx.x
float	vtot_loc = 0.0f
float	vtotElec_loc = 0.0f
__shared__ float3	sm_dynamicShmem []
float3 *	sm_fShiftLoc = sm_dynamicShmem
DeviceFloat4 *	gm_xq = reinterpret_cast<DeviceFloat4*>(gm_xq_in)
InteractionFunction	fType
bool	threadComputedPotential = false
static const int	simd_width = 1
	Define simd_width for memory allocation used for SIMD code.
static constexpr int	c_threadsPerBlock = 256
	Number of threads in a GPU block.
static constexpr int	sc_workGroupSize = 256
	Number of work-items in a work-group.
static const bool	c_disableAlternatingWait = (std::getenv("GMX_DISABLE_ALTERNATING_GPU_WAIT") != nullptr)
static const EnumerationArray < IncompatibilityReasons, std::string >	reasonStrings
	Strings explaining why the system is incompatible with update groups. More...
static constexpr InteractionFunction	c_ftypeVsiteStart = InteractionFunction::VirtualSite1
	The start value of the vsite indices in the ftype enum. More...
static constexpr InteractionFunction	c_ftypeVsiteEnd
	The start and end value of the vsite indices in the ftype enum. More...
static constexpr int	numFtypes = static_cast<int>(c_ftypeVsiteEnd) - static_cast<int>(c_ftypeVsiteStart)
const std::array < InteractionFunction, numFtypes >	vSiteFunctionTypes
const std::array < InteractionFunction, numFtypes >	vSiteFunctionTypesReversed
static constexpr real	sc_bU_bin_limit = 50
	The limit in kT for the histogram of insertion energies.
static constexpr real	sc_bU_logV_bin_limit = sc_bU_bin_limit + 10
	The limit in kT for the histogram of insertion energies including the log(volume) term.
static constexpr int32_t	sc_atomInfo_EnergyGroupIdMask = 0b11111111
	The first 8 bits are reserved for energy-group ID.
static const gmx::EnumerationArray < MtsForceGroups, std::string >	mtsForceGroupNames
	Names for the MTS force groups. More...
static constexpr int	s_maxNumThreadsForReduction = 256
	The max thread number is arbitrary, we used a fixed number to avoid memory management. Using more than 16 threads is probably never useful performance wise.
static constexpr EnumerationArray< NhcUsage, const char * >	nhcUsageNames = { "System", "Barostat" }
	boxVelocity_ { { 0 } }
	previousBox_ { { 0 } }
static constexpr int	STRIDE_XYZ = 3
	Stride for coordinate/force arrays with xyz coordinate storage.
static constexpr int	STRIDE_XYZQ = 4
	Stride for coordinate/force arrays with xyzq coordinate storage.
static constexpr int	c_packX4 = 4
	Size of packs of x, y or z with SIMD 4-grouped packed coordinates/forces.
static constexpr int	c_packX8 = 8
	Size of packs of x, y or z with SIMD 8-grouped packed coordinates/forces.
static constexpr int	STRIDE_P4 = DIM * c_packX4
	Stridefor a pack of 4 coordinates/forces.
static constexpr int	STRIDE_P8 = DIM * c_packX8
	Stridefor a pack of 8 coordinates/forces.
static constexpr int	c_numBoundingBoxBounds1D = 2
	The number of bounds along one dimension of a bounding box.
constexpr real	c_minDistanceSquared = 1.0e-12_real
	Lower limit for square interaction distances in nonbonded kernels. More...
constexpr real	c_maxRInvSix = 1.0e15_real
	Higher limit for r^-6 used for Lennard-Jones interactions. More...
static constexpr int	c_sciHistogramSize = 8192
	Number of separate bins used during sorting of plist on gpu. More...
static constexpr int	c_sciSortingThreadsPerBlock = 256
	Number of threads per block used by the gpu sorting kernel. More...
static constexpr int	c_sciSortingItemsPerThread = 16
static constexpr int	c_pruneKernelJPackedConcurrency = 4
	Default for the prune kernel's jPacked processing concurrency.
static constexpr int	c_sortGridRatio = 4
	Ratio of grid cells to atoms.
static constexpr int	c_sortGridMaxSizeFactor = c_sortGridRatio + 1
	Maximum ratio of holes used, in the worst case all particles end up in the last hole and we need num. atoms extra holes at the end.
static const unsigned int	gpu_min_ci_balanced_factor = 44
NBParamGpu	nbparam
NBParamGpu GpuPairlist	plist
template<PairlistType pairlistType>
__device__ constexpr int	c_subWarp = sc_gpuParallelExecutionWidth(pairlistType)
template<PairlistType pairlistType>
__device__ constexpr int	c_clSizeLog2 = StaticLog2<sc_gpuClusterSize(pairlistType)>::value
	Log of the i and j cluster size. change this together with c_clSize !
template<PairlistType pairlistType>
__device__ constexpr int	c_clSizeSq = sc_gpuClusterSize(pairlistType) * sc_gpuClusterSize(pairlistType)
	Square of cluster size.
template<PairlistType pairlistType>
static __device__ constexpr int	c_fbufStride = c_clSizeSq<pairlistType>
static constexpr auto	refPairlistLayoutType = PairlistType::Hierarchical8x8x8
static constexpr int	c_clSize = sc_gpuClusterSize(refPairlistLayoutType)
constexpr int	c_numElecTypes = static_cast<int>(ElecType::Count)
	Number of possible ElecType values.
constexpr int	c_numVdwTypes = static_cast<int>(VdwType::Count)
	Number of possible VdwType values.
static constexpr real	c_nbnxmRlistIncreaseOutsideFactor = 0.6
static constexpr int	c_maxGridsPerKernelLaunch = 8
	Maximum number of grids supported in a single fused kernel launch.
	eElec { 1, { hostAllocationPolicy } }
	dvdlLJ { 1, { hostAllocationPolicy } }
	dvdlElec { 1, { hostAllocationPolicy } }
	fShift { c_numShiftVectors, { hostAllocationPolicy } }
	eLJForeign { hostAllocationPolicy }
	eElecForeign { hostAllocationPolicy }
	dvdlLJForeign { hostAllocationPolicy }
	dvdlElecForeign
	hostAllocationPolicy { deviceContext, PinningPolicy::PinnedIfSupported }
static const float	epsilon
const float	sigma6 = sigma2 * sigma2 * sigma2
const float	c6 = epsilon * sigma6
const float	c12 = c6 * sigma6
	return { c6, c12 }
static const shift_consts_t	repulsionShift
static const shift_consts_t const float	rVdwSwitch
static const shift_consts_t const float const float const float const float	rInv
static const shift_consts_t const float const float const float const float const float	r2
static const shift_consts_t const float const float const float const float const float float *	f
static const shift_consts_t const float const float const float const float const float float float *	eLJ
const float	dispShiftV3 = dispersionShift.c3
const float	repuShiftV2 = repulsionShift.c2
const float	repuShiftV3 = repulsionShift.c3
const float	r = r2 * rInv
const float	rSwitch = gmxGpuFDim(r, rVdwSwitch)
	else
static const int	typeI
static const char *	nb_kfunc_noener_noprune_ptr [c_numElecTypes][c_numVdwTypes]
	Force-only kernel function names.
static const char *	nb_kfunc_ener_noprune_ptr [c_numElecTypes][c_numVdwTypes]
	Force + energy kernel function pointers.
static const char *	nb_kfunc_noener_prune_ptr [c_numElecTypes][c_numVdwTypes]
	Force + pruning kernel function pointers.
static const char *	nb_kfunc_ener_prune_ptr [c_numElecTypes][c_numVdwTypes]
	Force + energy + pruning kernel function pointers.
static unsigned int	gpu_min_ci_balanced_factor = 50
	This parameter should be determined heuristically from the kernel execution times. More...
static const char *	kernel_electrostatic_family_definitions []
	Array of the defines needed to generate a specific eel flavour. More...
static const char *	kernel_VdW_family_definitions []
	Array of the defines needed to generate a specific vdw flavour. More...
constexpr bool	c_pbcShiftBackward = true
const int	max_nrj_fep = 40
static constexpr auto	sc_layoutType = PairlistType::Hierarchical8x8x8
	Currently hard coded default GPU pairlist layout.
constexpr float	c_nbnxmMinDistanceSquared = 3.82e-07F
	Lower limit for square interaction distances in nonbonded kernels. More...
static const int	nbnxmReferenceNstlist = 10
	Cost of non-bonded kernels. More...
const int	nstlist_try [] = { 20, 25, 40, 50, 80, 100 }
	The values to try when switching.
static const float	c_nbnxmListSizeFactorCpu = 1.25
	Target pair-list size increase ratio for CPU.
static const float	c_nbnxmListSizeFactorGPU = 1.4
	Target pair-list size increase ratio for GPU.
static const float	c_nbnxmListSizeFactorMargin = 0.1
	Never increase the size of the pair-list more than the factor above plus this margin.
static constexpr int	c_nbnxmGpuRollingListPruningInterval = 2
	The interval in steps at which we perform dynamic, rolling pruning on a GPU. More...
static const int	c_nbnxmCpuDynamicListPruningMinLifetime = 5
	The minimum nstlist for dynamic pair list pruning on CPUs. More...
static constexpr int	c_nbnxmGpuDynamicListPruningMinLifetime = 4
	The minimum nstlist for dynamic pair list pruning om GPUs. More...
static constexpr gmx::EnumerationArray < PairlistType, int >	IClusterSizePerListType
	Gives the i-cluster size for each pairlist type. More...
static constexpr gmx::EnumerationArray < PairlistType, int >	JClusterSizePerListType
	Gives the j-cluster size for each pairlist type. More...
static constexpr bool	sc_calculateShiftForces = true
	Whether we calculate shift forces, always true, because it's cheap anyhow.
static constexpr int	c_syclPruneKernelJPackedConcurrency = c_pruneKernelJPackedConcurrency
	Prune kernel's jPacked processing concurrency. More...
constexpr int	c_centralShiftIndex = detail::c_numIvecs / 2
constexpr int	c_numShiftVectors = detail::c_numIvecs
static constexpr EnumerationArray < ChannelHistory, const char * >	ChannelString
	Names for the channels. More...
static constexpr EnumerationArray< Domain, const char * >	DomainString
	Names for the domains. More...
static const t_tab_props	tprops [etabNR]
static const int	NOTSET = -92637
static gmx_bool	bCase = FALSE
static const int	sc_indentationIncrement = 3
constexpr double	c_angstrom = 1e-10
constexpr double	c_kilo = 1e3
constexpr double	c_nano = 1e-9
constexpr double	c_pico = 1e-12
constexpr double	c_nm2A = c_nano / c_angstrom
constexpr double	c_cal2Joule = 4.184
constexpr double	c_electronCharge = 1.602176634e-19
constexpr double	c_amu = 1.66053906660e-27
constexpr double	c_boltzmann = 1.380649e-23
constexpr double	c_avogadro = 6.02214076e23
constexpr double	c_universalGasConstant = c_boltzmann * c_avogadro
constexpr double	c_boltz = c_universalGasConstant / c_kilo
constexpr double	c_faraday = c_electronCharge * c_avogadro
constexpr double	c_planck1 = 6.62607015e-34
constexpr double	c_planck = (c_planck1 * c_avogadro / (c_pico * c_kilo))
constexpr double	c_epsilon0Si = 8.8541878128e-12
constexpr double	c_epsilon0
constexpr double	c_speedOfLight = 2.99792458e05
constexpr double	c_rydberg = 1.0973731568160e-02
constexpr double	c_one4PiEps0 = (1.0 / (4.0 * 3.14159265358979323846 * c_epsilon0))
constexpr double	c_barMdunits = (1e5 * c_nano * c_pico * c_pico / c_amu)
constexpr double	c_presfac = 1.0 / c_barMdunits
constexpr double	c_debye2Enm = (1e-15 / (c_speedOfLight * c_electronCharge))
constexpr double	c_enm2Debye = 1.0 / c_debye2Enm
constexpr double	c_fieldfac = c_faraday / c_kilo
constexpr double	c_hartree2Kj = ((2.0 * c_rydberg * c_planck * c_speedOfLight) / c_avogadro)
constexpr double	c_bohr2Nm = 0.0529177210903
constexpr double	c_hartreeBohr2Md = (c_hartree2Kj * c_avogadro / c_bohr2Nm)
constexpr double	c_rad2Deg = 180.0 / 3.14159265358979323846
constexpr double	c_deg2Rad = 3.14159265358979323846 / 180.0
template<std::string_view const &... inputStrings>
static constexpr auto	CompileTimeStringJoin_v = CompileTimeStringJoin<inputStrings...>::value
static constexpr int32_t	sc_atomInfo_FreeEnergyPerturbation = 1 << 8
	Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo. More...
static constexpr int32_t	sc_atomInfo_HasPerturbedCharge = 1 << 9
static constexpr int32_t	sc_atomInfo_Exclusion = 1 << 10
static constexpr int32_t	sc_atomInfo_Constraint = 1 << 11
static constexpr int32_t	sc_atomInfo_Settle = 1 << 12
static constexpr int32_t	sc_atomInfo_BondCommunication = 1 << 13
static constexpr int32_t	sc_atomInfo_HasVdw = 1 << 14
static constexpr int32_t	sc_atomInfo_HasCharge = 1 << 15
static constexpr int32_t	sc_atomInfo_IsFillerParticle = 1 << 16
template<enum VdwType vdwType>
constexpr bool	ljComb = EnergyFunctionProperties<ElecType::Count, vdwType>().vdwComb
	Templated constants to shorten kernel function declaration.
template<enum ElecType elecType>
constexpr bool	elecEwald = EnergyFunctionProperties<elecType, VdwType::Count>().elecEwald
template<enum ElecType elecType>
constexpr bool	elecEwaldTab = EnergyFunctionProperties<elecType, VdwType::Count>().elecEwaldTab
template<enum VdwType vdwType>
constexpr bool	ljEwald = EnergyFunctionProperties<ElecType::Count, vdwType>().vdwEwald
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJ_F_ref
	All the different CPU reference kernel functions.
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJFsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJPsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombGeom_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombLB_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJ_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJFsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJPsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombLB_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJ_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJ_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJFsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJPsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombGeom_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombLB_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJ_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJFsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJPsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJ_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJFsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJPsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombGeom_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecRF_VdwLJEwCombLB_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJ_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJFsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJPsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTab_VdwLJEwCombLB_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJ_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_1x1_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJ_F_ref
	All the different CPU reference kernel functions.
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJFsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJPsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombGeom_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombLB_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJ_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJFsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJPsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombLB_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJ_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJ_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJFsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJPsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombGeom_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombLB_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJ_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJFsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJPsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJ_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJFsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJPsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombGeom_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecRF_VdwLJEwCombLB_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJ_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJFsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJPsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTab_VdwLJEwCombLB_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJ_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref
NbnxmKernelFunc	nbnxm_kernel_4x4_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref
constexpr unsigned int	NBNXM_INTERACTION_MASK_ALL = 0xffffffffU
	Cluster-pair Interaction masks. More...
constexpr int	c_dBoxZ = 1
	Maximum dimensions of grid expressing shifts across PBC.
constexpr int	c_dBoxY = 1
constexpr int	c_dBoxX = 2

Higher-level SIMD utility functions, double precision.
These include generic functions to work with triplets of data, typically coordinates, and a few utility functions to load and update data in the nonbonded kernels. These functions should be available on all implementations.
static const int	c_simdBestPairAlignmentDouble = 2
	Best alignment to use for aligned pairs of double data. More...
template<int align>
static void gmx_simdcall	gatherLoadTranspose (const double *base, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1, SimdDouble *v2, SimdDouble *v3)
	Load 4 consecutive double from each of GMX_SIMD_DOUBLE_WIDTH offsets, and transpose into 4 SIMD double variables. More...
template<int align>
static void gmx_simdcall	gatherLoadTranspose (const double *base, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1)
	Load 2 consecutive double from each of GMX_SIMD_DOUBLE_WIDTH offsets, and transpose into 2 SIMD double variables. More...
template<int align>
static void gmx_simdcall	gatherLoadUTranspose (const double *base, const std::int32_t offset[], SimdDouble *v0, SimdDouble *v1, SimdDouble *v2)
	Load 3 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets, and transpose into 3 SIMD double variables. More...
template<int align>
static void gmx_simdcall	transposeScatterStoreU (double *base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
	Transpose and store 3 SIMD doubles to 3 consecutive addresses at GMX_SIMD_DOUBLE_WIDTH offsets. More...
template<int align>
static void gmx_simdcall	transposeScatterIncrU (double *base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
	Transpose and add 3 SIMD doubles to 3 consecutive addresses at GMX_SIMD_DOUBLE_WIDTH offsets. More...
template<int align>
static void gmx_simdcall	transposeScatterDecrU (double *base, const std::int32_t offset[], SimdDouble v0, SimdDouble v1, SimdDouble v2)
	Transpose and subtract 3 SIMD doubles to 3 consecutive addresses at GMX_SIMD_DOUBLE_WIDTH offsets. More...
static void gmx_simdcall	expandScalarsToTriplets (SimdDouble scalar, SimdDouble *triplets0, SimdDouble *triplets1, SimdDouble *triplets2)
	Expand each element of double SIMD variable into three identical consecutive elements in three SIMD outputs. More...
template<int align>
static void gmx_simdcall	gatherLoadBySimdIntTranspose (const double *base, SimdDInt32 offset, SimdDouble *v0, SimdDouble *v1, SimdDouble *v2, SimdDouble *v3)
	Load 4 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets specified by a SIMD integer, transpose into 4 SIMD double variables. More...
template<int align>
static void gmx_simdcall	gatherLoadUBySimdIntTranspose (const double *base, SimdDInt32 offset, SimdDouble *v0, SimdDouble *v1)
	Load 2 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets (unaligned) specified by SIMD integer, transpose into 2 SIMD doubles. More...
template<int align>
static void gmx_simdcall	gatherLoadBySimdIntTranspose (const double *base, SimdDInt32 offset, SimdDouble *v0, SimdDouble *v1)
	Load 2 consecutive doubles from each of GMX_SIMD_DOUBLE_WIDTH offsets specified by a SIMD integer, transpose into 2 SIMD double variables. More...
static double gmx_simdcall	reduceIncr4ReturnSum (double *m, SimdDouble v0, SimdDouble v1, SimdDouble v2, SimdDouble v3)
	Reduce each of four SIMD doubles, add those values to four consecutive doubles in memory, return sum. More...

Higher-level SIMD utility functions, single precision.
These include generic functions to work with triplets of data, typically coordinates, and a few utility functions to load and update data in the nonbonded kernels. These functions should be available on all implementations, although some wide SIMD implementations (width>=8) also provide special optional versions to work with half or quarter registers to improve the performance in the nonbonded kernels.
static const int	c_simdBestPairAlignmentFloat = 2
	Best alignment to use for aligned pairs of float data. More...
template<int align>
static void gmx_simdcall	gatherLoadTranspose (const float *base, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1, SimdFloat *v2, SimdFloat *v3)
	Load 4 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets, and transpose into 4 SIMD float variables. More...
template<int align>
static void gmx_simdcall	gatherLoadTranspose (const float *base, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1)
	Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets, and transpose into 2 SIMD float variables. More...
template<int align>
static void gmx_simdcall	gatherLoadUTranspose (const float *base, const std::int32_t offset[], SimdFloat *v0, SimdFloat *v1, SimdFloat *v2)
	Load 3 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets, and transpose into 3 SIMD float variables. More...
template<int align>
static void gmx_simdcall	transposeScatterStoreU (float *base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
	Transpose and store 3 SIMD floats to 3 consecutive addresses at GMX_SIMD_FLOAT_WIDTH offsets. More...
template<int align>
static void gmx_simdcall	transposeScatterIncrU (float *base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
	Transpose and add 3 SIMD floats to 3 consecutive addresses at GMX_SIMD_FLOAT_WIDTH offsets. More...
template<int align>
static void gmx_simdcall	transposeScatterDecrU (float *base, const std::int32_t offset[], SimdFloat v0, SimdFloat v1, SimdFloat v2)
	Transpose and subtract 3 SIMD floats to 3 consecutive addresses at GMX_SIMD_FLOAT_WIDTH offsets. More...
static void gmx_simdcall	expandScalarsToTriplets (SimdFloat scalar, SimdFloat *triplets0, SimdFloat *triplets1, SimdFloat *triplets2)
	Expand each element of float SIMD variable into three identical consecutive elements in three SIMD outputs. More...
template<int align>
static void gmx_simdcall	gatherLoadBySimdIntTranspose (const float *base, SimdFInt32 offset, SimdFloat *v0, SimdFloat *v1, SimdFloat *v2, SimdFloat *v3)
	Load 4 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets specified by a SIMD integer, transpose into 4 SIMD float variables. More...
template<int align>
static void gmx_simdcall	gatherLoadUBySimdIntTranspose (const float *base, SimdFInt32 offset, SimdFloat *v0, SimdFloat *v1)
	Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets (unaligned) specified by SIMD integer, transpose into 2 SIMD floats. More...
template<int align>
static void gmx_simdcall	gatherLoadBySimdIntTranspose (const float *base, SimdFInt32 offset, SimdFloat *v0, SimdFloat *v1)
	Load 2 consecutive floats from each of GMX_SIMD_FLOAT_WIDTH offsets specified by a SIMD integer, transpose into 2 SIMD float variables. More...
static float gmx_simdcall	reduceIncr4ReturnSum (float *m, SimdFloat v0, SimdFloat v1, SimdFloat v2, SimdFloat v3)
	Reduce each of four SIMD floats, add those values to four consecutive floats in memory, return sum. More...

SIMD data types
The actual storage of these types is implementation dependent. The documentation is generated from the reference implementation, but for normal usage this will likely not be what you are using.
typedef SimdFloat	SimdReal
	Real precision floating-point SIMD datatype. More...
typedef SimdFBool	SimdBool
	Boolean SIMD type for usage with SimdReal. More...
typedef SimdFInt32	SimdInt32
	32-bit integer SIMD type. More...
typedef SimdFIBool	SimdIBool
	Boolean SIMD type for usage with SimdInt32. More...
typedef Simd4Float	Simd4Real
	Real precision floating-point SIMD4 datatype. More...
typedef Simd4FBool	Simd4Bool
	Boolean SIMD4 type for usage with SimdReal. More...
const int	c_simdBestPairAlignment = c_simdBestPairAlignmentFloat

High-level SIMD proxy objects to disambiguate load/set operations
using	Simd4NFloat = SimdFloat
using	Simd4NDouble = SimdDouble
using	Simd4NReal = Simd4NFloat
template<typename T >
static std::remove_const_t< T >	load (const internal::SimdTraitsT< T > *m)
	Load function that returns SIMD or scalar. More...
template<typename T >
static T	load (const std::enable_if_t< std::is_arithmetic_v< T >, T > *m)
template<typename T , size_t N>
static T gmx_simdcall	load (const AlignedArray< internal::SimdTraitsT< T >, N > &m)
template<typename T >
static T	loadU (const internal::SimdTraitsT< T > *m)
	Load function that returns SIMD or scalar based on template argument. More...
template<typename T >
static T	loadU (const std::enable_if_t< std::is_arithmetic_v< T >, T > *m)
template<typename T , size_t N>
static T gmx_simdcall	loadU (const AlignedArray< internal::SimdTraitsT< T >, N > &m)
static SimdSetZeroProxy gmx_simdcall	setZero ()
	Helper function to set any SIMD or scalar variable to zero. More...
template<typename T >
T	load (const internal::Simd4TraitsT< T > *m)
template<typename T >
T	loadU (const internal::Simd4TraitsT< T > *m)
static Simd4NFloat gmx_simdcall	loadUNDuplicate4 (const float *f)
static Simd4NFloat gmx_simdcall	load4DuplicateN (const float *f)
static Simd4NFloat gmx_simdcall	loadU4NOffset (const float *f, int)
static Simd4NDouble gmx_simdcall	loadUNDuplicate4 (const double *f)
static Simd4NDouble gmx_simdcall	load4DuplicateN (const double *f)
static Simd4NDouble gmx_simdcall	loadU4NOffset (const double *f, int)

Typedef Documentation

template<class T >

using gmx::AlignedAllocator = typedef Allocator<T, AlignedAllocationPolicy>

Aligned memory allocator.

Template Parameters

T	Type of objects to allocate

This convenience partial specialization can be used for the optional allocator template parameter in standard library containers, which is necessary e.g. to use SIMD aligned load and store operations on data in those containers. The memory will always be aligned according to the behavior of AlignedAllocationPolicy.

typedef std::vector< hsize_t > gmx::DataSetDims

Dimensions of a HDF5 data set.

Dimensions of HDF5 data sets and spaces.

template<class T >

using gmx::HostAllocator = typedef Allocator<T, HostAllocationPolicy>

Memory allocator that uses HostAllocationPolicy.

Template Parameters

T	Type of objects to allocate

This convenience partial specialization can be used for the optional allocator template parameter in standard library containers whose memory may be used for e.g. GPU transfers. The memory will always be allocated according to the behavior of HostAllocationPolicy.

using gmx::Index = typedef std::ptrdiff_t

Integer type for indexing into arrays or vectors.

Same as ptrdiff_t.

using gmx::Matrix3x3 = typedef BasicMatrix3x3<real>

Three-by-three real number matrix.

Note

will replace the C-style real[3][3] "matrix"

template<class T >

using gmx::PageAlignedAllocator = typedef Allocator<T, PageAlignedAllocationPolicy>

PageAligned memory allocator.

Template Parameters

T	Type of objects to allocate

This convenience partial specialization can be used for the optional allocator template parameter in standard library containers, which is necessary for locking memory pages for asynchronous transfer between a GPU device and the host. The memory will always be aligned according to the behavior of PageAlignedAllocationPolicy.

using gmx::PairlistEntry = typedef std::pair<std::pair<int, int>, int>

For compatibility with pairlist data structure in MDModulesPairlistConstructedSignal. Contains pairs like ((atom1, atom2), shiftIndex).

typedef std::random_device gmx::RandomDevice

Random device.

For now this is identical to the standard library, but since we use the GROMACS random module for all other random engines and distributions it is convenient to have this too in the same module.

typedef double(* gmx::real_space_grid_contribution_computer)(double, double)

Function pointer to calculate the grid contribution for coulomb/LJ.

Used to tell table_spline3_fill_ewald_lr whether it should calculate the grid contribution for electrostatics or LJ.

typedef Simd4FBool gmx::Simd4Bool

Boolean SIMD4 type for usage with SimdReal.

This type is only available if GMX_SIMD4_HAVE_REAL is 1.

If GMX_DOUBLE is 1, this will be set to Simd4DBool internally, otherwise Simd4FBool. This is necessary since some SIMD implementations use bitpatterns for marking truth, so single- vs. double precision booleans are not necessarily exchangable. As long as you just use this type you will not have to worry about precision.

Note

This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

typedef Simd4Float gmx::Simd4Real

Real precision floating-point SIMD4 datatype.

This type is only available if GMX_SIMD4_HAVE_REAL is 1.

Simd4Double if GMX_DOUBLE is 1, otherwise Simd4Float.

Note

This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

typedef SimdFBool gmx::SimdBool

Boolean SIMD type for usage with SimdReal.

This type is only available if GMX_SIMD_HAVE_REAL is 1.

If GMX_DOUBLE is 1, this will be set to SimdDBool internally, otherwise SimdFBool. This is necessary since some SIMD implementations use bitpatterns for marking truth, so single- vs. double precision booleans are not necessarily exchangable. As long as you just use this type you will not have to worry about precision.

See SimdIBool for an explanation of real vs. integer booleans.

Note

This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

typedef SimdFIBool gmx::SimdIBool

Boolean SIMD type for usage with SimdInt32.

This type is only available if GMX_SIMD_HAVE_INT32_ARITHMETICS is 1.

If GMX_DOUBLE is 1, this will be set to SimdDIBool internally, otherwise SimdFIBool. This is necessary since some SIMD implementations use bitpatterns for marking truth, so single- vs. double precision booleans are not necessarily exchangable, and while a double-precision boolean might be represented with a 64-bit mask, the corresponding integer might only use a 32-bit mask.

We provide conversion routines for these cases, so the only thing you need to keep in mind is to use SimdBool when working with SimdReal while you pick SimdIBool when working with SimdInt32 .

To convert between them, use cvtB2IB and cvtIB2B.

Note

This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

typedef SimdFInt32 gmx::SimdInt32

32-bit integer SIMD type.

If GMX_DOUBLE is 1, this will be set to SimdDInt32 internally, otherwise SimdFInt32. This might seem a strange implementation detail, but it is because some SIMD implementations use different types/widths of integers registers when converting from double vs. single precision floating point. As long as you just use this type you will not have to worry about precision.

Note

This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

typedef SimdFloat gmx::SimdReal

Real precision floating-point SIMD datatype.

This type is only available if GMX_SIMD_HAVE_REAL is 1.

SimdDouble if GMX_DOUBLE is 1, otherwise SimdFloat.

Note

This variable cannot be placed inside other structures or classes, since some compilers (including at least clang-3.7) appear to lose the alignment. This is likely particularly severe when allocating such memory on the heap, but it occurs for stack structures too.

Enumeration Type Documentation

anonymous enum

Kinds of Van der Waals treatments in NBNxM SIMD kernels.

The LJCUT_COMB refers to the LJ combination rule for the short range. The EWALDCOMB refers to the combination rule for the grid part. vdwktNR is the number of VdW treatments for the SIMD kernels. vdwktNR_ref is the number of VdW treatments for the C reference kernels. These two numbers differ, because currently only the reference kernels support LB combination rules for the LJ-Ewald grid part.

anonymous enum

Enumerated type to describe the interaction types in a table.

Enumerator
etiCOUL	Coulomb.
etiLJ6	Dispersion.
etiLJ12	Repulsion.
etiNR	Total number of interaction types.

enum gmx::ActiveFmmBackend

strong

Indicates which FMM backend is active based on MDP configuration.

Only one FMM backend should be active at a time. This enum reflects the active backend as determined by user-specified MDP options.

Enumerator
Inactive	No FMM backend is active.
ExaFmm	ExaFMM backend is active.
FMSolvr	FMSolvr backend is active.

enum gmx::AppendingBehavior

strong

Enumeration for mdrun appending behavior.

Enumerator
Auto	Append only if user command-line and file input is correct.
Appending	Must append.
NoAppending	Must not append.

enum gmx::Architecture

strong

Enum for GROMACS CPU hardware detection support.

Enumerator
Unknown	Not one of the cases below.
X86	X86.
Arm	ARM.
PowerPC	IBM PowerPC.
RiscV32	32-bit RISC-V
RiscV64	64-bit RISC-V
Loongarch64	64-bit Loongarch

enum gmx::AtomLocality : int

strong

Atom locality indicator: local, non-local, all.

Used for calls to: gridding, force calculation, x/f buffer operations

Enumerator
Local	Local atoms.
NonLocal	Non-local atoms.
All	Both local and non-local atoms.
Count	The number of atom locality types.

enum gmx::AwhOutputEntryType

strong

Enum with the AWH variables to write.

Enumerator
MetaData	Meta data.
CoordValue	Coordinate value.
Pmf	The pmf.
Bias	The bias.
Visits	The number of visits.
Weights	The weights.
Target	The target distribition.
SharedForceCorrelationVolume	The force correlation volume shared between multiple walkers.
SharedFrictionTensor	The full friction tensor shared between multiple walkers.

enum gmx::AwhOutputMetaData

strong

Enum with the types of metadata to write.

Enumerator
NumBlock	The number of blocks.
TargetError	The target error.
ScaledSampleWeight	The logarithm of the sample weight relative to a sample weight of 1 at the initial time.
Count	The number of enum values, not including Count.

enum gmx::CheckpointSignal

strong

Checkpoint signals.

Signals set and read by CheckpointHandler. Possible signals include

• nothing to signal
• do checkpoint (at next NS step)

enum gmx::CheckPointVersion : int

strong

Enum of values that describe the contents of a cpt file whose format matches a version number.

The enum helps the code be more self-documenting and ensure merges do not silently resolve when two patches make the same bump. When changing checkpoint contents, add a new element just above Count in this enumeration, and write code that does the right thing according to the value of file_version.

Enumerator
UnknownVersion0	Unknown initial version.
UnknownVersion1	Unknown version 1.
AddMagicNumber	Store magic number to validate file.
SafeSimulationPart	Store which sim this is.
EkinDataAndFlags	Store energy data.
SafeSteps	Store current step.
Version45	Cutoff before version 4.5.
UnknownVersion7	Unknown version 7.
FileChecksumAndSize	Store checksum.
UnknownVersion9	Unknown version 9.
NoseHooverThermostat	Safe NH chains for thermostat.
NoseHooverBarostat	Safe NH chains for barostat.
HostInformation	Safe host info.
DoublePrecisionBuild	Activate double build.
LambdaStateAndHistory	Lambda stuff.
EssentialDynamics	ED stuff.
SwapState	Swap state stuff.
AwhHistoryFlags	AWH history flags added.
RemoveBuildMachineInformation	Remove functionality that makes mdrun builds non-reproducible.
ComPrevStepAsPullGroupReference	Allow using COM of previous step as pull group PBC reference.
PullAverage	Added possibility to output average pull force and position.
MDModules	Added checkpointing for MDModules.
ModularSimulator	Added checkpointing for modular simulator.
AwhLocalWeightSum	Added local (per walker) weight contribution to each point in AWH.
Count	The total number of checkpoint versions.
CurrentVersion	Current version.

enum gmx::ClusterDistanceKernelType : int

strong

The types of kernel for calculating the distance between pairs of atom clusters.

Enumerator
CpuPlainC_4x4	Plain-C for CPU 4x4 list.
CpuSimd_4xM	SIMD for CPU list for j-cluster size matching the SIMD width.
CpuSimd_2xMM	SIMD for CPU list for j-cluster size matching half the SIMD width.
Gpu	For GPU list, can be either plain-C or SIMD.
CpuPlainC_1x1	Plain-C for CPU 1x1 list.

enum gmx::DDBondedChecking : bool

strong

Options for checking bonded interactions.

These values must match the bool false and true used for mdrun -ddcheck

Enumerator
ExcludeZeroLimit	Do not check bonded interactions that go to 0 for large distances.
All	Check all bonded interactions.

enum gmx::DdRankOrder

strong

The options for the domain decomposition MPI task ordering.

Enumerator
select	First value (needed to cope with command-line parsing)
interleave	Interleave the PP and PME ranks.
pp_pme	First all PP ranks, all PME rank at the end.
cartesian	Use Cartesian communicators for PP, PME and PP-PME.
Count	The number of options.

enum gmx::DensityFittingAmplitudeMethod : int

strong

The methods that determine how amplitudes are spread on a grid in density guided simulations.

Enumerator
Unity	same spread amplitude, unity, for all atoms
Mass	atom mass is the spread amplitude
Charge	partial charge determines the spread amplitude

enum gmx::DensitySimilarityMeasureMethod : int

strong

The methods that determine how two densities are compared to one another.

Enumerator
innerProduct	Measure similarity between densities as normalized inner product of their voxel values.
relativeEntropy	Measure similarity between densities by negative relative entropy. Note Voxels with negative values are ignored.
crossCorrelation	Measure similarity between densities by cross correlation.

enum gmx::DeviceStreamType : int

strong

Class enum to describe the different logical streams used for GPU work.

Whether the actual streams differ is an implementation detail of the manager class.

Enumerator
NonBondedLocal	Stream primarily for short-ranged local nonbonded work.
NonBondedNonLocal	Stream primarily for short-ranged nonlocal nonbonded work.
Pme	Stream primarily for PME work.
PmePpTransfer	Stream primarily for data exchange between PME and PP ranks.
UpdateAndConstraints	Stream primarily for update and constraints.
HaloExchange	Stream used for GPU halo exchange.
Count	Conventional termination of the enumeration.

enum gmx::DlbOption

strong

The options for the dynamic load balancing.

Enumerator
select	First value (needed to cope with command-line parsing)
turnOnWhenUseful	Turn on DLB when we think it would improve performance.
no	Never turn on DLB.
yes	Turn on DLB from the start and keep it on.
Count	The number of options.

enum gmx::Domain : int

strong

Domain identifier.

Keeps track of from which compartment the ions came before passing the channel.

enum gmx::ElecType : int

strong

Nbnxm electrostatic GPU kernel flavors.

Types of electrostatics implementations available in the GPU non-bonded force kernels. These represent both the electrostatics types implemented by the kernels (cut-off, RF, and Ewald - a subset of what's defined in enums.h) as well as encode implementation details analytical/tabulated and single or twin cut-off (for Ewald kernels). Note that the cut-off and RF kernels have only analytical flavor and unlike in the CPU kernels, the tabulated kernels are ATM Ewald-only. The None option is used when Coulomb interactions are handled by an MD module, such as FMM.

The row-order of pointers to different electrostatic kernels defined in nbnxm_cuda.cu by the nb_*_kfunc_ptr function pointer table should match the order of enumerated types below.

Enumerator
Cut	Plain cut-off.
RF	Reaction field.
EwaldTab	Tabulated Ewald with single cut-off.
EwaldTabTwin	Tabulated Ewald with twin cut-off.
EwaldAna	Analytical Ewald with single cut-off.
EwaldAnaTwin	Analytical Ewald with twin cut-off.
None	No NBNxM electrostatics (e.g., when FMM uses its own direct kernel)
Fmm	Fast multipole method.
Count	Number of valid values.

enum gmx::EmulateGpuNonbonded : bool

strong

Help pass GPU-emulation parameters with type safety.

Enumerator
No	Do not emulate GPUs.
Yes	Do emulate GPUs.

enum gmx::EndianSwapBehavior : int

strong

Specify endian swapping behavoir.

Enumerator
DoNotSwap	Don't touch anything.
Swap	User-enforced swapping.
SwapIfHostIsBigEndian	Only swap if machine we execute on is big-endian.
SwapIfHostIsLittleEndian	Only swap if machine we execute on is little-endian.
Count	Number of possible behaviors.

enum gmx::EnergySignallerVirialMode

strong

When we calculate virial.

Enumerator
Off	No specific virial calculation - calculate when energy is calculated.
OnStep	Calculate on virial frequency steps.
OnStepAndNext	Calculate on virial frequency steps and on step after.
Count	The number of entries.

enum gmx::FftBackend

strong

Enumerator
Cufft	supports only single-GPU
OclVkfft	supports only single-GPU
Ocl	supports only single-GPU
CuFFTMp	supports only multi-gpu
HeFFTe_CUDA	supports only multi-gpu
HeFFTe_Sycl_OneMkl	supports only multi-gpu
HeFFTe_Sycl_Rocfft	supports only multi-gpu
HeFFTe_Sycl_cuFFT	supports only multi-gpu
HeFFTe_HIP	supports only multi-gpu
SyclMkl	supports only single-GPU
SyclOneMath	supports only single-GPU
SyclRocfft	supports only single-GPU
SyclVkfft	supports only single-GPU
SyclBbfft	supports only single-GPU
Sycl	stubs for not supported configurations
HipVkfft	supports only single-GPU
HipRocfft	supports only single-GPU

enum gmx::FlexibleConstraintTreatment

strong

Tells make_at2con how to treat flexible constraints.

Enumerator
Include	Include all flexible constraints.
Exclude	Exclude all flexible constraints.

enum gmx::FmmDirectProvider

strong

Enumeration of possible direct interaction providers.

Enumerator
Gromacs	Use GROMACS direct interactions.
Fmm	Use direct interactions from the FMM backend.

enum gmx::GpuAwareMpiStatus : int

strong

Enum describing GPU-aware support in underlying MPI library.

Ordinal, so that the lowest value can represent the minimal level of support found across a set of devices, perhaps across nodes or ranks.

Enumerator
NotSupported	GPU-aware support NOT available or not known.
Forced	GPU-aware support forced using env variable.
Supported	GPU-aware support available.
Count	Conventional final enum value.

enum gmx::GpuTask : int

strong

Types of compute tasks that can be run on a GPU.

These names refer to existing practice in GROMACS, which is not strictly accurate.

Enumerator
Nonbonded	Short-ranged interactions.
Pme	Long-ranged interactions.
Count	Number of possible tasks.

enum gmx::GraphState : int

strong

State of graph.

Enumerator
Invalid	Invalid, i.e before recording has started (including after reset)
Recording	Recording is underway and has not yet finished.
Recorded	Recording has finished, but graph is not yet instantiated.
Instantiated	Instantiated and ready to launch.
Count	Number of valid values.

enum gmx::H5mdCompression : int

strong

Data set compression options.

Enumerator
Uncompressed	No compression.
LosslessNoShuffle	Lossless, only gzip (deflate)
LosslessShuffle	Lossless, byte shuffle followed by gzip (deflate)

enum gmx::H5mdFileMode : char

strong

Enumerator
Write	Only read from the file.
Append	Write to the file, replaces it if it exists. Also allows reading from the file.

enum gmx::HaloMpiTag

strong

Enumerator
X	Coordinates.
F	Forces.
ZoneCorners	The corners of the zone.
GridCells	The number of grid cells.
GridDimensions	The contents of the grid cell.
AtomIndices	The dimensions of the grid. Global atom indices

enum gmx::HelpOutputFormat

Output format for help writing.

Enumerator
eHelpOutputFormat_Console	Plain text directly on the console.
eHelpOutputFormat_Rst	reStructuredText for online manual and man pages.
eHelpOutputFormat_Other	Used for extensions in other modules.
eHelpOutputFormat_NR	Used for the number of output formats.

enum gmx::ILJInteractions

strong

The fraction of i-particles for which LJ interactions need to be computed.

Enumerator
All	all i-particles
Half	the first half of the i-particles
None	none of i-particles

enum gmx::IMDMessageType : int

strong

Enum for types of IMD messages.

We use the same records as the NAMD/VMD IMD implementation.

Enumerator
Disconnect	client disconnect
Energies	energy data
FCoords	atomic coordinates
Go	start command for the simulation
Handshake	handshake to determine little/big endianness
Kill	terminates the simulation
Mdcomm	force data
Pause	pauses the simulation
TRate	sets the IMD transmission and processing rate
IOerror	I/O error.
Count	number of entries

enum gmx::InteractionLocality : int

strong

Interaction locality indicator: local, non-local, all.

Used for calls to: pair-search, force calculation, x/f buffer operations

Enumerator
Local	Interactions between local atoms only.
NonLocal	Interactions between non-local and (non-)local atoms.
Count	The number of interaction locality types.

enum gmx::KernelCoulombType

strong

List of type of Nbnxm kernel coulomb type implementations.

Enumerator
RF	Reaction-field, also used for plain cut-off.
EwaldAnalytical	Ewald with analytical reciprocal contribution correction.
EwaldTabulated	Ewald with tabulated reciprocal contribution correction.
None	If FMM implementation has its own Coulomb kernels.

enum gmx::LJCombinationRule : int

strong

LJ combination rules.

Enumerator
Geometric	Geometric.
LorentzBerthelot	Lorentz-Berthelot.
None	No rule.
Count	Size of the enum.

enum gmx::LJKernelType

strong

The free-energy kernel Lennard-Jones functional shape.

Enumerator
Cutoff	Plain cut-off with or without potential shift.
ForceSwitch	Force switch.
PotentialSwitch	Potential Switch.
Ewald	Ewald for dispersion.

enum gmx::MoleculePatchType

strong

Declare different types of hacks for later check.

Enumerator
Add	Hack adds atom to structure/rtp.
Delete	Hack deletes atom.
Replace	Hack replaces atom.

enum gmx::MrcDataMode : int32_t

strong

The type of density data stored in an mrc file. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014" Modes 0-4 are defined by the standard. NOTE only mode 2 is currently implemented and used.

Enumerator
uInt8	compressed data mode, 8 bits, signed byte (range -128 to 127, ISO/IEC 10967)
int16	16 bits, signed integer (range -32768 to 32767, ISO/IEC 10967)
float32	32 bits, floating point number (IEEE 754)
complexInt32	32 bits, complex signed integers (ISO/IEC 10967)
complexFloat64	64 bits, complex floating point numbers (IEEE 754)

enum gmx::MtsForceGroups : int

strong

Force group available for selection for multiple time step integration.

Enumerator
LongrangeNonbonded	PME-mesh or Ewald for electrostatics and/or LJ.
Nonbonded	Non-bonded pair interactions.
Pair	Bonded pair interactions.
Dihedral	Dihedrals, including cmap (not restraints)
Angle	Bonded angle potentials (not restraints)
Pull	COM pulling.
Awh	Accelerated weight histogram method.
Count	The number of groups above.

enum gmx::NhcUsage

strong

The usages of Nose-Hoover chains.

Enumerator
System	Couple system to temperature bath.
Barostat	Couple barostat to temperature bath.
Count	Number of enum entries.

enum gmx::NNPotEmbedding

strong

Enum to specify embedding scheme used for NNP/MM interaction.

Enumerator
Mechanical	Mechanical embedding: NNP/MM interaction calculated classically.
ElectrostaticModel	Electrostatic embedding calculated within NNP model (e.g.g EMLE-engine)

enum gmx::Normalization

strong

Enum with different ways of normalizing the output.

Enumerator
None	No normalization.
Coordinate	Scale using the internal/user input coordinate scaling factor.
FreeEnergy	Normalize free energy values by subtracting the minimum value.
Distribution	Normalize the distribution to 1.

enum gmx::NumTempScaleValues

strong

Sets the number of different temperature coupling values.

This is needed to template the kernel

Todo:

Unify with similar enum in CPU update module

Enumerator
None	No temperature coupling.
Single	Single T-scaling value (one group)
Multiple	Multiple T-scaling values, need to use T-group indices.
Count	Number of valid values.
None	No temperature scaling.
Single	Single T-scaling value (either one group or all values =1)
Multiple	Multiple T-scaling values, need to use T-group indices.

enum gmx::NumTempScaleValues

strong

Sets the number of different temperature coupling values.

Enumerator
None	No temperature coupling.
Single	Single T-scaling value (one group)
Multiple	Multiple T-scaling values, need to use T-group indices.
Count	Number of valid values.
None	No temperature scaling.
Single	Single T-scaling value (either one group or all values =1)
Multiple	Multiple T-scaling values, need to use T-group indices.

enum gmx::ObservablesReducerStatus : int

strong

Report whether the reduction has happened this step.

Enumerator
ReadyToReduce	Reduction has not yet happened this step.
AlreadyReducedThisStep	Reduction has happened this step.

enum gmx::OptionFlag : uint64_t

Flags for options.

These flags are not part of the public interface, even though they are in an installed header. They are needed in a few template class implementations.

Todo:

The flags related to default values are confusing, consider reorganizing them.

Enumerator
efOption_Set	Option has been set.
efOption_HasDefaultValue	The current value of the option is a programmatic default value.
efOption_ExplicitDefaultValue	An explicit default value has been provided for the option.
efOption_ClearOnNextSet	Next assignment to the option clears old values. This flag is set when a new option source starts, such that values from the new source will overwrite old ones.
efOption_Required	Option is required to be set.
efOption_MultipleTimes	Option can be specified multiple times.
efOption_Hidden	Option is hidden from standard help.
efOption_Vector	Option value is a vector, but a single value is also accepted. See Also AbstractOption::setVector()
efOption_DefaultValueIfSetExists	Option has a defaultValueIfSet() specified.
efOption_NoDefaultValue	Option does not support default values.
efOption_DontCheckMinimumCount	Storage object does its custom checking for minimum value count. If this flag is set, the class derived from OptionStorageTemplate should implement processSetValues(), processAll(), and possible other functions it provides such that it always fails if not enough values are provided. This is useful to override the default check, which is done in OptionStorageTemplate::processSet().

enum gmx::ParrinelloRahmanVelocityScaling

strong

Describes the properties of the Parrinello-Rahman pressure scaling matrix.

Enumerator
No	Do not apply velocity scaling (not a PR-coupling run or step)
Diagonal	Apply velocity scaling using a diagonal matrix.
Anisotropic	Apply velocity scaling using a matrix with off-diagonal elements.
No	Do not apply velocity scaling (not a PR-coupling run or step)
Diagonal	Apply velocity scaling using a diagonal matrix.
Anisotropic	Apply velocity scaling using a matrix with off-diagonal elements.

enum gmx::PbcMode

strong

PBC modes for vsite construction and spreading.

Enumerator
all	Apply normal, simple PBC for all vsites.
none	No PBC treatment needed.

enum gmx::PinningPolicy : int

strong

Helper enum for pinning policy of the allocation of HostAllocationPolicy.

For an efficient non-blocking transfer (e.g. to a GPU), the memory pages for a buffer need to be pinned to a physical page. Aligning such buffers to a physical page should miminize the number of pages that need to be pinned. However, some buffers that may be used for such transfers may also be used in either GROMACS builds or run paths that cannot use such a device, so the policy can be configured so that the resource consumption is no higher than required for correct, efficient operation in all cases.

enum gmx::QMMMElectrostaticCoupling

strong

Enumerator for the QM/MM electrostatic coupling generated for tight-binding CP2K.

Enumerator
PointCharge	Use CP2K's POINT_CHARGE coupling.
Gauss	Use CP2K's GAUSS coupling also known as GEEP (Gaussian Electrostatic Embedding Potential)

enum gmx::QMMMQMMethod

strong

Enumerator for supported QM methods Also could be INPUT which means external input file provided with the name determined by QMMMParameters::qminputfilename_.

Enumerator
PBE	DFT with PBE functional.
PBE_D3	DFT with PBE functional and D3 dispersion correction.
BLYP	DFT with BLYP functional.
BLYP_D3	DFT with BLYP functional and D3 dispersion correction.
PBE0	DFT with PBE0 functional.
PBE0_D3	DFT with PBE0 functional and D3 dispersion correction.
B3LYP	DFT with B3LYP functional.
B3LYP_D3	DFT with B3LYP functional and D3 dispersion correction.
CAM_B3LYP	DFT with CAM-B3LYP functional.
CAM_B3LYP_D3	DFT with CAM-B3LYP functional and D3 dispersion correction.
WB97X	DFT with WB97X functional.
WB97X_D3	DFT with WB97X functional and D3 dispersion correction.
SCC_DFTB	Self-consistent-charge density-functional tight binding.
GFN1_XTB	Semi-empirical GFN1-xTB through CP2K's tblite interface.
GFN2_XTB	Semi-empirical GFN2-xTB through CP2K's tblite interface.
INPUT	User provides suitable input file for QM package.

enum gmx::RandomDomain

strong

Enumerated values for fixed part of random seed (domain)

Random numbers are used in many places in GROMACS, and to avoid identical streams the random seeds should be different. Instead of keeping track of several different user-provided seeds, it is better to use the fact that generators like ThreeFry take two 64-bit keys, and combine a general user-provided 64-bit random seed with a second constant value from this list to make each stream guaranteed unique.

Note

There is no reason to go overboard with adding options; we only need to guarantee different streams for cases that might be present simultaneously in a single simulation. As an example, two different integrators (or thermostats) can reuse the same domain.

When you do add options, leave some space between the values so you can group new options with old ones without changing old values.

Enumerator
Other	Generic - stream uniqueness is not important.
MaxwellVelocities	Veolcity assignment from Maxwell distribution.
TestParticleInsertion	Test particle insertion.
UpdateCoordinates	Particle integrators.
UpdateConstraints	Second integrator step for constraints.
Thermostat	Stochastic temperature coupling.
Barostat	Stochastic pressure coupling.
ReplicaExchange	Replica exchange metropolis moves.
ExpandedEnsemble	Expanded ensemble lambda moves.
AwhBiasing	AWH biasing reference value moves.

enum gmx::ReductionRequirement : int

strong

Control whether reduction is required soon.

Enumerator
Soon	Reduce whenever the runner next checks with the ObservablesReducer.
Eventually	Reduce whenever the runner next checks with the ObservablesReducer after some module requires reduction Soon.

enum gmx::ResetSignal

strong

Reset signals.

Signals set and read by ResetHandler. Possible signals include

• nothing to signal
• reset counters (as soon as signal is received)

enum gmx::ScheduleOnInitStep

strong

Whether the element does schedule on the initial step.

Enumerator
Yes	Schedule on first step.
No	Do not schedule on first step.
Count	Number of enum entries.

enum gmx::SimdType

strong

Enumerated options for SIMD architectures.

Enumerator
None	Disable all SIMD support.
Reference	Gromacs reference software SIMD.
Generic	Placeholder for future support for gcc generic SIMD.
X86_Sse2	SSE2.
X86_Sse4_1	SSE4.1.
X86_Avx128Fma	128-bit Avx with FMA (Amd)
X86_Avx	256-bit Avx
X86_Avx2	AVX2.
X86_Avx2_128	128-bit AVX2, better than 256-bit for AMD Ryzen
X86_Avx512	AVX_512.
Arm_NeonAsimd	64-bit ARM AArch64 Advanced SIMD
Arm_Sve	ARM Scalable Vector Extensions.
Ibm_Vsx	IBM VSX SIMD (Power7 and later)

enum gmx::SpaceGroup : int32_t

strong

Space group in three dimensions.

Currently only "no symmetry" is supported, the complete enum class would hold 230 symbols.

Table 12.3.4.1 Standard space-group symbols, pages 824-831, International Tables for Crystallography, Volume A, fifth edition

Enumerator
P1	no symmetry

enum gmx::StartingBehavior : int

strong

Enumeration for describing how mdrun is (re)starting.

Enumerator
RestartWithAppending	Restarting with appending, if a checkpoint is supplied and other conditions are met.
RestartWithoutAppending	Restarting without appending, when a checkpoint is supplied.
NewSimulation	Not restarting.
Count	Mark the end of the enumeration.

enum gmx::StopSignal : int

strong

Stop signals.

Signals that stop conditions can send to all ranks. Possible signals include

• nothing to signal
• stop at the next neighbor-searching step
• stop as soon as signal is received

enum gmx::StoreUpdatedVelocities

strong

Sets whether we store the updated velocities.

Enumerator
Yes	Store the updated velocities.
No	Do not store the updated velocities.

enum gmx::StripStrings : int

strong

Enum class for whether StringToEnumValueConverter will strip strings of leading and trailing whitespace before comparison.

Enumerator
No	Do not strip strings.
Yes	Strip strings.

enum gmx::VdwType : int

strong

Nbnxm VdW GPU kernel flavors.

The enumerates values correspond to the LJ implementations in the GPU non-bonded kernels.

The column-order of pointers to different electrostatic kernels defined in nbnxm_cuda_ocl.cpp/.cu by the nb_*_kfunc_ptr function pointer table should match the order of enumerated types below.

Enumerator
Cut	Plain cut-off.
CutCombGeom	Cut-off with geometric combination rules.
CutCombLB	Cut-off with Lorentz-Berthelot combination rules.
FSwitch	Smooth force switch.
PSwitch	Smooth potential switch.
EwaldGeom	Ewald with geometric combination rules.
EwaldLB	Ewald with Lorentz-Berthelot combination rules.
Count	Number of valid values.

enum gmx::VirtualSiteVirialHandling : int

strong

Tells how to handle virial contributions due to virtual sites.

Enumerator
None	Do not compute virial contributions.
Pbc	Add contributions working over PBC to shift forces.
NonLinear	Compute contributions due to non-linear virtual sites.

enum gmx::VSiteOperation

strong

Whether we calculate vsite positions, velocities, or both.

Enumerator
Positions	Calculate only positions.
Velocities	Calculate only velocities.
PositionsAndVelocities	Calculate both positions and velocities.
Count	The number of entries.

Function Documentation

static gmx::__attribute__ ( (always_inline)  ) const

inlinestatic

Convert sigma and epsilon VdW parameters to c6,c12 pair.

Fetch C6 grid contribution coefficients and return the product of these.

Calculate force and energy for a pair of atoms, VdW force-switch flavor.

template<int threadsPerBlock>

gmx::__launch_bounds__

(

threadsPerBlock

)

HIP bucket sci sort kernel.

Sorts sci in order from most to least neighbours, using the count sort algorithm

Unlike the cpu version of sci sort, this kernel uses counts which only contain pairs which have not been masked out, giving an ordering which more accurately represents the work which will be done in the non bonded force kernel. The counts themselves are generated in the prune kernel.

Inputs:

• plist.sci = unsorted pair list
• plist.sorting.sciCount[i] = total number of sci with exactly i neighbours
• plist.sorting.sciOffset = exclusive prefix sum of sciCount. plist.sorting.sciOffset[i] represents the offset that the first sci with i neighbours will have in the sorted sci list. All other sci with i neighbours will be placed randomly in positions plist.sorting.sciOffset[i] to plist.sorting.sciOffset[i+1] exclusive

template<PairlistType pairlistType, bool haveFreshList, int threadZ, int minBlocksPp>

gmx::__launch_bounds__	(	c_clSizeSq< pairlistType > *	threadZ,
		minBlocksPp
	)

Prune-only kernel for NBNXM.

The number of threads per block is always c_clSizeSq, so we can use it here without having to pass another template argument. The remaining multipliers are architecture and kernel flavor specific and need to be passed in.

template<bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType, int nthreadZ, int minBlocksPerMp, PairlistType pairlistType>

gmx::__launch_bounds__	(	c_clSizeSq< pairlistType > *	nthreadZ,
		minBlocksPerMp
	)

Main kernel for NBNXM.

static float gmx::abs ( float  a )

inlinestatic

Float Floating-point abs().

Parameters

a	any floating point values

Returns

abs(a) for each element.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::abs ( double  a )

inlinestatic

double doubleing-point abs().

Parameters

a	any doubleing point values

Returns

abs(a) for each element.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::acos ( float  x )

inlinestatic

Float acos.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::acos ( double  x )

inlinestatic

Double acos.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::acosSingleAccuracy ( double  x )

inlinestatic

Double acos, but with single accuracy.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::add_cmap_param	(	InteractionsOfType *	ps,
		int	ai,
		int	aj,
		int	ak,
		int	al,
		int	am,
		ArrayRef< const real >	c,
		const char *	s
	)

Adds a CMAP interaction to the list of interactions.

Parameters

ps	List of interactions.
ai	First atom.
aj	Second atom.
ak	Third atom.
al	Fourth atom.
am	Fifth atom.
c	Two CMAP types: if specified, first is used to override the default for state A, second for state B.
s	Interaction name.

int gmx::add_h	(	t_atoms **	initialAtoms,
		t_atoms **	localAtoms,
		std::vector< gmx::RVec > *	xptr,
		gmx::ArrayRef< const MoleculePatchDatabase >	globalPatches,
		gmx::ArrayRef< const PreprocessResidue >	residueTopology,
		t_symtab *	symtab,
		int	nterpairs,
		gmx::ArrayRef< MoleculePatchDatabase *const >	ntdb,
		gmx::ArrayRef< MoleculePatchDatabase *const >	ctdb,
		gmx::ArrayRef< const int >	rN,
		gmx::ArrayRef< const int >	rC,
		bool	bMissing,
		gmx::ArrayRef< const int >	cyclicBondsIndex
	)

Generate hydrogen atoms and N and C terminal patches.

Parameters

[in,out]	initialAtoms	The input atoms data structure to be modified.
[in,out]	localAtoms	The extra atoms for reassigning the new entries.
[in,out]	xptr	Coordinates to be updated with those for new atoms.
[in]	globalPatches	The atom modifications to use.
[in]	residueTopology	The residue topology entries corresponding to the atoms.
[in,out]	symtab	Global symbol table for atom names.
[in]	nterpairs	Number of termini pairs in the molecule.
[in]	ntdb	Entries for N-terminus in each chain, each entry can be valid or nullptr.
[in]	ctdb	Entries for C-terminus in each cahin, each entry can be valid or nullptr.
[in]	rN	Residue number of the N-terminus of each chain.
[in]	rC	Residue number of the C-terminus of each chain.
[in]	bMissing	If routine should continue if atoms are not found.
[in]	cyclicBondsIndex	Index of cyclic bonds or empty.

Returns

New total number of atoms.

void gmx::add_param	(	InteractionsOfType *	ps,
		int	ai,
		int	aj,
		ArrayRef< const real >	c,
		const char *	s
	)

Adds an interaction to the list of interactions.

Parameters

ps	List of interactions.
ai	First atom.
aj	Second atom.
c	Interaction parameters.
s	Interaction name.

static void gmx::add_to_list ( int  ci, t_compartment *  comp, real  distance  )

static

Add the atom with collective index ci to the atom list in compartment 'comp'.

This atom is expected to be the first atom of a molecule.

Parameters

[in]	ci	Index of this ion in the collective xc array.
[in,out]	comp	Compartment to add this atom to.
[in]	distance	Shortest distance of this atom to the bulk layer, from which ion/water pairs are selected for swapping.

void gmx::addEmbeddedNBExclusions	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const MDLogger &	logger
	)

Build exclusion list for non-bonded interactions between embedded atoms.

Adds embedded atoms to mtop->intermolecularExclusionGroup

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	logger	MDLogger for logging info about modifications

void gmx::addMdpOutputComment ( KeyValueTreeObjectBuilder *  builder, std::string_view  moduleName, std::string_view  optionName, const std::string &  comment  )

inline

Add a comment for an mdp value with a module-prefixed name.

Parameters

[in]	builder	Builder for KVT output
[in]	moduleName	Module name prefix
[in]	optionName	Suffix of the mdp option name
[in]	comment	Comment text to write

template<class ValueType >

void gmx::addMdpOutputValue	(	KeyValueTreeObjectBuilder *	builder,
		std::string_view	moduleName,
		std::string_view	optionName,
		const ValueType &	optionValue
	)

Add an mdp value to output KVT with a module-prefixed name.

Template Parameters

ValueType

Type of the value described by the option

Parameters

[in]	builder	Builder for KVT output
[in]	moduleName	Module name prefix
[in]	optionName	Suffix of the mdp option name
[in]	optionValue	Value to write

template<class ToType , class TransformWithFunctionType >

void gmx::addMdpTransformFromString	(	IKeyValueTreeTransformRules *	rules,
		TransformWithFunctionType	transformationFunction,
		std::string_view	moduleName,
		std::string_view	optionName
	)

Helper to declare mdp transform rules.

Enforces uniform mdp option transformation for a given module.

Template Parameters

ToType	type to be transformed to
TransformWithFunctionType	type of transformation function from std::string to ToType

Parameters

[in]	rules	KVT transformation rules
[in]	transformationFunction	function to transform string to ToType
[in]	moduleName	module name prepended to the option name
[in]	optionName	suffix of the mdp option name

template<int packSize>

static void gmx::addNbatFPackedToFPart ( const nbnxm_atomdata_output_t &  out, const int  a0, const int  a1, const int *  cellIndices, ArrayRef< RVec >  forces  )

static

Adds forces in SIMD packed layout to an RVec array.

Template Parameters

packSize

The stride of the packs in out

Parameters

[in]	out	Nbnxm thread output data containing the forces to be added
[in]	a0	The start of the atom range to add forces for
[in]	a1	The end of the atom range to add forces for
[in]	cellIndices	List of NBNxM cell indices, when nullptr the identity mapping is used
[in,out]	forces	The force buffer to add into

static OutputAdapterContainer gmx::addOutputAdapters ( const OutputRequirements &  requirements, AtomsDataPtr  atoms, const Selection &  sel, unsigned long  abilities  )

static

Creates a new container object with the user requested IOutputAdapter derived methods attached to it.

Parameters

[in]	requirements	Specifications for modules to add.
[in]	atoms	Local copy of atom information to use.
[in]	sel	Selection to use for choosing atoms to write out.
[in]	abilities	Specifications for what the output method can do.

Returns

New container for IoutputAdapter derived methods.

void gmx::addWithCoupled ( ArrayRef< const int >  iatoms, const int  stride, const gmx::ListOfLists< AtomsAdjacencyListElement > &  atomsAdjacencyList, ArrayRef< int >  splitMap, const int  c, int *  currentMapIndex  )

inline

Add constraint to splitMap with all constraints coupled to it.

Adds the constraint c from the constrain list iatoms to the map splitMap if it was not yet added. Then goes through all the constraints coupled to c and calls itself recursively. This ensures that all the coupled constraints will be added to neighboring locations in the final data structures on the device, hence mapping all coupled constraints to the same thread block. A value of -1 in the splitMap is used to flag that constraint was not yet added to the splitMap.

Parameters

[in]	iatoms	The list of constraints.
[in]	stride	Number of elements per constraint in iatoms.
[in]	atomsAdjacencyList	Information about connections between atoms.
[out]	splitMap	Map of sequential constraint indexes to indexes to be on the device
[in]	c	Sequential index for constraint to consider adding.
[in,out]	currentMapIndex	The rolling index for the constraints mapping.

static void gmx::adjustAtomInformation ( t_atoms *  atoms, t_atoms *  selectionAtoms, const Selection &  sel  )

static

Modify atoms information in coordinate frame to fit output selection.

Changes the information contained in the coordinate frame t_atoms struct to match the selection provided to the module.

Parameters

[in]	atoms	Pointer to original t_atoms.
[in]	selectionAtoms	Pointer to local atoms.
[in]	sel	Reference to selection.

bool gmx::advancePointInSubgrid	(	const BiasGrid &	grid,
		const awh_ivec	subgridOrigin,
		const awh_ivec	subgridNpoints,
		int *	gridPointIndex
	)

Find the next grid point in the sub-part of the grid given a starting point.

The given grid point index is updated to the next valid grid point index by traversing the sub-part of the grid, here termed the subgrid. Since the subgrid range might extend beyond the actual size of the grid, the subgrid is traversed until a point both in the subgrid and grid is found. If no point is found, the function returns false and the index is not modified. The starting point needs to be inside of the subgrid. However, if this index is not given, meaning < 0, then the search is initialized at the subgrid origin, i.e. in this case the "next" grid point index is defined to be the first common grid/subgrid point.

Parameters

[in]	grid	The grid.
[in]	subgridOrigin	Vector locating the subgrid origin relative to the grid origin.
[in]	subgridNpoints	Number of points along each subgrid dimension.
[in,out]	gridPointIndex	Pointer to the starting/next grid point index.

Returns

true if the grid point was updated.

static void gmx::alternatePmeNbGpuWaitReduce ( nonbonded_verlet_t *  nbv, gmx_pme_t *  pmedata, ForceOutputs *  forceOutputsNonbonded, ForceOutputs *  forceOutputsPme, gmx_enerdata_t *  enerd, const real  lambdaQ, const StepWorkload &  stepWork, const SimulationWorkload &  simulationWork, gmx_wallcycle *  wcycle  )

static

Polling wait for either of the PME or nonbonded GPU tasks.

Instead of a static order in waiting for GPU tasks, this function polls checking which of the two tasks completes first, and does the associated force buffer reduction overlapped with the other task. By doing that, unlike static scheduling order, it can always overlap one of the reductions, regardless of the GPU task completion order.

Parameters

[in]	nbv	Nonbonded verlet structure
[in,out]	pmedata	PME module data
[in,out]	forceOutputsNonbonded	Force outputs for the non-bonded forces and shift forces
[in,out]	forceOutputsPme	Force outputs for the PME forces and virial
[in,out]	enerd	Energy data structure results are reduced into
[in]	lambdaQ	The Coulomb lambda of the current system state.
[in]	stepWork	Step schedule flags
[in]	simulationWork	Simulation schedule flags
[in]	wcycle	The wallcycle structure

static float gmx::andNot ( float  a, float  b  )

inlinestatic

Bitwise andnot for two scalar float variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::andNot ( double  a, double  b  )

inlinestatic

Bitwise andnot for two scalar double variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::andNot ( std::int32_t  a, std::int32_t  b  )

inlinestatic

Bitwise andnot for two scalar integer variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static bool gmx::anyBiasIsScaledByMetric ( const AwhParams &  awhParams )

static

Checks whether any bias scales the target distribution based on the AWH friction metric.

Parameters

[in]

awhParams

The AWH params to check.

Returns

true if any of the biases scale the target distribution by the friction metric.

static bool gmx::anyDimUsesProvider ( const AwhBiasParams &  awhBiasParams, const AwhCoordinateProviderType  awhCoordProvider  )

static

Checks whether any dimension uses the given coordinate provider type.

Parameters

[in]	awhBiasParams	The bias params to check.
[in]	awhCoordProvider	The type of coordinate provider

Returns

true if any dimension of the bias is linked to the given provider

static bool gmx::anyDimUsesProvider ( const AwhParams &  awhParams, const AwhCoordinateProviderType  awhCoordProvider  )

static

Checks whether any dimension uses the given coordinate provider type.

Parameters

[in]	awhParams	The AWH params to check.
[in]	awhCoordProvider	The type of coordinate provider

Returns

true if any dimension of awh is linked to the given provider type.

static bool gmx::anyTrue ( bool  a )

inlinestatic

Returns if the boolean is true.

Parameters

a	Logical variable.

Returns

true if a is true, otherwise false.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::applyGlobalSimulationState	(	const SimulationInput &	simulationInput,
		PartialDeserializedTprFile *	partialDeserializedTpr,
		t_state *	globalState,
		t_inputrec *	inputrec,
		gmx_mtop_t *	globalTopology
	)

Get the global simulation input.

Acquire global simulation data structures from the SimulationInput handle. Note that global data is returned in the calling thread. In parallel computing contexts, the client is responsible for calling only where needed.

Example: if (SIMMAIN(cr)) { // Only the main rank has the global state globalState = globalSimulationState(simulationInput);

// Read (nearly) all data required for the simulation applyGlobalInputRecord(simulationInput, inputrec); applyGlobalTopology(simulationInput, &mtop); }

Todo:

Factor the logic for global/local and main-rank-checks. The SimulationInput utilities should behave properly for the various distributed data scenarios. Consider supplying data directly to the consumers rather than exposing the implementation details of the legacy aggregate types.

void gmx::applyLocalState	(	const SimulationInput &	simulationInput,
		t_fileio *	logfio,
		const MpiComm &	mpiCommSimulation,
		t_inputrec *	ir,
		t_state *	state,
		ObservablesHistory *	observablesHistory,
		bool	reproducibilityRequested,
		const MDModulesNotifiers &	notifiers,
		ReadCheckpointDataHolder *	modularSimulatorCheckpointData,
		bool	useModularSimulator
	)

Initialize local stateful simulation data.

Establish an invariant for the simulator at a trajectory point. Call on all ranks (after domain decomposition and task assignments).

After this call, the simulator has all of the information it will receive in order to advance a trajectory from the current step. Checkpoint information has been applied, if applicable, and stateful data has been (re)initialized.

Warning

Mdrunner instances do not clearly distinguish between global and local versions of t_state.

Todo:

Factor the distributed data aspects of simulation input data into the SimulationInput implementation.

Todo:

Consider refactoring to decouple the checkpoint facility from its consumers (state, observablesHistory, mdModulesNotifiers, and parts of ir).

Warning

It is the caller’s responsibility to make sure that preconditions are satisfied for the parameter objects.

See Also

globalSimulationState()

applyGlobalInputRecord()

applyGlobalTopology()

static void gmx::applySetup ( pme_setup_t *  setup, gmx_pme_t *  oldPmedata, const t_inputrec &  ir, interaction_const_t *  ic, nonbonded_verlet_t *  nbv, gmx_domdec_t *  dd, const PmePpComm *  pmePpComm  )

static

Updates all the mdrun machinery for setup.

setup->pmedata is set when empty or when running PME on GPU oldPmedata is not modified, except that the GPU object is moved out, when present

static float gmx::asin ( float  x )

inlinestatic

float asin.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::asin ( double  x )

inlinestatic

Double asin.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::asinSingleAccuracy ( double  x )

inlinestatic

Double asin, but with single accuracy.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::assertMatrixIsBoxMatrix ( const Matrix3x3 gmx_used_in_debug &  m )

inlinestatic

Assert that the matrix m describes a simulation box.

The GROMACS convention is that all simulation box descriptions are normalized to have zero entries in the upper triangle. This function asserts if that is not true.

static void gmx::assertMatrixIsBoxMatrix ( const matrix gmx_used_in_debug  m )

inlinestatic

Assert that the matrix m describes a simulation box.

The GROMACS convention is that all simulation box descriptions are normalized to have zero entries in the upper triangle. This function asserts if that is not true.

static void gmx::assignVsitesToThread ( VsiteThread *  tData, const int  thread, const int  numThreads, const int  numAtomsPerThread, gmx::ArrayRef< int >  taskIndex, const gmx::EnumerationArray< InteractionFunction, InteractionList > &  ilist, ArrayRef< const t_iparams >  ip, ArrayRef< const ParticleType >  ptype  )

static

Here we try to assign all vsites that are in our local range.

Our task local atom range is tData->rangeStart - tData->rangeEnd. Vsites that depend only on local atoms, as indicated by taskIndex[]==thread, are assigned to task tData->ilist. Vsites that depend on non-local atoms but not on other vsites are assigned to task tData->id_task.ilists. taskIndex[] is set for all vsites in our range, either to our local tasks or to the single last task as taskIndex[]=2*numThreads.

static float gmx::atan ( float  x )

inlinestatic

Float atan.

Parameters

x	The argument to evaluate atan for

Returns

Atan(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::atan ( double  x )

inlinestatic

Double atan.

Parameters

x	The argument to evaluate atan for

Returns

Atan(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::atan2 ( float  y, float  x  )

inlinestatic

Float atan2(y,x).

Parameters

y	Y component of vector, any quartile
x	X component of vector, any quartile

Returns

Atan(y,x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::atan2 ( double  y, double  x  )

inlinestatic

Double atan2(y,x).

Parameters

y	Y component of vector, any quartile
x	X component of vector, any quartile

Returns

Atan(y,x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::atan2SingleAccuracy ( double  y, double  x  )

inlinestatic

Double atan2(y,x), but with single accuracy.

Parameters

y	Y component of vector, any quartile
x	X component of vector, any quartile

Returns

Atan(y,x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::atanSingleAccuracy ( double  x )

inlinestatic

Double atan, but with single accuracy.

Parameters

x	The argument to evaluate atan for

Returns

Atan(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static bool gmx::atom_is_present_in_nnb ( const t_nextnb *  nnb, int  atom, int  highest_order, int  query  )

static

Return true of neighbor is already present in some exclusion level.

To avoid exploding complexity when processing exclusions for highly connected molecules with lots of exclusions, this routine is used to check whether a particular neighbor has already been excluded at any lower bond distance, in which case we should not add it to avoid creating loops.

Parameters

nnb	Valid initialized next-neighbor structure
atom	The host atom whose neighbors we are searching
highest_order	The highest-rank neighbor list to search.
query	Atom index to look for

Returns

True if query is present as an exclusion of up to highest_order (inclusive) from atom. For instance, if highest_order is 2, the routine will return true if the query atom is already listed as first or second neighbor (exclusion) in nnb.

static InteractionLocality gmx::atomToInteractionLocality ( const AtomLocality  atomLocality )

inlinestatic

Convert atom locality to interaction locality.

In the current implementation the this is straightforward conversion: local to local, non-local to non-local.

Parameters

[in]

atomLocality

Atom locality specifier

Returns

Interaction locality corresponding to the atom locality passed.

static real gmx::averageKineticEnergyEstimate ( const t_grpopts &  groupOptions )

static

Return an estimate of the average kinetic energy or 0 when unreliable.

Parameters

groupOptions

Group options, containing T-coupling options

static gmx_bool gmx::bConvertFromOldTpr ( t_swapcoords *  sc )

static

Returns TRUE if we started from an old .tpr.

Then we need to re-sort anions and cations into separate groups

template<class BasicMdspan >

constexpr std::enable_if_t<BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer> gmx::begin

(

const BasicMdspan &

basicMdspan

)

Free begin function addressing memory of a contiguously laid out basic_mdspan.

Note

Changing the elements that basic_mdspan views does not change the view itself, so a single begin that takes a const view suffices.

void gmx::bench	(	int	sizeFactor,
		const NbnxmKernelBenchOptions &	options
	)

Sets up and runs one or more Nbnxm kernel benchmarks.

The simulated system is a box of 1000 SPC/E water molecules scaled by the factor sizeFactor, which has to be a power of 2. One or more benchmarks are run, as specified by options. Benchmark settings and timings are printed to stdout.

Parameters

[in]	sizeFactor	How much should the system size be increased.
[in]	options	How the benchmark will be run.

void gmx::biasesAreCompatibleForSharingBetweenSimulations	(	const AwhParams &	awhParams,
		ArrayRef< const size_t >	pointSize,
		const BiasSharing &	biasSharing
	)

Checks whether biases are compatible for sharing between simulations, throws when not.

Should be called simultaneously on the main rank of every simulation. Note that this only checks for technical compatibility. It is up to the user to check that the sharing physically makes sense. Throws an exception when shared biases are not compatible.

Parameters

[in]	awhParams	The AWH parameters.
[in]	pointSize	Vector of grid-point sizes for each bias.
[in]	biasSharing	Object for communication for sharing bias data over simulations.

static float gmx::blend ( float  a, float  b, bool  sel  )

inlinestatic

Blend float selection.

Parameters

a	First source
b	Second source
sel	Boolean selector

Returns

Select b if sel is true, a otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::blend ( double  a, double  b, bool  sel  )

inlinestatic

Blend double selection.

Parameters

a	First source
b	Second source
sel	Boolean selector

Returns

Select b if sel is true, a otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::blend ( std::int32_t  a, std::int32_t  b, bool  sel  )

inlinestatic

Blend integer selection.

Parameters

a	First source
b	Second source
sel	Boolean selector

Returns

Select b if sel is true, a otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::blockaToExclusionBlocks	(	const t_blocka *	b,
		gmx::ArrayRef< ExclusionBlock >	b2
	)

Convert the exclusions.

Convert t_blocka exclusions in b into ExclusionBlock form and include them in b2.

Parameters

[in]	b	Exclusions in t_blocka form.
[in,out]	b2	ExclusionBlocks to populate with t_blocka exclusions.

std::unique_ptr< BoxDeformation > gmx::buildBoxDeformation	(	const Matrix3x3 &	initialBox,
		DDRole	ddRole,
		NumRanks	numRanks,
		MPI_Comm	communicator,
		const t_inputrec &	inputrec
	)

Factory function for box deformation module.

If the inputrec specifies the use of box deformation during the update phase, communicates the initialBox from SIMMAIN to other ranks, and constructs and returns an object to manage that update.

Exceptions

NotImplementedError

if the inputrec specifies an unsupported combination.

std::vector< int > gmx::buildEmbeddedAtomNumbers

(

const gmx_mtop_t &

mtop

)

Builds and returns a vector of atom numbers for all atoms in mtop.

Parameters

[in]

mtop

topology to be processed

Returns

vector of atom numbers for all atoms

std::vector< LinkFrontierAtom > gmx::buildLinkFrontier	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const std::vector< bool > &	isEmbeddedBlock,
		const MDLogger &	logger
	)

Builds link frontier vector with pairs of atoms indicting broken embedded - MM chemical bonds.

Also performs search of constrained bonds within embedded subsystem.

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	isEmbeddedBlock	vector with flags for embedded atom-containing blocks
[in]	logger	MDLogger for logging info about modifications

Returns

vector of link atom pairs

bool gmx::buildSupportsListedForcesGpu

(

std::string *

error

)

Checks whether the GROMACS build allows to compute bonded interactions on a GPU.

Parameters

[out]

error

If non-null, the diagnostic message when bondeds cannot run on a GPU.

Returns

true when this build can run bonded interactions on a GPU, false otherwise.

Exceptions

std::bad_alloc

when out of memory.

constexpr bool gmx::c_avoidFloatingPointAtomics

(

PairlistType

layoutType

)

Should we avoid FP atomics to the same location from the same work-group?

Intel GPUs without native floating-point operations emulate them via CAS-loop, which is very, very slow when two threads from the same group write to the same global location. We don't specialize the kernels by vendor, so we use c_clSize == 4 as a proxy to detect such devices.

static int gmx::calc_shmem_required_prune ( const int  num_threads_z )

inlinestatic

Calculates the amount of shared memory required by the prune kernel.

Note that for the sake of simplicity we use the CUDA terminology "shared memory" for OpenCL local memory.

Parameters

[in]

num_threads_z

cjPacked concurrency equal to the number of threads/work items in the 3-rd dimension.

Returns

the amount of local memory in bytes required by the pruning kernel

template<int packSize>

static gmx_unused void gmx::calcBoundingBoxHalves ( const int  numAtoms, const real *  x, BoundingBox *  bb, BoundingBox *  bbj  )

static

Computes the whole plus half bounding boxes for packed coordinates.

Template Parameters

packSize

The pack size for the coordinates, also the number of atoms per cell

Parameters

[in]	numAtoms	The actual number of atoms in this cell
[in]	x	Packed coodinates
[out]	bb	Pointer to the bounding box for the whole cell
[out]	bbj	Pointer to the bounding boxes for the two halves of the cell

template<int packSize>

static void gmx::calcBoundingBoxXPacked ( const int  numAtoms, const real *  x, BoundingBox *  bb  )

static

Computes the bounding box for packed coordinates.

Template Parameters

packSize

The pack size for the coordinates, also the number of atoms per cell

Parameters

[in]	numAtoms	The actual number of atoms in this cell
[in]	x	Packed coodinates
[out]	bb	Pointer to the bounding box

static real gmx::calcPruneVerletBufferSize ( const CalcVerletBufferParameters &  params, const int  nstlist  )

static

Wrapper for calcVerletBufferSize() for determining the pruning cut-off.

Parameters

[in]	params	References to most parameters for calcVerletBufferSize()
[in]	nstlist	The pruning interval, also used for setting the list lifetime

Returns

The cut-off for pruning the pairlist

real gmx::calculateAcceptanceWeight	(	LambdaWeightCalculation	calculationMode,
		real	lambdaEnergyDifference
	)

Calculates the acceptance weight for a lambda state transition.

Parameters

[in]	calculationMode	How the lambda weights are calculated
[in]	lambdaEnergyDifference	The difference in energy between the two states

Returns

The acceptance weight

static bool gmx::canSkipNonbondedWork ( const NbnxmGpu &  nb, InteractionLocality  iloc  )

inlinestatic

An early return condition for empty NB GPU workloads.

This is currently used for non-local kernels/transfers only. Skipping the local kernel is more complicated, since the local part of the force array also depends on the non-local kernel. The skip of the local kernel is taken care of separately.

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::cbrt ( float  x )

inlinestatic

Float cbrt(x). This is the cubic root.

Parameters

x	Argument, should be >= 0.

Returns

The cubic root of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::cbrt ( double  x )

inlinestatic

Double cbrt(x). This is the cubic root.

Parameters

x	Argument, should be >= 0.

Returns

The cubic root of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::centerAtomPositions ( ArrayRef< RVec >  nnPositions, ArrayRef< RVec >  mmPositions, const matrix &  box, const PbcType &  pbcType  )

static

Center positions of NN and MM atoms in the box.

For treatment of the NNP-MM interactions, we assume that the embedding model expects all atom positions to be centered around the NNP region.

const char * gmx::centerTypeNames

(

CenteringType

type

)

Get names for the different centering types.

Parameters

[in]

type

What name needs to be provided.

template<typename PinnableVector >

void gmx::changePinningPolicy	(	PinnableVector *	v,
		PinningPolicy	pinningPolicy
	)

Helper function for changing the pinning policy of a pinnable vector.

If the vector has contents, then a full reallocation and buffer copy are needed if the policy change requires tighter restrictions, and desirable even if the policy change requires looser restrictions. That cost is OK, because GROMACS will do this operation very rarely (e.g. when auto-tuning and deciding to switch whether a task will run on a GPU, or not).

Asserts from v->get_allocator().context() when the allocator of v was not constructed to be potentially suited for GPU transfers.

void gmx::check_ir	(	const char *	mdparin,
		MDModules *	mdModules,
		t_inputrec *	ir,
		t_gromppopts *	opts,
		WarningHandler *	wi
	)

Performs all validation on ir that can be done without index groups and topology.

Any errors, warnings or notes are added to wi

void gmx::checkAndUpdateHardwareOptions	(	const MDLogger &	mdlog,
		gmx_hw_opt_t *	hw_opt,
		bool	isSimulationMainRank,
		int	nPmeRanks,
		const t_inputrec *	inputrec
	)

Checks what our hardware options are based on how Gromacs was compiled and user-set options.

Parameters

[in]	mdlog	Logger
[in,out]	hw_opt	Hardware-related and threading options
[in]	isSimulationMainRank
[in]	nPmeRanks	Number of PME ranks
[in]	inputrec	The input record, should point to a valid object when isSimulationMainRank = true

void gmx::checkAndUpdateRequestedNumOpenmpThreads	(	gmx_hw_opt_t *	hw_opt,
		const gmx_hw_info_t &	hwinfo,
		const MpiComm &	mpiCommMySim,
		const gmx_multisim_t *	ms,
		int	numRanksOnThisNode,
		PmeRunMode	pmeRunMode,
		const gmx_mtop_t &	mtop,
		const t_inputrec &	inputrec
	)

Check, and if necessary update, the number of OpenMP threads requested.

Should be called when we know the MPI rank count and PME run mode.

void gmx::checkAwhParams	(	const AwhParams &	awhParams,
		const t_inputrec &	inputrec,
		WarningHandler *	wi
	)

Check the AWH parameters.

Parameters

[in]	awhParams	The AWH parameters.
[in]	inputrec	Input parameter struct.
[in,out]	wi	Struct for bookeeping warnings.

void gmx::checkConstrainedBonds	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const std::vector< bool > &	isEmbeddedBlock,
		WarningHandler *	wi
	)

Checks for constrained bonds within embedded subsystem.

Provides warnings via WarningHandler if any are found. Separated from buildLinkFrontier for better modularity.

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	isEmbeddedBlock	vector with flags for embedded atom-containing blocks
[in]	wi	WarningHandler for handling warnings

void gmx::checkDeviceError ( const hipError_t  deviceError, const std::string_view  errorMessage  )

inline

Check if API returned an error and throw an exception with information on it.

Parameters

[in]	deviceError	The error to assert hipSuccess on.
[in]	errorMessage	Undecorated error message.

Exceptions

InternalError

if deviceError is not a success.

static DeviceStatus gmx::checkGpu ( size_t  deviceId, const DeviceInformation &  deviceInfo  )

static

Check whether the ocl_gpu_device is suitable for use by mdrun.

Runs sanity checks: checking that the runtime can compile a dummy kernel and this can be executed; Runs compatibility checks verifying the device OpenCL version requirement and vendor/OS support.

Parameters

[in]	deviceId	The runtime-reported numeric ID of the device.
[in]	deviceInfo	The device info pointer.

Returns

A DeviceStatus to indicate if the GPU device is supported and if it was able to run basic functionality checks.

static bool gmx::checkIfRandomDeviceIsFunctional ( )

static

Check if the RDRAND random device functioning correctly.

Due to a bug in AMD Ryzen microcode, RDRAND may always return -1 (0xFFFFFFFF). To avoid that, fall back to using PRNG instead of RDRAND if this happens.

Returns

The result of the checks.

static void gmx::checkInputConsistencyInterval ( const AwhParams &  awhParams, WarningHandler *  wi  )

static

Check if the starting configuration is consistent with the given interval.

Parameters

[in]	awhParams	AWH parameters.
[in,out]	wi	Struct for bookeeping warnings.

static std::optional<std::string> gmx::checkKernelSetup ( const NbnxmKernelBenchOptions &  options )

static

Checks the kernel setup.

Returns an error string when the kernel is not available.

GpuAwareMpiStatus gmx::checkMpiCudaAwareSupport

(

)

Wrapper on top of MPIX_Query_cuda_support() For MPI implementations which don't support this function, it returns NotSupported. Even when an MPI implementation does support this function, MPI library might not be robust enough to detect CUDA-aware support at runtime correctly e.g. when UCX PML is used or CUDA is disabled at runtime.

Returns

CUDA-aware status in MPI implementation

GpuAwareMpiStatus gmx::checkMpiHipAwareSupport

(

)

Wrapper on top of MPIX_Query_hip_support() or MPIX_Query_rocm_support(). For MPI implementations which don't support this function, it returns NotSupported.

Currently, this function is only supported by MPICH and OpenMPI 5.0-rc, and is not very reliable.

Returns

HIP-aware status in MPI implementation

GpuAwareMpiStatus gmx::checkMpiZEAwareSupport

(

)

Wrapper on top of MPIX_Query_ze_support() (for MPICH) or custom logic (for IntelMPI).

For other MPI implementations which perhaps don't support the above function, it returns NotSupported.

Returns

LevelZero-aware status in MPI implementation

std::vector< std::string > gmx::checkMtsRequirements

(

const t_inputrec &

ir

)

Checks whether the MTS requirements on other algorithms and output frequencies are met.

Note: exits with an assertion failure when ir.useMts == true && haveValidMtsSetup(ir) == false

Parameters

[in]

ir

Complete input record

Returns

list of error messages, empty when all MTS requirements are met

template<typename VersionEnum >

VersionEnum gmx::checkpointVersion	(	const ReadCheckpointData *	checkpointData,
		const std::string &	key,
		const VersionEnum	programVersion
	)

Read a checkpoint version enum variable.

This reads the checkpoint version from file. The read version is returned.

If the read version is more recent than the code version, this throws an error, since we cannot know what has changed in the meantime. Using newer checkpoint files with old code is not a functionality we can offer. Note, however, that since the checkpoint version is saved by module, older checkpoint files of all simulations that don't use that specific module can still be used.

Allowing backwards compatibility of files (i.e., reading an older checkpoint file with a newer version of the code) is in the responsibility of the caller module. They can use the returned file checkpoint version to do that:

const auto fileVersion = checkpointVersion(checkpointData, "version", c_currentVersion);
if (fileVersion >= CheckpointVersion::AddedX)
{
    checkpointData->scalar("x", &x_));
}

Template Parameters

VersionEnum

The type of the checkpoint version enum

Parameters

checkpointData	A reading checkpoint data object
key	The key under which the version is saved - also used for error output
programVersion	The checkpoint version of the current code

Returns

The checkpoint version read from file

template<typename VersionEnum >

VersionEnum gmx::checkpointVersion	(	WriteCheckpointData *	checkpointData,
		const std::string &	key,
		const VersionEnum	programVersion
	)

Write the current code checkpoint version enum variable.

Write the current program checkpoint version to the checkpoint data object. Returns the written checkpoint version to mirror the signature of the reading version.

Template Parameters

VersionEnum

The type of the checkpoint version enum

Parameters

checkpointData	A writing checkpoint data object
key	The key under which the version is saved
programVersion	The checkpoint version of the current code

Returns

The checkpoint version written to file

static void gmx::checkPotentialEnergyValidity ( int64_t  step, const gmx_enerdata_t &  enerd, const t_inputrec &  inputrec  )

static

This routine checks that the potential energy is finite.

Always checks that the potential energy is finite. If step equals inputrec.init_step also checks that the magnitude of the potential energy is reasonable. Terminates with a fatal error when a check fails. Note that passing this check does not guarantee finite forces, since those use slightly different arithmetics. But in most cases there is just a narrow coordinate range where forces are not finite and energies are finite.

Parameters

[in]	step	The step number, used for checking and printing
[in]	enerd	The energy data; the non-bonded group energies need to be added to enerd.term[InteractionFunction::PotentialEnergy] before calling this routine
[in]	inputrec	The input record

void gmx::checkRBDihedralSum	(	const gmx_mtop_t &	mtop,
		const t_inputrec &	ir,
		WarningHandler *	wi
	)

Check that RB/Fourier style dihedral sums to zero in free-energy computation.

Searches for, and emits a warning when dihedral of function type 3 (Ryckaert-Bellemans or Fourier) have a sum of coefficient different from zero, when performing a free-energy computation, in stateA and stateB, as this is likely a parameter mistake that can produce erroneous dHdl values.

void gmx::checkUserGpuIds	(	ArrayRef< const std::unique_ptr< DeviceInformation >>	deviceInfoList,
		ArrayRef< const int >	compatibleGpus,
		ArrayRef< const int >	gpuIds
	)

Check that all user-selected GPUs are compatible.

Given the gpuIds and hardwareInfo, throw if any selected GPUs is not compatible.

The error is given with a suitable descriptive message, which will have context if this check is done after the hardware detection results have been reported to the user. However, note that only the GPUs detected on the main rank are reported, because of the existing limitations of that reporting.

Todo:

Note that the selected GPUs can be different on each rank, and the IDs of compatible GPUs can be different on each node, so this routine ought to do communication to determine whether all ranks are able to proceed. Currently this relies on the MPI runtime to kill the other processes because GROMACS lacks the appropriate infrastructure to do a good job of coordinating error messages and behaviour across MPMD ranks and multiple simulations.

Parameters

[in]	deviceInfoList	Information on the GPUs on this physical node.
[in]	compatibleGpus	Vector of GPUs that are compatible
[in]	gpuIds	The GPU IDs selected by the user.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the assigned GPUs are not valid

std::optional< std::string > gmx::checkVsiteHierarchy

(

const gmx_mtop_t &

mtop

)

Checks whether constructing atom are vsites with the same or higher function type.

Also checks whether vsites are used as constructing atoms for VsiteN (not allowed).

Returns

an error string when the restrictions are not satisfied

MoleculePatchDatabase * gmx::choose_ter	(	gmx::ArrayRef< MoleculePatchDatabase * >	tb,
		const char *	title
	)

Interactively select one terminus.

Parameters

[in]	tb	List of possible entries, with pointer to actual entry or nullptr.
[in]	title	Name of entry.

Returns

The modification block selected.

template<KernelLayoutClusterRatio clusterRatio>

static int gmx::cjFromCi ( const int  iCluster )

inlinestatic

Returns the j-cluster index for the given i-cluster index.

Template Parameters

clusterRatio

The ratio of cluster size, supported are 0.5,1,2, checked at compile time

Parameters

iCluster

The index of the i-cluster

Returns

the j-cluster index corresponding to iCluster

template<ClusterDistanceKernelType kernelType, int jSubClusterIndex>

static gmx_unused int gmx::cjFromCi ( int  ci )

inlinestatic

Returns the j-cluster index given the i-cluster index.

Template Parameters

kernelType	The kernel type
jSubClusterIndex	The j-sub-cluster index (0/1), used when size(j-cluster) < size(i-cluster)

Parameters

[in]

ci

The i-cluster index

void gmx::clean_vsite_bondeds	(	EnumerationArray< InteractionFunction, InteractionsOfType > &	ps,
		int	natoms,
		bool	bRmVSiteBds,
		const MDLogger &	logger
	)

Clean up the bonded interactions.

Throw away all obsolete bonds, angles and dihedrals. Throw away all constraints.

template<int numComponentsPerElement>

static void gmx::clearBufferFlagged ( const int  outputIndex, ArrayRef< const gmx_bitmask_t >  flags, ArrayRef< real >  buffer  )

static

Clears elements of size and stride numComponentsPerElement.

Only elements with flags in nbat set for index outputIndex are cleared.

void gmx::clearModificationBlock

(

MoleculePatchDatabase *

globalPatches

)

Reset modification block.

Parameters

[in,out]

globalPatches

Block to reset.

Todo:

Remove once constructor/destructor takes care of all of this.

static float gmx::clusterBoundingBoxDistance2 ( const BoundingBox &  bb_i, const BoundingBox &  bb_j  )

inlinestatic

Returns the distance^2 between two bounding boxes.

Uses 4-wide SIMD operations when available.

Parameters

[in]	bb_i	First bounding box, has to be aligned for 4-wide SIMD
[in]	bb_j	Second bounding box, has to be aligned for 4-wide SIMD

static void gmx::combineMtsForces ( const int  numAtoms, ArrayRef< RVec >  forceMtsLevel0, ArrayRef< RVec >  forceMts, const real  mtsFactor  )

static

Combines MTS level0 and level1 force buffers into a full and MTS-combined force buffer.

Parameters

[in]	numAtoms	The number of atoms to combine forces for
[in,out]	forceMtsLevel0	Input: F_level0, output: F_level0 + F_level1
[in,out]	forceMts	Input: F_level1, output: F_level0 + mtsFactor * F_level1
[in]	mtsFactor	The factor between the level0 and level1 time step

static gmx_bool gmx::compartment_contains_atom ( real  w1, real  w2, real  x, real  l, real  bulkOffset, real *  distance_from_b  )

static

Return TRUE if position x of ion (or water) is found in the compartment, i.e. between w1 and w2.

One can define and additional offset "b" if one wants to exchange ions/water to or from a plane not directly in the middle of w1 and w2. The offset can be in ]-1.0, ..., +1.0 [. A bulkOffset of 0.0 means 'no offset', so the swap-layer is directly in the middle between w1 and w2. Offsets -1.0 < b < 0.0 will yield swaps nearer to w1, whereas offsets 0.0 < 0 < +1.0 will yield swaps nearer to w2.

*
* ||--------------+-------------|-------------+------------------------||
*                w1  ? ? ? ? ? ? ? ? ? ? ?   w2
* ||--------------+-------------|----b--------+------------------------||
*                -1            0.0           +1
*
* 

Parameters

[in]	w1	Position of 'wall' atom 1.
[in]	w2	Position of 'wall' atom 2.
[in]	x	Position of the ion or the water molecule under consideration.
[in]	l	Length of the box, from || to || in the sketch.
[in]	bulkOffset	Where is the bulk layer "b" to be found between w1 and w2?
[out]	distance_from_b	Distance of x to the bulk layer "b".

Returns

TRUE if x is between w1 and w2.

Also computes the distance of x to the compartment center (the layer that is normally situated in the middle of w1 and w2 that would be considered as having the bulk concentration of ions).

static double gmx::computeDerivativeForTransformationPullCoord ( pull_coord_work_t *  coord, const int  variablePcrdIndex  )

static

Calculates and returns the derivative of a transformation pull coordinate from a dependent coordinate.

Note #1: this requires that getTransformationPullCoordinateValue() has been called before with the current coordinates.

Note #2: this method will not compute inner derivates. That is taken care of in the regular pull code

Parameters

[in]	coord	The (transformation) coordinate to compute the value for
[in]	variablePcrdIndex	Pull coordinate index of a variable.

static int gmx::computeExpectedNumGlobalBondedInteractions ( const gmx_mtop_t &  mtop, const DDBondedChecking  ddBondedChecking, const bool  useUpdateGroups  )

static

Compute the total bonded interaction count.

Parameters

[in]	mtop	The global system topology
[in]	ddBondedChecking	Which interactions to check
[in]	useUpdateGroups	Whether update groups are in use

When using domain decomposition without update groups, constraint-type interactions can be split across domains, and so we do not consider them in this correctness check. Otherwise, we include them.

int gmx::computeFepPeriod	(	const t_inputrec &	inputrec,
		const ReplicaExchangeParameters &	replExParams
	)

Compute the period at which FEP calculation is performed.

This harmonizes the free energy calculation period specified by nstdhdl with the periods specified by expanded ensemble, replica exchange, and AWH.

Parameters

inputrec	The input record (contains outputControl)
replExParams	The replica exchange parameters

Returns

The period required by the involved algorithms

real gmx::computeMaxUpdateGroupRadius	(	const gmx_mtop_t &	mtop,
		ArrayRef< const RangePartitioning >	updateGroupingPerMoleculeType,
		real	temperature
	)

Returns the maximum update group radius.

Note

When updateGroups is empty, 0 is returned.

Parameters

[in]	mtop	The system topology
[in]	updateGroupingPerMoleculeType	List of update group, size should match the number of moltypes in mtop or be 0
[in]	temperature	The maximum reference temperature, pass -1 when unknown or not applicable

static int gmx::computeNumGlobalPerturbedExclusions ( const gmx_mtop_t &  mtop )

static

Compute the number of exclusions involving perturbed atoms.

Parameters

[in]

mtop

The global system topology

Returns

the total number of exclusions exclusions (one-way) that involve at least one perturbed atom, including self-exclusions.

RVec gmx::computeQMBoxVec	(	const RVec &	a,
		const RVec &	b,
		const RVec &	c,
		real	h,
		real	minNorm,
		real	maxNorm
	)

Transforms vector a such as distance from it to the plane defined by vectors b and c will be h minimum length will be milL and maximum length maxL.

Parameters

[in]	a	Vector which should be scaled
[in]	b	First vector that forms the plane
[in]	c	Second vector that forms the plane
[in]	h	Distance from the end of a to the plane of (b,c)
[in]	minNorm	Minimum norm of vector
[in]	maxNorm	Maximum norm of vector

static void gmx::computeSpecialForces ( FILE *  fplog, const MpiComm &  mpiComm, const gmx_domdec_t *  dd, const t_inputrec &  inputrec, Awh *  awh, gmx_enfrot *  enforcedRotation, ImdSession *  imdSession, pull_t *  pull_work, int64_t  step, double  t, gmx_wallcycle *  wcycle, ForceProviders *  forceProviders, const matrix  box, ArrayRef< const RVec >  x, const t_mdatoms *  mdatoms, ArrayRef< const real >  lambda, const StepWorkload &  stepWork, ForceWithVirial *  forceWithVirialMtsLevel0, ForceWithVirial *  forceWithVirialMtsLevel1, gmx_enerdata_t *  enerd, edsam *  ed, bool  didNeighborSearch  )

static

Compute forces and/or energies for special algorithms.

The intention is to collect all calls to algorithms that compute forces on local atoms only and that do not contribute to the local virial sum (but add their virial contribution separately). Eventually these should likely all become ForceProviders. Within this function the intention is to have algorithms that do global communication at the end, so global barriers within the MD loop are as close together as possible.

Parameters

[in]	fplog	The log file
[in]	mpiComm	The communication object for my group
[in]	dd	Pointer to the domdec object, is nullptr when DD is not in use
[in]	inputrec	The input record
[in]	awh	The Awh module (nullptr if none in use).
[in]	enforcedRotation	Enforced rotation module.
[in]	imdSession	The IMD session
[in]	pull_work	The pull work structure.
[in]	step	The current MD step
[in]	t	The current time
[in,out]	wcycle	Wallcycle accounting struct
[in,out]	forceProviders	Pointer to a list of force providers
[in]	box	The unit cell
[in]	x	The coordinates
[in]	mdatoms	Per atom properties
[in]	lambda	Array of free-energy lambda values
[in]	stepWork	Step schedule flags
[in,out]	forceWithVirialMtsLevel0	Force and virial for MTS level0 forces
[in,out]	forceWithVirialMtsLevel1	Force and virial for MTS level1 forces, can be nullptr
[in,out]	enerd	Energy buffer
[in,out]	ed	Essential dynamics pointer
[in]	didNeighborSearch	Tells if we did neighbor searching this step, used for ED sampling

Todo:

Remove didNeighborSearch, which is used incorrectly.

Convert all other algorithms called here to ForceProviders.

void gmx::constrain_coordinates	(	gmx::Constraints *	constr,
		bool	computeRmsd,
		int64_t	step,
		t_state *	state,
		ArrayRefWithPadding< RVec >	xp,
		real *	dhdlambda,
		bool	computeVirial,
		tensor	constraintsVirial
	)

Constrain the coordinates.

Constrain the coordinates xp using reference coordinates in state. When present, the velocities in state are also constrained. The dhdlambda contribution has to be added to the bonded interactions.

Parameters

[in,out]	constr	The constraints object
[in]	computeRmsd	Tells whether the constraint RMS deviation should be computed
[in]	step	The integration step index
[in,out]	state	The state, x is read and halo data updated, v is constrained
[in,out]	xp	The coordinates to constrain
[out]	dhdlambda	The dHdlambda contraint contribution is returned in this
[in]	computeVirial	Whether the constraint virial contribution should be computed
[out]	constraintsVirial	The constraint virial is returned in this

bool gmx::constrain_lincs	(	bool	computeRmsd,
		const t_inputrec &	ir,
		int64_t	step,
		Lincs *	lincsd,
		ArrayRef< const real >	invmass,
		gmx_domdec_t *	dd,
		const gmx_multisim_t *	ms,
		ArrayRefWithPadding< const RVec >	x,
		ArrayRefWithPadding< RVec >	xprime,
		ArrayRef< RVec >	min_proj,
		const matrix	box,
		t_pbc *	pbc,
		bool	hasMassPerturbed,
		real	lambda,
		real *	dvdlambda,
		real	invdt,
		ArrayRef< RVec >	v,
		bool	bCalcVir,
		tensor	vir_r_m_dr,
		ConstraintVariable	econq,
		t_nrnb *	nrnb,
		int	maxwarn,
		int *	warncount,
		gmx_wallcycle *	wcycle
	)

Applies LINCS constraints.

Returns

true if the constraining succeeded.

void gmx::constrain_velocities	(	gmx::Constraints *	constr,
		bool	computeRmsd,
		int64_t	step,
		t_state *	state,
		real *	dhdlambda,
		bool	computeVirial,
		tensor	constraintsVirial
	)

Constrain the velocities only.

The dhdlambda contribution has to be added to the bonded interactions

Parameters

[in,out]	constr	The constraints object
[in]	computeRmsd	Tells whether the constraint RMS deviation should be computed
[in]	step	The integration step index
[in,out]	state	The state, x is read and halo data updated, v is constrained
[out]	dhdlambda	The dHdlambda contraint contribution is returned in this
[in]	computeVirial	Whether the constraint virial contribution should be computed
[out]	constraintsVirial	The constraint virial is returned in this

template<int numPartnerAtoms>

static real gmx::constraintGroupRadius ( const gmx_moltype_t &  moltype, gmx::ArrayRef< const t_iparams >  iparams, const int  centralAtom, const ListOfLists< int > &  at2con, const std::unordered_multimap< int, int > &  angleIndices, const real  constraintLength, const real  temperature  )

static

When possible, computes the maximum radius of constrained atom in an update group.

Supports groups with 2 or 3 atoms where all partner atoms are connected to each other by angle potentials. The temperature is used to compute a radius that is not exceeded with a chance of 10^-9. Note that this computation assumes there are no other strong forces working on these angular degrees of freedom. The return value is -1 when all partners are not connected to each other by one angle potential, when a potential is perturbed or when an angle could reach more than 180 degrees.

template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>

static void gmx::construct_vsites ( const ThreadingInfo *  threadingInfo, ArrayRef< RVec >  x, ArrayRef< RVec >  v, ArrayRef< const t_iparams >  ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &  ilists, const DomainInfo &  domainInfo, const matrix  box  )

static

Dispatch the vsite construction tasks for all threads.

Parameters

[in]	threadingInfo	Used to divide work over threads when != nullptr
[in,out]	x	Coordinates to construct vsites for
[in,out]	v	When not empty, velocities are generated for virtual sites
[in]	ip	Interaction parameters for all interaction, only vsite parameters are used
[in]	ilists	The interaction lists, only vsites are usesd
[in]	domainInfo	Information about PBC and DD
[in]	box	Used for PBC when PBC is set in domainInfo

template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>

static void gmx::construct_vsites_thread ( ArrayRef< RVec >  x, ArrayRef< RVec >  v, ArrayRef< const t_iparams >  ip, const gmx::EnumerationArray< InteractionFunction, InteractionList > &  ilists, const t_pbc *  pbc_null  )

static

Executes the vsite construction task for a single thread.

Template Parameters

calculatePosition	Whether we are calculating positions
calculateVelocity	Whether we are calculating velocities

Parameters

[in,out]	x	Coordinates to construct vsites for
[in,out]	v	Velocities are generated for virtual sites if calculateVelocity is true
[in]	ip	Interaction parameters for all interaction, only vsite parameters are used
[in]	ilists	The interaction lists, only vsites are used
[in]	pbc_null	PBC struct, used for PBC distance calculations when !=nullptr

void gmx::constructVirtualSites	(	ArrayRef< RVec >	x,
		ArrayRef< const t_iparams >	ip,
		const gmx::EnumerationArray< InteractionFunction, InteractionList > &	ilists
	)

Create positions of vsite atoms based for the local system.

Parameters

[in,out]	x	The coordinates
[in]	ip	Interaction parameters
[in]	ilists	The interaction lists

void gmx::constructVirtualSitesGlobal	(	const gmx_mtop_t &	mtop,
		ArrayRef< RVec >	x
	)

Create positions of vsite atoms for the whole system assuming all molecules are wholex.

Parameters

[in]	mtop	The global topology
[in,out]	x	The global coordinates

void gmx::convertInteractionsOfType	(	int	atnr,
		const EnumerationArray< InteractionFunction, InteractionsOfType > &	nbtypes,
		ArrayRef< const MoleculeInformation >	mi,
		const MoleculeInformation *	intermolecular_interactions,
		CombinationRule	comb,
		double	reppow,
		real	fudgeQQ,
		gmx_mtop_t *	mtop
	)

Convert the raw arrays of parameters read from the topology file to those which match the interaction type and fill into mtop.

This can involve pre-computation e.g. for G96 interactions. Interaction parameter sets that are all zero are not added to mtop

Parameters

[in]	atnr	Number of atoms
[in]	nbtypes	Non-bonded interaction types
[in]	mi	Molecule types read from topology file containing bonded-style interactions
[in]	intermolecular_interactions	Molecule type for inter-molecular interactions
[in]	comb	The combination rule
[in]	reppow	The repulsion power
[in]	fudgeQQ	The 1-4 scaling factor
[out]	mtop	The molecular topology containing the converted parameters

static void gmx::convertOldToNewGroupFormat ( t_swapcoords *  sc, const gmx_mtop_t &  mtop, gmx_bool  bVerbose, const gmx::MpiComm &  mpiComm  )

static

Converts old .tpr file CompEL contents to new data layout.

If we have read an old .tpr file (tpxv <= tpxv_CompElPolyatomicIonsAndMultipleIonTypes), anions and cations are stored together in group #3. In the new format we store each ion type in a separate group. The 'classic' groups are: #0 split group 0 - OK #1 split group 1 - OK #2 solvent - OK #3 anions - contains also cations, needs to be converted #4 cations - empty before conversion

static CheckpointSignal gmx::convertToCheckpointSignal ( signed char  sig )

inlinestatic

Convert signed char (as used by SimulationSignal) to CheckpointSignal enum.

Expected values are sig == 0 – no signal sig >= 1 – signal received

static ResetSignal gmx::convertToResetSignal ( signed char  sig )

inlinestatic

Convert signed char (as used by SimulationSignal) to ResetSignal enum.

Expected values are sig == 0 – no signal sig >= 1 – signal received

static StopSignal gmx::convertToStopSignal ( signed char  sig )

inlinestatic

Convert signed char (as used by SimulationSignal) to StopSignal enum.

• Expected values are sig == 0 – no signal sig >= 1 – stop at next NS sig <= -1 – stop asap

template<typename Callable >

auto gmx::coordinateExceptionHandling	(	MPI_Comm	communicator,
		Callable	callable
	)		-> typename std::invoke_result_t<Callable>

Call the callable and then make sure all MPI ranks of communicator have consistent exception-throwing behaviour.

Any rank that threw an exception in callable will re-throw it. If so, any other rank will throw ParallelConsistencyError. Otherwise, does not throw.

Note that the callable must not require any arguments to be passed, so judicious use of a function object, lambda or std::function may be required.

Parameters

[in]	communicator	The MPI communicator over which exception-throwing behaviour should be coordinated
[in]	callable	The "callable," which can be a function, function object, lambda, or std::function object. It may return a value, but is not required to do so.

void gmx::copy_gpu_fepparams	(	NbnxmGpu gmx_unused *	nb,
		bool gmx_unused	bFepGpuNonBonded,
		float gmx_unused	alphaCoul,
		float gmx_unused	alphaVdw,
		int gmx_unused	lambdaPower,
		float gmx_unused	sigma6WithInvalidSigma,
		float gmx_unused	sigma6Minimum,
		float gmx_unused	lambdaCoul,
		float gmx_unused	lambdaVdw,
		int gmx_unused	nLambda,
		const EnumerationArray< FreeEnergyPerturbationCouplingType, std::vector< double >> gmx_unused &	all_lambda
	)

Copy FEP parameters to GPU.

static void gmx::copyIndicesToGroup ( gmx::ArrayRef< const int >  indIons, t_swapGroup *  group, const gmx::MpiComm &  mpiComm  )

static

Sorts anions and cations into two separate groups.

This routine should be called for the 'anions' and 'cations' group, of which the indices were lumped together in the older version of the code.

void gmx::copyModificationBlocks	(	const MoleculePatchDatabase &	s,
		MoleculePatchDatabase *	d
	)

Copy all information from datastructure.

Parameters

[in]	s	Source information.
[in,out]	d	Destination to copy to.

void gmx::copyPreprocessResidues	(	const PreprocessResidue &	s,
		PreprocessResidue *	d,
		t_symtab *	symtab
	)

Copy residue information.

Parameters

[in]	s	Source information.
[in]	d	Destination to copy to.
[in,out]	symtab	Symbol table for names.

Todo:

Remove once copy can be done directly.

template<int packSize>

static void gmx::copyRVecToNbatPackedReal ( int  numAtoms, const rvec *  x, real *  xnb, int  a0  )

static

Copies coordinates with RVec layout to SIMD layout with X/Y/Z packs.

Template Parameters

packSize

The stride of the packs in xnb

Parameters

[in]	numAtoms	The number of atoms to copy coordinates for
[in]	x	The coordinates to copy
[in,out]	xnb	The NBNxM coordainate buffer
[in]	a0	The index of the first atom to copy coordinates for

static float gmx::copysign ( float  x, float  y  )

inlinestatic

Composes single value with the magnitude of x and the sign of y.

Parameters

x	Value to set sign for
y	Value used to set sign

Returns

Magnitude of x, sign of y

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::copysign ( double  x, double  y  )

inlinestatic

Composes double value with the magnitude of x and the sign of y.

Parameters

x	Value to set sign for
y	Value used to set sign

Returns

Magnitude of x, sign of y

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::cos ( float  x )

inlinestatic

Float cos.

Parameters

x	The argument to evaluate cos for

Returns

Cos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::cos ( double  x )

inlinestatic

Double cos.

Parameters

x	The argument to evaluate cos for

Returns

Cos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::cosSingleAccuracy ( double  x )

inlinestatic

Double cos, but with single accuracy.

Parameters

x	The argument to evaluate cos for

Returns

Cos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

int gmx::count_triangle_constraints	(	const InteractionLists &	ilist,
		const ListOfLists< int > &	at2con
	)

Counts the number of constraint triangles, i.e. triplets of atoms connected by three constraints.

Parameters

[in]	ilist	The interaction list to count constraints triangles for
[in]	at2con	The atom to constraints map

Returns

the number of constraint triangles

int gmx::countInterUpdategroupVsites	(	const gmx_mtop_t &	mtop,
		ArrayRef< const RangePartitioning >	updateGroupingsPerMoleculeType
	)

Return the number of virtual sites that cross update groups.

Parameters

[in]	mtop	The global topology
[in]	updateGroupingsPerMoleculeType	Update grouping per molecule type, pass empty when not using update groups

static void gmx::countPruneKernelTime ( GpuTimers *  timers, gmx_wallclock_gpu_nbnxm_t *  timings, const InteractionLocality  iloc  )

static

Count pruning kernel time if either kernel has been triggered.

We do the accounting for either of the two pruning kernel flavors:

• 1st pass prune: ran during the current step (prior to the force kernel);
• rolling prune: ran at the end of the previous step (prior to the current step H2D xq);

Note that the resetting of GpuTimers::didPrune and GpuTimers::didRollingPrune should happen after calling this function.

Parameters

[in]	timers	structs with GPU timer objects
[in,out]	timings	GPU task timing data
[in]	iloc	interaction locality

static int64_t gmx::countSamples ( ArrayRef< const PointState >  pointState )

static

Count the total number of samples / sample weight over all grid points.

Parameters

[in]

pointState

The state of the points in a bias.

Returns

the total sample count.

static int gmx::countTrailingZeroRows ( const MultiDimArray< std::vector< double >, dynamicExtents2D > &  data, int  numRows, int  numColumns  )

static

Count trailing data rows containing only zeros.

Parameters

[in]	data	2D data array.
[in]	numRows	Number of rows in array.
[in]	numColumns	Number of cols in array.

Returns

the number of trailing zero rows.

static std::vector<char*> gmx::cpp_opts ( const char *  define, const char *  include, WarningHandler *  wi  )

static

Parses define and include flags.

Returns a vector of parsed include/define flags, with an extra nullptr entry at the back for consumers that expect null-terminated char** structures.

std::string gmx::cpuFftDescription

(

)

Construct a string that describes the library that provides CPU FFT support to this build.

Returns information for describing the CPU FFT support.

bool gmx::cpuIsAmdZen1

(

const CpuInfo &

cpuInfo

)

Return true if the CPU is a first generation AMD Zen (produced by AMD or Hygon)

Parameters

cpuInfo

Object with cpu information

Returns

True if running on a first generation AMD Zen

bool gmx::cpuIsNeoverseV2

(

const CpuInfo &

cpuInfo

)

Return true if the CPU has Neoverse V2 cores (including Grace and Graviton 4)

Parameters

cpuInfo

Object with cpu information

Returns

True if running on Neoverse V2

bool gmx::cpuIsX86Nehalem

(

const CpuInfo &

cpuInfo

)

Return true if the CPU is an Intel x86 Nehalem.

Parameters

cpuInfo

Object with cpu information

Returns

True if running on Nehalem CPU

hid_t gmx::createGroup	(	hid_t	container,
		const char *	name
	)

Create an H5MD group, and intermediate groups if they do not exist.

Parameters

[in]	container	The ID of the container where the group is located, or should be created.
[in]	name	The name of the group.

Returns

the ID of the group.

Exceptions

H5mdError

If the group cannot be created, such as if it already exists.

SimulationWorkload gmx::createSimulationWorkload	(	const gmx::MDLogger &	mdlog,
		const t_inputrec &	inputrec,
		bool	haveDynamicBox,
		bool	useReplicaExchange,
		bool	disableNonbondedCalculation,
		const DevelopmentFeatureFlags &	devFlags,
		bool	haveFillerParticlesInLocalState,
		bool	havePpDomainDecomposition,
		bool	haveSeparatePmeRank,
		bool	useGpuForNonbonded,
		bool	useGpuForNonbondedFE,
		PmeRunMode	pmeRunMode,
		bool	useGpuForBonded,
		bool	useGpuForUpdate,
		bool	useGpuDirectHalo,
		bool	canUseDirectGpuComm,
		bool	useGpuPmeDecomposition
	)

Build datastructure that contains decisions whether to run different workload task on GPUs.

Parameters

[in]	mdlog	Logger object.
[in]	inputrec	The input record
[in]	haveDynamicBox	Whether the simulation box is dynamic (ie. changes each step)
[in]	useReplicaExchange	Whether we are using replica exchange
[in]	disableNonbondedCalculation	Disable calculation of nonbonded forces
[in]	devFlags	The development feature flags
[in]	haveFillerParticlesInLocalState	Whether filler particles are part of the local state.
[in]	havePpDomainDecomposition	Whether PP domain decomposition is used in this run.
[in]	haveSeparatePmeRank	Whether separate PME rank(s) are used in this run.
[in]	useGpuForNonbonded	Whether we have short-range nonbonded interaction calculations on GPU(s).
[in]	useGpuForNonbondedFE	Whether we have nonbonded free-energy interaction calculations on GPU(s).
[in]	pmeRunMode	Run mode indicating what resource is PME executed on.
[in]	useGpuForBonded	Whether bonded interactions are calculated on GPU(s).
[in]	useGpuForUpdate	Whether coordinate update and constraint solving is performed on GPU(s).
[in]	useGpuDirectHalo	Whether halo exchange is performed directly between GPUs
[in]	canUseDirectGpuComm	Whether direct GPU communication can be used in this run.
[in]	useGpuPmeDecomposition	GPU based PME decomposition used.

Returns

Simulation lifetime constant workload description.

std::unique_ptr< TrajectoryFrameWriter > gmx::createTrajectoryFrameWriter	(	const gmx_mtop_t *	top,
		const Selection &	sel,
		const std::filesystem::path &	filename,
		AtomsDataPtr	atoms,
		OutputRequirements	requirements
	)

Factory function for TrajectoryFrameWriter.

Used to initialize a new instance of TrajectoryFrameWriter with the user supplied information for writing trajectory data to disk. Information needed is the file type, file name corresponding to the type, if available topology information and selection information.

If supplied, the modules contained within adapters are registered on the TrajectoryFrameWriter if possible.

The factory function is responsible for the initial santity checks concerning file types and availability of topology information, with the registration of modules being the second part.

Parameters

[in]	top	Pointer to full topology or null.
[in]	sel	Reference to global selection used to construct the object.
[in]	filename	Name of new output file, used to deduce file type.
[in]	atoms	Smart Pointer to atoms data or null.
[in]	requirements	Container for settings obtained to specify which OutputAdapters should be registered.

Exceptions

InconsistentInputError

When user input and requirements don't match.

void gmx::cshake	(	const int	iatom[],
		int	ncon,
		int *	nnit,
		int	maxnit,
		ArrayRef< const real >	constraint_distance_squared,
		ArrayRef< RVec >	positions,
		const t_pbc *	pbc,
		ArrayRef< const RVec >	initial_displacements,
		ArrayRef< const real >	half_of_reduced_mass,
		real	omega,
		ArrayRef< const real >	invmass,
		ArrayRef< const real >	distance_squared_tolerance,
		ArrayRef< real >	scaled_lagrange_multiplier,
		int *	nerror
	)

Inner kernel for SHAKE constraints.

Regular iterative shake.

Original implementation from R.C. van Schaik and W.F. van Gunsteren (ETH Zuerich, June 1992), adapted for GROMACS by David van der Spoel November 1992.

The algorithm here is based section five of Ryckaert, Ciccotti and Berendsen, J Comp Phys, 23, 327, 1977.

Parameters

[in]	iatom	Mini-topology of triplets of constraint type (unused in this function) and indices of two atoms involved
[in]	ncon	Number of constraints
[out]	nnit	Number of iterations performed
[in]	maxnit	Maximum number of iterations permitted
[in]	constraint_distance_squared	The objective value for each constraint
[in,out]	positions	The initial (and final) values of the positions of all atoms
[in]	pbc	PBC information
[in]	initial_displacements	The initial displacements of each constraint
[in]	half_of_reduced_mass	Half of the reduced mass for each constraint
[in]	omega	SHAKE over-relaxation factor (set non-1.0 by using shake-sor=yes in the .mdp, but there is no documentation anywhere)
[in]	invmass	Inverse mass of each atom
[in]	distance_squared_tolerance	Multiplicative tolerance on the difference in the square of the constrained distance (see code)
[out]	scaled_lagrange_multiplier	Scaled Lagrange multiplier for each constraint (-2 * eta from p. 336 of the paper, divided by the constraint distance)
[out]	nerror	Zero upon success, returns one more than the index of the problematic constraint if the input was malformed

Todo:

Make SHAKE use better data structures, in particular for iatom.

gmx::EnumerationArray< FreeEnergyPerturbationCouplingType, real > gmx::currentLambdas	(	int64_t	step,
		const t_lambda &	fepvals,
		int	currentLambdaState
	)

Evaluate the current lambdas.

Parameters

[in]	step	the current simulation step
[in]	fepvals	describing the lambda setup
[in]	currentLambdaState	the lambda state to use to set the lambdas, -1 if not set

Returns

the current lambda-value array

static bool gmx::cvtB2IB ( bool  a )

inlinestatic

Just return a boolean (mimicks SIMD real-to-int bool conversions)

Parameters

a

boolean

Returns

same boolean

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::cvtD2F ( double  a )

inlinestatic

Convert double to float (mimicks SIMD conversion)

Parameters

a

double

Returns

a, as float

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::cvtF2D ( float  a )

inlinestatic

Convert float to double (mimicks SIMD conversion)

Parameters

a

float

Returns

a, as double double

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::cvtI2R ( std::int32_t  a )

inlinestatic

Return integer.

This function mimicks the SIMD integer-to-real conversion routines. By simply returning an integer, we let the compiler sort out whether the conversion should be to float or double rather than using proxy objects.

Parameters

a

integer

Returns

same value (a)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static bool gmx::cvtIB2B ( bool  a )

inlinestatic

Just return a boolean (mimicks SIMD int-to-real bool conversions)

Parameters

a

boolean

Returns

same boolean

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::cvtR2I ( float  a )

inlinestatic

Round single precision floating point to integer.

Parameters

a

float

Returns

Integer format, a rounded to nearest integer.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::cvtR2I ( double  a )

inlinestatic

Round single precision doubleing point to integer.

Parameters

a

double

Returns

Integer format, a rounded to nearest integer.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::cvttR2I ( float  a )

inlinestatic

Truncate single precision floating point to integer.

Parameters

a

float

Returns

Integer format, a truncated to integer.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::cvttR2I ( double  a )

inlinestatic

Truncate single precision doubleing point to integer.

Parameters

a

double

Returns

Integer format, a truncated to integer.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::dd_make_local_ed_indices	(	gmx_domdec_t *	dd,
		edsam *	ed
	)

Make a selection of the home atoms for the ED groups.

Should be called at every domain decomposition.

Parameters

dd	Domain decomposition data.
ed	Essential dynamics and flooding data.

void gmx::dd_partition_system	(	FILE *	fplog,
		const gmx::MDLogger &	mdlog,
		const SimulationWorkload &	simulationWork,
		int64_t	step,
		gmx_domdec_t *	dd,
		bool	bMainState,
		t_state *	state_global,
		const gmx_mtop_t &	top_global,
		const t_inputrec &	inputrec,
		const MDModulesNotifiers &	mdModulesNotifiers,
		gmx::ImdSession *	imdSession,
		pull_t *	pull_work,
		t_state *	state_local,
		StatePropagatorDataGpu *	stateGpu,
		gmx::ForceBuffers *	f,
		gmx::MDAtoms *	mdAtoms,
		gmx_localtop_t *	top_local,
		t_forcerec *	fr,
		gmx::VirtualSitesHandler *	vsite,
		gmx::Constraints *	constr,
		t_nrnb *	nrnb,
		gmx_wallcycle *	wcycle,
		bool	bVerbose
	)

TODO Remove fplog when group scheme and charge groups are gone.

Partition the system over the nodes.

step is only used for printing error messages. If bMainState==TRUE then state_global from the main node is used, else state_local is redistributed between the nodes. When f!=NULL, *f will be reallocated to the size of state_local.

Parameters

[in]	fplog	Pointer to the log file
[in]	mdlog	MD file logger
[in]	simulationWork	The simulation workload
[in]	step	Current step
[in,out]	dd	The domain decomposition struct, can not be nullptr
[in]	bMainState	Is it a main state
[in]	state_global	Global state
[in]	top_global	Global topology
[in]	inputrec	Input record
[in]	mdModulesNotifiers	MDModules notifications handler
[in]	imdSession	IMD handle
[in]	pull_work	Pulling data
[in]	state_local	Local state
[in]	stateGpu	The state-on-GPU manager, can be NULL
[in]	f	Force buffer
[in]	mdAtoms	MD atoms
[in]	top_local	Local topology
[in]	fr	Force record
[in]	vsite	Virtual sites handler
[in]	constr	Constraints
[in]	nrnb	Cycle counters
[in]	wcycle	Timers
[in]	bVerbose	Be verbose

bool gmx::decideWhetherDirectGpuCommunicationCanBeUsed	(	gmx::GpuAwareMpiStatus	mpiStatus,
		bool	haveMts,
		bool	useReplicaExchange,
		bool	haveSwapCoords,
		bool	gpusWereDetected,
		const gmx::MDLogger &	mdlog
	)

Decide whether direct GPU communication can be used.

Takes into account the build type which determines feature support as well as GPU development feature flags, determines whether this run can use direct GPU communication. The final decision whether the run will use direct communication for either of the features which rely on it is made during task assignment / simulationWorkload initialization.

Parameters

[in]	mpiStatus	Information about GPU-aware availability
[in]	haveMts	Whether the simulation uses multiple time stepping
[in]	useReplicaExchange	Whether replica exchange is used
[in]	haveSwapCoords	Whether the swap-coords functionality is active
[in]	gpusWereDetected	Whether we have any GPUs
[in]	mdlog	MD logger.

Returns

Whether the MPI-parallel runs can use direct GPU communication.

bool gmx::decideWhetherToUseGpuForHalo	(	bool	havePPDomainDecomposition,
		bool	useGpuForNonbonded,
		bool	canUseDirectGpuComm,
		bool	useModularSimulator,
		bool	doRerun,
		bool	haveEnergyMinimization,
		const gmx::MDLogger &	mdlog
	)

Decide whether to use GPU for halo exchange.

Parameters

[in]	havePPDomainDecomposition	Whether PP domain decomposition is in use.
[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	canUseDirectGpuComm	Whether direct GPU communication can be used.
[in]	useModularSimulator	Whether modularsimulator is in use.
[in]	doRerun	Whether this is a rerun.
[in]	haveEnergyMinimization	Whether energy minimization is in use.
[in]	mdlog	MD logger.

Returns

Whether halo exchange can be run on GPU.

bool gmx::decideWhetherToUseGpuForUpdate	(	bool	isDomainDecomposition,
		bool	useUpdateGroups,
		PmeRunMode	pmeRunMode,
		bool	havePmeOnlyRank,
		bool	useGpuForNonbonded,
		TaskTarget	updateTarget,
		bool	gpusWereDetected,
		const t_inputrec &	inputrec,
		const gmx_mtop_t &	mtop,
		bool	useEssentialDynamics,
		bool	doOrientationRestraints,
		bool	haveFrozenAtoms,
		bool	useModularSimulator,
		bool	doRerun,
		const gmx::MDLogger &	mdlog
	)

Decide whether to use GPU for update.

Parameters

[in]	isDomainDecomposition	Whether there more than one domain.
[in]	useUpdateGroups	If the constraints can be split across domains.
[in]	pmeRunMode	PME running mode: CPU, GPU or mixed.
[in]	havePmeOnlyRank	If there is a PME-only rank in the simulation.
[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	updateTarget	User choice for running simulation on GPU.
[in]	gpusWereDetected	Whether compatible GPUs were detected on any node.
[in]	inputrec	The user input.
[in]	mtop	The global topology.
[in]	useEssentialDynamics	If essential dynamics is active.
[in]	doOrientationRestraints	If orientation restraints are enabled.
[in]	haveFrozenAtoms	If this simulation has frozen atoms (see Issue #3920).
[in]	useModularSimulator	Whether the modular simulator is used
[in]	doRerun	It this is a rerun.
[in]	mdlog	MD logger.

Returns

Whether complete simulation can be run on GPU.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

bool gmx::decideWhetherToUseGpusForBonded	(	bool	useGpuForNonbonded,
		bool	useGpuForPme,
		TaskTarget	bondedTarget,
		const t_inputrec &	inputrec,
		const gmx_mtop_t &	mtop,
		int	numPmeRanksPerSimulation,
		bool	gpusWereDetected
	)

Decide whether the simulation will try to run bonded tasks on GPUs.

Parameters

[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	useGpuForPme	Whether GPUs will be used for PME interactions.
[in]	bondedTarget	The user's choice for mdrun -bonded for where to assign tasks.
[in]	inputrec	The user input.
[in]	mtop	The global topology.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation, can be -1 for auto.
[in]	gpusWereDetected	Whether compatible GPUs were detected on any node.

Returns

Whether the simulation will run bondeded tasks on GPUs.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

bool gmx::decideWhetherToUseGpusForNonbonded	(	TaskTarget	nonbondedTarget,
		const std::vector< int > &	userGpuTaskAssignment,
		EmulateGpuNonbonded	emulateGpuNonbonded,
		bool	canUseNonbondedOnGpu,
		bool	binaryReproducibilityRequested,
		bool	gpusWereDetected
	)

Decide whether the simulation will try to run nonbonded tasks on GPUs.

The final decision cannot be made until after the duty of the rank is known. But we need to know if nonbonded will run on GPUs for setting up DD (particularly rlist) and determining duty. If the user requires GPUs for the tasks of that duty, then it will be an error when none are found.

With thread-MPI, calls have been made to decideWhetherToUseGpusForNonbondedWithThreadMpi() and decideWhetherToUseGpusForPmeWithThreadMpi() to help determine the number of ranks and run some checks, but the final decision is made in this routine, along with many more consistency checks.

Parameters

[in]	nonbondedTarget	The user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	emulateGpuNonbonded	Whether we will emulate GPU calculation of nonbonded interactions.
[in]	canUseNonbondedOnGpu	Whether GROMACS was build with GPU support and simulation parameters are compatible.
[in]	binaryReproducibilityRequested	Whether binary reproducibility was requested
[in]	gpusWereDetected	Whether compatible GPUs were detected on any node.

Returns

Whether the simulation will run nonbonded and PME tasks, respectively, on GPUs.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

bool gmx::decideWhetherToUseGpusForNonbondedFE	(	bool	useGpuForNonbonded,
		TaskTarget	nonBondedFeTarget,
		const t_inputrec &	inputrec
	)

Decide whether the simulation will try to run nonbonde FE tasks on GPUs.

Parameters

[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	nonBondedFeTarget	The user's choice for mdrun -nbfe for where to assign tasks.
[in]	inputrec	The user input

Returns

Whether the simulation will run nonbonded fe tasks on GPUs.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

bool gmx::decideWhetherToUseGpusForNonbondedWithThreadMpi	(	TaskTarget	nonbondedTarget,
		bool	haveAvailableDevices,
		const std::vector< int > &	userGpuTaskAssignment,
		EmulateGpuNonbonded	emulateGpuNonbonded,
		bool	canUseNonbondedOnGpu,
		bool	binaryReproducibilityRequested,
		int	numRanksPerSimulation
	)

Decide whether this thread-MPI simulation will run nonbonded tasks on GPUs.

The number of GPU tasks and devices influences both the choice of the number of ranks, and checks upon any such choice made by the user. So we need to consider this before any automated choice of the number of thread-MPI ranks.

Parameters

[in]	nonbondedTarget	The user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]	haveAvailableDevices	Whether there are available devices.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	emulateGpuNonbonded	Whether we will emulate GPU calculation of nonbonded interactions.
[in]	canUseNonbondedOnGpu	Whether GROMACS was built with GPU support and simulation parameters are compatible.
[in]	binaryReproducibilityRequested	Whether binary reproducibility was requested
[in]	numRanksPerSimulation	The number of ranks in each simulation.

Returns

Whether the simulation will run nonbonded tasks on GPUs.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

bool gmx::decideWhetherToUseGpusForPme	(	bool	useGpuForNonbonded,
		TaskTarget	pmeTarget,
		TaskTarget	pmeFftTarget,
		const std::vector< int > &	userGpuTaskAssignment,
		const t_inputrec &	inputrec,
		int	numRanksPerSimulation,
		int	numPmeRanksPerSimulation,
		bool	gpusWereDetected
	)

Decide whether the simulation will try to run tasks of different types on GPUs.

The final decision cannot be made until after the duty of the rank is known. But we need to know if nonbonded will run on GPUs for setting up DD (particularly rlist) and determining duty. If the user requires GPUs for the tasks of that duty, then it will be an error when none are found.

With thread-MPI, calls have been made to decideWhetherToUseGpusForNonbondedWithThreadMpi() and decideWhetherToUseGpusForPmeWithThreadMpi() to help determine the number of ranks and run some checks, but the final decision is made in this routine, along with many more consistency checks.

Parameters

[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	pmeTarget	The user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]	pmeFftTarget	The user's choice for mdrun -pmefft for where to do FFT for PME.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	inputrec	The user input
[in]	numRanksPerSimulation	The number of ranks in each simulation.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation.
[in]	gpusWereDetected	Whether compatible GPUs were detected on any node.

Returns

Whether the simulation will run nonbonded and PME tasks, respectively, on GPUs.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

bool gmx::decideWhetherToUseGpusForPmeWithThreadMpi	(	bool	useGpuForNonbonded,
		TaskTarget	pmeTarget,
		TaskTarget	pmeFftTarget,
		int	numDevicesToUse,
		const std::vector< int > &	userGpuTaskAssignment,
		const t_inputrec &	inputrec,
		int	numRanksPerSimulation,
		int	numPmeRanksPerSimulation
	)

Decide whether this thread-MPI simulation will run PME tasks on GPUs.

The number of GPU tasks and devices influences both the choice of the number of ranks, and checks upon any such choice made by the user. So we need to consider this before any automated choice of the number of thread-MPI ranks.

Parameters

[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	pmeTarget	The user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]	pmeFftTarget	The user's choice for mdrun -pmefft for where to run FFT.
[in]	numDevicesToUse	The number of compatible GPUs that the user permitted us to use.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	inputrec	The user input
[in]	numRanksPerSimulation	The number of ranks in each simulation.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation.

Returns

Whether the simulation will run PME tasks on GPUs.

Exceptions

std::bad_alloc

If out of memory InconsistentInputError If the user requirements are inconsistent.

static void gmx::deepCopy_t_trxframe ( const t_trxframe &  input, t_trxframe *  copy, RVec *  xvec, RVec *  vvec, RVec *  fvec, int *  indexvec  )

static

Create a deep copy of a t_trxframe input into copy.

When running the analysis tools and changing values with the outputadapters, a deep copy of the input coordinate frame has to be created first to ensure that the data is not changed if it is needed for other tools following with analysis later. Therefore, the data is passed to copy by performing a deep copy first.

The method allocates new storage for coordinates of the x, v, and f arrays in the new coordinate frame. This means that those arrays need to be free'd after the frame has been processed and been written to disk.

Parameters

[in]	input	Reference input coordinate frame.
[in,out]	copy	Pointer to new output frame that will receive the deep copy.
[in]	xvec	Pointer to local coordinate storage vector.
[in]	vvec	Pointer to local velocity storage vector.
[in]	fvec	Pointer to local force storage vector.
[in]	indexvec	Pointer to local index storage vector.

static std::string gmx::describeAtomsForRBDihedralOfGivenType ( const gmx_mtop_t &  mtop, int  interactionType  )

static

Describe molecule and involved atoms for a dihedral interaction of a given type.

Searches in the dihedrals of type 3 (Ryckaert-Bellemans or Fourier) for an interaction type matching the interactionType input parameters, returning for the first match a string with the name of the molecule and the 4 involved atoms.

Precondition: the interaction should exist in the topology

MrcDensityMapHeader gmx::deserializeMrcDensityMapHeader

(

ISerializer *

serializer

)

Deserializes an MrcDensityMapHeader from a given serializer.

Parameters

[in]

serializer

the serializer

Returns

mrc density map header

static void gmx::detect_flux_per_channel ( t_swapgrp *  group, int  iAtom, Compartment  comp, const gmx::RVec  atomPosition, Domain *  comp_now, Domain *  comp_from, ChannelHistory *  channel_label, const t_swapcoords &  sc, SwapCoords::Impl *  s, real  cyl0_r2, real  cyl1_r2, int64_t  step, gmx_bool  bRerun, FILE *  fpout  )

static

Determine the per-channel ion flux.

To determine the flux through the individual channels, we remember the compartment and channel history of each ion. An ion can be either in channel0 or channel1, or in the remaining volume of compartment A or B.

*    +-----------------+
*    |                 | B
*    |                 | B compartment
*    ||||||||||0|||||||| bilayer with channel 0
*    |                 | A
*    |                 | A
*    |                 | A compartment
*    |                 | A
*    |||||1||||||||||||| bilayer with channel 1
*    |                 | B
*    |                 | B compartment
*    +-----------------+
*
* 

static void gmx::detect_flux_per_channel_init ( SwapCoords::Impl *  s, swaphistory_t *  swapstate, const bool  isRestart  )

static

Initialize channel ion flux detection routine.

Initialize arrays that keep track of where the ions come from and where they go.

static DeviceDetectionResult gmx::detectAllDeviceInformation ( const PhysicalNodeCommunicator &  physicalNodeComm )

static

Detect GPUs when that makes sense to attempt.

Parameters

[in]

physicalNodeComm

The communicator across this physical node

Returns

The result of the detection, perhaps including diagnostic messages to issue later.

Todo:

Coordinating the efficient detection of devices across multiple ranks per node should be separated from the lower-level hardware detection. See https://gitlab.com/gromacs/gromacs/-/issues/3650.

static torch::Device gmx::determineDevice ( const MDLogger &  logger, const MpiComm &  mpiComm  )

static

Determine which device to use depending on GMX_NN_DEVICE environment variable.

Should be "gpu" or "cpu". "cuda" option is deprecated. Defaults to GPU if no environment variable is set. Throws an error if CUDA/HIP is requested but no compatible device is available. Also throws an error if the environment variable is set to an invalid value.

PmeRunMode gmx::determinePmeRunMode	(	bool	useGpuForPme,
		const TaskTarget &	pmeFftTarget,
		const t_inputrec &	inputrec
	)

Determine PME run mode.

Given the PME task assignment in useGpuForPme and the user-provided FFT task target in pmeFftTarget, returns a PME run mode for the current run. It also checks the compatibility of the two.

Note

Aborts the run upon incompatible values of useGpuForPme and pmeFftTarget.

Parameters

[in]	useGpuForPme	PME task assignment, true if PME task is mapped to the GPU.
[in]	pmeFftTarget	The user's choice for -pmefft for where to assign the FFT work of the PME task.
[in]	inputrec	The user input record

template<typename T , int iClusterSize, int jClusterSize>

constexpr std::array<T, jClusterSize / iClusterSize> gmx::diagonalMaskJLargerI

(

)

Returns a diagonal interaction mask with atoms j>i masked out.

Template Parameters

T	Integer type, should have at least iClusterSize*jClusterSize bits
iClusterSize	The i-cluster size
jClusterSize	The j-cluster size

Condition: jClusterSize >= iClusterSize

template<typename T , int iClusterSize, int jClusterSize>

constexpr std::array<T, iClusterSize / jClusterSize> gmx::diagonalMaskJSmallerI

(

)

Returns a diagonal interaction mask with atoms j<i masked out.

Template Parameters

T	Integer type, should have at least iClusterSize*jClusterSize bits
iClusterSize	The i-cluster size
jClusterSize	The j-cluster size

Condition: jClusterSize <= iClusterSize

template<typename ElementType >

BasicMatrix3x3<ElementType> gmx::diagonalMatrix

(

const ElementType

value

)

Create a diagonal matrix of ElementType.

Template Parameters

ElementType

type of matrix elements

Parameters

value

The value that fills the leading diagonal

Returns

a matrix with values value where row equals column index and null where row does not equal column index

void gmx::distributeTransformationPullCoordForce	(	pull_coord_work_t *	pcrd,
		gmx::ArrayRef< pull_coord_work_t >	variableCoords
	)

Distributes the force on a transformation pull coordinates to the involved coordinates of lower rank.

Note: There is no recursion applied here, which means that this function needs to be called in a reverse loop over the pull coordinates to ensure that forces on recursive transformation coordinates are distributed correctly.

Parameters

[in,out]	pcrd	The transformation pull coordinate to act on
[in,out]	variableCoords	List of variable coords up to the coord index of pcrd

template<typename T >

constexpr T gmx::divideRoundUp	(	T	numerator,
		T	denominator
	)

Return numerator divided by denominator rounded up to the next integer.

Parameters

[in]	numerator	Numerator, a non-negative integer.
[in]	denominator	Denominator, a positive integer.

Warning

The sum of numerator and denominator should fit into T

void gmx::do_edsam	(	const t_inputrec *	ir,
		int64_t	step,
		const MpiComm &	mpiComm,
		ArrayRef< RVec >	coords,
		ArrayRef< RVec >	velocities,
		const matrix	box,
		edsam *	ed
	)

Applies essential dynamics constrains as defined in the .edi input file.

Parameters

ir	MD input parameter record.
step	Number of the time step.
mpiComm	Communication object for my group.
coords	The local positions on this processor.
velocities	The local velocities.
box	The simulation box.
ed	The essential dynamics data.

static bool gmx::do_em_step ( const t_commrec *  cr, const t_inputrec *  ir, const t_mdatoms *  md, t_state *  s1, const real  stepSize, ArrayRef< const RVec >  force, em_state_t *  ems2, Constraints *  constr, const int64_t  count  )

static

Do one minimization step.

Parameters

[in]	cr	Communication record
[in]	ir	Run parameters
[in]	md	Atom properties
[in]	s1	Coordinates to take the step from, non-const for constrained halo atoms
[in]	stepSize	Step size in nm/(kJ/mol/nm)
[in]	force	The force for the coordinates in s1
[in,out]	ems2	Buffer for returning the new coordinates, the force buffer is resize
[in,out]	constr	Constraint object
[in]	count	Step count, only used for reporting

Returns

true when the step succeeded, false when a constraint error occurred

void gmx::do_flood	(	const MpiComm &	mpiComm,
		const t_inputrec &	ir,
		ArrayRef< const RVec >	coords,
		ArrayRef< RVec >	force,
		edsam *	ed,
		const matrix	box,
		int64_t	step,
		bool	bNS
	)

Evaluate the flooding potential(s) and forces as requested in the .edi input file.

Parameters

mpiComm	Communication object for my group.
ir	MD input parameter record.
coords	Positions on the local processor.
force	Forcefield forces to which the flooding forces are added.
ed	The essential dynamics data.
box	The simulation box.
step	Number of the time step.
bNS	Are we in a neighbor searching step?

void gmx::do_h_mass	(	const InteractionsOfType &	psb,
		ArrayRef< const VsiteTypeAndSign >	vsiteType,
		t_atoms *	at,
		real	mHmult,
		bool	deuterate
	)

Optionally, change masses of hydrogens.

Parameters

[in]	psb	List of bond interations
[in]	vsiteType	Array with vsites with their type and sign, only type is used
[in,out]	at	Atom information, masses may be modified
[in]	mHmult	Factor to multiply the masses of hydrogens with
[in]	deuterate	When false, subtract the increase in hydrogen mass from the bonded heavt atom

gmx_bool gmx::do_swapcoords	(	const MpiComm &	mpiComm,
		int64_t	step,
		double	t,
		const t_inputrec *	ir,
		SwapCoords *	s,
		gmx_wallcycle *	wcycle,
		ArrayRef< RVec >	x,
		matrix	box,
		gmx_bool	bVerbose,
		gmx_bool	bRerun
	)

"Computational Electrophysiology" main routine within MD loop.

Parameters

[in]	mpiComm	Communicator object for my group.
[in]	step	The number of the MD time step.
[in]	t	The time.
[in]	ir	Structure containing MD input parameters
[in,out]	s	The structure needed for position swapping.
[in]	wcycle	Count wallcycles of swap routines for diagnostic output.
[in]	x	Positions of home particles this node owns.
[in]	box	The simulation box.
[in]	bVerbose	Should we be quiet or verbose?
[in]	bRerun	Are we doing a rerun?

Returns

Whether at least one pair of molecules was swapped.

void gmx::doDeviceTransfers	(	const DeviceContext &	deviceContext,
		ArrayRef< const char >	input,
		ArrayRef< char >	output
	)

Helper function for GPU test code to be platform agnostic.

Transfers input to device 0, if present, and transfers it back into output. Both sizes must match. If no devices are present, do a simple host-side buffer copy instead.

Exceptions

InternalError

Upon any GPU API error condition.

template<class BasicMdspan >

constexpr std::enable_if_t<BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer> gmx::end

(

const BasicMdspan &

basicMdspan

)

Free end function addressing memory of a contiguously laid out basic_mdspan.

Note

Changing the elements that basic_mdspan views does not change the view itself, so a single end that takes a const view suffices.

void gmx::ensureNoPendingDeviceError ( const std::string_view  errorMessage )

inline

Helper function to ensure no pending error silently disrupts error handling.

Asserts in a debug build if an unhandled error is present. Issues a warning at run time otherwise.

Parameters

[in]

errorMessage

Undecorated error message.

static void gmx::ensureStateAndRunConsistency ( const BiasParams &  params, const BiasState &  state  )

static

Check if the state (loaded from checkpoint) and the run are consistent.

When the state and the run setup are inconsistent, an exception is thrown.

Parameters

[in]	params	The parameters of the bias.
[in]	state	The state of the bias.

static const char* gmx::enumValueToString ( AtomLocality  enumValue )

static

Get the human-friendly name for atom localities.

Parameters

[in]

enumValue

The enum value to get the name for.

static const char* gmx::enumValueToString ( InteractionLocality  enumValue )

static

Get the human-friendly name for interaction localities.

Parameters

[in]

enumValue

The enum value to get the name for.

static float gmx::erf ( float  x )

inlinestatic

Float erf(x).

Parameters

x

Argument.

Returns

erf(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::erf ( double  x )

inlinestatic

Double erf(x).

Parameters

x

Argument.

Returns

erf(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::erfc ( float  x )

inlinestatic

Float erfc(x).

Parameters

x

Argument.

Returns

erfc(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::erfc ( double  x )

inlinestatic

Double erfc(x).

Parameters

x

Argument.

Returns

erfc(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::erfcSingleAccuracy ( double  x )

inlinestatic

Double erfc(x), but with single accuracy.

Parameters

x

Argument.

Returns

erfc(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

double gmx::erfinv

(

double

x

)

Inverse error function, double precision.

Parameters

x	Argument, should be in the range -1.0 < x < 1.0

Returns

The inverse of the error function if the argument is inside the range, +/- infinity if it is exactly 1.0 or -1.0, and NaN otherwise.

float gmx::erfinv

(

float

x

)

Inverse error function, single precision.

Parameters

x	Argument, should be in the range -1.0 < x < 1.0

Returns

The inverse of the error function if the argument is inside the range, +/- infinity if it is exactly 1.0 or -1.0, and NaN otherwise.

static double gmx::erfSingleAccuracy ( double  x )

inlinestatic

Double erf(x), but with single accuracy.

Parameters

x

Argument.

Returns

erf(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<typename Iterator , typename Callback >

std::pair<size_t, size_t> gmx::estimateBufferSize	(	Iterator	begin,
		Iterator	end,
		Callback	cStringFromIterator
	)

Iterate over a list of objects and calculate the maximum string length via a callback function.

Template Parameters

Iterator	The type of the iterator of the source strings.
Callback	The type of the callback function to convert iterator to C-string.

Parameters

[in]	begin	Iterator to the beginning of the source vector of strings.
[in]	end	Iterator to the end of the source vector of strings.
[in]	cStringFromIterator	The callback function to convert iterator to C-string.

Returns

The maximum length of the strings and the number of strings in the vector.

real gmx::ewald_spline3_table_scale	(	const interaction_const_t &	ic,
		bool	generateCoulombTables,
		bool	generateVdwTables
	)

Compute scaling for the Ewald quadratic spline tables.

Parameters

ic	Pointer to interaction constant structure
generateCoulombTables	Take the spacing for Coulomb Ewald corrections into account
generateVdwTables	Take the spacing for Van der Waals Ewald corrections into account

Returns

The scaling factor in units 1/nm

constexpr int32_t gmx::exactDiv	(	int32_t	a,
		int32_t	b
	)

Exact integer division, 32bit.

Parameters

a	dividend. Function asserts that it is a multiple of divisor
b	divisor

Returns

quotient of division

std::string gmx::exaFmmTreeTypeName

(

ExaFmmTreeType

treeType

)

Returns the string name for a given ExaFmm Tree Type.

Parameters

treeType

The ExaFmmTreeType enum value.

Returns

The corresponding tree type name as a std::string.

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::exp ( float  x )

inlinestatic

Float exp(x).

Parameters

x

Argument.

Returns

exp(x). Undefined if input argument caused overflow.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::exp ( double  x )

inlinestatic

Double exp(x).

Parameters

x

Argument.

Returns

exp(x). Undefined if input argument caused overflow.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::exp2 ( float  x )

inlinestatic

Float 2^x.

Parameters

x

Argument.

Returns

2^x. Undefined if input argument caused overflow.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::exp2 ( double  x )

inlinestatic

Double 2^x.

Parameters

x

Argument.

Returns

2^x. Undefined if input argument caused overflow.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::exp2SingleAccuracy ( double  x )

inlinestatic

Double 2^x, but with single accuracy.

Parameters

x

Argument.

Returns

2^x. Undefined if input argument caused overflow.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::expandScalarsToTriplets ( float  scalar, float *  triplets0, float *  triplets1, float *  triplets2  )

inlinestatic

Copy single float to three variables.

Parameters

	scalar	Floating-point input.
[out]	triplets0	Copy 1.
[out]	triplets1	Copy 2.
[out]	triplets2	Copy 3.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::expandScalarsToTriplets ( double  scalar, double *  triplets0, double *  triplets1, double *  triplets2  )

inlinestatic

Copy single double to three variables.

Parameters

	scalar	Floating-point input.
[out]	triplets0	Copy 1.
[out]	triplets1	Copy 2.
[out]	triplets2	Copy 3.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

ExponentialMovingAverageState gmx::exponentialMovingAverageStateFromKeyValueTree

(

const KeyValueTreeObject &

object

)

Sets the exponential moving average state from a key-value-tree object.

Sets the expoential moving average state from a key-value-tree object.

static double gmx::expSingleAccuracy ( double  x )

inlinestatic

Double exp(x), but with single accuracy.

Parameters

x

Argument.

Returns

exp(x). Undefined if input argument caused overflow.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::fep_list_new_nri_copy ( AtomPairlist *  nlist, int  energyGroupPair = -1  )

inlinestatic

Add a new entry to the i-list as a copy of the last entry.

If the last i-entry has no j-entries, it will be replaced instead of creating a new entry.

static void gmx::fillin_ocl_structures ( NBParamGpu *  nbp, cl_nbparam_params_t *  nbparams_params  )

static

Initializes data structures that are going to be sent to the OpenCL device.

The device can't use the same data structures as the host for two main reasons:

• OpenCL restrictions (pointers are not accepted inside data structures)
• some host side fields are not needed for the OpenCL kernels.

This function is called before the launch of both nbnxm and prune kernels.

static FixedCapacityVector<int, 12> gmx::fillSupportedSubGroupSizes ( const cl_device_id  devId, const DeviceVendor  deviceVendor  )

static

Return the list of sub-group sizes supported by the device.

Parameters

devId	OpenCL device ID.
deviceVendor	Device vendor.

Returns

the list of sub-group sizes supported by the device

std::vector< MoleculePatchDatabase * > gmx::filter_ter	(	gmx::ArrayRef< MoleculePatchDatabase >	tb,
		const char *	resname
	)

Return entries for modification blocks that match a residue name.

Parameters

[in]	tb	Complete modification database.
[in]	resname	Residue name for terminus.

Returns

A list of pointers to entries that match, or of nullptr for no matching entry.

GpuTasksOnRanks gmx::findAllGpuTasksOnThisNode	(	ArrayRef< const GpuTask >	gpuTasksOnThisRank,
		const PhysicalNodeCommunicator &	physicalNodeComm
	)

Returns container of all tasks on all ranks of this node that are eligible for GPU execution.

Perform all necessary communication for preparing for task assignment. Separating this aspect makes it possible to unit test the logic of task assignment.

static int gmx::findCmapType ( EnumerationArray< InteractionFunction, InteractionsOfType > &  bondtype, const t_atoms &  at, const PreprocessingAtomTypes &  atypes, const InteractionOfType &  p, WarningHandler *  wi  )

static

Find the appropriate type for the current CMAP p interaction.

The CMAP type looked up in the list available for this forcefield, either via the index supplied in the user's topology for this interaction, or via atom-type name and/or residue-type name lookup (according to the how the forcefield does lookups for default CMAP types).

When no CMAP type matches p, a fatal error is issued.

void gmx::findConstraintGroupSizes	(	int	numConstraints,
		ArrayRef< const AtomPair >	constraintsHost,
		ArrayRef< int >	constraintGroupSize
	)

Calculate constraint group sizes.

Allows reducing the number of contested atomics in LINCS GPU kernel.

Parameters

[in]	numConstraints	Number of constraints in system.
[in]	constraintsHost	The host constraint array to get sizes from.
[in,out]	constraintGroupSize	Number of constraints in a block.

std::vector< GpuTask > gmx::findGpuTasksOnThisRank	(	bool	haveGpusOnThisPhysicalNode,
		TaskTarget	nonbondedTarget,
		TaskTarget	nonbondedFeTarget,
		TaskTarget	pmeTarget,
		TaskTarget	bondedTarget,
		TaskTarget	updateTarget,
		bool	useGpuForNonbonded,
		bool	useGpuForPme,
		bool	rankHasPpTask,
		bool	rankHasPmeTask
	)

Returns container of all tasks on this rank that are eligible for GPU execution.

Parameters

[in]	haveGpusOnThisPhysicalNode	Whether there are any GPUs on this physical node.
[in]	nonbondedTarget	The user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]	nonbondedFeTarget	The user's choice for mdrun -nbfe for where to assign nonbonded fe interaction tasks.
[in]	pmeTarget	The user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]	bondedTarget	The user's choice for mdrun -bonded for where to assign tasks.
[in]	updateTarget	The user's choice for mdrun -update for where to assign tasks.
[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	useGpuForPme	Whether GPUs will be used for PME interactions.
[in]	rankHasPpTask	Whether this rank has a PP task
[in]	rankHasPmeTask	Whether this rank has a PME task

std::filesystem::path gmx::findLibraryFile	(	const std::filesystem::path &	filename,
		bool	bAddCWD = true,
		bool	bFatal = true
	)

Finds full path for a library file.

Searches in the configured library directories for filename. If bAddCWD is true, searches first in the current directory. Fatal error results if the file is not found in any location and bFatal is true.

static void gmx::flagInteractionsForType ( const InteractionFunction  ftype, const InteractionList &  il, const reverse_ilist_t &  ril, const Range< int > &  atomRange, const int  numAtomsPerMolecule, ArrayRef< const int >  globalAtomIndices, ArrayRef< int >  isAssigned  )

static

Checks whether interactions have been assigned for one function type.

Loops over a list of interactions in the local topology of one function type and flags each of the interactions as assigned in the global isAssigned list. Exits with an inconsistency error when an interaction is assigned more than once.

static float gmx::fma ( float  a, float  b, float  c  )

inlinestatic

Float Fused-multiply-add. Result is a*b + c.

Parameters

a	factor1
b	factor2
c	term

Returns

a*b + c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::fma ( double  a, double  b, double  c  )

inlinestatic

double Fused-multiply-add. Result is a*b + c.

Parameters

a	factor1
b	factor2
c	term

Returns

a*b + c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

std::string gmx::fmmBackendName

(

ActiveFmmBackend

backend

)

Returns the string name for a given FMM backend.

Parameters

backend

The FMM backend enum value.

Returns

The corresponding backend name as a std::string.

std::string gmx::fmmDirectProviderName

(

FmmDirectProvider

directProvider

)

Returns the string name for a given FMM direct provider.

Parameters

directProvider

The FmmDirectProvider enum value.

Returns

The corresponding direct provider name as a std::string.

static float gmx::fms ( float  a, float  b, float  c  )

inlinestatic

Float Fused-multiply-subtract. Result is a*b - c.

Parameters

a	factor1
b	factor2
c	term

Returns

a*b - c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::fms ( double  a, double  b, double  c  )

inlinestatic

double Fused-multiply-subtract. Result is a*b - c.

Parameters

a	factor1
b	factor2
c	term

Returns

a*b - c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::fnma ( float  a, float  b, float  c  )

inlinestatic

Float Fused-negated-multiply-add. Result is -a*b + c.

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b + c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::fnma ( double  a, double  b, double  c  )

inlinestatic

double Fused-negated-multiply-add. Result is - a*b + c.

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b + c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::fnms ( float  a, float  b, float  c  )

inlinestatic

Float Fused-negated-multiply-subtract. Result is -a*b - c.

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b - c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::fnms ( double  a, double  b, double  c  )

inlinestatic

double Fused-negated-multiply-subtract. Result is -a*b - c.

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b - c

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static int gmx::forceGroupMtsLevel ( ArrayRef< const MtsLevel >  mtsLevels, const MtsForceGroups  mtsForceGroup  )

inlinestatic

Returns the MTS level at which a force group is to be computed.

Parameters

[in]	mtsLevels	List of force groups for each MTS level, can be empty without MTS
[in]	mtsForceGroup	The force group to query the MTS level for

static std::string gmx::formatListSetup ( const std::string &  listName, int  nstList, int  nstListForSpacing, real  rList, real  interactionCutoff  )

static

Returns a string describing the setup of a single pair-list.

Parameters

[in]	listName	Short name of the list, can be ""
[in]	nstList	The list update interval in steps
[in]	nstListForSpacing	Update interval for setting the number characters for printing nstList
[in]	rList	List cut-off radius
[in]	interactionCutoff	The interaction cut-off, use for printing the list buffer size

static void gmx::freeGpuProgram ( cl_program  program )

static

Free the OpenCL program.

The function releases the OpenCL program assuciated with the device that the calling PP rank is running on.

Parameters

program

[in] OpenCL program to release.

template<int align>

static void gmx::gatherLoadBySimdIntTranspose ( const float *  base, std::int32_t  offset, float *  v0, float *  v1, float *  v2, float *  v3  )

inlinestatic

Load 4 floats from base/offsets and store into variables.

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Aligned pointer to the start of the memory.
	offset	Integer type with offset to the start of each triplet.
[out]	v0	First float, base[align*offset[0]].
[out]	v1	Second float, base[align*offset[0] + 1].
[out]	v2	Third float, base[align*offset[0] + 2].
[out]	v3	Fourth float, base[align*offset[0] + 3].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadBySimdIntTranspose ( const float *  base, std::int32_t  offset, float *  v0, float *  v1  )

inlinestatic

Load 2 floats from base/offsets and store into variables (aligned).

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Aligned pointer to the start of the memory.
	offset	Integer type with offset to the start of each triplet.
[out]	v0	First float, base[align*offset[0]].
[out]	v1	Second float, base[align*offset[0] + 1].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadBySimdIntTranspose ( const double *  base, std::int32_t  offset, double *  v0, double *  v1, double *  v2, double *  v3  )

inlinestatic

Load 4 doubles from base/offsets and store into variables.

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Aligned pointer to the start of the memory.
	offset	Integer type with offset to the start of each triplet.
[out]	v0	First double, base[align*offset[0]].
[out]	v1	Second double, base[align*offset[0] + 1].
[out]	v2	Third double, base[align*offset[0] + 2].
[out]	v3	Fourth double, base[align*offset[0] + 3].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadBySimdIntTranspose ( const double *  base, std::int32_t  offset, double *  v0, double *  v1  )

inlinestatic

Load 2 doubles from base/offsets and store into variables (aligned).

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Aligned pointer to the start of the memory.
	offset	Integer type with offset to the start of each triplet.
[out]	v0	First double, base[align*offset[0]].
[out]	v1	Second double, base[align*offset[0] + 1].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadTranspose ( const float *  base, const std::int32_t  offset[], float *  v0, float *  v1, float *  v2, float *  v3  )

inlinestatic

Load 4 consecutive floats from base/offset into four variables.

Template Parameters

align

Alignment of the memory from which we read.

Parameters

	base	Pointer to the start of the memory area
	offset	Index to data.
[out]	v0	1st float, base[align*offset[0]].
[out]	v1	2nd float, base[align*offset[0] + 1].
[out]	v2	3rd float, base[align*offset[0] + 2].
[out]	v3	4th float, base[align*offset[0] + 3].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadTranspose ( const float *  base, const std::int32_t  offset[], float *  v0, float *  v1  )

inlinestatic

Load 2 consecutive floats from base/offset into four variables.

Template Parameters

align

Alignment of the memory from which we read.

Parameters

	base	Pointer to the start of the memory area
	offset	Index to data.
[out]	v0	1st float, base[align*offset[0]].
[out]	v1	2nd float, base[align*offset[0] + 1].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadTranspose ( const double *  base, const std::int32_t  offset[], double *  v0, double *  v1, double *  v2, double *  v3  )

inlinestatic

Load 4 consecutive doubles from base/offset into four variables.

Template Parameters

align

Alignment of the memory from which we read.

Parameters

	base	Pointer to the start of the memory area
	offset	Index to data.
[out]	v0	1st double, base[align*offset[0]].
[out]	v1	2nd double, base[align*offset[0] + 1].
[out]	v2	3rd double, base[align*offset[0] + 2].
[out]	v3	4th double, base[align*offset[0] + 3].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadTranspose ( const double *  base, const std::int32_t  offset[], double *  v0, double *  v1  )

inlinestatic

Load 2 consecutive doubles from base/offset into four variables.

Template Parameters

align

Alignment of the memory from which we read.

Parameters

	base	Pointer to the start of the memory area
	offset	Index to data.
[out]	v0	1st double, base[align*offset[0]].
[out]	v1	2nd double, base[align*offset[0] + 1].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadUBySimdIntTranspose ( const float *  base, std::int32_t  offset, float *  v0, float *  v1  )

inlinestatic

Load 2 floats from base/offsets and store into variables (unaligned).

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Aligned pointer to the start of the memory.
	offset	Integer type with offset to the start of each triplet.
[out]	v0	First float, base[align*offset[0]].
[out]	v1	Second float, base[align*offset[0] + 1].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadUBySimdIntTranspose ( const double *  base, std::int32_t  offset, double *  v0, double *  v1  )

inlinestatic

Load 2 doubles from base/offsets and store into variables (unaligned).

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Aligned pointer to the start of the memory.
	offset	Integer type with offset to the start of each triplet.
[out]	v0	First double, base[align*offset[0]].
[out]	v1	Second double, base[align*offset[0] + 1].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadUTranspose ( const float *  base, const std::int32_t  offset[], float *  v0, float *  v1, float *  v2  )

inlinestatic

Load 3 consecutive floats from base/offsets, store into three vars.

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Pointer to the start of the memory area
	offset	Offset to the start of data.
[out]	v0	1st value, base[align*offset[0]].
[out]	v1	2nd value, base[align*offset[0] + 1].
[out]	v2	3rd value, base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::gatherLoadUTranspose ( const double *  base, const std::int32_t  offset[], double *  v0, double *  v1, double *  v2  )

inlinestatic

Load 3 consecutive doubles from base/offsets, store into three vars.

Template Parameters

align

Alignment of the memory from which we read, i.e. distance (measured in elements, not bytes) between index points.

Parameters

	base	Pointer to the start of the memory area
	offset	Offset to the start of data.
[out]	v0	1st double, base[align*offset[0]].
[out]	v1	2nd double, base[align*offset[0] + 1].
[out]	v2	3rd double, base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::gen_pad	(	t_atoms *	atoms,
		ArrayRef< const PreprocessResidue >	rtpFFDB,
		EnumerationArray< InteractionFunction, InteractionsOfType > &	plist,
		t_excls	excls[],
		ArrayRef< MoleculePatchDatabase >	globalPatches,
		bool	bAllowMissing,
		ArrayRef< const int >	cyclicBondsIndex,
		ArrayRef< const DisulfideBond >	ssbonds
	)

Generate pairs, angles and dihedrals from .rtp settings.

Parameters

[in,out]	atoms	Global information about atoms in topology.
[in]	rtpFFDB	Residue type database from force field.
[in,out]	plist	Information about listed interactions.
[in,out]	excls	Pair interaction exclusions.
[in,out]	globalPatches	Information about possible residue modifications.
[in]	bAllowMissing	True if missing interaction information is allowed. AKA allow cartoon physics
[in]	cyclicBondsIndex	Information about bonds creating cyclic molecules. Empty if no such bonds exist.
[in]	ssbonds	Information regarding special bonds and custom improper dihedrals from specbond. Empty if no such bonds exist.

static void gmx::generate_qmexcl_moltype ( gmx_moltype_t *  molt, const unsigned char *  grpnr, t_inputrec *  ir, const MDLogger &  logger  )

static

Exclude molecular interactions for QM atoms handled by MiMic.

Update the exclusion lists to include all QM atoms of this molecule, replace bonds between QM atoms with InteractionFunction::ConnectBonds and set charges of QM atoms to 0.

Parameters

[in,out]	molt	molecule type with QM atoms
[in]	grpnr	group informatio
[in,out]	ir	input record
[in]	logger	Handle to logging interface.

template<class RealType = real, unsigned int Bits, class Rng >

RealType gmx::generateCanonical

(

Rng &

g

)

Generate a floating-point value with specified number of random bits.

Template Parameters

RealType	Floating-point type to generate
Bits	Number of random bits to generate
Rng	Random number generator class

Parameters

g	Random number generator to use

This implementation avoids the bug in libc++ and stdlibc++ (which is due to the C++ standard being unclear) where 1.0 can be returned occasionally.

EwaldCorrectionTables gmx::generateEwaldCorrectionTables	(	int	numPoints,
		double	tableScaling,
		real	beta,
		real_space_grid_contribution_computer	v_lr
	)

Construct tables with the Ewald long-range force interaction.

Creates and fills tables of numPoints points with the spacing set to 1/tableScaling with the Ewald long-range (mesh) force. There are three separate tables with format F, V, FDV0. This function interpolates the Ewald mesh potential contribution with coefficient beta using a quadratic spline. The force is then be interpolated linearly.

Parameters

numPoints	Number of points in the tables
tableScaling	1/spacing, units 1/nm
beta	Ewald splitting parameter, units 1/nm
v_lr	Pointer to function calculating real-space grid contribution

Returns

a set of Ewald correction tables

std::vector< int > gmx::genQmmmIndices

(

const gmx_mtop_t &

mtop

)

Generates the list of QM atoms.

This function generates vector containing global IDs of QM atoms based on the information stored in the QM/MM group (egcQMMM)

Parameters

[in]

mtop

Global topology object

Returns

The list of global IDs of QM atoms

static int gmx::get_group_apm_check ( const t_swapgrp &  group, gmx_bool  bVerbose, const gmx_mtop_t &  mtop  )

static

Get the number of atoms per molecule for this group.

Also ensure that all the molecules in this group have this number of atoms.

static int gmx::get_index_of_distant_atom ( t_compartment *  comp, const std::string &  molname  )

static

Return the index of an atom or molecule suitable for swapping.

Returns the index of an atom that is far off the compartment boundaries, that is near to the bulk layer to/from which the swaps take place. Other atoms of the molecule (if any) will directly follow the returned index.

Parameters

[in]	comp	Structure containing compartment-specific data.
[in]	molname	Name of the molecule.

Returns

Index of the first atom of the molecule chosen for a position exchange.

static void gmx::get_initial_ioncounts_from_cpt ( const t_swapcoords &  sc, SwapCoords::Impl *  s, swaphistory_t *  swapstate, const gmx::MpiComm &  mpiComm, gmx_bool  bVerbose  )

static

Copy history of ion counts from checkpoint file.

When called, the checkpoint file has already been read in. Here we copy over the values from .cpt file to the swap data structure.

void gmx::get_ir	(	const char *	mdparin,
		const char *	mdparout,
		MDModules *	mdModules,
		t_inputrec *	ir,
		t_gromppopts *	opts,
		WriteMdpHeader	writeMdpHeader,
		WarningHandler *	wi
	)

Parse input, apply defaults, prepare mdp output.

Read from the mdp input file, parse data from it, and fill inputrec. Also prints the read mdp contents plus applicable defaults back to mdparout.

static gmx::RVec gmx::get_molecule_center ( gmx::ArrayRef< const gmx::RVec >  x, gmx::ArrayRef< const real >  weights, t_pbc *  pbc  )

static

Get the center of a group of nat atoms.

Since with PBC an atom group might not be whole, use the first atom as the reference atom and determine the center with respect to this reference.

static double gmx::get_pull_coord_period ( const t_pull_coord &  pullCoordParams, const t_pbc &  pbc, const real  intervalLength  )

static

Gets the period of a pull coordinate.

Parameters

[in]	pullCoordParams	The parameters for the pull coordinate.
[in]	pbc	The PBC setup
[in]	intervalLength	The length of the AWH interval for this pull coordinate

Returns

the period (or 0 if not periodic).

template<typename ValueType >

std::optional< ValueType > gmx::getAttribute	(	hid_t	container,
		const char *	attributeName
	)

Read an attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to read

Parameters

[in]	container	The HDF5 container (group or dataset) to read the attribute from.
[in]	attributeName	The name of the attribute to read.

Returns

The value of the desired type, or std::nullopt if the attribute does not exist.

template<>

std::optional< std::string > gmx::getAttribute< std::string >	(	hid_t	container,
		const char *	attributeName
	)

Read an attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to read

Parameters

[in]	container	The HDF5 container (group or dataset) to read the attribute from.
[in]	attributeName	The name of the attribute to read.

Returns

The value of the desired type, or std::nullopt if the attribute does not exist. Specialization of getAttribute() for reading attributes of string type.

template<typename ValueType >

std::optional< std::vector< ValueType > > gmx::getAttributeVector	(	hid_t	container,
		const char *	attributeName
	)

Read a vector-like attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to read

Parameters

[in]	container	The HDF5 container (group or dataset) to read the attribute from.
[in]	attributeName	The name of the attribute to read.

Returns

The 1D vector of the desired data, or std::nullopt if the attribute does not exist.

template<>

std::optional< std::vector< std::string > > gmx::getAttributeVector< std::string >	(	hid_t	container,
		const char *	attributeName
	)

Read a vector-like attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to read

Parameters

[in]	container	The HDF5 container (group or dataset) to read the attribute from.
[in]	attributeName	The name of the attribute to read.

Returns

The 1D vector of the desired data, or std::nullopt if the attribute does not exist. Specialization of getAttributeVector() for reading attributes of string type.

TranslateAndScale gmx::getCoordinateTransformationToLattice

(

const MrcDensityMapHeader &

header

)

Extract the transformation into lattice coordinates.

Note

Transformation into lattice coordinates is not treated uniformly in different implementations for the mrc format,e.g., vmd, pymol and chimera have different conventions. Following the vmd implementation here.

In determining the density origin coordinates, explicit ORIGIN records (also called origin2k) in the user defined floats 13 - 15, corresponding to words 50,51 and 52 in the mrc header, precedence over ColumnRowSectionStart. Only if above values are zero, using the column, row and section start to determine the translation vector.

Parameters

[in]

header

from which the coordinate transformation is to be extracted

Returns

a functor that transforms real space coordinates into the lattice

gmx::ArrayRef< const PreprocessResidue >::const_iterator gmx::getDatabaseEntry	(	const std::string &	rtpname,
		gmx::ArrayRef< const PreprocessResidue >	rtpDBEntry
	)

Returns matching entry in database.

Parameters

[in]	rtpname	Name of the entry looked for.
[in]	rtpDBEntry	Database to search.

Exceptions

If	the name can not be found in the database.

double gmx::getDeviationFromPointAlongGridAxis	(	const BiasGrid &	grid,
		int	dimIndex,
		int	pointIndex,
		double	value
	)

Get the deviation along one dimension from the given value to a point in the grid.

Parameters

[in]	grid	The grid.
[in]	dimIndex	Dimensional index in [0, ndim -1].
[in]	pointIndex	BiasGrid point index.
[in]	value	Value along the given dimension.

Returns

the deviation of the given value to the given point.

double gmx::getDeviationFromPointAlongGridAxis	(	const BiasGrid &	grid,
		int	dimIndex,
		int	pointIndex1,
		int	pointIndex2
	)

Get the deviation from one point to another along one dimension in the grid.

Parameters

[in]	grid	The grid.
[in]	dimIndex	Dimensional index in [0, ndim -1].
[in]	pointIndex1	Grid point index of the first point.
[in]	pointIndex2	Grid point index of the second point.

Returns

the deviation of the two points along the given axis.

std::string gmx::getDeviceErrorString ( const hipError_t  deviceError )

inline

Add the API information on the specific error to the error message.

Parameters

[in]

deviceError

The error to assert hipSuccess on.

Returns

A description of the API error. Returns '(HIP error #0 (hipSuccess): no error)' in case deviceError is hipSuccess.

dynamicExtents3D gmx::getDynamicExtents3D

(

const MrcDensityMapHeader &

header

)

Extract the extents of the density data.

Parameters

[in]

header

from which the extents are to be extracted

Returns

density data extents in three dimensions.

size_t gmx::getExclusiveScanWorkingArraySize	(	GpuPairlist *	plist,
		const DeviceStream &	deviceStream
	)

Calculates working memory required for exclusive sum, used in neighbour list sorting on GPU.

This is only used for CUDA/HIP, where the actual size is calculate based on the list. For SYCL, the default value of 0 is important for the code to work correctly, this is why we have it set here.

static int gmx::getExpectedLocalFReadyOnDeviceConsumptionCount ( const SimulationWorkload &  simulationWork, const DomainLifetimeWorkload &  domainWork, const StepWorkload &  stepWork, bool  useOrEmulateGpuNb, bool  alternateGpuWait  )

static

Compute the number of times the "local forces ready on device" GPU event will be used as a synchronization point.

In GROMACS, we usually follow the "mark once - wait once" approach. But this event is "consumed" (that is, waited upon either on host or on the device) multiple times, since many tasks in different streams depend on the local forces.

Parameters

simulationWork	Simulation workload flags.
domainWork	Domain workload flags.
stepWork	Step workload flags.
useOrEmulateGpuNb	Whether GPU non-bonded calculations are used or emulated.
alternateGpuWait	Whether alternating wait/reduce scheme is used.

Returns

The number of times the event will be consumed based on this step's workload.

static int gmx::getExpectedLocalXReadyOnDeviceConsumptionCount ( const SimulationWorkload &  simulationWork, const StepWorkload &  stepWork, const DomainLifetimeWorkload &  domainWork, const bool  pmeSendCoordinatesFromGpu  )

static

Compute the number of times the "local coordinates ready on device" GPU event will be used as a synchronization point.

When some work is offloaded to GPU, force calculation should wait for the atom coordinates to be ready on the device. The coordinates can come either from H2D copy at the beginning of the step, or from the GPU integration at the end of the previous step.

In GROMACS, we usually follow the "mark once - wait once" approach. But this event is "consumed" (that is, waited upon either on host or on the device) multiple times, since many tasks in different streams depend on the coordinates.

This function return the number of times the event will be consumed based on this step's workload.

Parameters

simulationWork	Simulation workload flags.
stepWork	Step workload flags.
domainWork	Domain workload flags.
pmeSendCoordinatesFromGpu	Whether peer-to-peer communication is used for PME coordinates.

Returns

static int gmx::getFileType ( const std::filesystem::path &  filename )

static

Get the internal file type from the filename.

Parameters

[in]

filename

Filename of output file.

Exceptions

InvalidInputError

When unable to work on an emoty file name.

Returns

integer value of file type.

static Range<int> gmx::getGpuAtomRange ( const NBAtomDataGpu *  atomData, const AtomLocality  atomLocality  )

inlinestatic

Calculate atom range and return start index and length.

Parameters

[in]	atomData	Atom descriptor data structure
[in]	atomLocality	Atom locality specifier

Returns

Range of indexes for selected locality.

std::optional<std::string> gmx::getHandleBaseName ( const hid_t  handle )

inline

Return the base name (last component of the HDF-path) of an HDF5 handle.

Parameters

[in]

handle

HDF5 handle to get the base name of.

Returns

The base name of the handle, the full name if no '/' found in its paths, or std::nullopt on error.

std::optional<std::string> gmx::getHandlePath ( const hid_t  handle )

inline

Return the full name (HDF-path) of an HDF5 handle.

Parameters

[in]

handle

HDF5 handle to get the name of.

Returns

The full name of the handle, or std::nullopt if the handle is invalid.

template<int iClusterSize, int jClusterSize>

static gmx_unused uint32_t gmx::getImask ( const bool  maskOutSubDiagonal, const int  ci, const int  cj  )

static

Returns a diagonal or off-diagonal interaction mask.

Template Parameters

iClusterSize	The i-cluster size
jClusterSize	The j-cluster size

Parameters

[in]	maskOutSubDiagonal	Whether to mask out the sub-diagonal interactions
[in]	ci	The i-cluster index
[in]	cj	The j-cluster index

static std::tuple<std::vector<RVec>, std::vector<real> > gmx::getMMPositionsAndCharges ( const std::unique_ptr< LocalAtomSet > &  mmAtoms, ArrayRef< const RVec >  positions, ArrayRef< const real >  charges  )

static

Helper function to gather the positions of the NNP atoms from the input.

Parameters

[in]	mmAtoms	set of MM atoms
[in]	positions	positions of all atoms
[in]	charges	charges of all atoms

Returns

positions and charges of the MM atoms

static int gmx::getNearestIndexInGrid ( const awh_dvec  value, ArrayRef< const GridAxis >  axis  )

static

Map a value to the nearest point in the grid.

Parameters

[in]	value	Value.
[in]	axis	The grid axes.

Returns

the point index nearest to the value.

static std::size_t gmx::getPageSize ( )

static

Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes).

Todo:

Move this function into sysinfo.cpp where other OS-specific code/includes live

static PbcMode gmx::getPbcMode ( const t_pbc *  pbcPtr )

static

Returns the PBC mode based on the system PBC and vsite properties.

Parameters

[in]

pbcPtr

A pointer to a PBC struct or nullptr when no PBC treatment is required

double gmx::getSqrtDeterminant

(

gmx::ArrayRef< const double >

correlationIntegral

)

Returns the volume element of the correlation metric.

The matrix of the metric equals the time-integrated correlation matrix. The volume element of the metric therefore equals the square-root of the absolute value of its determinant according to the standard formula for a volume element in a metric space.

The order of the tensor elements is: 1-dimensional tensor: [0] 2-dimensional tensor: [0 1; 1 2] 3-dimensional tensor: [0 1 3; 1 2 4; 3 4 5]

Parameters

[in]

correlationIntegral

A pre-filled vector of time integral elements. The correlation index lists the elements of the upper-triangular correlation matrix row-wise, so e.g. in 3D: 0 (0,0), 1 (1,0), 2 (1,1), 3 (2,0), 4 (2,1), 5 (2,2).

Returns

the volume element.

static unsigned long gmx::getSupportedOutputAdapters ( int  filetype )

static

Get the flag representing the requirements for a given file output.

Also checks if the supplied topology is sufficient through the pointer to mtop.

Parameters

[in]

filetype

Internal file type used to check requirements.

Exceptions

InvalidInputError

When encountering an invalid file type.

Returns

Requirements represent by the bitmask in the return type.

static RVec gmx::getTargetCellLength ( const Grid::Geometry &  geometry, const real  atomDensity  )

static

Get approximate dimensions of the grid cells.

Only the X and Y-components are used for the actual grid, which is 2D. The Z-component is only used for creating a 3D grid for computing the effective atom density.

void gmx::getThreadAtomRange	(	int	numThreads,
		int	threadIndex,
		int	numAtoms,
		int *	startAtom,
		int *	endAtom
	)

Computes the atom range for a thread to operate on, ensuring SIMD aligned ranges.

Parameters

[in]	numThreads	The number of threads to divide atoms over
[in]	threadIndex	The thread to get the range for
[in]	numAtoms	The total number of atoms (on this rank)
[out]	startAtom	The start of the atom range
[out]	endAtom	The end of the atom range, note that this is in general not a multiple of the SIMD width

double gmx::getTransformationPullCoordinateValue	(	pull_coord_work_t *	coord,
		ArrayRef< const pull_coord_work_t >	variableCoords,
		double	t
	)

Calculates pull->coord[coord_ind].spatialData.value for a transformation pull coordinate.

This requires the values of the pull coordinates of lower indices to be set

Parameters

[in]	coord	The (transformation) coordinate to compute the value for
[in]	variableCoords	Pull coordinates used as variables, entries 0 to coord->coordIndex will be used
[in]	t	The time

Returns

Transformation value for pull coordinate.

Exceptions

InconsistentInputError

when the expression uses coordinates with index equal to or larger than the index of coord.

int gmx::gmx_check	(	int	argc,
		char *	argv[]
	)

Implements gmx check.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

std::unique_ptr< gmx_hw_info_t > gmx::gmx_detect_hardware	(	const PhysicalNodeCommunicator &	physicalNodeComm,
		MPI_Comm	libraryCommWorld
	)

Run detection and make correct and consistent hardware information available on all ranks.

May do communication on libraryCommWorld when compiled with real MPI.

This routine is designed to be called once on each process. In a thread-MPI configuration, it may only be called before the threads are spawned. With real MPI, communication is needed to coordinate the results. In all cases, any thread within a process may use the returned handle.

int gmx::gmx_eneconv	(	int	argc,
		char *	argv[]
	)

Implements gmx eneconv.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

int gmx::gmx_grompp	(	int	argc,
		char *	argv[]
	)

Must be done after do_index, so we do it here before the triple check

int gmx::gmx_make_ndx	(	int	argc,
		char *	argv[]
	)

Implements gmx make_ndx.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

int gmx::gmx_mdrun	(	int	argc,
		char *	argv[]
	)

Implements C-style main function for mdrun.

This implementation detects hardware itself, as suits the gmx wrapper binary.

Parameters

[in]	argc	Number of C-style command-line arguments
[in]	argv	C-style command-line argument strings

int gmx::gmx_mdrun	(	MPI_Comm	communicator,
		const gmx_hw_info_t &	hwinfo,
		int	argc,
		char *	argv[]
	)

Implements C-style main function for mdrun.

This implementation facilitates reuse of infrastructure. This includes the information about the hardware detected across the given communicator. That suits e.g. efficient implementation of test fixtures.

Parameters

[in]	communicator	The communicator to use for the simulation
[in]	hwinfo	Describes the hardware detected on the physical nodes of the communicator
[in]	argc	Number of C-style command-line arguments
[in]	argv	C-style command-line argument strings

Todo:

Progress on https://gitlab.com/gromacs/gromacs/-/issues/3774 will remove the need of test binaries to call gmx_mdrun in a way that is different from the command-line and gmxapi.

int gmx::gmx_mk_angndx	(	int	argc,
		char *	argv[]
	)

Implements gmx mk_angndx.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

void gmx::gmx_nb_free_energy_kernel	(	const AtomPairlist &	nlist,
		const ArrayRefWithPadding< const RVec > &	coords,
		bool	useSimd,
		int	ntype,
		const interaction_const_t &	ic,
		ArrayRef< const RVec >	shiftvec,
		ArrayRef< const real >	nbfp,
		ArrayRef< const real >	nbfp_grid,
		ArrayRef< const real >	chargeA,
		ArrayRef< const real >	chargeB,
		ArrayRef< const int >	typeA,
		ArrayRef< const int >	typeB,
		bool	computeForeignLambda,
		const StepWorkload *	stepWork,
		ArrayRef< const real >	lambda,
		t_nrnb *gmx_restrict	nrnb,
		ArrayRefWithPadding< RVec >	threadForceBuffer,
		rvec *	threadForceShiftBuffer,
		ArrayRef< real >	threadVc,
		ArrayRef< real >	threadVv,
		ArrayRef< real >	threadDvdl
	)

The non-bonded free-energy kernel.

Parameters

[in]	nlist	A plain atom pair list containing only perturbed interactions
[in]	coords	The list of local and non-local coordinates
[in]	useSimd	Whether to use the SIMD intrinsics kernel
[in]	ntype	The number of non-bonded atom types
[in]	ic	The non-bonded interactions constants
[in]	shiftvec	The periodic shift vectors
[in]	nbfp	The matrix of LJ parameters between atom types
[in]	nbfp_grid	The matrix of LJ parameters for PME grid corrections
[in]	chargeA	List of charges per atom for state A
[in]	chargeB	List of charges per atom for state B
[in]	typeA	List of LJ atom types per atom for state A
[in]	typeB	List of LJ atom types per atom for state B
[in]	computeForeignLambda	When true, only compute energies and dV/dlambda, igore stepWork
[in]	stepWork	Tells what to compute, ignored and can be nullptr when computeForeignLambda=true
[in]	lambda	List of free-energy lambdas for different components
[in,out]	nrnb	Flop counters to add to
[in,out]	threadForceBuffer	Thread-local force buffer to accumulate into
[in,out]	threadForceShiftBuffer	Thread-local shift force buffer to accumulate into
[in,out]	threadVc	Thread-local Coulomb energy group pair buffer to accumulate into
[in,out]	threadVv	Thread-local VdW energy group pair buffer to accumulate into
[in,out]	threadDvdl	Thread-local dV/dlambda component buffer to accumulate into

Exceptions

InvalidInputError

when an excluded pair is beyond the rcoulomb with reaction-field.

int gmx::gmx_pme_error	(	int	argc,
		char *	argv[]
	)

Implements gmx pme_error.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

int gmx::gmx_trjcat	(	int	argc,
		char *	argv[]
	)

Implements gmx trjcat.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

int gmx::gmx_trjconv	(	int	argc,
		char *	argv[]
	)

Implements gmx trjconv.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

int gmx::gmx_tune_pme	(	int	argc,
		char *	argv[]
	)

Implements gmx tune_pme.

Parameters

[in]	argc	argc value passed to main().
[in]	argv	argv array passed to main().

template<typename GpuPairlist >

static void gmx::gpu_accumulate_timings ( gmx_wallclock_gpu_nbnxm_t *  timings, GpuTimers *  timers, const GpuPairlist *  plist, AtomLocality  atomLocality, const StepWorkload &  stepWork, bool  doTiming  )

inlinestatic

Do the per-step timing accounting of the nonbonded tasks.

Does timing accumulation and call-count increments for the nonbonded kernels. Note that this function should be called after the current step's nonbonded nonbonded tasks have completed with the exception of the rolling pruning kernels that are accounted for during the following step.

NOTE: if timing with multiple GPUs (streams) becomes possible, the counters could end up being inconsistent due to not being incremented on some of the node when this is skipped on empty local domains!

Template Parameters

GpuPairlist

Pair list type

Parameters

[out]	timings	Pointer to the NB GPU timings data
[in]	timers	Pointer to GPU timers data
[in]	plist	Pointer to the pair list data
[in]	atomLocality	Atom locality specifier
[in]	stepWork	Force schedule flags
[in]	doTiming	True if timing is enabled.

void gmx::gpu_clear_outputs	(	NbnxmGpu gmx_unused *	nb,
		bool gmx_unused	computeVirial
	)

Clears GPU outputs: nonbonded force, shift force and energy.

void gmx::gpu_copy_xq_to_gpu	(	NbnxmGpu gmx_unused *	nb,
		const struct nbnxm_atomdata_t gmx_unused *	nbdata,
		AtomLocality gmx_unused	aloc
	)

Launch asynchronously the xq buffer host to device copy.

The nonlocal copy is skipped if there is no dependent work to do, neither non-local nonbonded interactions nor bonded GPU work.

Parameters

[in]	nb	GPU nonbonded data.
[in]	nbdata	Host-side atom data structure.
[in]	aloc	Atom locality flag.

void gmx::gpu_free

(

NbnxmGpu gmx_unused *

nb

)

Frees all GPU resources used for the nonbonded calculations.

void gmx::gpu_free_platform_specific

(

NbnxmGpu *

nb

)

Releases the NBNXM GPU data structures.

This function is documented in the header file.

struct gmx_wallclock_gpu_nbnxm_t* gmx::gpu_get_timings

(

NbnxmGpu gmx_unused *

nb

)

Returns the GPU timings structure or NULL if GPU is not used or timing is off.

NbnxmGpu* gmx::gpu_init	(	const DeviceStreamManager gmx_unused &	deviceStreamManager,
		const interaction_const_t gmx_unused *	ic,
		const PairlistParams gmx_unused &	listParams,
		const nbnxm_atomdata_t gmx_unused *	nbat,
		bool gmx_unused	bLocalAndNonlocal,
		const std::optional< size_t > gmx_unused	nLambda
	)

Initializes the data structures related to GPU nonbonded calculations.

void gmx::gpu_init_atomdata	(	NbnxmGpu gmx_unused *	nb,
		const nbnxm_atomdata_t gmx_unused *	nbat
	)

Initializes atom-data on the GPU, called at every pair search step.

void gmx::gpu_init_feppairlist	(	NbnxmGpu gmx_unused *	nb,
		const AtomPairlist gmx_unused &	h_feplist,
		InteractionLocality gmx_unused	iloc,
		ArrayRef< const int > gmx_unused	atomIndices
	)

Initializes fep pair-list data for GPU, called at every pair search step.

void gmx::gpu_init_pairlist	(	NbnxmGpu gmx_unused *	nb,
		const struct NbnxmPairlistGpu gmx_unused *	h_nblist,
		InteractionLocality gmx_unused	iloc
	)

Initializes pair-list data for GPU, called at every pair search step.

bool gmx::gpu_is_kernel_ewald_analytical

(

const NbnxmGpu gmx_unused *

nb

)

Returns if analytical Ewald GPU kernels are used.

void gmx::gpu_launch_free_energy_kernel	(	NbnxmGpu gmx_unused *	nb,
		const SimulationWorkload gmx_unused &	simulationWork,
		const gmx::StepWorkload gmx_unused &	stepWork,
		const InteractionLocality gmx_unused	iloc
	)

Launch asynchronously the nonbonded free energy calculations.

Launch the Nonbonded free energy GPU kernels.

void gmx::gpu_launch_kernel	(	NbnxmGpu gmx_unused *	nb,
		const StepWorkload gmx_unused &	stepWork,
		InteractionLocality gmx_unused	iloc
	)

Launch asynchronously the nonbonded force calculations.

Also launches the initial pruning of a fresh list after search.

The local and non-local interaction calculations are launched in two separate streams. If there is no work (i.e. empty pair list), the force kernel launch is omitted.

void gmx::gpu_launch_kernel	(	NbnxmGpu *	nb,
		const gmx::StepWorkload &	stepWork,
		const InteractionLocality	iloc
	)

Launch GPU kernel.

As we execute nonbonded workload in separate queues, before launching the kernel we need to make sure that he following operations have completed:

• atomdata allocation and related H2D transfers (every nstlist step);
• pair list H2D transfer (every nstlist step);
• shift vector H2D transfer (every nstlist step);
• force (+shift force and energy) output clearing (every step).

These operations are issued in the local queue at the beginning of the step and therefore always complete before the local kernel launch. The non-local kernel is launched after the local on the same device/context, so this is inherently scheduled after the operations in the local stream (including the above "misc_ops"). However, for the sake of having a future-proof implementation, we use the misc_ops_done event to record the point in time when the above operations are finished and synchronize with this event in the non-local stream.

void gmx::gpu_launch_kernel_pruneonly	(	NbnxmGpu gmx_unused *	nb,
		InteractionLocality gmx_unused	iloc,
		int gmx_unused	numParts
	)

Launch asynchronously the nonbonded prune-only kernel.

The local and non-local list pruning are launched in their separate streams.

Notes for future scheduling tuning: Currently we schedule the dynamic pruning between two MD steps after both local and nonlocal force D2H transfers completed. We could launch already after the cpyback is launched, but we want to avoid prune kernels (especially in the non-local high prio-stream) competing with nonbonded work.

However, this is not ideal as this schedule does not expose the available concurrency. The dynamic pruning kernel:

• should be allowed to overlap with any task other than force compute, including transfers (F D2H and the next step's x H2D as well as force clearing).
• we'd prefer to avoid competition with non-bonded force kernels belonging to the same rank and ideally other ranks too.

In the most general case, the former would require scheduling pruning in a separate stream and adding additional event sync points to ensure that force kernels read consistent pair list data. This would lead to some overhead (due to extra cudaStreamWaitEvent calls, 3-5 us/call) which we might be able to live with. The gains from additional overlap might not be significant as long as update+constraints anyway takes longer than pruning, but there will still be use-cases where more overlap may help (e.g. multiple ranks per GPU, no/hbonds only constraints). The above second point is harder to address given that multiple ranks will often share a GPU. Ranks that complete their nonbondeds sooner can schedule pruning earlier and without a third priority level it is difficult to avoid some interference of prune kernels with force tasks (in particular preemption of low-prio local force task).

Parameters

[in,out]	nb	GPU nonbonded data.
[in]	iloc	Interaction locality flag.
[in]	numParts	Number of parts the pair list is split into in the rolling kernel.

int gmx::gpu_min_ci_balanced

(

NbnxmGpu gmx_unused *

nb

)

Calculates the minimum size of proximity lists to improve SM load balance with GPU non-bonded kernels.

static void gmx::gpu_reduce_staged_foreign_term ( const NBStagingData &  nbst, const InteractionLocality  iLocality, const int  nLambda, ForeignLambdaTerms *  foreign_term  )

inlinestatic

Reduce free energy lambda data staged internally in the nbnxm module.

Parameters

[in]	nbst	Nonbonded staging data
[in]	iLocality	Interaction locality specifier
[in]	nLambda	Number of foreign lambdas
[out]	foreign_term	Variable to accumulate foreign lambda terms into

static void gmx::gpu_reduce_staged_outputs ( const NBStagingData &  nbst, const InteractionLocality  iLocality, const bool  reduceEnergies, const bool  reduceFshift, real *  e_lj, real *  e_el, double *  dvdl_lj, double *  dvdl_el, rvec *  fshift  )

inlinestatic

Reduce data staged internally in the nbnxm module.

Shift forces and electrostatic/LJ energies copied from the GPU into a module-internal staging area are immediately reduced (CPU-side buffers passed) after having waited for the transfers' completion.

Note that this function should always be called after the transfers into the staging buffers has completed.

Parameters

[in]	nbst	Nonbonded staging data
[in]	iLocality	Interaction locality specifier
[in]	reduceEnergies	True if energy reduction should be done
[in]	reduceFshift	True if shift force reduction should be done
[out]	e_lj	Variable to accumulate LJ energy into
[out]	e_el	Variable to accumulate electrostatic energy into
[out]	dvdl_lj	Variable to accumulate LJ energy derivatives into
[out]	dvdl_el	Variable to accumulate electrostatic energy derivatives into
[out]	fshift	Pointer to the array of shift forces to accumulate into

void gmx::gpu_reset_timings

(

struct nonbonded_verlet_t gmx_unused *

nbv

)

Resets nonbonded GPU timings.

bool gmx::gpu_try_finish_task	(	NbnxmGpu gmx_unused *	nb,
		const StepWorkload gmx_unused &	stepWork,
		AtomLocality gmx_unused	aloc,
		real gmx_unused *	e_lj,
		real gmx_unused *	e_el,
		double gmx_unused *	dvdl_lj,
		double gmx_unused *	dvdl_el,
		ArrayRef< RVec > gmx_unused	shiftForces,
		ForeignLambdaTerms gmx_unused *	foreign_term,
		GpuTaskCompletion gmx_unused	completionKind
	)

Attempts to complete nonbonded GPU task.

This function attempts to complete the nonbonded task (both GPU and CPU auxiliary work). Success, i.e. that the tasks completed and results are ready to be consumed, is signaled by the return value (always true if blocking wait mode requested).

The completionKind parameter controls whether the behavior is non-blocking (achieved by passing GpuTaskCompletion::Check) or blocking wait until the results are ready (when GpuTaskCompletion::Wait is passed). As the "Check" mode the function will return immediately if the GPU stream still contain tasks that have not completed, it allows more flexible overlapping of work on the CPU with GPU execution.

Note that it is only safe to use the results, and to continue to the next MD step when this function has returned true which indicates successful completion of

• All nonbonded GPU tasks: both compute and device transfer(s)
• auxiliary tasks: updating the internal module state (timing accumulation, list pruning states) and
• internal staging reduction of (fshift, e_el, e_lj).

In GpuTaskCompletion::Check mode this function does the timing and keeps correct count for the nonbonded task (incrementing only once per task), in the GpuTaskCompletion::Wait mode timing is expected to be done in the caller.

TODO: improve the handling of outputs e.g. by ensuring that this function explicitly returns the force buffer (instead of that being passed only to nbnxm_gpu_launch_cpyback()) and by returning the energy and Fshift contributions for some external/centralized reduction.

Parameters

[in]	nb	The nonbonded data GPU structure
[in]	stepWork	Step schedule flags
[in]	aloc	Atom locality identifier
[out]	e_lj	Pointer to the LJ energy output to accumulate into
[out]	e_el	Pointer to the electrostatics energy output to accumulate into
[out]	dvdl_lj	Pointer to the LJ DvDL output to accumulate into
[out]	dvdl_el	Pointer to the electrostatics DVDL output to accumulate into
[out]	shiftForces	Shift forces buffer to accumulate into
[out]	foreign_term	Foreign lambda terms buffer to accumulate into
[in]	completionKind	Indicates whether nonbonded task completion should only be checked rather than waited for

Returns

True if the nonbonded tasks associated with aloc locality have completed

bool gmx::gpu_try_finish_task	(	NbnxmGpu *	nb,
		const StepWorkload &	stepWork,
		const AtomLocality	aloc,
		real *	e_lj,
		real *	e_el,
		double *	dvdl_lj,
		double *	dvdl_el,
		ArrayRef< RVec >	shiftForces,
		ForeignLambdaTerms *	foreign_term,
		GpuTaskCompletion	completionKind
	)

Attempts to complete nonbonded GPU task.

See documentation in nbnxm_gpu.h for details.

Todo:

Move into shared source file, perhaps including cuda_runtime.h if needed for any remaining CUDA-specific objects.

void gmx::gpu_upload_shiftvec	(	NbnxmGpu gmx_unused *	nb,
		const nbnxm_atomdata_t gmx_unused *	nbatom
	)

Uploads shift vector to the GPU if the box is dynamic (otherwise just returns).

float gmx::gpu_wait_finish_task	(	NbnxmGpu gmx_unused *	nb,
		const StepWorkload gmx_unused &	stepWork,
		AtomLocality gmx_unused	aloc,
		const bool gmx_unused	haveSoftCore,
		gmx_enerdata_t gmx_unused *	enerd,
		ArrayRef< RVec > gmx_unused	shiftForces,
		gmx_wallcycle gmx_unused *	wcycle
	)

Completes the nonbonded GPU task blocking until GPU tasks and data transfers to finish.

Also does timing accounting and reduction of the internal staging buffers. As this is called at the end of the step, it also resets the pair list and pruning flags.

Parameters

[in]	nb	The nonbonded data GPU structure
[in]	stepWork	Step schedule flags
[in]	aloc	Atom locality identifier
[in]	haveSoftCore	Whether SoftCore has been used
[out]	enerd	Pointer to the energy data to accumulate energies into
[out]	shiftForces	Shift forces buffer to accumulate into
[out]	wcycle	Pointer to wallcycle data structure

float gmx::gpu_wait_finish_task	(	NbnxmGpu *	nb,
		const StepWorkload &	stepWork,
		AtomLocality	aloc,
		const bool	haveSoftCore,
		gmx_enerdata_t *	enerd,
		ArrayRef< RVec >	shiftForces,
		gmx_wallcycle *	wcycle
	)

Wait for the asynchronously launched nonbonded tasks and data transfers to finish.

Also does timing accounting and reduction of the internal staging buffers. As this is called at the end of the step, it also resets the pair list and pruning flags.

Parameters

[in]	nb	The nonbonded data GPU structure
[in]	stepWork	Force schedule flags
[in]	aloc	Atom locality identifier
[in]	haveSoftCore	Whether SoftCore has been used
[out]	enerd	Pointer to the energy data to accumulate energies into
[out]	shiftForces	Shift forces buffer to accumulate into
[out]	wcycle	Pointer to wallcycle data structure

Returns

The number of cycles the gpu wait took

std::string gmx::gpuFftDescription

(

)

Construct a string that describes the library that provides GPU FFT support to this build.

Returns information for describing the GPU FFT support.

std::int64_t gmx::greatestCommonDivisor	(	std::int64_t	p,
		std::int64_t	q
	)

Find greatest common divisor of two numbers.

Parameters

p	First number, positive
q	Second number, positive

Returns

Greatest common divisor of p and q

template<int subGroupSize, int groupSize>

static float gmx::groupReduce ( const sycl::nd_item< 3 >  itemIdx, const unsigned int  tidxi, sycl::local_ptr< float >  sm_buf, float  valueToReduce  )

inlinestatic

Do workgroup-level reduction of a single float.

While SYCL has sycl::reduce_over_group, it currently (oneAPI 2021.3.0) uses a very large shared memory buffer, which leads to a reduced occupancy.

Note

The caller must make sure there are no races when reusing the sm_buf.

Template Parameters

subGroupSize	Size of a sub-group.
groupSize	Size of a work-group.

Parameters

itemIdx	Current thread's sycl::nd_item.
tidxi	Current thread's linearized local index.
sm_buf	Accessor for local reduction buffer.
valueToReduce	Current thread's value. Must have length of at least 1.

Returns

For thread with tidxi 0: sum of all valueToReduce. Other threads: unspecified.

static bool gmx::groupsCloserThanCutoffWithPbc ( t_pbc *  pbc, rvec  x[], ArrayRef< const int >  smallerGroupIndices, ArrayRef< const int >  largerGroupIndices, real  minimumDistance  )

static

Return whether any atoms of two groups are below minimum distance.

Parameters

[in]	pbc	the periodic boundary conditions
[in]	x	the coordinates
[in]	smallerGroupIndices	the atom indices of the first group to check
[in]	largerGroupIndices	the atom indices of the second group to check
[in]	minimumDistance	the minimum required distance betwenn any atom in the first and second group

Returns

true if any distance between an atom from group A and group B is smaller than a minimum distance.

static void gmx::hacksearch_atom ( int *  ii, int *  jj, const char *  name, ArrayRef< const std::vector< MoleculePatch >>  patches, int  resind, const t_atoms *  pdba  )

static

Return the index of the first atom whose residue index matches and which has a patch with the given name.

Parameters

[out]	ii	Index of the first atom in the residue that matches, -1 if no match occurs.
[out]	jj	Index of the patch that matches, unchanged if no match occurs.
[in]	name	Name of the desired patch to match
[in]	patches	The patch database to search
[in]	resind	The residue index to match
[in]	pdba	The atoms to work with

Todo:

The short-circuit logic will be simpler if this returned a std::pair<int, int> as soon as the first double match is found.

bool gmx::handleIsValid ( const hid_t  handle )

inlinenoexcept

Return whether HDF5 handle is valid.

Parameters

[in]

handle

HDF5 handle to check.

Returns

True if the handle is valid, otherwise false.

std::tuple< StartingBehavior, LogFilePtr > gmx::handleRestart	(	bool	isSimulationMain,
		MPI_Comm	communicator,
		const gmx_multisim_t *	ms,
		AppendingBehavior	appendingBehavior,
		int	nfile,
		t_filenm	fnm[]
	)

Handle startup of mdrun, particularly regarding -cpi and -append.

If there is a checkpoint file, then prepare to start from that state. If possible/required, do so with appending. If some files are not found when appending should be done, we will instead issue a fatal error to avoid unintentional problems.

If there is no checkpoint file, we return a value to indicate a new simulation is starting.

On return, fnm is updated with suffix strings for part numbers if we are doing a restart from checkpoint and are not appending. Output files may have been truncated if we are restarting from a checkpoint and are appending.

The routine also does communication to coordinate behaviour between all simulations, including for error conditions.

Note that this function looks like it does lots of different things that could be separated, but that is actually difficult. The starting behaviour can depend on the state of the filesystem and the contents of the checkpoint header, each of which we only want to read once, so we can't easily separate the decision of what to do from the details of doing it (e.g. changing output filenames or truncating output files).

Exceptions

FileIOError	When the filesystem behavior prevents the user's choices being implemented.
InconsistentInputError	When the users's choices cannot be implemented.
ParallelConsistencyError	On ranks upon which the error condition was not detected.

Parameters

[in]	isSimulationMain	Whether this rank is the main rank of a simulation
[in]	communicator	MPI communicator across which error behaviour must be kept consistent
[in]	ms	Handles multi-simulations.
[in]	appendingBehavior	User choice for appending
[in]	nfile	Size of fnm struct
[in,out]	fnm	Filename parameters to mdrun

Returns

Description of how mdrun is starting and log file pointer

static bool gmx::hasIncompatibleVsites ( const gmx_moltype_t &  moltype, gmx::ArrayRef< const t_iparams >  iparams  )

static

Returns whether moltype has incompatible vsites.

For simplicity the only compatible vsites are linear 2 or 3 atom sites that are constructed in between the 2 or 3 contructing atoms,

static bool gmx::hasPmeOrNonbondedTask ( const GpuTaskMapping &  mapping )

static

Function for whether the mapping has the GPU PME or Nonbonded task.

Parameters

[in]

mapping

Current GPU task mapping.

Returns

If PME on Nonbonded GPU task was assigned to this mapping.

template<GpuTask TaskType>

static bool gmx::hasTaskType ( const GpuTaskMapping &  mapping )

static

Function for whether the task of mapping has value TaskType.

Parameters

[in]

mapping

Current GPU task mapping.

Returns

If TaskType task was assigned to the mapping.

bool gmx::haveBiasSharingWithinSimulation

(

const AwhParams &

awhParams

)

Returns if any bias is sharing within a simulation.

Parameters

[in]

awhParams

The AWH parameters.

bool gmx::haveGpuShortRangeWork	(	const NbnxmGpu gmx_unused *	nb,
		InteractionLocality gmx_unused	interactionLocality
	)

Returns true if there is GPU short-range work for the given interaction locality.

Note that as, unlike nonbonded tasks, bonded tasks are not split into local/nonlocal, and therefore if there are GPU offloaded bonded interactions, this function will return true for both local and nonlocal atom range.

Parameters

[in,out]	nb	Pointer to the nonbonded GPU data structure
[in]	interactionLocality	Interaction locality identifier

Returns

Whether there is short range work for a given locality.

static bool gmx::haveSpecialForces ( const t_inputrec &  inputrec, const gmx::ForceProviders &  forceProviders, const pull_t *  pull_work, const edsam *  ed  )

static

Return true if there are special forces computed.

The conditionals exactly correspond to those in sim_util.cpp:computeSpecialForces().

bool gmx::haveValidMtsSetup

(

const t_inputrec &

ir

)

Returns whether we use MTS and the MTS setup is internally valid.

Note that setupMtsLevels would have returned at least one error message when this function returns false

template<typename ValueType >

hid_t gmx::hdf5DataTypeFor ( )

noexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

template<>

hid_t gmx::hdf5DataTypeFor< double > ( )

inlinenoexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

template<>

hid_t gmx::hdf5DataTypeFor< float > ( )

inlinenoexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

template<>

hid_t gmx::hdf5DataTypeFor< int32_t > ( )

inlinenoexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

template<>

hid_t gmx::hdf5DataTypeFor< int64_t > ( )

inlinenoexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

template<>

hid_t gmx::hdf5DataTypeFor< uint32_t > ( )

inlinenoexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

template<>

hid_t gmx::hdf5DataTypeFor< uint64_t > ( )

inlinenoexcept

Return a handle to a native HDF5 type corresponding to the templated value type.

The data type referenced by the handle is immutable and does not need to be closed.

Template Parameters

ValueType

Type of value.

Returns

Handle to native HDF5 type.

hid_t gmx::hdf5DataTypeForFixedLengthString ( const hsize_t  maxStringLength )

inline

Return a handle to a HDF5 data type for fixed-length strings.

The string type is created with a UTF8 character set and null termination, so stored strings may be shorter than the maximum length but a fixed amount of memory is always allocated. Data sets of fixed length strings are contiguous in memory and can be compressed.

The returned handle must be closed with a call to H5Tclose to avoid leaking resources.

Parameters

[in]

maxStringLength

Fixed maximum length of string.

Exceptions

H5mdError

if maxStringLength is not a positive value.

int gmx::identifyAvx512FmaUnits

(

)

Test whether machine has dual AVX512 FMA units.

Returns

1 or 2 for the number of AVX512 FMA units if AVX512 support is present, 0 if we know the hardware does not have AVX512 support, or -1 if the test cannot run because the compiler lacked AVX512 support.

template<typename ElementType >

BasicMatrix3x3<ElementType> gmx::identityMatrix

(

)

Create an identity matrix of ElementType.

Template Parameters

ElementType

type of matrix elements

Returns

a matrix with values one where row equals column index and null where row does not equal column index

static bool gmx::imd_recv_mdcomm ( IMDSocket *  socket, int32_t  nforces, int32_t *  forcendx, float *  forces  )

static

Receive force indices and forces.

The number of forces was previously communicated via the header.

static int gmx::imd_send_rvecs ( IMDSocket *  socket, int  nat, rvec *  x, char *  buffer  )

static

Send positions from rvec.

We need a separate send buffer and conversion to Angstrom.

int gmx::imd_sock_listen

(

IMDSocket *

sock

)

Set socket to listening state.

Prints out an error message if unsuccessful.

Parameters

sock	The IMD socket.

Returns

0 if successful.

IMDSocket * gmx::imdsock_accept

(

IMDSocket *

sock

)

Accept incoming connection and redirect to client socket.

Prints out an error message if unsuccessful.

Parameters

sock	The IMD socket.

Returns

IMD socket if successful, NULL otherwise.

int gmx::imdsock_bind	(	IMDSocket *	sock,
		int	port
	)

Bind the IMD socket to address and port.

Prints out an error message if unsuccessful. If port == 0, bind() assigns a free port automatically.

Parameters

sock	The IMD socket.
port	The port to bind to.

Returns

0 if successful.

IMDSocket * gmx::imdsock_create

(

)

Create an IMD main socket.

Returns

The IMD socket if successful. Otherwise prints an error message and returns NULL.

int gmx::imdsock_destroy

(

IMDSocket *

sock

)

Close the socket and free the sock struct memory.

Writes an error message if unsuccessful.

Parameters

sock	The IMD socket.

Returns

1 on success, or 0 if unsuccessful.

int gmx::imdsock_getport	(	IMDSocket *	sock,
		int *	port
	)

Get the port number used for IMD connection.

Prints out an error message if unsuccessful.

Parameters

sock	The IMD socket.
port	The assigned port number.

Returns

0 if successful, an error code otherwise.

int gmx::imdsock_read	(	IMDSocket *	sock,
		char *	buffer,
		int	length
	)

Read from socket.

Parameters

sock	The IMD socket.
buffer	Buffer to put the read data.
length	Number of bytes to read.

Returns

The number of bytes read, or -1 for errors.

void gmx::imdsock_shutdown

(

IMDSocket *

sock

)

Shutdown the socket.

Parameters

sock	The IMD socket.

int gmx::imdsock_tryread	(	IMDSocket *	sock,
		int	timeoutsec,
		int	timeoutusec
	)

Try to read from the socket.

Time out after waiting the interval specified. Print an error message if unsuccessful.

Parameters

sock	The IMD socket.
timeoutsec	Time out seconds
timeoutusec	Time out microseconds

int gmx::imdsock_write	(	IMDSocket *	sock,
		const char *	buffer,
		int	length
	)

Write to socket.

Parameters

sock	The IMD socket.
buffer	The data to write.
length	Number of bytes to write.

Returns

The number of bytes written, or -1.

void gmx::increaseNstlist	(	FILE *	fplog,
		const MpiComm &	mpiCommSimulation,
		t_inputrec *	ir,
		int	nstlistOnCmdline,
		const gmx_mtop_t *	mtop,
		const matrix	box,
		real	effectiveAtomDensity,
		bool	useOrEmulateGpuForNonbondeds
	)

Try to increase nstlist when using the Verlet cut-off scheme.

Parameters

[in,out]	fplog	Log file
[in]	mpiCommSimulation	MPI communicator for the whole simulation
[in]	ir	The input parameter record
[in]	nstlistOnCmdline	The value of nstlist provided on the command line
[in]	mtop	The global topology
[in]	box	The unit cell
[in]	effectiveAtomDensity	The effective atom density
[in]	useOrEmulateGpuForNonbondeds	Tells if we are using a GPU for non-bondeds

template<PairlistType pairlistType, typename T >

__device__ size_t gmx::incrementSharedMemorySlotPtr ( )

inline

Increment the pointer into shared memory.

Template Parameters

T	which type we use to calculate the new offset

std::unique_ptr< EssentialDynamics > gmx::init_edsam	(	const MDLogger &	mdlog,
		const char *	ediFileName,
		const char *	edoFileName,
		const gmx_mtop_t &	mtop,
		const t_inputrec &	ir,
		const MpiComm &	mpiComm,
		const gmx_domdec_t *	dd,
		Constraints *	constr,
		const t_state *	globalState,
		ObservablesHistory *	oh,
		const gmx_output_env_t *	oenv,
		StartingBehavior	startingBehavior
	)

Initializes the essential dynamics and flooding module.

Parameters

mdlog	Logger.
ediFileName	Essential dynamics input file.
edoFileName	Output file for essential dynamics data.
mtop	Molecular topology.
ir	MD input parameter record.
mpiComm	Communication object for my group.
dd	Domain decomposition object, pass nullptr when DD is not active.
constr	Data structure keeping the constraint information.
globalState	The global state, only used on the main rank.
oh	The observables history container.
oenv	The output environment information.
startingBehavior	Describes whether this is a restart appending to output files

Returns

A pointer to the ED data structure.

void gmx::init_parrinellorahman	(	const PressureCouplingOptions &	pressureCouplingOptions,
		const tensor	deform,
		real	couplingTimePeriod,
		const tensor	box,
		tensor	box_rel,
		tensor	boxv,
		Matrix3x3 *	M,
		Matrix3x3 *	mu
	)

Initialize the Parrinello-Rahman mu and M tensors.

mu describes the relative change in box vectors introduced by the coupling and applied at each step. This ensures there is no large jump in box-vector values.

M is used in the update code to couple the change in particle velocities to that of the box vectors introduced by mu.

Parameters

[in]	pressureCouplingOptions	The pressure-coupling options
[in]	deform	The matrix describing any box deformation
[in]	couplingTimePeriod	The period between changes to the pressure coupling
[in]	box	The simulation box vectors
[in]	box_rel	The relative box vectors
[in]	boxv	The simulation box vector velocity for Parrinello-Rahman coupling
[out]	M	The scaling factor for particle velocities
[out]	mu	The scaling factor for box vectors

gmx_repl_ex_t gmx::init_replica_exchange	(	FILE *	fplog,
		const gmx_multisim_t *	ms,
		int	numAtomsInSystem,
		const t_inputrec *	ir,
		const ReplicaExchangeParameters &	replExParams
	)

Setup function.

Should only be called on the main ranks

shellfc_t * gmx::init_shell_flexcon	(	FILE *	fplog,
		const gmx_mtop_t &	mtop,
		int	nflexcon,
		int	nstcalcenergy,
		bool	usingDomainDecomposition,
		const DeviceStreamManager *	deviceStreamManager,
		const SimulationWorkload &	simulationWork
	)

Initialization function, also predicts the initial shell positions.

Parameters

fplog	Pointer to the log stream. Can be set to nullptr to disable verbose log.
mtop	Pointer to a global system topology object.
nflexcon	Number of flexible constraints.
nstcalcenergy	How often are energies calculated. Must be provided for sanity check.
usingDomainDecomposition	Whether domain decomposition is used. Must be provided for sanity check.
deviceStreamManager	Pointer to the device stream manager
simulationWork	The simulation workload.

Returns

a pointer to an initialized shellfc object.

std::unique_ptr< SwapCoords > gmx::init_swapcoords	(	FILE *	fplog,
		const t_inputrec *	ir,
		const char *	fn,
		const gmx_mtop_t &	mtop,
		const t_state *	globalState,
		ObservablesHistory *	oh,
		const MpiComm &	mpiComm,
		const gmx_domdec_t *	dd,
		LocalAtomSetManager *	atomSets,
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions,
		StartingBehavior	startingBehavior
	)

Initialize ion / water position swapping ("Computational Electrophysiology").

This routine does the memory allocation for various helper arrays, opens the output file, sets up swap data checkpoint writing, etc. and returns it.

Parameters

[in]	fplog	General output file, normally md.log.
[in]	ir	Structure containing MD input parameters, among those also the structure needed for position swapping.
[in]	fn	Output file name for swap data.
[in]	mtop	Molecular topology.
[in]	globalState	The global state, only used on the main rank.
[in]	oh	Contains struct with swap data that is read from or written to checkpoint.
[in]	mpiComm	Communicator object for my group.
[in]	dd	Domain decomposition object, is nullptr when DD is not active.
[in]	atomSets	Manager tending to swap atom indices.
[in]	oenv	Needed to open the swap output XVGR file.
[in]	mdrunOptions	Options for mdrun.
[in]	startingBehavior	Describes whether this is a restart appending to output files

static void gmx::init_swapstate ( swaphistory_t *  swapstate, SwapCoords::Impl *  s, const gmx_mtop_t &  mtop, gmx::ArrayRef< const gmx::RVec >  x, const matrix  box, const t_inputrec *  ir  )

static

Initialize the swapstate structure, used for checkpoint writing.

The swapstate struct stores the information we need to make the channels whole again after restarts from a checkpoint file. Here we do the following: a) If we did not start from .cpt, we prepare the struct for proper .cpt writing, b) if we did start from .cpt, we copy over the last whole structures from .cpt, c) in any case, for subsequent checkpoint writing, we set the pointers in swapstate to the x_old arrays, which contain the correct PBC representation of multimeric channels at the last time step.

void gmx::initCorrelationGridHistory	(	CorrelationGridHistory *	correlationGridHistory,
		int	numCorrelationTensors,
		int	tensorSize,
		int	blockDataListSize
	)

Initialize correlation grid history, sets all sizes.

Parameters

[in,out]	correlationGridHistory	Correlation grid history for main rank.
[in]	numCorrelationTensors	Number of correlation tensors in the grid.
[in]	tensorSize	Number of correlation elements in each tensor.
[in]	blockDataListSize	The number of blocks in the list of each tensor element.

CorrelationGridHistory gmx::initCorrelationGridHistoryFromState

(

const CorrelationGrid &

corrGrid

)

Allocate a correlation grid history with the same structure as the given correlation grid.

This function would be called at the start of a new simulation. Note that only sizes and memory are initialized here. History data is set by updateCorrelationGridHistory.

Parameters

[in,out]

corrGrid

Correlation grid state to initialize with.

Returns

the correlation grid history struct.

static void gmx::initializeProjectionMatrix ( const real  invmO, const real  invmH, const real  dOH, const real  dHH, matrix  inverseCouplingMatrix  )

static

Initializes a projection matrix.

Parameters

[in]	invmO	Reciprocal oxygen mass
[in]	invmH	Reciprocal hydrogen mass
[in]	dOH	Target O-H bond length
[in]	dHH	Target H-H bond length
[out]	inverseCouplingMatrix	Inverse bond coupling matrix for the projection version of SETTLE

bool gmx::inputSupportsListedForcesGpu	(	const t_inputrec &	ir,
		const gmx_mtop_t &	mtop,
		std::string *	error
	)

Checks whether the input system allows to compute bonded interactions on a GPU.

Parameters

[in]	ir	Input system.
[in]	mtop	Complete system topology to search for supported interactions.
[out]	error	If non-null, the error message if the input is not supported on GPU.

Returns

true if PME can run on GPU with this input, false otherwise.

static bool gmx::intervalIsInPeriodicInterval ( double  origin, double  end, double  period  )

static

Checks if the given interval is defined in the correct periodic interval.

Parameters

[in]	origin	Start value of interval.
[in]	end	End value of interval.
[in]	period	Period (or 0 if not periodic).

Returns

true if the end point values are in the correct periodic interval.

static float gmx::inv ( float  x )

inlinestatic

Calculate 1/x for float.

Parameters

x	Argument that must be nonzero. This routine does not check arguments.

Returns

1/x. Result is undefined if your argument was invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::inv ( double  x )

inlinestatic

Calculate 1/x for double.

Parameters

x	Argument that must be nonzero. This routine does not check arguments.

Returns

1/x. Result is undefined if your argument was invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::invcbrt ( float  x )

inlinestatic

Calculate inverse cube root of x in single precision.

Parameters

x

Argument

Returns

x^(-1/3)

This routine is typically faster than using std::pow().

static double gmx::invcbrt ( double  x )

inlinestatic

Calculate inverse sixth root of x in double precision.

Parameters

x

Argument

Returns

x^(-1/3)

This routine is typically faster than using std::pow().

static double gmx::invcbrt ( int  x )

inlinestatic

Calculate inverse sixth root of integer x in double precision.

Parameters

x

Argument

Returns

x^(-1/3)

This routine is typically faster than using std::pow().

static Matrix3x3 gmx::invertBoxMatrix ( const Matrix3x3 &  src )

inlinestatic

Invert a simulation-box matrix.

This routine assumes that src is a simulation-box matrix, i.e. has zeroes in the upper-right triangle.

Exceptions

RangeError

if the product of the leading diagonal is too small.

static void gmx::invertBoxMatrix ( const matrix  src, matrix  dest  )

inlinestatic

Invert a simulation-box matrix in src, return in dest.

This routine assumes that src is a simulation-box matrix, i.e. has zeroes in the upper-right triangle. A fatal error occurs if the product of the leading diagonal is too small. The inversion can be done "in place", i.e src and dest can be the same matrix.

static std::vector<int> gmx::invertIndexGroup ( int  nrAtoms, std::vector< int >  indexGroup  )

static

Return all atom indices that do not belong to an index group.

Parameters

[in]	nrAtoms	the total number of atoms
[in]	indexGroup	the index group to be inverted. Note that a copy is made in order to sort the group indices

Returns

the inverted group indices

void gmx::invertMatrix	(	const matrix	src,
		matrix	dest
	)

Invert a general 3x3 matrix in src, return in dest.

A fatal error occurs if the determinant is too small. src and dest cannot be the same matrix.

static double gmx::invSingleAccuracy ( double  x )

inlinestatic

Calculate 1/x for double, but with single accuracy.

Parameters

x	Argument that must be nonzero. This routine does not check arguments.

Returns

1/x. Result is undefined if your argument was invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::invsixthroot ( float  x )

inlinestatic

Calculate inverse sixth root of x in single precision.

Parameters

x	Argument, must be greater than zero.

Returns

x^(-1/6)

This routine is typically faster than using std::pow().

static double gmx::invsixthroot ( double  x )

inlinestatic

Calculate inverse sixth root of x in double precision.

Parameters

x	Argument, must be greater than zero.

Returns

x^(-1/6)

This routine is typically faster than using std::pow().

static double gmx::invsixthroot ( int  x )

inlinestatic

Calculate inverse sixth root of integer x in double precision.

Parameters

x	Argument, must be greater than zero.

Returns

x^(-1/6)

This routine is typically faster than using std::pow().

static float gmx::invsqrt ( float  x )

inlinestatic

Calculate 1.0/sqrt(x) in single precision.

Parameters

x	Positive value to calculate inverse square root for

For now this is implemented with std::sqrt(x) since gcc seems to do a decent job optimizing it. However, we might decide to use instrinsics or compiler-specific functions in the future.

Returns

1.0/sqrt(x)

static double gmx::invsqrt ( double  x )

inlinestatic

Calculate 1.0/sqrt(x) in double precision, but single range.

Parameters

x	Positive value to calculate inverse square root for, must be in the input domain valid for single precision.

For now this is implemented with std::sqrt(x). However, we might decide to use instrinsics or compiler-specific functions in the future, and then we want to have the freedom to do the first step in single precision.

Returns

1.0/sqrt(x)

static double gmx::invsqrt ( int  x )

inlinestatic

Calculate 1.0/sqrt(x) for integer x in double precision.

Parameters

x	Positive value to calculate inverse square root for.

Returns

1.0/sqrt(x)

static void gmx::invsqrtPair ( float  x0, float  x1, float *  out0, float *  out1  )

inlinestatic

Calculate 1/sqrt(x) for two floats.

Parameters

	x0	First argument, x0 must be positive - no argument checking.
	x1	Second argument, x1 must be positive - no argument checking.
[out]	out0	Result 1/sqrt(x0)
[out]	out1	Result 1/sqrt(x1)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::invsqrtPair ( double  x0, double  x1, double *  out0, double *  out1  )

inlinestatic

Calculate 1/sqrt(x) for two doubles.

Parameters

	x0	First argument, x0 must be positive - no argument checking.
	x1	Second argument, x1 must be positive - no argument checking.
[out]	out0	Result 1/sqrt(x0)
[out]	out1	Result 1/sqrt(x1)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::invsqrtPairSingleAccuracy ( double  x0, double  x1, double *  out0, double *  out1  )

inlinestatic

Calculate 1/sqrt(x) for two doubles, but with single accuracy.

Parameters

	x0	First argument, x0 must be positive - no argument checking.
	x1	Second argument, x1 must be positive - no argument checking.
[out]	out0	Result 1/sqrt(x0)
[out]	out1	Result 1/sqrt(x1)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::invsqrtSingleAccuracy ( double  x )

inlinestatic

Calculate 1/sqrt(x) for double, but with single accuracy.

Parameters

x	Argument that must be >0. This routine does not check arguments.

Returns

1/sqrt(x). Result is undefined if your argument was invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static gmx_bool gmx::is_in_channel ( const gmx::RVec  point, const gmx::RVec  center, real  d_up, real  d_down, real  r_cyl2, t_pbc *  pbc, int  normal  )

static

Check whether point is in channel.

A channel is a cylinder defined by a disc with radius r around its center c. The thickness of the cylinder is d_up - d_down.

*               ^  d_up
*               |
*     r         |
*     <---------c--------->
*               |
*               v  d_down
*
* 

Parameters

[in]	point	The position (xyz) under consideration.
[in]	center	The center of the cylinder.
[in]	d_up	The upper extension of the cylinder.
[in]	d_down	The lower extension.
[in]	r_cyl2	Cylinder radius squared.
[in]	pbc	Structure with info about periodic boundary conditions.
[in]	normal	The membrane normal direction is typically 3, i.e. z, but can be x or y also.

Returns

Whether the point is inside the defined cylindric channel.

static DeviceStatus gmx::isDeviceFunctional ( const DeviceInformation &  deviceInfo )

static

Checks that device deviceInfo is compatible with GROMACS.

Vendor and OpenCL version support checks are executed an the result of these returned.

Parameters

[in]

deviceInfo

The device info pointer.

Returns

The status enumeration value for the checked device:

static bool gmx::isDeviceFunctional ( const DeviceInformation &  deviceInfo, std::string *  errorMessage  )

static

Checks that device deviceInfo is sane (ie can run a kernel).

Compiles and runs a dummy kernel to determine whether the given OpenCL device functions properly.

Parameters

[in]	deviceInfo	The device info pointer.
[out]	errorMessage	An error message related to a failing OpenCL API call.

Exceptions

std::bad_alloc

When out of memory.

Returns

Whether the device passed sanity checks

template<typename EnumerationArrayType >

EnumerationArrayType::EnumerationWrapperType gmx::keysOf

(

const EnumerationArrayType &

)

Returns an object that provides iterators over the keys associated with EnumerationArrayType.

This helper function is useful in contexts where there is an object of an EnumerationArray, and we want to use a range-based for loop over the keys associated with it, and it would be inconvenient to use the very word EnumerationArray<...> type, nor introduce a using statement for this purpose. It is legal in C++ to call a static member function (such as keys()) via an object rather than the type, but clang-tidy warns about that. So instead we make available a free function that calls that static method.

void gmx::labelInternalTopologyVersion

(

hid_t

baseContainer

)

Label the version of the internal topology module.

Parameters

[in]

baseContainer

The HDF5 container to write to.

void gmx::labelTopologyName	(	hid_t	baseContainer,
		const char *	topName
	)

Label the name of the simulation system.

Parameters

[in]	baseContainer	The HDF5 container to write to.
[in]	topName	The name of the topology.

void gmx::launchForceReductionKernel	(	int	numAtoms,
		int	atomStart,
		bool	addRvecForce,
		bool	accumulate,
		const DeviceBuffer< Float3 >	d_nbnxmForceToAdd,
		const DeviceBuffer< Float3 >	d_rvecForceToAdd,
		DeviceBuffer< Float3 >	d_baseForce,
		DeviceBuffer< int >	d_cell,
		const DeviceStream &	deviceStream,
		DeviceBuffer< uint64_t >	d_forcesReadyNvshmemFlags,
		const uint64_t	forcesReadyNvshmemFlagsCounter
	)

Backend-specific function to launch GPU Force Reduction kernel.

Select templated Force reduction kernel and launch it.

In pseudocode:

* for (int i = 0; i < numAtoms; i++) {
*     totalForce = d_nbnxmForceToAdd[d_cell[i]]
*     if (accumulate)
*         totalForce += d_baseForce[atomStart + i]
*     if (addRvecForce)
*         totalForce += d_rvecForceToAdd[atomStart + i]
*     d_baseForce[atomStart + i] = totalForce[i]
* }
* 

Parameters

numAtoms	Number of atoms subject to reduction.
atomStart	First atom index (for d_rvecForceToAdd and d_baseForce).
addRvecForce	When false, d_rvecForceToAdd is ignored.
accumulate	When false, the previous values of d_baseForce are discarded.
d_nbnxmForceToAdd	Buffer containing Nbnxm forces in Nbnxm layout.
d_rvecForceToAdd	Optional buffer containing arbitrary forces in linear layout.
d_baseForce	Destination buffer for forces in linear layout.
d_cell	Atom index to Nbnxm cell index.
deviceStream	Device stream for kernel submission.
d_forcesReadyNvshmemFlags	NVSHMEM signals from PME to PP force transfer.
forcesReadyNvshmemFlagsCounter	Tracks NVSHMEM signal from PME to PP force transfer.

void gmx::launchLeapFrogKernel	(	int	numAtoms,
		DeviceBuffer< Float3 >	d_x,
		DeviceBuffer< Float3 >	d_x0,
		DeviceBuffer< Float3 >	d_v,
		DeviceBuffer< Float3 >	d_f,
		DeviceBuffer< float >	d_inverseMasses,
		float	dt,
		bool	doTemperatureScaling,
		int	numTempScaleValues,
		DeviceBuffer< unsigned short >	d_tempScaleGroups,
		DeviceBuffer< float >	d_lambdas,
		ParrinelloRahmanVelocityScaling	parrinelloRahmanVelocityScaling,
		Float3	prVelocityScalingMatrixDiagonal,
		const DeviceStream &	deviceStream
	)

Backend-specific function to launch GPU Leap Frog kernel.

Parameters

	numAtoms	Total number of atoms.
[in,out]	d_x	Buffer containing initial coordinates, and where the updated ones will be written.
[out]	d_x0	Buffer where a copy of the initial coordinates will be written.
[in,out]	d_v	Buffer containing initial velocities, and where the updated ones will be written.
[in]	d_f	Buffer containing forces.
[in]	d_inverseMasses	Buffer containing atoms' reciprocal masses.
	dt	Timestep.
	doTemperatureScaling	Whether temperature scaling is needed.
	numTempScaleValues	Number of different T-couple values.
	d_tempScaleGroups	Mapping of atoms into temperature scaling groups.
	d_lambdas	Temperature scaling factors (one per group).
	parrinelloRahmanVelocityScaling	The properties of the Parrinello-Rahman velocity scaling matrix.
	prVelocityScalingMatrixDiagonal	Diagonal elements of Parrinello-Rahman velocity scaling matrix.
	deviceStream	Device stream for kernel launch.

void gmx::launchLincsGpuKernel	(	LincsGpuKernelParameters *	kernelParams,
		const DeviceBuffer< Float3 > &	d_x,
		DeviceBuffer< Float3 >	d_xp,
		bool	updateVelocities,
		DeviceBuffer< Float3 >	d_v,
		real	invdt,
		bool	computeVirial,
		const DeviceStream &	deviceStream
	)

Backend-specific function to launch LINCS kernel.

Parameters

kernelParams	LINCS parameters.
d_x	Initial coordinates before the integration.
d_xp	Coordinates after the integration which will be updated.
updateVelocities	Whether to also update velocities.
d_v	Velocities to update (ignored if updateVelocities is false).
invdt	Reciprocal of timestep.
computeVirial	Whether to compute the virial.
deviceStream	Device stream for kernel launch.

void gmx::launchNbnxmKernel	(	NbnxmGpu *	nb,
		const StepWorkload &	stepWork,
		InteractionLocality	iloc,
		bool	doPrune
	)

Launch HIP NBNXM kernel.

Launch SYCL NBNXM kernel.

Parameters

nb	Non-bonded parameters.
stepWork	Workload flags for the current step.
iloc	Interaction locality.
doPrune	Whether to do neighborlist pruning.

void gmx::launchNbnxmKernelPruneOnly	(	NbnxmGpu *	nb,
		const InteractionLocality	iloc,
		const int *	numParts,
		const int	numSciInPart
	)

Launch HIP NBNXM prune-only kernel.

Parameters

nb	Non-bonded parameters.
iloc	Interaction locality.
numParts	Total number of rolling-prune parts.
numSciInPart	Number of superclusters in part.

void gmx::launchNbnxmKernelPruneOnly	(	NbnxmGpu *	nb,
		const InteractionLocality	iloc,
		const int	numParts,
		const int	numSciInPartMax
	)

Launch SYCL NBNXM prune-only kernel.

Parameters

nb	Non-bonded parameters.
iloc	Interaction locality.
numParts	Total number of rolling-prune parts.
numSciInPartMax	Maximum number of superclusters in a part.

void gmx::launchNbnxmKernelTransformXToXq	(	const FusedXToXqLaunchParams &	launchParams,
		NbnxmGpu *	nb,
		DeviceBuffer< Float3 >	d_x,
		const DeviceStream &	deviceStream
	)

Launch the fused coordinate layout conversion kernel.

Processes all grids in a single kernel launch by mapping cells from all grids into a flat set of GPU blocks. Uses blockIdx.y for global cell indexing across grids, and a prefix-sum lookup to determine which grid each cell belongs to. All parameters are pre-computed at pair-list setup and stored per interaction locality in NbnxmGpu::xToXqLaunchParams.

Parameters

[in]	launchParams	Pre-computed kernel launch parameters.
[in,out]	nb	Nbnxm main structure.
[in]	d_x	Source atom coordinates.
[in]	deviceStream	Device stream for kernel submission.

static void gmx::launchPmeGpuFftAndGather ( gmx_pme_t *  pmedata, const real  lambdaQ, gmx_wallcycle *  wcycle, const PmeStepWorkload &  stepWork  )

static

Launch the FFT and gather stages of PME GPU.

This function only implements setting the output forces (no accumulation).

Parameters

[in]	pmedata	The PME structure
[in]	lambdaQ	The Coulomb lambda of the current system state.
[in]	wcycle	The wallcycle structure
[in]	stepWork	Step schedule flags

static void gmx::launchPmeGpuSpread ( gmx_pme_t *  pmedata, const matrix  box, const SimulationWorkload &  simulationWork, const PmeStepWorkload &  stepWork, GpuEventSynchronizer *  xReadyOnDevice, const real  lambdaQ, gmx_wallcycle *  wcycle  )

inlinestatic

Launch the prepare_step and spread stages of PME GPU.

Parameters

[in]	pmedata	The PME structure
[in]	box	The box matrix
[in]	simulationWork	Simulation schedule flags
[in]	stepWork	Step schedule flags
[in]	xReadyOnDevice	Event synchronizer indicating that the coordinates are ready in the device memory.
[in]	lambdaQ	The Coulomb lambda of the current state.
[in]	wcycle	The wallcycle structure

void gmx::launchScaleCoordinatesKernel	(	int	numAtoms,
		DeviceBuffer< Float3 >	d_coordinates,
		const ScalingMatrix &	mu,
		const DeviceStream &	deviceStream
	)

Launches positions of velocities scaling kernel.

Parameters

[in]	numAtoms	Number of atoms in the system.
[in]	d_coordinates	Device buffer with position or velocities to be scaled.
[in]	mu	Scaling matrix.
[in]	deviceStream	Stream to launch kernel in.

void gmx::launchSettleGpuKernel	(	int	numSettles,
		const DeviceBuffer< WaterMolecule > &	d_atomIds,
		const SettleParameters &	settleParameters,
		const DeviceBuffer< Float3 > &	d_x,
		DeviceBuffer< Float3 >	d_xp,
		bool	updateVelocities,
		DeviceBuffer< Float3 >	d_v,
		real	invdt,
		bool	computeVirial,
		DeviceBuffer< float >	d_virialScaled,
		const PbcAiuc &	pbcAiuc,
		const DeviceStream &	deviceStream
	)

Apply SETTLE.

Applies SETTLE to coordinates and velocities, stored on GPU. Data at pointers d_xp and d_v change in the GPU memory. The results are not automatically copied back to the CPU memory. Method uses this class data structures which should be updated when needed using update method.

Parameters

[in]	numSettles	Number of SETTLE constraints.
[in]	d_atomIds	Device buffer with indices of atoms to be SETTLEd.
[in]	settleParameters	Parameters for SETTLE constraints.
[in]	d_x	Coordinates before timestep (in GPU memory)
[in,out]	d_xp	Coordinates after timestep (in GPU memory). The resulting constrained coordinates will be saved here.
[in]	updateVelocities	If the velocities should be updated.
[in,out]	d_v	Velocities to update (in GPU memory, can be nullptr if not updated)
[in]	invdt	Reciprocal timestep (to scale Lagrange multipliers when velocities are updated)
[in]	computeVirial	If virial should be updated.
[in,out]	d_virialScaled	Scaled virial tensor to be updated.
[in]	pbcAiuc	PBC data.
[in]	deviceStream	Device stream to launch kernel in.

template<NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>

auto gmx::leapFrogKernel	(	Float3 *__restrict__	gm_x,
		Float3 *__restrict__	gm_x0,
		Float3 *__restrict__	gm_v,
		const Float3 *__restrict__	gm_f,
		const float *__restrict__	gm_inverseMasses,
		float	dt,
		const float *__restrict__	gm_lambdas,
		const unsigned short *__restrict__	gm_tempScaleGroups,
		Float3	prVelocityScalingMatrixDiagonal
	)

Main kernel for the Leap-Frog integrator.

The coordinates and velocities are updated on the GPU. Also saves the intermediate values of the coordinates for further use in constraints.

Each GPU thread works with a single particle.

Template Parameters

numTempScaleValues	The number of different T-couple values.
parrinelloRahmanVelocityScaling	The properties of the Parrinello-Rahman velocity scaling matrix.

Parameters

[in,out]	gm_x	Coordinates to update upon integration.
[out]	gm_x0	A copy of the coordinates before the integration (for constraints).
[in,out]	gm_v	Velocities to update.
[in]	gm_f	Atomic forces.
[in]	gm_inverseMasses	Reciprocal masses.
[in]	dt	Timestep.
[in]	gm_lambdas	Temperature scaling factors (one per group).
[in]	gm_tempScaleGroups	Mapping of atoms into groups.
[in]	prVelocityScalingMatrixDiagonal	Diagonal elements of Parrinello-Rahman velocity scaling matrix.

static void gmx::lincs_matrix_expand ( const Lincs &  lincsd, const Task &  li_task, gmx::ArrayRef< const real >  blcc, gmx::ArrayRef< real >  rhs1, gmx::ArrayRef< real >  rhs2, gmx::ArrayRef< real >  sol  )

static

Do a set of nrec LINCS matrix multiplications.

This function will return with up to date thread-local constraint data, without an OpenMP barrier.

template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, typename CommandGroupHandler >

auto gmx::lincsKernel	(	CommandGroupHandler &	cgh,
		const int	numConstraintsThreads,
		const AtomPair *__restrict__	gm_constraints,
		const float *__restrict__	gm_constraintsTargetLengths,
		const int *__restrict__	gm_coupledConstraintsCounts,
		const int *__restrict__	gm_coupledConstraintsIndices,
		const float *__restrict__	gm_massFactors,
		float *__restrict__	gm_matrixA,
		const float *__restrict__	gm_inverseMasses,
		const int	numIterations,
		const int	expansionOrder,
		const Float3 *__restrict__	gm_x,
		Float3 *__restrict__	gm_xp,
		const float	invdt,
		Float3 *__restrict__	gm_v,
		float *__restrict__	gm_virialScaled,
		PbcAiuc	pbcAiuc
	)

Main kernel for LINCS constraints.

See Hess et al., J. Comput. Chem. 18: 1463-1472 (1997) for the description of the algorithm.

In GPU version, one thread is responsible for all computations for one constraint. The blocks are filled in a way that no constraint is coupled to the constraint from the next block. This is achieved by moving active threads to the next block, if the correspondent group of coupled constraints is to big to fit the current thread block. This may leave some 'dummy' threads in the end of the thread block, i.e. threads that are not required to do actual work. Since constraints from different blocks are not coupled, there is no need to synchronize across the device. However, extensive communication in a thread block are still needed.

Todo:

Reduce synchronization overhead. Some ideas are:

1. Consider going to warp-level synchronization for the coupled constraints.
2. Move more data to local/shared memory and try to get rid of atomic operations (at least on the device level).
3. Use analytical solution for matrix A inversion.
4. Introduce mapping of thread id to both single constraint and single atom, thus designating Nth threads to deal with Nat <= Nth coupled atoms and Nc <= Nth coupled constraints. See Issue #2885 for details (https://gitlab.com/gromacs/gromacs/-/issues/2885)

The use of restrict for gm_xp and gm_v causes failure, probably because of the atomic operations. Investigate this issue further.

Template Parameters

updateVelocities	Whether velocities should be updated this step.
computeVirial	Whether virial tensor should be computed this step.
haveCoupledConstraints	If there are coupled constraints (i.e. LINCS iterations are needed).
CommandGroupHandler	Type of real or dummy command group handler

Parameters

[in]	cgh	SYCL handler.
[in]	numConstraintsThreads	Total number of threads.
[in]	gm_constraints	List of constrained atoms.
[in]	gm_constraintsTargetLengths	Equilibrium distances for the constraints.
[in]	gm_coupledConstraintsCounts	Number of constraints, coupled with the current one.
[in]	gm_coupledConstraintsIndices	List of coupled with the current one.
[in]	gm_massFactors	Mass factors.
[in]	gm_matrixA	Elements of the coupling matrix.
[in]	gm_inverseMasses	1/mass for all atoms.
[in]	numIterations	Number of iterations used to correct the projection.
[in]	expansionOrder	Order of expansion when inverting the matrix.
[in]	gm_x	Unconstrained positions.
[in,out]	gm_xp	Positions at the previous step, will be updated.
[in]	invdt	Inverse timestep (needed to update velocities).
[in,out]	gm_v	Velocities of atoms, will be updated if updateVelocities.
[in,out]	gm_virialScaled	Scaled virial tensor (6 floats: [XX, XY, XZ, YY, YZ, ZZ]). Will be updated if updateVirial.
[in]	pbcAiuc	Periodic boundary data.

void gmx::linearArrayIndexToMultiDim	(	int	indexLinear,
		int	ndim,
		const awh_ivec	numPointsDim,
		awh_ivec	indexMulti
	)

Convert a linear array index to a multidimensional one.

Parameters

[in]	indexLinear	Linear array index
[in]	ndim	Number of dimensions of the array.
[in]	numPointsDim	Number of points for each dimension.
[out]	indexMulti	The multidimensional index.

void gmx::linearGridindexToMultiDim	(	const BiasGrid &	grid,
		int	indexLinear,
		awh_ivec	indexMulti
	)

Convert a linear grid point index to a multidimensional one.

Parameters

[in]	grid	The grid.
[in]	indexLinear	Linear grid point index to convert to a multidimensional one.
[out]	indexMulti	The multidimensional index.

template<typename T >

static std::remove_const_t<T> gmx::load ( const internal::SimdTraitsT< T > *  m )

inlinestatic

Load function that returns SIMD or scalar.

Note that a load of T* where T is const returns a value, which is a copy, and the caller cannot be constrained to not change it, so the return type uses std::remove_const_t.

Template Parameters

T	Type to load (type is always mandatory)

Parameters

m	Pointer to aligned memory

Returns

Loaded value

template<typename T >

static T gmx::loadU ( const internal::SimdTraitsT< T > *  m )

inlinestatic

Load function that returns SIMD or scalar based on template argument.

Template Parameters

T	Type to load (type is always mandatory)

Parameters

m	Pointer to unaligned memory

Returns

Loaded SimdFloat/Double/Int or basic scalar type

static float gmx::log ( float  x )

inlinestatic

Float log(x). This is the natural logarithm.

Parameters

x	Argument, should be >0.

Returns

The natural logarithm of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::log ( double  x )

inlinestatic

Double log(x). This is the natural logarithm.

Parameters

x	Argument, should be >0.

Returns

The natural logarithm of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

unsigned int gmx::log2I

(

std::uint32_t

x

)

Compute floor of logarithm to base 2, 32 bit unsigned argument.

Parameters

x	32-bit unsigned argument

Returns

log2(x)

Note

This version of the overloaded function uses unsigned arguments to be able to handle arguments using all 32 bits.

unsigned int gmx::log2I

(

std::uint64_t

x

)

Compute floor of logarithm to base 2, 64 bit unsigned argument.

Parameters

x	64-bit unsigned argument

Returns

log2(x)

Note

This version of the overloaded function uses unsigned arguments to be able to handle arguments using all 64 bits.

unsigned int gmx::log2I

(

std::int32_t

x

)

Compute floor of logarithm to base 2, 32 bit signed argument.

Parameters

x	32-bit signed argument

Returns

log2(x)

Note

This version of the overloaded function will assert that x is not negative.

unsigned int gmx::log2I

(

std::int64_t

x

)

Compute floor of logarithm to base 2, 64 bit signed argument.

Parameters

x	64-bit signed argument

Returns

log2(x)

Note

This version of the overloaded function will assert that x is not negative.

void gmx::logHardwareDetectionWarnings	(	const gmx::MDLogger &	mdlog,
		const gmx_hw_info_t &	hardwareInformation
	)

Issue warnings to mdlog that were decided during detection.

Parameters

[in]	mdlog	Logger
[in]	hardwareInformation	The hardwareInformation

static double gmx::logSingleAccuracy ( double  x )

inlinestatic

Double log(x), but with single accuracy. This is the natural logarithm.

Parameters

x	Argument, should be >0.

Returns

The natural logarithm of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::logValidationMessages	(	const MDLogger &	mdlog,
		const SimulationWorkload &	simulationWorkload,
		bool	haveFillerParticlesInLocalState,
		bool	useH5mdOutputFile,
		bool	useModularSimulator,
		IntegrationAlgorithm	integrationAlgorithm,
		const DeviceInformation *	deviceInfo
	)

Write a messages for lists of features with status "experimental" and "validation pending" to the log.

Parameters

[in]	mdlog	The logger
[in]	simulationWorkload	Describes the simulation workload
[in]	haveFillerParticlesInLocalState	Whether direct-halo communication is in use
[in]	useH5mdOutputFile	Whether a trajectory output file uses H5md format.
[in]	useModularSimulator	Whether the modular simulator is in use
[in]	integrationAlgorithm	Whether integration algorithm is in use
[in]	deviceInfo	Handle to device information object, can be nullptr

void gmx::lsq_y_ax_b	(	int	n,
		real	x[],
		real	y[],
		real *	a,
		real *	b,
		real *	r,
		real *	chi2
	)

Fit a straight line y=ax+b thru the n data points x, y.

Parameters

[in]	n	number of points
[in]	x	data points x
[in]	y	data point y
[out]	a	slope
[out]	b	intercept
[out]	r	correlation coefficient
[out]	chi2	quality of fit

Exceptions

InconsistentInputError

if given no points to fit

void gmx::lsq_y_ax_b_error	(	int	n,
		real	x[],
		real	y[],
		real	dy[],
		real *	a,
		real *	b,
		real *	da,
		real *	db,
		real *	r,
		real *	chi2
	)

Fit a straight line y=ax+b thru the n data points x, y.

Parameters

[in]	n	number of points
[in]	x	data points x
[in]	y	data point y
[in]	dy	uncertainty in data point y
[out]	a	slope
[out]	b	intercept
[out]	da	error in slope
[out]	db	error in intercept
[out]	r	correlation coefficient
[out]	chi2	quality of fit

Exceptions

InconsistentInputError

if given no points to fit

void gmx::lsq_y_ax_b_xdouble	(	int	n,
		double	x[],
		real	y[],
		real *	a,
		real *	b,
		real *	r,
		real *	chi2
	)

Fit a straight line y=ax+b thru the n data points x, y.

Parameters

[in]	n	number of points
[in]	x	data points x
[in]	y	data point y
[out]	a	slope
[out]	b	intercept
[out]	r	correlation coefficient
[out]	chi2	quality of fit

Exceptions

InconsistentInputError

if given no points to fit Suits cases where x is already always computed in double precision even in a mixed-precision build configuration.

ListOfLists< int > gmx::make_at2con	(	int	numAtoms,
		const gmx::EnumerationArray< InteractionFunction, InteractionList > &	ilist,
		ArrayRef< const t_iparams >	iparams,
		FlexibleConstraintTreatment	flexibleConstraintTreatment
	)

Returns a ListOfLists object to go from atoms to constraints.

The object will contain constraint indices with lower indices directly matching the order in InteractionFunction::Constraints and higher indices matching the order in InteractionFunction::ConstraintsNoCoupling offset by the number of constraints in InteractionFunction::Constraints.

Parameters

[in]	numAtoms	The number of atoms to construct the list for
[in]	ilist	Interaction list, size InteractionFunction::Count
[in]	iparams	Interaction parameters, can be null when flexibleConstraintTreatment==Include
[in]	flexibleConstraintTreatment	The flexible constraint treatment, see enum above

Returns

a ListOfLists object with all constraints for each atom

ListOfLists< int > gmx::make_at2con	(	const gmx_moltype_t &	moltype,
		gmx::ArrayRef< const t_iparams >	iparams,
		FlexibleConstraintTreatment	flexibleConstraintTreatment
	)

Returns a ListOfLists object to go from atoms to constraints.

The object will contain constraint indices with lower indices directly matching the order in InteractionFunction::Constraints and higher indices matching the order in InteractionFunction::ConstraintsNoCoupling offset by the number of constraints in InteractionFunction::Constraints.

Parameters

[in]	moltype	The molecule data
[in]	iparams	Interaction parameters, can be null when flexibleConstraintTreatment==Include
[in]	flexibleConstraintTreatment	The flexible constraint treatment, see enum above

Returns

a ListOfLists object with all constraints for each atom

bondedtable_t gmx::make_bonded_table	(	FILE *	fplog,
		const char *	fn,
		int	angle
	)

Return a table for bonded interactions,.

Parameters

fplog	Pointer to log file
fn	File name
angle	Type of angle: bonds 0, angles 1, dihedrals 2

Returns

New bonded table datatype

void gmx::make_local_shells	(	const gmx_domdec_t *	dd,
		const t_mdatoms &	md,
		shellfc_t *	shfc
	)

Gets the local shell with domain decomposition.

Parameters

[in]	dd	Domain decomposition struct, can be nullptr
[in]	md	The MD atom data
[in,out]	shfc	The shell/flexible-constraint data

std::unique_ptr< t_forcetable > gmx::make_tables	(	FILE *	fp,
		const interaction_const_t &	ic,
		const char *	fn,
		real	rtab,
		int	flags
	)

Return tables for inner loops.

Parameters

fp	Log file pointer
ic	Non-bonded interaction constants
fn	File name from which to read user tables
rtab	Largest interaction distance to tabulate
flags	Flags to select table settings

Returns

Pointer to inner loop table structure

ArrayRef< bool > gmx::makeArrayRef

(

std::vector< BoolType > &

boolVector

)

Create ArrayRef to bool from reference to std::vector<BoolType>.

Allow to easily make views of bool from vectors of BoolType.

See Also

ArrayRef

template<typename T >

ArrayRef<std::conditional_t<std::is_const_v<T>, const typename T::value_type, typename T::value_type> > gmx::makeArrayRef

(

T &

c

)

Create ArrayRef from container with type deduction.

See Also

ArrayRef

static ListOfLists<int> gmx::makeAtomsToConstraintsList ( int  numAtoms, const gmx::EnumerationArray< InteractionFunction, InteractionList > &  ilists, ArrayRef< const t_iparams >  iparams, FlexibleConstraintTreatment  flexibleConstraintTreatment  )

static

Returns a block struct to go from atoms to constraints.

The block struct will contain constraint indices with lower indices directly matching the order in InteractionFunction::Constraints and higher indices matching the order in InteractionFunction::ConstraintsNoCoupling offset by the number of constraints in InteractionFunction::Constraints.

Parameters

[in]	numAtoms	The number of atoms to construct the list for
[in]	ilists	The interaction lists, size InteractionFunction::Count
[in]	iparams	Interaction parameters, can be null when flexibleConstraintTreatment==Include
[in]	flexibleConstraintTreatment	The flexible constraint treatment, see enum above

Returns

a block struct with all constraints for each atom

static std::vector<ListOfLists<int> > gmx::makeAtomToConstraintMappings ( const gmx_mtop_t &  mtop, FlexibleConstraintTreatment  flexibleConstraintTreatment  )

static

Makes a per-moleculetype container of mappings from atom indices to constraint indices.

Note that flexible constraints are only enabled with a dynamical integrator.

static std::vector<int> gmx::makeAtomToGroupMapping ( const gmx::RangePartitioning &  grouping )

static

Returns the an array with group indices for each atom.

Parameters

[in]

grouping

The partitioning of the atom range into atom groups

void gmx::makeClusterListSimd2xMM	(	const Grid &	jGrid,
		NbnxmPairlistCpu *	nbl,
		int	icluster,
		int	firstCell,
		int	lastCell,
		bool	excludeSubDiagonal,
		const real *gmx_restrict	x_j,
		real	rlist2,
		float	rbb2,
		int *gmx_restrict	numDistanceChecks
	)

SIMD code for checking and adding cluster-pairs to the list using the 2xMM layout.

Checks bounding box distances and possibly atom pair distances. This is an accelerated version of make_cluster_list_simple.

Parameters

[in]	jGrid	The j-grid
[in,out]	nbl	The pair-list to store the cluster pairs in
[in]	icluster	The index of the i-cluster
[in]	firstCell	The first cluster in the j-range, using i-cluster size indexing
[in]	lastCell	The last cluster in the j-range, using i-cluster size indexing
[in]	excludeSubDiagonal	Exclude atom pairs with i-index > j-index
[in]	x_j	Coordinates for the j-atom, in SIMD packed format
[in]	rlist2	The squared list cut-off
[in]	rbb2	The squared cut-off for putting cluster-pairs in the list based on bounding box distance only
[in,out]	numDistanceChecks	The number of distance checks performed

void gmx::makeClusterListSimd4xM	(	const Grid &	jGrid,
		NbnxmPairlistCpu *	nbl,
		int	icluster,
		int	firstCell,
		int	lastCell,
		bool	excludeSubDiagonal,
		const real *gmx_restrict	x_j,
		real	rlist2,
		float	rbb2,
		int *gmx_restrict	numDistanceChecks
	)

SIMD code for checking and adding cluster-pairs to the list using the 4xM layout.

Checks bounding box distances and possibly atom pair distances. This is an accelerated version of make_cluster_list_simple.

Parameters

[in]	jGrid	The j-grid
[in,out]	nbl	The pair-list to store the cluster pairs in
[in]	icluster	The index of the i-cluster
[in]	firstCell	The first cluster in the j-range, using i-cluster size indexing
[in]	lastCell	The last cluster in the j-range, using i-cluster size indexing
[in]	excludeSubDiagonal	Exclude atom pairs with i-index > j-index
[in]	x_j	Coordinates for the j-atom, in SIMD packed format
[in]	rlist2	The squared list cut-off
[in]	rbb2	The squared cut-off for putting cluster-pairs in the list based on bounding box distance only
[in,out]	numDistanceChecks	The number of distance checks performed

ArrayRef< const bool > gmx::makeConstArrayRef

(

const std::vector< BoolType > &

boolVector

)

Create ArrayRef to const bool from reference to std::vector<BoolType>.

Allow to easily make views of const bool from vectors of BoolType.

See Also

ArrayRef

template<typename T >

ArrayRef<const typename T::value_type> gmx::makeConstArrayRef

(

const T &

c

)

Create ArrayRef to const T from container with type deduction.

See Also

ArrayRef

template<typename... Args>

std::unique_ptr<Constraints> gmx::makeConstraints	(	const gmx_mtop_t &	mtop,
		const t_inputrec &	ir,
		pull_t *	pull_work,
		bool	havePullConstraintsWork,
		bool	doEssentialDynamics,
		Args &&...	args
	)

Factory function for Constraints.

We only want an object to manage computing constraints when the simulation requires one. Checking for whether the object was made adds overhead to simulations that use constraints, while avoiding overhead on those that do not, so is a design trade-off we might reconsider some time.

Using a private constructor and a factory function ensures that we can only make a Constraints object when the prerequisites are satisfied, ie. that something needs them and if necessary has already been initialized.

Using the parameter pack insulates the factory function from changes to the type signature of the constructor that don't affect the logic here.

static std::string gmx::makeDefinesForKernelTypes ( bool  bFastGen, enum ElecType  elecType, enum VdwType  vdwType  )

static

Returns a string with the compiler defines required to avoid all flavour generation.

For example if flavour ElecType::RF with VdwType::FSwitch, the output will be such that the corresponding kernel flavour is generated: -DGMX_OCL_FASTGEN (will replace flavour generator nbnxm_ocl_kernels.clh with nbnxm_ocl_kernels_fastgen.clh) -DEL_RF (The ElecType::RF flavour) -DEELNAME=_ElecRF (The first part of the generated kernel name ) -DLJ_EWALD_COMB_GEOM (The VdwType::FSwitch flavour) -DVDWNAME=_VdwLJEwCombGeom (The second part of the generated kernel name )

prune/energy are still generated as originally. It is only the flavour-level that has changed, so that only the required flavour for the simulation is compiled.

If elecType is single-range Ewald, then we need to add the twin-cutoff flavour kernels to the JIT, because PME tuning might need it. This path sets -DGMX_OCL_FASTGEN_ADD_TWINCUT, which triggers the use of nbnxm_ocl_kernels_fastgen_add_twincut.clh. This hard-codes the generation of extra kernels that have the same base flavour, and add the required -DVDW_CUTOFF_CHECK and "TwinCut" to the kernel name.

If FastGen is not active, then nothing needs to be returned. The JIT defaults to compiling all kernel flavours.

Parameters

[in]	bFastGen	Whether FastGen should be used
[in]	elecType	Electrostatics kernel flavour for FastGen
[in]	vdwType	VDW kernel flavour for FastGen

Returns

String with the defines if FastGen is active

Exceptions

std::bad_alloc

if out of memory

std::unique_ptr< t_forcetable > gmx::makeDispersionCorrectionTable	(	FILE *	fp,
		const interaction_const_t &	ic,
		real	rtab,
		const char *	tabfn
	)

Construct and return tabulated dispersion and repulsion interactions.

This table can be used to compute long-range dispersion corrections. Returns pointer owning nothing when tabfn=nullptr.

std::vector< real > gmx::makeExclusionDistances	(	const t_atoms *	a,
		AtomProperties *	aps,
		real	defaultDistance,
		real	scaleFactor
	)

Allocate and fill an array of inter-atomic half distances.

These are either scaled VDW radii taken from vdwradii.dat, or the default value. Used directly and indirectly by solvate and insert-molecules for deciding whether molecules clash. The return pointer should be freed by the caller.

std::vector< int > gmx::makeGpuIds	(	ArrayRef< const int >	compatibleGpus,
		size_t	numGpuTasks
	)

Make a vector containing numGpuTasks IDs of the IDs found in compatibleGpus.

Exceptions

std::bad_alloc

If out of memory

Returns

A sorted vector of IDs of compatible vectors, whose length matches that of the number of GPU tasks required. If more tasks are required than compatible GPUs, then some GPU IDs will appear more than once.

std::string gmx::makeGpuIdString	(	const std::vector< int > &	gpuIds,
		int	totalNumberOfTasks
	)

Convert a container of GPU deviced IDs to a string that can be used by gmx tune_pme as input to mdrun -gputasks.

Produce a valid input for mdrun -gputasks that refers to the device IDs in gpuIds but produces a mapping for totalNumberOfTasks tasks. Note that gmx tune_pme does not currently support filling mdrun -gputasks.

Parameters

[in]	gpuIds	Container of device IDs
[in]	totalNumberOfTasks	Total number of tasks for the output mapping produced by the returned string.

Returns

A string that is suitable to pass to mdrun -gputasks.

Exceptions

std::bad_alloc

If out of memory.

static CommSetup gmx::makeGroupCommunicators ( const MDLogger &  mdlog, const DDSettings &  ddSettings, const DdRankOrder  ddRankOrder, const DDRankSetup &  ddRankSetup, const MpiComm &  mpiCommSimulation  )

static

Makes the PP communicator and the PME communicator, when needed.

Returns the Cartesian rank setup and the rank duties. Sets cr->mpi_comm_mygroup For PP ranks, sets the DD PP cell index in ddCellIndex. With separate PME ranks in interleaved order, set the PME ranks in pmeRanks.

enum H5mdFileMode char H5md * gmx::makeH5md ( const std::filesystem::path &  fileName, H5mdFileMode  mode  )

strong

Builder method to isolate creation from callers.

This should replaced by an impl class to hide the dependency on hdf5 types.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdAttributeGuard

(

hid_t

object

)

Helper function for guarding an HDF5 attribute with H5Aclose.

Parameters

[in]

object

Object to guard.

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdDataSetGuard

(

hid_t

object

)

Helper function for guarding an HDF5 data set with H5Dclose.

Parameters

[in]

object

Object to guard.

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdDataSpaceGuard

(

hid_t

object

)

Helper function for guarding an HDF5 data space with H5Sclose.

Parameters

[in]

object

Object to guard.

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdGroupGuard

(

hid_t

object

)

Helper function for guarding an HDF5 group with H5Gclose.

Parameters

[in]

object

Object to guard.

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdGuard	(	hid_t	object,
		H5mdCloseType	unboundCloser
	)

Helper function for guarding an HDF5 object with a closing function (H5Gclose, etc.).

When the returned scope guard goes out of scope the closing function is called with the object identifier as its argument, ensuring that the resource is freed. If the identifier needs to be stored for later use it should not be guarded using these functions.

Intended use is for the object to be the result of an opening or creating function call, which is why it is returned along with the guard. E.g. to open a group:

auto [object, guard] = makeH5mdGuard(openOrCreateGroup(<...>), H5Gclose);

Parameters

[in]	object	Object to guard.
[in]	unboundCloser	Callback function used to close the guarded object

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdPropertyListGuard

(

hid_t

object

)

Helper function for guarding an HDF5 property list with H5Pclose.

Parameters

[in]

object

Object to guard.

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

std::pair< hid_t, H5mdGuard > gmx::makeH5mdTypeGuard

(

hid_t

object

)

Helper function for guarding an HDF5 type with H5Tclose.

Parameters

[in]

object

Object to guard.

Returns

Pair of the (object, guard), where object is the id and guard is the scope guard which closes the object once it exits scope.

HostAllocationPolicy gmx::makeHostAllocationPolicy	(	bool	pinBuffers,
		const DeviceStreamManager *	deviceStreamManager,
		bool	propagateDuringContainerCopyConstruction = false
	)

Helper function to make a suitable HostAllocationPolicy.

Parameters

[in]	pinBuffers	Whether to pin buffers (for GPU transfers)
[in]	deviceStreamManager	Manager of device streams (must be valid when GPU will be used)
[in]	propagateDuringContainerCopyConstruction	Default is chosen to be consistent with copy assignment

std::unique_ptr< ImdSession > gmx::makeImdSession	(	const t_inputrec *	ir,
		const MpiComm &	mpiComm,
		const gmx_domdec_t *	dd,
		gmx_wallcycle *	wcycle,
		gmx_enerdata_t *	enerd,
		const gmx_multisim_t *	ms,
		const gmx_mtop_t &	top_global,
		const MDLogger &	mdlog,
		gmx::ArrayRef< const gmx::RVec >	coords,
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const ImdOptions &	options,
		StartingBehavior	startingBehavior
	)

Makes and returns an initialized IMD session, which may be inactive.

This function is called before the main MD loop over time steps.

Parameters

ir	The inputrec structure containing the MD input parameters
mpiComm	Communication object for my group.
dd	Domain decomposition object, pass nullptr when DD is not active.
wcycle	Count wallcycles of IMD routines for diagnostic output.
enerd	Contains the GROMACS energies for the different interaction types.
ms	Handler for multi-simulations.
top_global	The topology of the whole system.
mdlog	Logger
coords	The starting positions of the atoms.
nfile	Number of files.
fnm	Struct containing file names etc.
oenv	Output options.
options	Options for interactive MD.
startingBehavior	Describes whether this is a restart appending to output files

std::vector< int > gmx::makeListOfAvailableDevices	(	gmx::ArrayRef< const std::unique_ptr< DeviceInformation >>	deviceInfoList,
		const std::string &	devicesSelectedByUserString
	)

Implement GPU ID selection by returning the available GPU IDs on this physical node that are compatible.

If the string supplied by the user is empty, then return the IDs of all compatible GPUs on this physical node. Otherwise, check the user specified compatible GPUs and return their IDs.

Parameters

[in]	deviceInfoList	Information on the GPUs on this physical node.
[in]	devicesSelectedByUserString	String like "013" or "0,1,3" typically supplied by the user to mdrun -gpu_id. Must contain only unique decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is acceptable (and required to specify a single ID that is larger than 9).

Returns

A vector of unique compatible GPU IDs on this physical node.

Exceptions

std::bad_alloc

If out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',') or if identifiers are duplicated in the specifier list. InvalidInputError If devicesSelectedByUserString specifies IDs of the devices that are not compatible.

std::unique_ptr< MDAtoms > gmx::makeMDAtoms	(	FILE *	fp,
		const gmx_mtop_t &	mtop,
		const t_inputrec &	ir,
		const bool	rankHasPmeGpuTask,
		const DeviceStreamManager *	deviceStreamManager
	)

Builder function for MdAtomsWrapper.

Builder function.

std::string gmx::makeOpenClInternalErrorString ( const char *  message, cl_int  status  )

inline

Make an error string following an OpenCL API call.

It is meant to be called with status != CL_SUCCESS, but it will work correctly even if it is called with no OpenCL failure.

Todo:

Make use of this function more.

Parameters

[in]	message	Supplies context, e.g. the name of the API call that returned the error.
[in]	status	OpenCL API status code

Returns

A string describing the OpenCL error.

template<typename T >

T gmx::makePeriodic	(	const T	x,
		const T	period
	)

Return x modulo period such that it is within the interval [-0.5*period, 0.5*period].

A shift of +/- 'period' is applied, if needed.

Parameters

[in]	x	Value to correct, should be within the interval [-1.5*period, 1.5*period]
[in]	period	The period

Returns

x modulo period that is within the interval [-0.5*period, 0.5*period]

uint64_t gmx::makeRandomSeed

(

)

Return 64 random bits from the random device, suitable as seed.

If the internal random device output is smaller than 64 bits, this routine will use multiple calls internally until we have 64 bits of random data.

Returns

64-bit unsigned integer with random bits.

template<typename GeneratorType >

static uint64_t gmx::makeRandomSeedInternal ( GeneratorType &  gen )

static

Get the next pure or pseudo-random number.

Returns the next random number taken from the hardware generator or from PRNG.

Parameters

[in]

gen

Pseudo-random/random numbers generator/device to use.

Returns

Random or pseudo-random number.

std::variant< std::vector< RangePartitioning >, std::string > gmx::makeUpdateGroupingsPerMoleculeType

(

const gmx_mtop_t &

mtop

)

Returns a vector with update groups for each moleculetype in mtop or an error string when the criteria (see below) are not satisfied.

An error string is returned when at least one moleculetype does not obey the restrictions of update groups, e.g. more than two constraints in a row.

Currently valid update groups are:

• a single atom which is not a virtual site and does not have constraints;
• or a group of atoms where all virtual sites are constructed from atoms within the group and at least one non-vsite atom is constrained to all other non-vsite atoms.

To have update groups, all virtual sites should be linear 2 or 3 atom constructions with coefficients >= 0 and sum of coefficients <= 1.

This vector is generally consumed in constructing an UpdateGroups object.

Parameters

[in]

mtop

The system topology

UpdateGroups gmx::makeUpdateGroups	(	const gmx::MDLogger &	mdlog,
		std::vector< RangePartitioning > &&	updateGroupingPerMoleculeType,
		real	maxUpdateGroupRadius,
		bool	doRerun,
		bool	useDomainDecomposition,
		bool	systemHasConstraintsOrVsites,
		real	cutoffMargin
	)

Builder for update groups.

Checks the conditions for using update groups, and logs a message if they cannot be used, along with the reason why not.

updateGroupingPerMoleculeType can not be empty (is asserted).

If PP domain decomposition is not in use, there is no reason to use update groups.

All molecule types in the system topology must be conform to the requirements, such that makeUpdateGroupingsPerMoleculeType() returns a non-empty vector.

mdrun -rerun does not support update groups (PBC corrections needed).

When we have constraints and/or vsites, it is beneficial to use update groups (when possible) to allow independent update of groups. But if there are no constraints or vsites, then there is no need to use update groups at all.

To use update groups, the large domain-to-domain cutoff distance should be compatible with the box size.

std::unique_ptr< VirtualSitesHandler > gmx::makeVirtualSitesHandler	(	const gmx_mtop_t &	mtop,
		gmx_domdec_t *	domdec,
		PbcType	pbcType,
		ArrayRef< const RangePartitioning >	updateGroupingPerMoleculeType
	)

Create the virtual site handler.

Parameters

[in]	mtop	The global topology
[in]	domdec	The domain decomposition struct, pass nullptr when DD is not in use
[in]	pbcType	The type of PBC
[in]	updateGroupingPerMoleculeType	Update grouping per molecule type, pass empty when not using update groups

Returns

A valid vsite handler object or nullptr when there are no virtual sites

static DevelopmentFeatureFlags gmx::manageDevelopmentFeatures ( const MDLogger &  mdlog, const PmeRunMode  pmeRunMode, const int  numRanksPerSimulation, const int  numPmeRanksPerSimulation, const bool  canUseGpuAwareMpi  )

static

Manage any development feature flag variables encountered.

The use of dev features indicated by environment variables is logged in order to ensure that runs with such features enabled can be identified from their log and standard output. Any cross dependencies are also checked, and if unsatisfied, a fatal error issued.

Note that some development features overrides are applied already here: the GPU communication flags are set to false in non-tMPI and non-CUDA builds.

Parameters

[in]	mdlog	Logger object.
[in]	pmeRunMode	Run mode indicating what resource is PME executed on.
[in]	numRanksPerSimulation	The number of ranks in each simulation.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation, can be -1
[in]	canUseGpuAwareMpi	Whether GPU-aware MPI can be used.

Returns

The object populated with development feature flags.

void gmx::mapGridToDataGrid	(	std::vector< int > *	gridpointToDatapoint,
		const MultiDimArray< std::vector< double >, dynamicExtents2D > &	data,
		int	numDataPoints,
		const std::string &	dataFilename,
		const BiasGrid &	grid,
		const std::string &	correctFormatMessage
	)

Maps each point in the grid to a point in the data grid.

This functions maps an AWH bias grid to a user provided input data grid. The value of data grid point i along dimension d is given by data[d][i]. The number of dimensions of the data should equal that of the grid. A fatal error is thrown if extracting the data fails or the data does not cover the whole grid.

Parameters

[out]	gridpointToDatapoint	Array mapping each grid point to a data point index.
[in]	data	2D array in format ndim x ndatapoints with data grid point values.
[in]	numDataPoints	Number of data points.
[in]	dataFilename	The data filename.
[in]	grid	The grid.
[in]	correctFormatMessage	String to include in error message if extracting the data fails.

IndexMap gmx::mapSelectionToInternalIndices

(

ArrayRef< const int32_t >

selectedIndices

)

Map the selected atoms to local internal indices.

Parameters

[in]

selectedIndices

An array of selected atom indices.

Returns

A index map with the original index as key and internal index as value.

static float gmx::maskAdd ( float  a, float  b, float  m  )

inlinestatic

Add two float variables, masked version.

Parameters

a	term1
b	term2
m	mask

Returns

a+b where mask is true, a otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskAdd ( double  a, double  b, double  m  )

inlinestatic

Add two double variables, masked version.

Parameters

a	term1
b	term2
m	mask

Returns

a+b where mask is true, a otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::maskzFma ( float  a, float  b, float  c, float  m  )

inlinestatic

Float fused multiply-add, masked version.

Parameters

a	factor1
b	factor2
c	term
m	mask

Returns

a*b+c where mask is true, 0.0 otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskzFma ( double  a, double  b, double  c, double  m  )

inlinestatic

double fused multiply-add, masked version.

Parameters

a	factor1
b	factor2
c	term
m	mask

Returns

a*b+c where mask is true, 0.0 otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::maskzInv ( float  x, bool  m  )

inlinestatic

Calculate 1/x for masked entry of float.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out float will not lead to floating-point exceptions.

Parameters

x	Argument that must be nonzero if masked-in.
m	Mask

Returns

1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskzInv ( double  x, bool  m  )

inlinestatic

Calculate 1/x for masked entry of double.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be nonzero if masked-in.
m	Mask

Returns

1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskzInvSingleAccuracy ( double  x, bool  m  )

inlinestatic

Calculate 1/x for masked entry of double, but with single accuracy.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be nonzero if masked-in.
m	Mask

Returns

1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::maskzInvsqrt ( float  x, bool  m  )

inlinestatic

Calculate 1/sqrt(x) for masked entry of float.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out float will not lead to floating-point exceptions.

Parameters

x	Argument that must be >0 if masked-in.
m	Mask

Returns

1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskzInvsqrt ( double  x, bool  m  )

inlinestatic

Calculate 1/sqrt(x) for masked entry of double.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be >0 if masked-in.
m	Mask

Returns

1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskzInvsqrtSingleAccuracy ( double  x, bool  m  )

inlinestatic

Calculate 1/sqrt(x) for masked entry of double, but with single accuracy.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be >0 if masked-in.
m	Mask

Returns

1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::maskzMul ( float  a, float  b, float  m  )

inlinestatic

Multiply two float variables, masked version.

Parameters

a	factor1
b	factor2
m	mask

Returns

a*b where mask is true, 0.0 otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::maskzMul ( double  a, double  b, double  m  )

inlinestatic

Multiply two double variables, masked version.

Parameters

a	factor1
b	factor2
m	mask

Returns

a*b where mask is true, 0.0 otherwise.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx_simdcall gmx::maskzRcp ( float  x, float  m  )

inlinestatic

Float 1.0/x, masked version.

Parameters

x	Argument, x>0 for entries where mask is true.
m	Mask

Returns

1/x. The result for masked-out entries will be 0.0.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx_simdcall gmx::maskzRcp ( double  x, double  m  )

inlinestatic

Double 1.0/x, masked version.

Parameters

x	Argument, x>0 for entries where mask is true.
m	Mask

Returns

Approximation of 1/x. The result for masked-out entries will be 0.0.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::max ( float  a, float  b  )

inlinestatic

Set each float element to the largest from two variables.

Parameters

a	Any floating-point value
b	Any floating-point value

Returns

max(a,b) for each element.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::max ( double  a, double  b  )

inlinestatic

Set each double element to the largest from two variables.

Parameters

a	Any doubleing-point value
b	Any doubleing-point value

Returns

max(a,b) for each element.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::maxwell_speed	(	real	tempi,
		int	seed,
		gmx_mtop_t *	mtop,
		rvec	v[],
		const MDLogger &	logger
	)

Generate Maxwellian velocities.

Parameters

[in]	tempi	Temperature to generate around
[in]	seed	Random number generator seed. A new one is generated if this is -1.
[in]	mtop	Molecular Topology
[out]	v	Velocities
[in]	logger	Handle to logging interface.

void gmx::mdAlgorithmsSetupAtomData	(	const SimulationWorkload &	simulationWork,
		gmx_domdec_t *	dd,
		const t_inputrec &	inputrec,
		const gmx_mtop_t &	top_global,
		gmx_localtop_t *	top,
		t_forcerec *	fr,
		ForceBuffers *	force,
		MDAtoms *	mdAtoms,
		Constraints *	constr,
		VirtualSitesHandler *	vsite,
		shellfc_t *	shellfc,
		StatePropagatorDataGpu *	stateGpu,
		gmx_wallcycle *	wcycle
	)

Sets atom data for several MD algorithms.

Most MD algorithms require two different setup calls: one for initialization and parameter setting and one for atom data setup. This routine sets the atom data for the (locally available) atoms. This is called at the start of serial runs and during domain decomposition.

Parameters

[in]	simulationWork	The simulation workload
[in,out]	dd	Domain decomposition struct, can be nullptr
[in]	inputrec	Input parameter record
[in]	top_global	The global topology
[in,out]	top	The local topology
[in,out]	fr	The force calculation parameter/data record
[out]	force	The force buffer
[out]	mdAtoms	The MD atom data
[in,out]	constr	The constraints handler, can be NULL
[in,out]	vsite	The virtual site data, can be NULL
[in,out]	shellfc	The shell/flexible-constraint data, can be NULL
[in]	stateGpu	The state-on-GPU manager, can be NULL
[in]	wcycle	The wallcycle counter manager, can be NULL

static void gmx::mdrunner_start_fn ( const void *  arg )

static

The callback used for running on spawned threads.

Obtains the pointer to the main mdrunner object from the one argument permitted to the thread-launch API call, copies it to make a new runner for this thread, reinitializes necessary data, and proceeds to the simulation.

void gmx::mergeAtomAndBondModifications	(	const MoleculePatchDatabase &	s,
		MoleculePatchDatabase *	d
	)

Add the individual modifications in s to d.

Parameters

[in]	s	Source information.
[in,out]	d	Destination to copy to.

void gmx::mergeAtomModifications	(	const MoleculePatchDatabase &	s,
		MoleculePatchDatabase *	d
	)

Add the individual modifications in s to d.

Parameters

[in]	s	Source information.
[in,out]	d	Destination to copy to.

bool gmx::mergeBondedInteractionList	(	ArrayRef< const BondedInteractionList >	s,
		ArrayRef< BondedInteractionList >	d,
		bool	bMin,
		bool	bPlus
	)

Add bond information in s to d.

Parameters

[in]	s	Source information to copy.
[in,out]	d	Destination to copy to.
[in]	bMin	don't copy bondeds with atoms starting with '-'.
[in]	bPlus	don't copy bondeds with atoms starting with '+'.

Returns

if bonds were removed at the termini.

void gmx::mergeExclusions	(	ListOfLists< int > *	excl,
		gmx::ArrayRef< ExclusionBlock >	b2
	)

Merge the contents of b2 into excl.

Requires that b2 and excl describe the same number of particles, if b2 describes a non-zero number.

static float gmx::min ( float  a, float  b  )

inlinestatic

Set each float element to the smallest from two variables.

Parameters

a	Any floating-point value
b	Any floating-point value

Returns

min(a,b) for each element.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::min ( double  a, double  b  )

inlinestatic

Set each double element to the smallest from two variables.

Parameters

a	Any doubleing-point value
b	Any doubleing-point value

Returns

min(a,b) for each element.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

void gmx::modifyEmbeddedFourCenterInteractions	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const std::vector< bool > &	isEmbeddedBlock,
		const MDLogger &	logger
	)

Modifies four-centers interactions.

Removes any other four-centers bonded interactions including 3 or more embedded atoms Any restraints and constraints will be kept

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	isEmbeddedBlock	vector with flags for embedded atom-containing blocks
[in]	logger	MDLogger for logging info about modifications

void gmx::modifyEmbeddedThreeCenterInteractions	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const std::vector< bool > &	isEmbeddedBlock,
		const MDLogger &	logger
	)

Modifies three-centers interactions (i.e. Angles, Settles)

Removes any other three-centers bonded interactions including 2 or more embedded atoms Any restraints and constraints will be kept Any F_SETTLE containing embedded atoms will be converted to the pair of F_CONNBONDS

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	isEmbeddedBlock	vector with flags for embedded atom-containing blocks
[in]	logger	MDLogger for logging info about modifications

void gmx::modifyEmbeddedTwoCenterInteractions	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const std::vector< bool > &	isEmbeddedBlock,
		const MDLogger &	logger
	)

Modifies pairwise bonded interactions.

Removes any other pairwise bonded interactions between embedded atoms Creates F_CONNBOND between embedded atoms Any restraints and constraints will be kept

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	isEmbeddedBlock	vector with flags for embedded atom-containing blocks
[in]	logger	MDLogger for logging info about modifications

void gmx::MPI_Comm_free_wrapper

(

MPI_Comm *

comm

)

Wrapper function for RAII-style cleanup.

This is needed to discard the return value so it can be used as a deleter by a smart pointer.

bool gmx::mrcHeaderIsSane

(

const MrcDensityMapHeader &

header

)

Checks if the values in the header are sane.

Checks extents and numbers of columns, rows and sections, as well as unit cell angles for positivity and to be within bounds.

Bounds are set generously not to hamper future creative uses of mrc files.

Returns

true if all header values are within resonable albeit generous bounds

int gmx::multiDimArrayIndexToLinear	(	const awh_ivec	indexMulti,
		int	numDim,
		const awh_ivec	numPointsDim
	)

Convert multidimensional array index to a linear one.

Parameters

[in]	indexMulti	Multidimensional index to convert to a linear one.
[in]	numDim	Number of dimensions of the array.
[in]	numPointsDim	Number of points of the array.

Returns

the linear index.

Note

This function can be used without having an initialized grid.

int gmx::multiDimGridIndexToLinear	(	const BiasGrid &	grid,
		const awh_ivec	indexMulti
	)

Convert a multidimensional grid point index to a linear one.

Parameters

[in]	grid	The grid.
[in]	indexMulti	Multidimensional grid point index to convert to a linear one.

Returns

the linear index.

std::string gmx::multiGpuFftDescription

(

)

Construct a string that describes the library (if any) that provides multi-GPU FFT support to this build.

Returns information for describing the multi-GPU FFT support.

void gmx::nbnxm_atomdata_copy_x_to_nbat_x	(	const GridSet &	gridSet,
		AtomLocality	locality,
		const rvec *	coordinates,
		nbnxm_atomdata_t *	nbat
	)

Transform coordinates to xbat layout.

Creates a copy of the coordinates buffer using short-range ordering.

Parameters

[in]	gridSet	The grids data.
[in]	locality	If the transformation should be applied to local or non local coordinates.
[in]	coordinates	Coordinates in plain rvec format.
[in,out]	nbat	Data in NBNXM format, used for mapping formats and to locate the output buffer.

real gmx::nbnxm_get_rlist_effective_inc	(	int	clusterSize,
		const RVec &	averageClusterBoundingBox
	)

Returns the effective list radius of the pair-list.

Due to the cluster size the effective pair-list is longer than that of a simple atom pair-list. This function gives the extra distance.

Note

This routine does not know which cluster layout is used and assumes the most common one. Therefore this should only be used to estimates, not for setting a pair list buffer.

void gmx::nbnxm_gpu_compile_kernels

(

NbnxmGpu *

nb

)

Compiles nbnxm kernels for OpenCL GPU given by mygpu.

With OpenCL, a call to this function must not precede nbnxm_gpu_init() (which also calls it).

Doing bFastGen means only the requested kernels are compiled, significantly reducing the total compilation time. If false, all OpenCL kernels are compiled.

A fatal error results if compilation fails.

Parameters

[in,out]

nb

Manages OpenCL non-bonded calculations; compiled kernels returned in deviceInfo members

Does not throw

void gmx::nbnxm_gpu_x_to_nbat_x	(	NbnxmGpu gmx_unused *	gpu_nbv,
		DeviceBuffer< RVec > gmx_unused	d_x,
		GpuEventSynchronizer gmx_unused *	xReadyOnDevice,
		AtomLocality gmx_unused	locality
	)

X buffer operations on GPU: performs conversion from rvec to nb format.

Processes all grids in a single fused kernel launch, using pre-stored launch parameters from gpu_nbv.

Parameters

[in,out]	gpu_nbv	The nonbonded data GPU structure.
[in]	d_x	Device-side coordinates in plain rvec format.
[in]	xReadyOnDevice	Event synchronizer indicating that the coordinates are ready in the device memory.
[in]	locality	Copy coordinates for local or non-local atoms.

static void gmx::nbnxm_kernel_cpu ( const PairlistSet &  pairlistSet, const NbnxmKernelSetup &  kernelSetup, nbnxm_atomdata_t *  nbat, const interaction_const_t &  ic, gmx::ArrayRef< const gmx::RVec >  shiftVectors, const gmx::StepWorkload &  stepWork, int  clearF, real *  vCoulomb, real *  vVdw, gmx_wallcycle *  wcycle  )

static

Dispatches the non-bonded N versus M atom cluster CPU kernels.

OpenMP parallelization is performed within this function. Energy reduction, but not force and shift force reduction, is performed within this function.

Parameters

[in]	pairlistSet	Pairlists with local or non-local interactions to compute
[in]	kernelSetup	The non-bonded kernel setup
[in,out]	nbat	The atomdata for the interactions
[in]	ic	Non-bonded interaction constants
[in]	shiftVectors	The PBC shift vectors
[in]	stepWork	Flags that tell what to compute
[in]	clearF	Enum that tells if to clear the force output buffer
[out]	vCoulomb	Output buffer for Coulomb energies
[out]	vVdw	Output buffer for Van der Waals energies
[in]	wcycle	Pointer to cycle counting data structure.

void gmx::nbnxm_put_on_grid_nonlocal	(	nonbonded_verlet_t *	nb_verlet,
		const gmx::DomdecZones &	zones,
		ArrayRef< const int32_t >	atomInfo,
		ArrayRef< const RVec >	x
	)

As nbnxm_put_on_grid, but for the non-local atoms.

with domain decomposition. Should be called after calling nbnxm_search_put_on_grid for the local atoms / home zone.

void gmx::nbnxmInsertNonlocalGpuDependency	(	NbnxmGpu gmx_unused *	nb,
		InteractionLocality gmx_unused	interactionLocality
	)

Sync the nonlocal stream with dependent tasks in the local queue.

As the point where the local stream tasks can be considered complete happens at the same call point where the nonlocal stream should be synced with the the local, this function records the event if called with the local stream as argument and inserts in the GPU stream a wait on the event on the nonlocal.

Parameters

[in]	nb	The nonbonded data GPU structure
[in]	interactionLocality	Local or NonLocal sync point

template<int subGroupSize, bool doPruneNBL, bool doCalcEnergies, enum ElecType elecType, enum VdwType vdwType, typename CommandGroupHandler >

static auto gmx::nbnxmKernel ( CommandGroupHandler  cgh, const Float4 *__restrict__  gm_xq, Float3 *__restrict__  gm_f, const Float3 *__restrict__  gm_shiftVec, Float3 *__restrict__  gm_fShift, float *__restrict__  gm_energyElec, float *__restrict__  gm_energyVdw, nbnxm_cj_packed_t *__restrict__  gm_plistCJPacked, const nbnxm_sci_t *__restrict__  gm_plistSci, const nbnxm_excl_t *__restrict__  gm_plistExcl, const Float2 *__restrict__  gm_ljComb, const int *__restrict__  gm_atomTypes, const Float2 *__restrict__  gm_nbfp, const Float2 *__restrict__  gm_nbfpComb, const float *__restrict__  gm_coulombTab, int *__restrict__  gm_sciHistogram, int *__restrict__  gm_sciCount, const int  numTypes, const float  rCoulombSq, const float  rVdwSq, const float  twoKRf, const float  ewaldBeta, const float  rlistOuterSq, const float  ewaldShift, const float  epsFac, const float  ewaldCoeffLJ_2, const float  cRF, const shift_consts_t  dispersionShift, const shift_consts_t  repulsionShift, const switch_consts_t  vdwSwitch, const float  rVdwSwitch, const float  ljEwaldShift, const float  coulombTabScale, const bool  calcShift  )

static

Main kernel for NBNXM.

static auto gmx::nbnxmKernelBucketSciSort ( const nbnxm_sci_t *__restrict__  gm_sci, const int *__restrict__  gm_sciCount, int *__restrict__  gm_sciOffset, nbnxm_sci_t *__restrict__  gm_sciSorted  )

static

SYCL bucket sci sort kernel.

Sorts sci in order from most to least neighbours, using the count sort algorithm

Unlike the cpu version of sci sort, this kernel uses counts which only contain pairs which have not been masked out, giving an ordering which more accurately represents the work which will be done in the non bonded force kernel. The counts themselves are generated in the prune kernel.

Parameters

gm_sci	Unsorted pair list.
gm_sciCount	Total number of sci with exactly i neighbours
gm_sciOffset	Exclusive prefix sum of gm_sciCount. gm_sciOffset[i] is the offset that the first sci with i neighbours will have in the sorted sci list. All other sci with i neighbours will be placed randomly in positions gm_sciOffset[i] to gm_sciOffset[i+1] exclusive.
gm_sciSorted	Sorted pair list.

template<int workGroupSize, int nElements>

static auto gmx::nbnxmKernelExclusivePrefixSum ( const int *__restrict__  gm_input, int *__restrict__  gm_output  )

static

SYCL exclusive prefix sum kernel for list sorting.

As of oneAPI 2024.1, oneapi::dpl::experimental::exclusive_scan_async for inputs <= 16384 elements simply launches a single work-group and uses sycl::joint_exclusive_scan. We have, somewhat arbitrary, input size of 8192, so we're fine replicating the same approach.

NVIDIA's CUB uses fancier approach ("Single-pass Parallel Prefix Scan with Decoupled Look-back"), but we are unlikely to need it here since this kernel is very small anyway.

Template Parameters

workGroupSize	Size of the (only) work-group.
nElements	Input array size; should be a multiple of workGroupSize.

Parameters

gm_input	Input data buffer, should contain nElements elements of type int.
gm_output	Output data buffer, should have enough space for nElements elements of type int.

Warning

This kernel should be launched with only a single work-group of size workGroupSize.

This kernel is inefficient for large inputs (oneDPL uses it with <= 16384 elements).

template<bool haveFreshList, PairlistType layoutType, typename CommandGroupHandler >

auto gmx::nbnxmKernelPruneOnly	(	CommandGroupHandler	cgh,
		const int	numSci,
		const int	numParts,
		const Float4 *__restrict__	gm_xq,
		const Float3 *__restrict__	gm_shiftVec,
		nbnxm_cj_packed_t *__restrict__	gm_plistCJPacked,
		const nbnxm_sci_t *__restrict__	gm_plistSci,
		unsigned int *__restrict__	gm_plistIMask,
		int *__restrict__	gm_rollingPruningPart,
		int *__restrict__	gm_sciHistogram,
		int *__restrict__	gm_sciCount,
		const float	rlistOuterSq,
		const float	rlistInnerSq
	)

Prune-only kernel for NBNXM.

template<KernelLayout kernelLayout, KernelCoulombType coulombType, VdwCutoffCheck vdwCutoffCheck, LJCombinationRule ljCombinationRule, InteractionModifiers vdwModifier, LJEwald ljEwald, EnergyOutput energyOutput>

void gmx::nbnxmKernelSimd	(	const NbnxmPairlistCpu &	pairlist,
		const nbnxm_atomdata_t &	nbat,
		const interaction_const_t &	ic,
		const rvec *	shift_vec,
		nbnxm_atomdata_output_t *	out
	)

The actual NBNxM SIMD kernel.

Template Parameters

kernelLayout	The kernel layout: either 2xMM or 4xM
coulombType	The type of Coulomb interaction
vdwCutoffCheck	Whether a separate check for the VdW cutoff is needed
ljCombinationRule	The combination rule for the LJ parameters
vdwModifier	The modifier for the LJ interactions
ljEwald	The type of LJ Ewald treatment, can be none
energyOutput	Which types of output are requested

Parameters

[in]	pairlist	The cluster pair list
[in]	nbat	Input data for atoms, including charges and LJ parameters
[in]	ic	The interaction constants
[in]	shift_vec	A list of PBC shift vectors
[in,out]	out	Struct for accumulating forces, energies and virial

static auto gmx::nbnxmKernelTransformXToXq ( Float4 *__restrict__  gm_xq, const Float3 *__restrict__  gm_x, const int *__restrict__  gm_atomIndex, const int *__restrict__  gm_numAtomsPerCell, const int *__restrict__  gm_cellToBin, int  numAtomsPerBin, int  gridBegin, int  numCellsMax, FusedXToXqGridParams  gridParams  )

static

SYCL kernel for transforming position coordinates from rvec to nbnxm layout.

Processes cells from multiple grids in a single kernel launch. itemIdx.get(0) covers atoms within a cell, itemIdx.get(1) maps to a global cell index across all grids. The grid membership of each cell is determined using gridParams: columnsPrefix[] holds the prefix sum of per-grid cell counts and binOffset[] the starting bin for each grid.

Parameters

[out]	gm_xq	Coordinates buffer in nbnxm layout.
[in]	gm_x	Coordinates buffer.
[in]	gm_atomIndex	Atom index mapping.
[in]	gm_numAtomsPerCell	Array of number of atoms per cell (all grids, stride numCellsMax).
[in]	gm_cellToBin	Array of bin indices per cell (all grids, stride numCellsMax).
[in]	numAtomsPerBin	Number of atoms per bin.
[in]	gridBegin	Index of first grid in gridset.
[in]	numCellsMax	Max cells per grid (stride for per-grid arrays).
[in]	gridParams	Per-grid parameters (prefix sums and bin offsets).

real gmx::nbnxmPairlistVolumeRadiusIncrease	(	bool	useGpu,
		real	atomDensity
	)

Returns the increase in pairlist radius when including volume of pairs beyond rlist.

Due to the cluster size the total volume of the pairlist is (much) more than 4/3*pi*rlist^3. This function returns the increase in radius required to match the volume of the pairlist including the atoms pairs that are beyond rlist.

Note

This routine does not know which cluster layout is used and assumes the most common one. Therefore this should only be used to estimates, not for setting a pair list buffer.

template<NbnxmKernelType kernelType>

void gmx::nbnxmRefPruneKernel	(	NbnxmPairlistCpu *	nbl,
		const nbnxm_atomdata_t *	nbat,
		ArrayRef< const RVec >	shiftvec,
		real	rlistInner
	)

Prune a single NbnxmPairlistCpu entry with distance rlistInner.

Reads a cluster pairlist nbl->ciOuter, nbl->cjOuter and writes all cluster pairs within rlistInner to nbl->ci, nbl->cj.

static bool gmx::nbnxmSimdSupported ( const MDLogger &  mdlog, const t_inputrec &  inputrec  )

static

Returns whether CPU SIMD support exists for the given inputrec.

If the return value is false, issue a warning to mdlog

static gmx_bool gmx::need_swap ( const t_swapcoords &  sc, SwapCoords::Impl *  s  )

static

Do we need to swap a molecule in any of the ion groups with a water molecule at this step?

From the requested and average molecule counts we determine whether a swap is needed at this time step.

bool gmx::needStateGpu ( SimulationWorkload  simulationWorkload )

inline

If StatePropagatorDataGpu object is needed.

Parameters

[in]

simulationWorkload

Simulation workload flags.

Returns

Whether the StatePropagatorDataGpu object is needed/was created for this run.

OptimisationResult gmx::nelderMead	(	const std::function< real(ArrayRef< const real >)> &	functionToMinimize,
		ArrayRef< const real >	initialGuess,
		real	minimumRelativeSimplexLength = 1e-8,
		int	maxSteps = 10'000
	)

Derivative-free downhill simplex optimisation.

Find a local minimum of an N-dimensional mapping using the downhill simplex algorithm by Nelder and Mead as described in

  Saša Singer and John Nelder (2009), Scholarpedia, 4(7):2928.
  doi:10.4249/scholarpedia.2928

Stops when the oriented simplex length is less than a constant factor times the initial lengths or when a maximum step size is reached.

For best performance pre-condition problem magnitudes to 1.

The following algorithm is implemented in this function 1 Define the N+1 vertices of the initial simplex The inital simplex is constructed from the initial guess and N additional vertices by adding 0.05 to the initial guess (or 0.0025 if the initial guess is the null vector) from the initial vertex (in line with usual implementations).

1a Sort vertices according to function value with the lowest function value first in order to minimize the function.

2 Calculate the centroid of the simplex as arithmetic mean of all vertices except the worst, .

3 Reflect the worst simplex vertex (the one with the highest function value) at the centroid to obtain a reflection point which lies outside the vertex.

3a Replace worst point with reflection point if reflection point function value is better than second worst point, but not better than best and go to 1a.

4 If the reflection point is better than all other points so far, attempt an expansion by calculating the expansion point at . Swap out the worst point in the vertex with the expansion point if better than reflection point, otherwise use the reflection point and go to 1a.

5 Attempt contraction, because reflection was not successful; . If the contraction point is better than the worst point, swap out worst point with contracted point and go to 1a.

6 Shrink the vertex. Replace all points except the best one with and go to 1a.

Parameters

[in]	functionToMinimize	function to be minimized
[in]	initialGuess	of coordinates
[in]	minimumRelativeSimplexLength	minimal oriented simplex length with respect to initial simplex
[in]	maxSteps	to run algorithm for

Returns

the lowest found function value and corresponding coordinates.

void gmx::niceHeader	(	TextWriter *	writer,
		const char *	fn,
		char	commentChar
	)

Prints creation time stamp and user information into a string as comments, and returns it.

Parameters

[out]	writer	Where to print the information.
[in]	fn	Name of the file being written; if nullptr, described as "unknown".
[in]	commentChar	Character to use as the starting delimiter for comments.

Exceptions

std::bad_alloc

if out of memory.

int gmx::nonbondedMtsFactor

(

const t_inputrec &

ir

)

Returns the interval in steps at which the non-bonded pair forces are calculated.

Note: returns 1 when multiple time-stepping is not activated.

template<typename T >

std::remove_const_t<T> gmx::norm

(

T *

v

)

Forward operations on C Array style vectors to C implementations.

Since vec.h and vectypes.h independently declare norm and norm2 in different namespaces, code that includes both headers but does not specify the namespace from which to use norm and norm2 cannot properly resolve overloads without the following helper templates.

Template Parameters

T	array element type (e.g. real, int, etc.)

Parameters

v	address of first vector element

Returns

magnitude or squared magnitude of vector

static void gmx::normalizeBlock ( AwhEnergyBlock *  block, const Bias &  bias  )

static

Normalizes block data for output.

Parameters

[in,out]	block	The block to normalize.
[in]	bias	The AWH bias.

static void gmx::normalizeFreeEnergyAndPmfSum ( std::vector< PointState > *  pointState )

static

Normalizes the free energy and PMF sum.

Parameters

[in]

pointState

The state of the points.

void gmx::normalizeSumPositiveValuesToUnity

(

ArrayRef< float >

data

)

Divide all values of a view by a constant so that the sum of all its positive values is one.

Note

Does nothing if there are no positive values

Parameters

[in,out]

data

the input data to be normalized

size_t gmx::numberOfExpectedDataItems

(

const MrcDensityMapHeader &

header

)

Return the number of density data items that are expected to follow this header.

Exceptions

InternalError

if the number of data items cannot be determined

Returns

the number of voxels

bool gmx::objectExists ( const hid_t  container, const char *  name  )

inlinenoexcept

Return whether object name exists in the given HDF5 container.

Parameters

[in]	container	Handle to container in which to check.
[in]	name	Name of object to look for.

Returns

True if the object exists, otherwise false.

hid_t gmx::openGroup	(	hid_t	container,
		const char *	name
	)

Open an existing HDF5 group.

Parameters

[in]	container	The ID of the container where the group is located, or should be created.
[in]	name	The name of the group.

Returns

the ID of the group.

Exceptions

H5mdError

If the group cannot be found.

FilePtr gmx::openLibraryFile	(	const std::filesystem::path &	filename,
		bool	bAddCWD = true,
		bool	bFatal = true
	)

Opens a library file for reading in an RAII-style FILE handle.

Works as findLibraryFile(), except that it opens the file and returns a file handle.

LogFilePtr gmx::openLogFile	(	const char *	lognm,
		bool	appendFiles
	)

Open the log file for writing/appending.

Exceptions

FileIOError

when the log file cannot be opened.

hid_t gmx::openOrCreateGroup	(	hid_t	container,
		const char *	name
	)

Open an existing HDF5 group or create it if it did not exist already.

NOTE: This function is deprecated and should not be used in new code.

Parameters

[in]	container	The ID of the container where the group is located, or should be created.
[in]	name	The name of the group.

Returns

the ID of the group.

Exceptions

H5mdError

If the group cannot be found or created.

static t_trxstatus* gmx::openTNG ( const std::filesystem::path &  name, const Selection &  sel, const gmx_mtop_t *  mtop  )

static

Method to open TNG file.

Only need extra method to open this kind of file as it may need access to a Selection sel, if it is valid. Otherwise atom indices will be taken from the topology mtop.

Parameters

[in]	name	Name of the output file.
[in]	sel	Reference to selection.
[in]	mtop	Pointer to topology, tested before that it is valid.

Todo:

Those should be methods in a replacement for t_trxstatus instead.

bool gmx::operator!=	(	const DensityFittingParameters &	lhs,
		const DensityFittingParameters &	rhs
	)

Check if two structs holding density fitting parameters are not equal.

Parameters

[in]	lhs	left hand side to be compared
[in]	rhs	right hand side to be compared

Returns

true if lhs is not equal rhs

template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>

constexpr bool gmx::operator!= ( const extents< LHS...> &  lhs, const extents< RHS...> &  rhs  )

noexcept

Check for non-equality.

Returns

true if extents are unequal

bool gmx::operator==	(	const DensityFittingParameters &	lhs,
		const DensityFittingParameters &	rhs
	)

Check if two structs holding density fitting parameters are equal.

Parameters

[in]	lhs	left hand side to be compared
[in]	rhs	right hand side to be compared

Returns

true if all elements in DensityFittingParameters are equal, else false

template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>

constexpr bool gmx::operator== ( const extents< LHS...> &  lhs, const extents< RHS...> &  rhs  )

noexcept

Comparison operator.

Returns

true if extents are equal

template<class T1 , class Policy1 , class T2 , class Policy2 >

bool gmx::operator==	(	const Allocator< T1, Policy1 > &	a,
		const Allocator< T2, Policy2 > &	b
	)

Return true if two allocators are identical.

True if they have identical policies that are defined to be always equal (which is generally true for a stateless policy). An allocation policy with state should typically define is_always_equal to std::false_type and provide a correct equality operator.

static void gmx::outputStartStructureIfWanted ( const gmx_mtop_t &  mtop, rvec *  x, PbcType  pbcType, const matrix  box  )

static

Outputs the initial structure to PDB file for debugging reasons.

Output the starting structure so that in case of multimeric channels the user can check whether we have the correct PBC image for all atoms. If this is not correct, the ion counts per channel will be very likely wrong.

template<typename Iterator , typename Callback >

std::vector<char> gmx::packBufferViaIterator	(	Iterator	begin,
		Iterator	end,
		std::vector< char > &&	packingBuffer,
		const size_t	maxStrLength,
		Callback	cStringFromIterator
	)

Pack a string buffer from a range of iterators and a callback function.

Caller that knows about their problem domain can pass in a buffer whose capacity meets that needed. Otherwise we fall back on the standard vector approach of resizing logarithmically

Registering a callback function avoids the H5md interface adding overloads and explicit specializations for multiple string types and multiple collection types

Template Parameters

Iterator	The type of the iterator to write.
Callback	The type of the callback function to convert iterator to C-string.

Parameters

[in]	begin	The beginning iterator of the data to write.
[in]	end	The ending iterator of the data to write.
[in]	packingBuffer	The buffer to write the strings into.
[in]	maxStrLength	The maximum length of the strings in the attribute.
[in]	cStringFromIterator	The callback function to convert iterator to C-string.

Returns

The packed buffer containing the strings.

std::size_t gmx::pageSize

(

)

Return the memory page size on this system.

Implements the "construct on first use" idiom to avoid the static initialization order fiasco where a possible static page-aligned container would be initialized before the alignment variable was.

Note that thread-safety is guaranteed by the C++11 language standard.

void gmx::parrinellorahman_pcoupl	(	const MDLogger &	mdlog,
		int64_t	step,
		const PressureCouplingOptions &	pressureCouplingOptions,
		const tensor	deform,
		real	couplingTimePeriod,
		const tensor	pres,
		const tensor	box,
		tensor	box_rel,
		tensor	boxv,
		Matrix3x3 *	M,
		Matrix3x3 *	mu
	)

Calculate the change in box vectors due to Parrinello-Rahman pressure coupling.

Parameters

[in]	mdlog	Log file for warning when pressure change is large
[in]	step	The MD step count for the above warning
[in]	pressureCouplingOptions	The pressure-coupling options
[in]	deform	The matrix describing any box deformation
[in]	couplingTimePeriod	The period between changes to the pressure coupling
[in]	pres	The current pressure
[in]	box	The simulation box vectors
[in]	box_rel	The relative box vectors
[in]	boxv	The simulation box vector velocity for Parrinello-Rahman coupling
[out]	M	The scaling factor for particle velocities
[out]	mu	The scaling factor for box vectors

This doesn't do any coordinate updating. It just integrates the box vector equations from the calculated acceleration due to pressure difference. We also compute the tensor M which is used in update to couple the particle coordinates to the box vectors.

We also do NOT update the box vectors themselves here, since we need them for shifting later. It is instead done last in the update routines.

In Nose and Klein (Mol.Phys 50 (1983) no 5., p 1055) this is given as

       -1    .           .     -1

M_nk = (h') * (h' * h + h' h) * h

with the dots denoting time derivatives, apostrophes denoting transposition, and h is the transformation from the scaled frame to the real frame, i.e. the TRANSPOSE of the box. This also goes for the pressure and M tensors - they are transposed relative to ours. Our equation thus becomes:

             -1       .    .           -1

M_gmx = M_nk' = b * (b * b' + b * b') * b'

where b is the gromacs box matrix. Our box accelerations are given by

.. .. b = vol/W inv(box') * (P-ref_P) (=h')

template<typename ValueType , int NumExpectedValues>

static std::optional<std::array<ValueType, NumExpectedValues> > gmx::parsedArrayFromInputString ( const std::string &  str )

inlinestatic

Convert a string into an array of values.

Template Parameters

ValueType	array element type to convert into
NumExpectedValues	number of values of the array

Returns

an array containing the converted string, optionally null if the white-space stripped string is empty

Exceptions

InvalidInputError	if splitting the string at whitespaces does not result in NumExpectedValues or zero substrings
InvalidInputError	if conversion of any of the NumExpectedValues substrings of the splitted input string fails

Converts a string into an array of type ValueType with exactly NumExpectedValues.

No result is returned if the string is empty or contains only whitespace .

static std::vector<int> gmx::parseGpuDeviceIdentifierList ( const std::string &  gpuIdString )

static

Parse a GPU ID specifier string into a container.

Parameters

[in]

gpuIdString

String like "013" or "0,1,3" typically supplied by the user. Must contain only unique decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is acceptable (and required to specify a single ID that is larger than 9).

Returns

A vector of numeric IDs extracted from gpuIdString.

Exceptions

std::bad_alloc

If out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',').

std::vector< int > gmx::parseUserGpuIdString

(

const std::string &

gpuIdString

)

Parse a GPU ID specifier string into a container describing device IDs exposed to the run.

Parameters

[in]

gpuIdString

String like "013" or "0,1,3" typically supplied by the user to mdrun -gpu_id. Must contain only unique decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is acceptable (and required to specify a single ID that is larger than 9).

Returns

A vector of unique GPU IDs.

Exceptions

std::bad_alloc

If out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',') or if identifiers are duplicated in the specifier list.

std::vector< int > gmx::parseUserTaskAssignmentString

(

const std::string &

gpuIdString

)

Parse a GPU ID specifier string into a container describing device ID to task mapping.

Parameters

[in]

gpuIdString

String like "0011" or "0,0,1,1" typically supplied by the user to mdrun -gputasks. Must contain only decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is acceptable (and required to specify a single ID that is larger than 9).

Returns

A vector of GPU IDs.

Exceptions

std::bad_alloc

If out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',').

static EwaldExclusionType gmx::pickNbnxmKernelCpuSimdExclusion ( const gmx_hw_info_t gmx_unused &  hardwareInfo )

static

Returns the most suitable CPU SIMD kernel exclusion type.

Environment variables GMX_NBNXM_EWALD_TABLE and GMX_NBNXM_EWALD_ANALYTICAL override all heuristics below.

Since table lookup's don't parallelize with SIMD, analytical will probably always be faster for a SIMD width of 8 or more. With FMA analytical is sometimes faster for a width if 4 as well. In single precision, this is faster on Bulldozer. On AMD Zen1, tabulated Ewald kernels are faster on all 4 combinations of single or double precision and 128 or 256-bit AVX2.

static NbnxmKernelType gmx::pickNbnxmKernelCpuSimdType ( const t_inputrec &  inputrec, const gmx_hw_info_t gmx_unused &  hardwareInfo  )

static

Returns the most suitable CPU SIMD kernel type.

Environment variables GMX_NBNXM_SIMD_4XN and GMX_NBNXM_SIMD_2XNN take priority. Then, as long as both 2x(N+N) and 4xN kernels are built, we choose between them. This is based on the SIMD acceleration choice and CPU information detected at runtime.

4xN calculates more (zero) interactions, but has less pair-search work and much better kernel instruction scheduling.

Up till now we have only seen that on Intel Sandy/Ivy Bridge, which doesn't have FMA, both the analytical and tabulated Ewald kernels have similar pair rates for 4x8 and 2x(4+4), so we choose 2x(4+4) because it results in significantly fewer pairs. For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4), 10% with HT, 50% without HT. As we currently don't detect the actual use of HT, use 4x8 to avoid a potential performance hit. On Intel Haswell 4x8 is always faster.

void gmx::placeCoordinatesWithCOMInBox	(	const PbcType &	pbcType,
		UnitCellType	unitCellType,
		CenteringType	centerType,
		const matrix	box,
		ArrayRef< RVec >	x,
		const gmx_mtop_t &	mtop,
		COMShiftType	comShiftType
	)

Moves collection of atoms along the center of mass into a box.

This ensures that the centre of mass (COM) of a molecule is placed within a predefined coordinate space (usually a simulation box).

Parameters

[in]	pbcType	What kind of PBC are we handling today.
[in]	unitCellType	Kind of unitcell used for the box.
[in]	centerType	How atoms should be centered.
[in]	box	The currently available box to place things into.
[in,out]	x	View in coordinates to shift.
[in]	mtop	Topology with residue and molecule information.
[in]	comShiftType	Whether residues or molecules are shifted.

static float gmx::pmeForceCorrection ( float  z2 )

inlinestatic

Calculate the force correction due to PME analytically in float.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on force

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::pmeForceCorrection ( double  z2 )

inlinestatic

Calculate the force correction due to PME analytically in double.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on force

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::pmeForceCorrectionSingleAccuracy ( double  z2 )

inlinestatic

Force correction due to PME in double, but with single accuracy.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on force

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::pmeGpuWaitAndReduce ( gmx_pme_t *  pme, const PmeStepWorkload &  stepWork, gmx_wallcycle *  wcycle, ForceWithVirial *  forceWithVirial, gmx_enerdata_t *  enerd, const real  lambdaQ  )

static

Blocks until PME GPU tasks are completed, and gets the output forces and virial/energy (if they were to be computed).

Parameters

[in]	pme	The PME data structure.
[in]	stepWork	The required work for this simulation step
[in]	wcycle	The wallclock counter.
[out]	forceWithVirial	The output force and virial
[out]	enerd	The output energies
[in]	lambdaQ	The Coulomb lambda to use when calculating the results.

static float gmx::pmePotentialCorrection ( float  z2 )

inlinestatic

Calculate the potential correction due to PME analytically in float.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on potential.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::pmePotentialCorrection ( double  z2 )

inlinestatic

Calculate the potential correction due to PME analytically in double.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on potential.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::pmePotentialCorrectionSingleAccuracy ( double  z2 )

inlinestatic

Potential correction due to PME in double, but with single accuracy.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on potential.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static int gmx::pointDistanceAlongAxis ( const GridAxis &  axis, double  x, double  x0  )

static

Returns the point distance between from value x to value x0 along the given axis.

Note that the returned distance may be negative or larger than the number of points in the axis. For a periodic axis, the distance is chosen to be in [0, period), i.e. always positive but not the shortest one.

Parameters

[in]	axis	BiasGrid axis.
[in]	x	From value.
[in]	x0	To value.

Returns

(x - x0) in number of points.

bool gmx::pointsAlongLambdaAxis	(	const BiasGrid &	grid,
		int	pointIndex1,
		int	pointIndex2
	)

Checks whether two points are along a free energy lambda state axis.

Parameters

[in]	grid	The grid.
[in]	pointIndex1	Grid point index of the first point.
[in]	pointIndex2	Grid point index of the second point.

Returns

true if the two points are along a free energy lambda state axis.

bool gmx::pointsHaveDifferentLambda	(	const BiasGrid &	grid,
		int	pointIndex1,
		int	pointIndex2
	)

Checks whether two points are different in the free energy lambda state dimension (if any).

Parameters

[in]	grid	The grid.
[in]	pointIndex1	Grid point index of the first point.
[in]	pointIndex2	Grid point index of the second point.

Returns

true if the two points have different lambda values.

template<typename T >

T gmx::power12

(

T

x

)

calculate x^12

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^12

template<typename T >

T gmx::power3

(

T

x

)

calculate x^3

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^3

template<typename T >

T gmx::power4

(

T

x

)

calculate x^4

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^4

template<typename T >

T gmx::power5

(

T

x

)

calculate x^5

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^5

template<typename T >

T gmx::power6

(

T

x

)

calculate x^6

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^6

std::unique_ptr< Awh > gmx::prepareAwhModule	(	FILE *	fplog,
		const t_inputrec &	inputRecord,
		t_state *	stateGlobal,
		const MpiComm &	mpiComm,
		const gmx_multisim_t *	multiSimRecord,
		bool	startingFromCheckpoint,
		bool	usingShellParticles,
		const std::string &	biasInitFilename,
		pull_t *	pull_work
	)

Makes an Awh and prepares to use it if the user input requests that.

Restores state from history in checkpoint if needed.

Parameters

[in,out]	fplog	General output file, normally md.log, can be nullptr.
[in]	inputRecord	General input parameters (as set up by grompp).
[in]	stateGlobal	A pointer to the global state structure.
[in]	mpiComm	The MPI communicator for intra-simulation communication.
[in]	multiSimRecord	Multi-sim handler
[in]	startingFromCheckpoint	Whether the simulation is starting from a checkpoint
[in]	usingShellParticles	Whether the user requested shell particles (which is unsupported)
[in]	biasInitFilename	Name of file to read PMF and target from.
[in,out]	pull_work	Pointer to a pull struct which AWH will couple to, has to be initialized, is assumed not to change during the lifetime of the Awh object.

Returns

An initialized Awh module, or nullptr if none was requested.

Exceptions

InvalidInputError

If another active module is not supported.

void gmx::prepareLogAppending

(

FILE *

fplog

)

Prepare to use the open log file when appending.

Does not throw.

static void gmx::prepareRerunState ( const t_trxframe &  rerunFrame, t_state *  globalState, bool  constructVsites, const VirtualSitesHandler *  vsite  )

static

Copy the state from rerunFrame to globalState and, if requested, construct vsites.

Parameters

[in]	rerunFrame	The trajectory frame to compute energy/forces for
[in,out]	globalState	The global state container
[in]	constructVsites	When true, vsite coordinates are constructed
[in]	vsite	Vsite setup, can be nullptr when constructVsites = false

template<PressureCoupling pressureCouplingType>

void gmx::pressureCouplingCalculateScalingMatrix	(	FILE *	fplog,
		int64_t	step,
		const PressureCouplingOptions &	pressureCoupling,
		int64_t	ld_seed,
		real	ensembleTemperature,
		real	delta_t,
		const tensor	pres,
		const matrix	box,
		const matrix	force_vir,
		const matrix	constraint_vir,
		Matrix3x3 *	mu,
		double *	baros_integral
	)

Calculate the pressure coupling scaling matrix.

Used by Berendsen and C-Rescale pressure coupling, this function computes the current value of the scaling matrix. The template parameter determines the pressure coupling algorithm.

template<PressureCoupling pressureCouplingType>

void gmx::pressureCouplingScaleBoxAndCoordinates	(	const PressureCouplingOptions &	pressureCoupling,
		const tensor	deform,
		const ivec *	nFreeze,
		const Matrix3x3 &	mu,
		matrix	box,
		matrix	box_rel,
		int	start,
		int	nr_atoms,
		ArrayRef< RVec >	x,
		ArrayRef< RVec >	v,
		ArrayRef< const unsigned short >	cFREEZE,
		t_nrnb *	nrnb,
		bool	scaleCoordinates
	)

Scale the box and coordinates.

Used by Berendsen and C-Rescale pressure coupling, this function scales the box, the positions, and the velocities (C-Rescale only) according to the scaling matrix mu. The template parameter determines the pressure coupling algorithm.

static void gmx::print_ionlist ( SwapCoords::Impl *  s, double  time, const char  comment[]  )

static

Prints output to CompEL output file.

Prints to swap output file how many ions are in each compartment, where the centers of the split groups are, and how many ions of each type passed the channels.

static void gmx::print_ionlist_legend ( const t_inputrec *  ir, SwapCoords::Impl *  s, const gmx_output_env_t *  oenv  )

static

Print the legend to the swap output file.

Also print the initial values of ion counts and position of split groups.

void gmx::print_replica_exchange_statistics	(	FILE *	fplog,
		gmx_repl_ex_t	re
	)

Prints replica exchange statistics to the log file.

Should only be called on the main ranks

void gmx::print_resall	(	FILE *	out,
		gmx::ArrayRef< const PreprocessResidue >	rtpDBEntry,
		const PreprocessingAtomTypes &	atype
	)

Print out database.

Parameters

[in]	out	File to write to.
[in]	rtpDBEntry	Database to write out.
[in]	atype	Atom type information.

void gmx::printBinaryInformation	(	FILE *	fp,
		const IProgramContext &	programContext,
		const BinaryInformationSettings &	settings
	)

Print basic information about the executable with custom settings.

Parameters

	fp	Where to print the information to.
[in]	programContext	Program information object to use.
[in]	settings	Specifies what to print.

See Also

BinaryInformationSettings

void gmx::printBinaryInformation	(	TextWriter *	writer,
		const IProgramContext &	programContext,
		const BinaryInformationSettings &	settings
	)

Print basic information about the executable with custom settings.

Needed to read the members without otherwise unnecessary accessors.

Parameters

[out]	writer	Where to print the information.
[in]	programContext	Program information object to use.
[in]	settings	Specifies what to print.

Exceptions

std::bad_alloc

if out of memory.

See Also

BinaryInformationSettings

static std::string gmx::printMissingInteractionsMolblock ( const MpiComm &  mpiComm, const gmx_domdec_t &  dd, const gmx_reverse_top_t &  rt, const char *  moltypename, const reverse_ilist_t &  ril, const Range< int > &  atomRange, const int  numAtomsPerMolecule, const int  numMolecules, const InteractionDefinitions &  idef  )

static

Help print error output when interactions are missing in a molblock.

Note

This function needs to be called on all ranks (contains a global summation)

void gmx::printNbnxmPressureError	(	const MDLogger &	mdlog,
		const t_inputrec &	inputrec,
		const gmx_mtop_t &	mtop,
		real	effectiveAtomDensity,
		const PairlistParams &	listParams
	)

Prints an estimate of the error in the pressure due to missing interactions.

The NBNxM algorithm tolerates a few missing pair interactions. Missing pair interactions will lead to a systematic overestimates of the pressure when dispersion forces dominate at the cut-off distance. This routine prints an overestimate of the error in the average pressure.

Parameters

[in,out]	mdlog	MD logger
[in]	inputrec	The input parameter record
[in]	mtop	The global topology
[in]	effectiveAtomDensity	The effective atom density of the system
[in]	listParams	The list setup parameters

static bool gmx::processCycles ( FILE *  fp_err, const MDLogger &  mdlog, const double  cycles, const int64_t  step, const bool  isInLastStage, pme_setup_t *  set  )

static

Checks the cycles and adds them to *set.

Returns

whether we should increase the number of stages by 1.

int gmx::processExceptionAtExitForCommandLine

(

const std::exception &

ex

)

Handles an exception and deinitializes after initForCommandLine.

Parameters

[in]

ex

Exception that is the cause for terminating the program.

Returns

Return code to return from main().

This method should be called as the last thing before terminating the program because of an exception. See processExceptionAtExit() for details. Additionally this method undoes the work done by initForCommandLine.

Does not throw.

PreprocessingAtomTypes gmx::read_atype

(

const std::filesystem::path &

ffdir

)

Read atom types into database.

Parameters

[in]

ffdir

Force field directory.

Returns

Atom type database.

void gmx::read_checkpoint_part_and_step	(	const std::filesystem::path &	filename,
		int *	simulation_part,
		int64_t *	step
	)

Read simulation step and part from a checkpoint file.

Used by tune_pme to handle tuning with a checkpoint file as part of the input.

Parameters

[in]	filename	Name of checkpoint file
[out]	simulation_part	The part of the simulation that wrote the checkpoint
[out]	step	The final step number of the simulation that wrote the checkpoint

Exceptions

FileIOError

if the file cannot be opened

CheckpointHeaderContents gmx::read_checkpoint_simulation_part_and_filenames	(	const std::filesystem::path &	filename,
		std::vector< gmx_file_position_t > *	outputfiles
	)

Return header information from an open checkpoint file.

Used by mdrun to handle restarts

Parameters

[in]	filename	Name of checkpoint file
[out]	outputfiles	Container of output file names from the previous run.

void gmx::read_checkpoint_trxframe	(	const std::filesystem::path &	filename,
		t_trxframe *	fr
	)

Read everything that can be stored in t_trxframe from a checkpoint file.

Parameters

[in]	filename	Name of checkpoint file from which to read
[out]	fr	Trajectory frame into which to read

int gmx::read_h_db	(	const std::filesystem::path &	ffdir,
		std::vector< MoleculePatchDatabase > *	globalPatches
	)

Read the databse from hdb file(s).

Parameters

[in]	ffdir	Directory for files.
[in,out]	globalPatches	The database for atom modifications to populate.

Returns

The number of modifications stored.

static std::unique_ptr<gmx_mtop_t> gmx::read_mtop_for_tng ( const char *  tps_file, const char *  input_file, const char *  output_file  )

static

Read a full molecular topology if useful and available.

If the input trajectory file is not in TNG format, and the output file is in TNG format, then we want to try to read a full topology (if available), so that we can write molecule information to the output file. The full topology provides better molecule information than is available from the normal t_topology data used by GROMACS tools.

Also, the t_topology is only read under (different) particular conditions. If both apply, then a .tpr file might be read twice. Trying to fix this redundancy while trjconv is still an all-purpose tool does not seem worthwhile.

Because of the way gmx_prepare_tng_writing is implemented, the case where the input TNG file has no molecule information will never lead to an output TNG file having molecule information. Since molecule information will generally be present if the input TNG file was written by a GROMACS tool, this seems like reasonable behaviour.

int gmx::read_ter_db	(	const std::filesystem::path &	ffdir,
		char	ter,
		std::vector< MoleculePatchDatabase > *	tbptr,
		PreprocessingAtomTypes *	atype
	)

Read database for N&C terminal modifications.

Parameters

[in]	ffdir	Directory for files.
[in]	ter	Which terminal side to read.
[in,out]	tbptr	Database for terminii entry to populate.
[in]	atype	Database for atomtype information.

Returns

Number of entries entered into database.

template<typename ValueType >

void gmx::readKvtCheckpointValue	(	compat::not_null< ValueType * >	value,
		std::string_view	name,
		std::string_view	identifier,
		const KeyValueTreeObject &	kvt
	)

Read to a key-value-tree value used for checkpointing.

Template Parameters

ValueType

Parameters

[in]	value	the value to be checkpointed
[in]	name	name of the value to be checkpointed
[in]	identifier	uniquely identifies the module that is checkpointing typically the module name
[in]	kvt	the key value tree to read from

Exceptions

InternalError

if kvt does not contain requested value.

Note

Triggers assertion if value type is not correct.

template void gmx::readKvtCheckpointValue	(	compat::not_null< std::int64_t * >	value,
		std::string_view	name,
		std::string_view	identifier,
		const KeyValueTreeObject &	kvt
	)

Read to a key-value-tree value used for checkpointing.

Template Parameters

ValueType

Parameters

[in]	value	the value to be checkpointed
[in]	name	name of the value to be checkpointed
[in]	identifier	uniquely identifies the module that is checkpointing typically the module name
[in]	kvt	the key value tree to read from

Exceptions

InternalError

if kvt does not contain requested value.

Note

Triggers assertion if value type is not correct.

template void gmx::readKvtCheckpointValue	(	compat::not_null< real * >	value,
		std::string_view	name,
		std::string_view	identifier,
		const KeyValueTreeObject &	kvt
	)

Read to a key-value-tree value used for checkpointing.

Template Parameters

ValueType

Parameters

[in]	value	the value to be checkpointed
[in]	name	name of the value to be checkpointed
[in]	identifier	uniquely identifies the module that is checkpointing typically the module name
[in]	kvt	the key value tree to read from

Exceptions

InternalError

if kvt does not contain requested value.

Note

Triggers assertion if value type is not correct.

void gmx::readResidueDatabase	(	const std::filesystem::path &	resdb,
		std::vector< PreprocessResidue > *	rtpDBEntry,
		PreprocessingAtomTypes *	atype,
		t_symtab *	tab,
		const gmx::MDLogger &	logger,
		bool	bAllowOverrideRTP
	)

Read in database, append to exisiting.

Parameters

[in]	resdb	Name of database file.
[in,out]	rtpDBEntry	Database to populate.
[in,out]	atype	Atomtype information.
[in,out]	tab	Symbol table for names.
[in]	logger	MDLogger interface.
[in]	bAllowOverrideRTP	If entries can be overwritten in the database.

static void gmx::readUserPmfAndTargetDistribution ( ArrayRef< const DimParams >  dimParams, const BiasGrid &  grid, const std::string &  filename, int  numBias, int  biasIndex, std::vector< PointState > *  pointState  )

static

Initializes the PMF and target with data read from an input table.

Parameters

[in]	dimParams	The dimension parameters.
[in]	grid	The grid.
[in]	filename	The filename to read PMF and target from.
[in]	numBias	Number of biases.
[in]	biasIndex	The index of the bias.
[in,out]	pointState	The state of the points in this bias.

static float gmx::reduce ( float  a )

inlinestatic

Return sum of all elements in float variable (i.e., the variable itself).

Parameters

a	variable to reduce/sum.

Returns

The argument variable itself.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::reduce ( double  a )

inlinestatic

Return sum of all elements in double variable (i.e., the variable itself).

Parameters

a	variable to reduce/sum.

Returns

The argument variable itself.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<PairlistType pairlistType>

static __device__ void gmx::reduceEnergyWarpShuffle ( float  localLJ, float  localEl, float *  gm_LJ, float *  gm_El, int  tidx  )

inlinestatic

Energy reduction kernel for regular nbnxm kernels.

Only works for power of two array sizes.

template<bool calculateShift, PairlistType pairlistType>

static __device__ void gmx::reduceForceI ( AmdPackedFloat3 *  input, float3 *  result, const int  tidxi, const int  tidxj, const int  tidx, const int  sci, float3 *  fShift, const int  shiftBase  )

inlinestatic

Reduce i forces.

Only works for array sizes that are power of 2. Depending on architecture, reduce using DPP shuffles for main forces or atomics. Final accumulation is always done using atomics, while shift forces are using DPP shuffles for non CDNA architectures.

template<bool useShuffleReduction, int subGroupSize, typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >

static void gmx::reduceForceIAndFShift ( sycl::local_ptr< float >  sm_buf, const FCiBufferWrapperX &  fCiBufX, const FCiBufferWrapperY &  fCiBufY, const FCiBufferWrapperZ &  fCiBufZ, const bool  calcFShift, const sycl::nd_item< 3 >  itemIdx, const int  tidxi, const int  tidxj, const int  sci, const int  shift, sycl::global_ptr< Float3 >  a_f, sycl::global_ptr< Float3 >  a_fShift  )

inlinestatic

Final i-force reduction.

Reduce c_nbnxmGpuNumClusterPerSupercluster i-force components stored in fCiBuf[] accumulating atomically into a_f. If calcFShift is true, further reduce shift forces and atomically accumulate into a_fShift.

This implementation works only with power of two array sizes.

template<typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >

static void gmx::reduceForceIAndFShiftGeneric ( sycl::local_ptr< float >  sm_buf, const FCiBufferWrapperX &  fCiBufX, const FCiBufferWrapperY &  fCiBufY, const FCiBufferWrapperZ &  fCiBufZ, const bool  calcFShift, const sycl::nd_item< 3 >  itemIdx, const int  tidxi, const int  tidxj, const int  sci, const int  shift, sycl::global_ptr< Float3 >  a_f, sycl::global_ptr< Float3 >  a_fShift  )

inlinestatic

Local memory-based i-force reduction.

Note that this reduction is unoptimized and some of the barrier synchronization used could be avoided on >=8-wide architectures.

template<int numShuffleReductionSteps, typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >

static std::enable_if_t<numShuffleReductionSteps != 1, void> gmx::reduceForceIAndFShiftShuffles ( const FCiBufferWrapperX &  fCiBufX, const FCiBufferWrapperY &  fCiBufY, const FCiBufferWrapperZ &  fCiBufZ, const bool  calcFShift, const sycl::nd_item< 3 >  itemIdx, const int  tidxi, const int  tidxj, const int  sci, const int  shift, sycl::global_ptr< Float3 >  a_f, sycl::global_ptr< Float3 >  a_fShift  )

inlinestatic

Shuffle-based i-force reduction.

We need to reduce c_clSize values spaced c_clSize threads apart (hardware threads are consecutive for tidxi, have stride c_clSize for tidxj).

We can have up to three reduction steps done with shuffles:

One step (e.g, Intel iGPU, c_clSize == 4, subGroupSize == 8): handled in a separate specialization. Two steps (e.g., NVIDIA, c_clSize == 8, subGroupSize == 32): after two shuffle reduction steps, we do atomicFetchAdd from each sub-group. Three steps (e.g., AMD CDNA, c_clSize == 8, subGroupSize == 64): similar to the two-step approach, but we have two times less atomicFetchAdd's.

template<int numShuffleReductionSteps, typename FCiBufferWrapperX , typename FCiBufferWrapperY , typename FCiBufferWrapperZ >

static std::enable_if_t<numShuffleReductionSteps == 1, void> gmx::reduceForceIAndFShiftShuffles ( const FCiBufferWrapperX &  fCiBufX, const FCiBufferWrapperY &  fCiBufY, const FCiBufferWrapperZ &  fCiBufZ, const bool  calcFShift, const sycl::nd_item< 3 >  itemIdx, const int  tidxi, const int  tidxj, const int  sci, const int  shift, sycl::global_ptr< Float3 >  a_f, sycl::global_ptr< Float3 >  a_fShift  )

inlinestatic

reduceForceIAndFShiftShuffles specialization for single-step reduction (e.g., Intel iGPUs).

We have three components to reduce, but only one reduction step, so it is not possible to gather the components in fx of different threads, like we do with 2 and more reduction steps.

Therefore, first even threads handle X and odd threads handle Y; then, even threads additionally handle Z. This also requires the second fShift buffer register.

After one step of reduction using shuffles is complete, we use atomicAdd to accumulate the results in the global memory. That causes a lot of atomic operations on a single memory location, which is poorly handled by some hardware (e.g., Intel Gen9-11 and Xe LP). This can be remediated by using local memory reduction after shuffles, but that's a TODO.

template<PairlistType pairlistType, bool calculateShift>

static __device__ float3 gmx::reduceForceIAtomics ( AmdPackedFloat3  input, float3 *  result, const int  tidxj, const int  aidx  )

inlinestatic

Lowest level i force reduction.

Only works for array sizes that are power of 2. Uses atomic operations instead of shuffles.

template<PairlistType pairlistType>

static __device__ float gmx::reduceForceIWarpShuffle ( AmdPackedFloat3  f, const int  tidxi, const int  tidxj  )

inlinestatic

Lowest level i force reduction.

Only works for array sizes that are power of 2. Uses AMD DPP instructions to avoid use of atomic operations.

static void gmx::reduceForceJGeneric ( sycl::local_ptr< float >  sm_buf, Float3  f, const sycl::nd_item< 3 > &  itemIdx, const int  tidxi, const int  tidxj, const int  aidx, sycl::global_ptr< Float3 >  a_f  )

inlinestatic

Reduce c_clSize j-force components using local memory and atomically accumulate into a_f.

c_clSize consecutive threads hold the force components of a j-atom which we reduced in cl_Size steps using shift and atomically accumulate them into a_f.

TODO: implement binary reduction flavor for the case where cl_Size is power of two.

static void gmx::reduceForceJShuffle ( Float3  f, const sycl::nd_item< 3 > &  itemIdx, const int  tidxi, const int  aidx, sycl::global_ptr< Float3 >  a_f  )

inlinestatic

Reduce c_clSize j-force components using shifts and atomically accumulate into a_f.

c_clSize consecutive threads hold the force components of a j-atom which we reduced in log2(cl_Size) steps using shift and atomically accumulate them into a_f.

template<PairlistType pairlistType>

static __device__ float gmx::reduceForceJWarpShuffle ( AmdPackedFloat3  f, const int  tidxi  )

inlinestatic

Reduce c_clSize j-force components using AMD DPP instruction.

c_clSize consecutive threads hold the force components of a j-atom which we reduced in log2(cl_Size) steps using shift

Note: This causes massive amount of spills with the tabulated kernel on gfx803 using ROCm 5.3. We don't disable it only for the tabulated kernel as the analytical is the default anyway.

static float gmx::reduceIncr4ReturnSum ( float *  m, float  v0, float  v1, float  v2, float  v3  )

inlinestatic

Add each float to four consecutive memory locations, return sum.

Parameters

m	Pointer to memory where four floats should be incremented
v0	float to be added to m[0]
v1	float to be added to m[1]
v2	float to be added to m[2]
v3	float to be added to m[3]

Returns

v0+v1+v2+v3.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::reduceIncr4ReturnSum ( double *  m, double  v0, double  v1, double  v2, double  v3  )

inlinestatic

Add each double to four consecutive memory locations, return sum.

Parameters

m	Pointer to memory where four floats should be incremented
v0	double to be added to m[0]
v1	double to be added to m[1]
v2	double to be added to m[2]
v3	double to be added to m[3]

Returns

v0+v1+v2+v3.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

std::vector< real > gmx::removeEmbeddedClassicalCharges	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices,
		const std::vector< bool > &	isEmbeddedBlock,
		real	refQ,
		const MDLogger &	logger,
		WarningHandler *	wi
	)

Removes classical charges from embedded atoms and virtual sites.

Also removes charges from virtual sites built from embedded atoms only.

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms
[in]	isEmbeddedBlock	vector with flags for embedded atom-containing blocks
[in]	refQ	reference total charge of the system, used for warning messages
[in]	logger	MDLogger for logging info about modifications
[in]	wi	WarningHandler for handling warnings

Returns

vector of point charges for all atoms in the modified topology

static void gmx::removeExtraSolventMolecules ( t_atoms *  atoms, std::vector< RVec > *  x, std::vector< RVec > *  v, int  numberToRemove  )

static

Removes a given number of solvent residues.

Parameters

[in,out]	atoms	Solvent atoms.
[in,out]	x	Solvent positions.
[in,out]	v	Solvent velocities (can be empty).
[in]	numberToRemove	Number of residues to remove.

This function is called last in the process of creating the solvent box, so it does not operate on the exclusion radii, as no code after this needs them.

static void gmx::removeSolventBoxOverlap ( t_atoms *  atoms, std::vector< RVec > *  x, std::vector< RVec > *  v, std::vector< real > *  r, const t_pbc &  pbc  )

static

Removes overlap of solvent atoms across the edges.

Parameters

[in,out]	atoms	Solvent atoms.
[in,out]	x	Solvent positions.
[in,out]	v	Solvent velocities (can be empty).
[in,out]	r	Solvent exclusion radii.
[in]	pbc	PBC information.

Solvent residues that lay on the edges that do not touch the origin are removed if they overlap with other solvent atoms across the PBC. This is done in this way as the assumption is that the input solvent configuration is already equilibrated, and so does not contain any undesirable overlap. The only overlap that should be removed is caused by cutting the box in half in replicateSolventBox() and leaving a margin of solvent outside those box edges; these atoms can then overlap with those on the opposite box edge in a way that is not part of the pre-equilibrated configuration.

static void gmx::removeSolventOutsideShell ( t_atoms *  atoms, std::vector< RVec > *  x_solvent, std::vector< RVec > *  v_solvent, std::vector< real > *  r, const t_pbc &  pbc, const std::vector< RVec > &  x_solute, real  rshell  )

static

Remove all solvent molecules outside a give radius from the solute.

Parameters

[in,out]	atoms	Solvent atoms.
[in,out]	x_solvent	Solvent positions.
[in,out]	v_solvent	Solvent velocities.
[in,out]	r	Atomic exclusion radii.
[in]	pbc	PBC information.
[in]	x_solute	Solute positions.
[in]	rshell	The radius outside the solute molecule.

static void gmx::removeSolventOverlappingWithSolute ( t_atoms *  atoms, std::vector< RVec > *  x, std::vector< RVec > *  v, std::vector< real > *  r, const t_pbc &  pbc, const std::vector< RVec > &  x_solute, const std::vector< real > &  r_solute  )

static

Removes solvent molecules that overlap with the solute.

Parameters

[in,out]	atoms	Solvent atoms.
[in,out]	x	Solvent positions.
[in,out]	v	Solvent velocities (can be empty).
[in,out]	r	Solvent exclusion radii.
[in]	pbc	PBC information.
[in]	x_solute	Solute positions.
[in]	r_solute	Solute exclusion radii.

void gmx::repartitionAtomMasses	(	gmx_mtop_t *	mtop,
		bool	useFep,
		real	massFactor,
		WarningHandler *	wi
	)

Scales the smallest masses in the system by up to massFactor.

First finds the smallest atom mass. Then sets all masses that are smaller than the smallest mass time massFactor to the smallest mass time massFactor. The additional mass is taken away from the atom bound to the light atom. A warning is generated when light atoms are present that are unbound. An error is generated when perturbed masses are affected or when a light atom is bound to multiple other atoms or when a bound atom does becomes lighter than the smallest mass times massFactor.

Parameters

[in,out]	mtop	The topology to modify
[in]	useFep	Whether free-energy perturbation is active
[in]	massFactor	The factor to scale the smallest mass by
[in,out]	wi	Warning handler

gmx_bool gmx::replica_exchange	(	FILE *	fplog,
		const t_commrec *	cr,
		const gmx_multisim_t *	ms,
		gmx_repl_ex_t	re,
		t_state *	state,
		const gmx_enerdata_t *	enerd,
		t_state *	state_local,
		int64_t	step,
		real	time
	)

Attempts replica exchange.

Should be called on all ranks. When running each replica in parallel, this routine collects the state on the main rank before exchange. With domain decomposition, the global state after exchange is stored in state and still needs to be redistributed over the ranks.

Returns

TRUE if the state has been exchanged.

static void gmx::replicateSolventBox ( t_atoms *  atoms, std::vector< RVec > *  x, std::vector< RVec > *  v, std::vector< real > *  r, const matrix  box, const matrix  boxTarget  )

static

Generates a solvent configuration of desired size by stacking solvent boxes.

Parameters

[in,out]	atoms	Solvent atoms.
[in,out]	x	Solvent positions.
[in,out]	v	Solvent velocities (*v can be NULL).
[in,out]	r	Solvent exclusion radii.
[in]	box	Initial solvent box.
[in]	boxTarget	Target box size.

The solvent box of desired size is created by stacking the initial box in the smallest k*l*m array that covers the box, and then removing any residue where all atoms are outside the target box (with a small margin). This function does not remove overlap between solvent atoms across the edges.

Note that the input configuration should be in the rectangular unit cell and have whole residues.

void gmx::reportGpuUsage	(	const MDLogger &	mdlog,
		ArrayRef< const GpuTaskAssignment >	gpuTaskAssignmentOnRanksOfThisNode,
		size_t	numGpuTasksOnThisNode,
		size_t	numPpRanks,
		bool	printHostName,
		PmeRunMode	pmeRunMode,
		const SimulationWorkload &	simulationWork
	)

Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation.

Todo:

It could be useful to report also whether any nodes differed, and in what way.

Parameters

[in]	mdlog	Logging object.
[in]	gpuTaskAssignmentOnRanksOfThisNode	The selected GPU IDs.
[in]	numGpuTasksOnThisNode	The number of GPU tasks on this node.
[in]	numPpRanks	Number of PP ranks on this node
[in]	printHostName	Print the hostname in the usage information
[in]	pmeRunMode	Describes the execution of PME tasks
[in]	simulationWork	Simulation workload descriptor

Exceptions

std::bad_alloc

if out of memory

void gmx::restoreCorrelationGridStateFromHistory	(	const CorrelationGridHistory &	corrGridHist,
		CorrelationGrid *	corrGrid
	)

Restores the correlation grid state from the correlation grid history.

Parameters

[in]	corrGridHist	Correlation grid history to read.
[in,out]	corrGrid	Correlation grid state to set.

void gmx::resumeIttTracingWhenAppropriate

(

)

Resume tracing when applicable.

When linked with Intel Tracing Technology (ITT, configured with GMX_USE_ITT), data collection can be started conditionally, or it may have been paused from the beginning. If so, resume (or start) collection now. This can help align how GROMACS reports wallcycle counting with how the tracing tool gathers data. If data collection was already started, this does nothing.

static float gmx::round ( float  a )

inlinestatic

Float round to nearest integer value (in floating-point format).

Parameters

a	Any floating-point value

Returns

The nearest integer, represented in floating-point format.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::round ( double  a )

inlinestatic

double round to nearest integer value (in doubleing-point format).

Parameters

a	Any doubleing-point value

Returns

The nearest integer, represented in doubleing-point format.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::roundedMoleculeCharge ( double  qMol, double  sumAbsQ  )

static

Returns the rounded charge of a molecule, when close to integer, otherwise returns the original charge.

The results of this routine are only used for checking and for printing warning messages. Thus we can assume that charges of molecules should be integer. If the user wanted non-integer molecular charge, an undesired warning is printed and the user should use grompp -maxwarn 1.

Parameters

qMol	The total, unrounded, charge of the molecule
sumAbsQ	The sum of absolute values of the charges, used for determining the tolerance for the rounding.

static int gmx::roundToInt ( float  x )

inlinestatic

Round float to int.

Rounding behavior is round to nearest. Rounding of halfway cases is implementation defined (either halfway to even or halfway away from zero).

int gmx::runCommandLineModule	(	int	argc,
		char *	argv[],
		ICommandLineModule *	module
	)

Implements a main() method that runs a single module.

Parameters

argc	argc passed to main().
argv	argv passed to main().
module	Module to run.

This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).

The signature assumes that module construction does not throw (because otherwise the caller would need to duplicate all the exception handling code). It is possible to move the construction inside the try/catch in this method using an indirection similar to TrajectoryAnalysisCommandLineRunner::runAsMain(), but until that is necessary, the current approach leads to simpler code.

Usage:

int main(int argc, char *argv[])
{
    CustomCommandLineModule module;
    return gmx::runCommandLineModule(argc, argv, &module);
}

Does not throw. All exceptions are caught and handled internally.

int gmx::runCommandLineModule	(	int	argc,
		char *	argv[],
		const char *	name,
		const char *	description,
		std::function< std::unique_ptr< ICommandLineOptionsModule >()>	factory
	)

Implements a main() method that runs a single module.

Parameters

	argc	argc passed to main().
	argv	argv passed to main().
[in]	name	Name for the module.
[in]	description	Short description for the module.
	factory	Factory method that creates the module to run.

This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).

Usage:

class CustomCommandLineOptionsModule : public ICommandLineOptionsModule
{
    // <...>
};

static ICommandLineOptionsModule *create()
{
    return new CustomCommandLineOptionsModule();
}

int main(int argc, char *argv[])
{
    return gmx::runCommandLineModule(
            argc, argv, "mymodule", "short description", &create);
}

Does not throw. All exceptions are caught and handled internally.

static bool gmx::runningOnCompatibleHWForAmd ( const DeviceInformation &  deviceInfo )

static

Return true if executing on compatible GPU for AMD OpenCL.

There are known issues with OpenCL when running on 32-wide AMD hardware, such as desktop GPUs with RDNA and RDNA2 architectures (gfx10xx).

Returns

true if running on 64-wide hardware (GCN, CDNA).

static bool gmx::runningOnCompatibleHWForNvidia ( const DeviceInformation &  deviceInfo )

static

Return true if executing on compatible GPU for NVIDIA OpenCL.

There are known issues with OpenCL when running on NVIDIA Volta or newer (CC 7+). As a workaround, we recommend using CUDA on such hardware.

This function relies on cl_nv_device_attribute_query. In case it's not functioning properly, we trust the user and mark the device as compatible.

Returns

true if running on Pascal (CC 6.x) or older, or if we can not determine device generation.

static bool gmx::runningOnCompatibleOSForAmd ( )

static

Return true if executing on compatible OS for AMD OpenCL.

This is assumed to be true for OS X version of at least 10.10.4 and all other OS flavors.

Uses the BSD sysctl() interfaces to extract the kernel version.

Returns

true if version is 14.4 or later (= OS X version 10.10.4), or OS is not Darwin.

static constexpr int gmx::sc_gpuClusterPairSplit ( const PairlistType  pairlistType )

static

The number of sub-parts used for data storage for a GPU cluster pair.

In CUDA the number of threads in a warp is 32 and we have cluster pairs of 8*8=64 atoms, so it's convenient to store data for cluster pair halves, i.e. split in 2.

On architectures with 64-wide execution however it is better to avoid splitting (e.g. AMD GCN, CDNA and later).

static constexpr int gmx::sc_jClusterSize ( const NbnxmKernelType  kernelType )

static

The nbnxm j-cluster size in atoms for the given NBNxM kernel type.

Note

When including this file in files compiled for SYCL devices only, this function can not be called for SIMD kernel types. This is asserted.

template<NumPositionScalingValues numPositionScalingValues>

static void gmx::scalePositions ( int  a, real  lambda, RVec *gmx_restrict  x  )

inlinestatic

Scale positions.

To maximize the ability of the compiler to optimize, all the arrays of RVec should be annotated with gmx_restrict, so the compiler knows there is no aliasing, and for the same reason we do not use ArrayRef<RVec> for them.

template<NumVelocityScalingValues numStartVelocityScalingValues>

static void gmx::scaleVelocities ( int  a, real  lambda, RVec *gmx_restrict  v  )

inlinestatic

Scale velocities.

To maximize the ability of the compiler to optimize, all the arrays of RVec should be annotated with gmx_restrict, so the compiler knows there is no aliasing, and for the same reason we do not use ArrayRef<RVec> for them.

std::optional< int > gmx::search_atom	(	const char *	atomName,
		int	start,
		const t_atoms *	atoms,
		const char *	bondtype,
		bool	bAllowMissing,
		ArrayRef< const int >	cyclicBondsIndex
	)

Search for an atom named atomName in atoms.

If atomName starts with '-', start from start. Will search backwards from that.

bondtype is only used for printing the error/warning string, when bondtype ="check" no error/warning is issued. When bAllowMissing = FALSE an fatal error is issued, otherwise a warning.

Parameters

[in]	atomName	Atom name string to match.
[in]	start	Possible atom index within atoms from which to begin search.
[in]	atoms	Global topology atoms information.
[in]	bondtype	Information what kind of bond, used for error messages.
[in]	bAllowMissing	If true, missing bond types are allowed. AKA allow cartoon physics.
[in]	cyclicBondsIndex	Information about bonds creating cyclic molecules, empty if no such bonds exist.

Returns

Atom index within atoms matching atomName, or std::nullopt if none found.

ArrayRef< const MoleculePatchDatabase >::iterator gmx::search_h_db	(	ArrayRef< const MoleculePatchDatabase >	globalPatches,
		const char *	key
	)

Search for an entry.

Parameters

[in]	globalPatches	Database to search.
[in]	key	Name to search for.

std::string gmx::searchResidueDatabase	(	const std::string &	key,
		gmx::ArrayRef< const PreprocessResidue >	rtpDBEntry,
		const gmx::MDLogger &	logger
	)

Search for an entry in the rtp database.

A mismatch of one character is allowed, if there is only one nearly matching entry in the database, a warning will be generated.

Parameters

[in]	key	The atomname to search for.
[in]	rtpDBEntry	Database with residue information.
[in]	logger	Logging object.

Returns

The rtp residue name.

static float gmx::selectByMask ( float  a, bool  mask  )

inlinestatic

Select from single precision variable where boolean is true.

Parameters

a	Floating-point variable to select from
mask	Boolean selector

Returns

a is selected for true, 0 for false.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::selectByMask ( double  a, bool  mask  )

inlinestatic

Select from double precision variable where boolean is true.

Parameters

a	double variable to select from
mask	Boolean selector

Returns

a is selected for true, 0 for false.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::selectByMask ( std::int32_t  a, bool  mask  )

inlinestatic

Select from integer variable where boolean is true.

Parameters

a	Integer variable to select from
mask	Boolean selector

Returns

a is selected for true, 0 for false.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::selectByNotMask ( float  a, bool  mask  )

inlinestatic

Select from single precision variable where boolean is false.

Parameters

a	Floating-point variable to select from
mask	Boolean selector

Returns

a is selected for false, 0 for true.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::selectByNotMask ( double  a, bool  mask  )

inlinestatic

Select from double precision variable where boolean is false.

Parameters

a	double variable to select from
mask	Boolean selector

Returns

a is selected for false, 0 for true.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static std::int32_t gmx::selectByNotMask ( std::int32_t  a, bool  mask  )

inlinestatic

Select from integer variable where boolean is false.

Parameters

a	Integer variable to select from
mask	Boolean selector

Returns

a is selected for false, 0 for true.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static cl_kernel gmx::selectPruneKernel ( cl_kernel  kernel_pruneonly[], bool  firstPrunePass  )

inlinestatic

Return a pointer to the prune kernel version to be executed at the current invocation.

Parameters

[in]	kernel_pruneonly	array of prune kernel objects
[in]	firstPrunePass	true if the first pruning pass is being executed

void gmx::serializeMrcDensityMapHeader	(	ISerializer *	serializer,
		const MrcDensityMapHeader &	mrcHeader
	)

Serializes an MrcDensityMapHeader from a given serializer.

Parameters

[in]	serializer	the serializer
[in]	mrcHeader	file header to be serialized

static real gmx::series_sinhx ( real  x )

inlinestatic

Maclaurin series for sinh(x)/x.

Used for NH chains and MTTK pressure control. Here, we compute it to 10th order, which might be an overkill. 8th is probably enough, but it's not very much more expensive.

template<typename ValueType >

void gmx::setAttribute	(	hid_t	container,
		const char *	attributeName,
		const ValueType &	value
	)

Write a scalar attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to write

Parameters

[in]	container	The HDF5 container (group or dataset) to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	value	The scalar to write.

void gmx::setAttribute	(	hid_t	container,
		const char *	attributeName,
		const char *	value
	)

Write a scalar attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to write

Parameters

[in]	container	The HDF5 container (group or dataset) to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	value	The scalar to write. Specialization of setAttribute() for writing attributes of char* type.

void gmx::setAttribute	(	hid_t	container,
		const char *	attributeName,
		const std::string &	value
	)

Write a scalar attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to write

Parameters

[in]	container	The HDF5 container (group or dataset) to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	value	The scalar to write. Specialization of setAttribute() for writing attributes of std::string type.

template<typename Iterator >

std::vector< char > gmx::setAttributeStringVector	(	hid_t	container,
		const char *	attributeName,
		std::vector< char > &&	buffer,
		Iterator	begin,
		Iterator	end
	)

Write a vector-like string attribute via iterators String data type is treated specially because of the HDF5 requirements for contiguous memory storage for fixed-length strings. A reusable character buffer is needed to avoid frequent memory allocations for multiple writing of different string attributes.

Template Parameters

Iterator

The type of the iterator to write.

Parameters

[in]	container	The HDF5 container (group or dataset) to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	buffer	The buffer to write the strings into, could leave it empty {}.
[in]	begin	The beginning iterator of the data to write.
[in]	end	The ending iterator of the data to write.

template<typename ValueType >

void gmx::setAttributeVector	(	hid_t	container,
		const char *	attributeName,
		ArrayRef< const ValueType >	value
	)

Write a vector-like attribute of a given data type.

Template Parameters

ValueType

The type of the attribute to write.

Parameters

[in]	container	The path of the group or dataset to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	value	The 1D-vector to write, provided as an ArrayRef.

void gmx::setAttributeVector	(	hid_t	container,
		const char *	attributeName,
		ArrayRef< const std::string >	values
	)

Write a vector-like attribute of strings.

Parameters

[in]	container	The path of the group or dataset to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	values	The 1D-vector to write, provided as an ArrayRef.

void gmx::setAttributeVector	(	hid_t	container,
		const char *	attributeName,
		ArrayRef< const char *const >	values
	)

Write a vector-like attribute of C-strings.

Parameters

[in]	container	The path of the group or dataset to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	values	The 1D-vector to write, provided as an ArrayRef.

void gmx::setBoxDeformationFlowMatrix	(	const matrix	boxDeformationVelocity,
		const matrix	box,
		matrix	flowMatrix
	)

Set a matrix for computing the flow velocity at coordinates.

Used with continuous box deformation for calculating the flow profile. Sets a matrix which can be used to multiply with coordinates to obtain the flow velocity at that coordinate.

Parameters

[in]	boxDeformationVelocity	The velocity of the box in nm/ps
[in]	box	The box in nm
[out]	flowMatrix	The deformation rate in ps^-1

static void gmx::setDynamicPairlistPruningParameters ( const t_inputrec &  inputrec, const gmx_mtop_t &  mtop, const real  effectiveAtomDensity, const bool  useGpuList, const VerletbufListSetup &  listSetup, const bool  userSetNstlistPrune, const interaction_const_t &  interactionConst, PairlistParams *  listParams  )

static

Set the dynamic pairlist pruning parameters in ic.

Parameters

[in]	inputrec	The input parameter record
[in]	mtop	The global topology
[in]	effectiveAtomDensity	The effective atom density of the system
[in]	useGpuList	Tells if we are using a GPU type pairlist
[in]	listSetup	The nbnxm pair list setup
[in]	userSetNstlistPrune	The user set ic->nstlistPrune (using an env.var.)
[in]	interactionConst	The nonbonded interactions constants
[in,out]	listParams	The list setup parameters

void gmx::setLibraryFileFinder

(

const DataFileFinder *

finder

)

Sets a finder for location data files from share/top/.

Parameters

[in]

finder

finder to set (can be NULL to restore the default finder).

The library does not take ownership of finder. The provided object must remain valid until the global instance is changed by another call to setLibraryFileFinder().

The global instance is used by findLibraryFile() and openLibraryFile().

This method is not thread-safe. See setProgramContext(); the same constraints apply here as well.

Does not throw.

void gmx::setOutputControlPreprocessingStrings	(	IMDModule *	module,
		inputrec_strings *	preprocessingStrings
	)

Set preprocessing-only string storage for an OutputControlModule.

Configures where the OutputControlModule stores group specifications (compressed-x-grps, energygrps) that are only used during grompp preprocessing. These strings are NOT part of OutputControl and are NOT serialized to TPR.

This must be called before assignOptionsToModules() when parsing MDP files in grompp. It is not needed when reading TPR files in mdrun/tools.

Parameters

[in]	module	The module (must be an OutputControlModule)
[in]	preprocessingStrings	Pointer to storage for preprocessing-only strings

Exceptions

InternalError

if module is not an OutputControlModule

void gmx::setOutputControlTarget	(	IMDModule *	module,
		OutputControl *	outputControl
	)

Set the target OutputControl for an OutputControlModule.

Configures the OutputControlModule to write to an external OutputControl (typically embedded in t_inputrec). This must be called before MDP options are parsed.

Parameters

[in]	module	The module (must be an OutputControlModule)
[in]	outputControl	Pointer to the OutputControl to write to

Exceptions

InternalError

if module is not an OutputControlModule

void gmx::setOutputControlWriteToMdpOutput	(	IMDModule *	module,
		bool	enable
	)

Enable MDP output writing for OutputControl module (for testing only)

By default, OutputControlModule::buildMdpOutput() does nothing to avoid duplication with the inp vector mechanism. This function enables output writing so tests can verify the module produces correct MDP output.

Parameters

[in]	module	The OutputControl module (must be an OutputControlModule)
[in]	enable	Whether to enable MDP output writing

Exceptions

InternalError

if module is not an OutputControlModule

void gmx::setStateDependentAwhParams	(	AwhParams *	awhParams,
		const pull_params_t &	pull_params,
		pull_t *	pull_work,
		const matrix	box,
		PbcType	pbcType,
		const tensor &	compressibility,
		const t_inputrec &	inputrec,
		real	initLambda,
		const gmx_mtop_t &	mtop,
		WarningHandler *	wi
	)

Sets AWH parameters that need state parameters such as the box vectors.

Parameters

[in,out]	awhParams	AWH parameters.
[in]	pull_params	Pull parameters.
[in,out]	pull_work	Pull working struct to register AWH bias in.
[in]	box	Box vectors.
[in]	pbcType	Periodic boundary conditions enum.
[in]	compressibility	Compressibility matrix for pressure coupling, pass all 0 without pressure coupling
[in]	inputrec	Input record, for checking the reference temperature
[in]	initLambda	The starting lambda, to allow using free energy lambda as reaction coordinate provider in any dimension.
[in]	mtop	The system topology.
[in,out]	wi	Struct for bookeeping warnings.

Note

This function currently relies on the function set_pull_init to have been called.

static void gmx::setStateDependentAwhPullDimParams ( AwhDimParams *  dimParams, const int  biasIndex, const int  dimIndex, const pull_params_t &  pull_params, pull_t *  pull_work, const t_pbc &  pbc, const tensor &  compressibility, WarningHandler *  wi  )

static

Sets AWH parameters, for one AWH pull dimension.

Parameters

[in,out]	dimParams	AWH dimension parameters.
[in]	biasIndex	The index of the bias containing this AWH pull dimension.
[in]	dimIndex	The index of this AWH pull dimension.
[in]	pull_params	Pull parameters.
[in,out]	pull_work	Pull working struct to register AWH bias in.
[in]	pbc	A pbc information structure.
[in]	compressibility	Compressibility matrix for pressure coupling, pass all 0 without pressure coupling.
[in,out]	wi	Struct for bookeeping warnings.

void gmx::setStringAttributeByBuffer	(	hid_t	container,
		const char *	attributeName,
		size_t	numberOfStrings,
		int	maxStrLength,
		ArrayRef< const char >	buffer
	)

Low-level utility function to write a string-vector attribute via a character buffer.

The size of the character buffer must be greater than or equal to numberOfStrings * (maxStrLength + 1).

Parameters

[in]	container	The HDF5 container to write the attribute to.
[in]	attributeName	The name of the attribute to write.
[in]	numberOfStrings	The number of strings in the vector.
[in]	maxStrLength	The maximum length of the strings in the vector.
[in]	buffer	The character buffer to write.

void gmx::setThrowForPerformanceProblems

(

bool

newValue

)

Flag for controlling behaviour in cases where performance might be low.

In mdrun, by default we will make an efficient task assignment by creating as many tasks as available GPUs. If users make a partial assigment that would likely be inefficient (e.g. using fewer ranks than GPUs, or like -nb gpu -pme cpu -npme 1), we want users to think about what they are doing and be fully specific if they really want to do things their way.

In tests, we want to be able to cover many code paths on the available hardware regardless of performance. This setter allows test code to avoid irrelevant fatal errors about performance.

SettleParameters gmx::settleParameters	(	real	mO,
		real	mH,
		real	invmO,
		real	invmH,
		real	dOH,
		real	dHH
	)

Computes and returns settle parameters.

Parameters

[in]	mO	Mass of oxygen atom
[in]	mH	Mass of hydrogen atom
[in]	invmO	Reciprocal mass of oxygen atom
[in]	invmH	Reciprocal mass of hydrogen atom
[in]	dOH	Target O-H bond length
[in]	dHH	Target H-H bond length

DomainLifetimeWorkload gmx::setupDomainLifetimeWorkload	(	const t_inputrec &	inputrec,
		const t_forcerec &	fr,
		const pull_t *	pull_work,
		const edsam *	ed,
		const t_mdatoms &	mdatoms,
		const SimulationWorkload &	simulationWork
	)

Set up workload flags that have the lifetime of the PP domain decomposition.

This function should be called every time after domain decomposition happens. Also note that fr->listedForcesGpu->updateHaveInteractions() should be called before this function anytime a change in listed forces assignment after repartitioning can be expected.

Parameters

[in]	inputrec	The input record
[in]	fr	The force record
[in]	pull_work	Pull data
[in]	ed	Essential dynamics data
[in]	mdatoms	Atom parameter data
[in]	simulationWork	Simulation workload flags

void gmx::setupDynamicPairlistPruning	(	const MDLogger &	mdlog,
		const t_inputrec &	inputrec,
		const gmx_mtop_t &	mtop,
		real	effectiveAtomDensity,
		const interaction_const_t &	interactionConst,
		PairlistParams *	listParams
	)

Set up the dynamic pairlist pruning.

Parameters

[in,out]	mdlog	MD logger
[in]	inputrec	The input parameter record
[in]	mtop	The global topology
[in]	effectiveAtomDensity	The effective atom density of the system
[in]	interactionConst	The nonbonded interactions constants
[in,out]	listParams	The list setup parameters

void gmx::setupFileFromInput	(	H5md *	h5md,
		const gmx_mtop_t &	topology,
		const t_inputrec &	inputRecord
	)

Set up the file from input data.

Parameters

[out]	h5md	Handle to H5md object
[in]	topology	Topology data of system.
[in]	inputRecord	Simulation parameters.

static ForceOutputs gmx::setupForceOutputs ( ForceHelperBuffers *  forceHelperBuffers, ArrayRefWithPadding< RVec >  force, const DomainLifetimeWorkload &  domainWork, const StepWorkload &  stepWork, const bool  havePpDomainDecomposition, gmx_wallcycle *  wcycle  )

static

Set up the different force buffers; also does clearing.

Parameters

[in]	forceHelperBuffers	Helper force buffers
[in]	force	force array
[in]	domainWork	Domain lifetime workload flags
[in]	stepWork	Step schedule flags
[in]	havePpDomainDecomposition	Whether we have a PP domain decomposition
[out]	wcycle	wallcycle recording structure

Returns

Cleared force output structure

void gmx::setupFromExistingFileForAppending	(	H5md *	h5md,
		int64_t	restartingFromStep,
		int64_t	numParticles
	)

Set up from an existing h5md file for restarting with appending.

Scans for trajectory data available in the /particles/system group of the HDF5 file. For trajectories written by GROMACS this group contains data for all atoms in the simulated system.

Note

Ignores trajectory data in other subgroups of /particles.

Parameters

[out]	h5md	Handle to H5md object
[in]	restartingFromStep	Step which we are restarting the simulation from
[in]	numParticles	Number of particles in system

Exceptions

H5mdError

if the existing file contents are not for a system of numParticles.

static FusedXToXqLaunchParams gmx::setupFusedXToXqLaunchParams ( ArrayRef< const Grid >  grids, int  gridBegin, int  numCellsMax  )

static

Compute all kernel launch parameters for a given set of grids.

Called once per pair-list setup; results are stored in NbnxmGpu.

Parameters

[in]	grids	Grids for one interaction locality.
[in]	gridBegin	Index of the first grid in the gridset (0 = local, 1 = non-local).
[in]	numCellsMax	Max. cells per grid; stride for per-grid device arrays.

void gmx::setupGpuShortRangeWorkLow	(	NbnxmGpu gmx_unused *	nb,
		const ListedForcesGpu gmx_unused *	listedForcesGpu,
		InteractionLocality gmx_unused	iLocality
	)

Set up internal flags that indicate what type of short-range work there is.

As nonbondeds and bondeds share input/output buffers and GPU queues, both are considered when checking for work in the current domain.

This function is expected to be called every time the work-distribution can change (i.e. at search/domain decomposition steps).

Parameters

[in,out]	nb	Pointer to the nonbonded GPU data structure
[in]	listedForcesGpu	Pointer to the GPU bonded data structure
[in]	iLocality	Interaction locality identifier

static void gmx::setupGroupCommunication ( const MDLogger &  mdlog, const DDSettings &  ddSettings, const int  numAtomsInSystem, gmx_domdec_t *  dd  )

static

For PP ranks, sets or makes the communicator.

For PME ranks get the rank id. For PP only ranks, sets the PME-only rank.

static void gmx::setupLocalGpuForceReduction ( const MdrunScheduleWorkload &  runScheduleWork, nonbonded_verlet_t *  nbv, StatePropagatorDataGpu *  stateGpu, GpuForceReduction *  gpuForceReduction, PmePpCommGpu *  pmePpCommGpu, const gmx_pme_t *  pmedata, const gmx_domdec_t *  dd  )

static

Setup for the local GPU force reduction: reinitialization plus the registration of forces and dependencies.

Parameters

[in]	runScheduleWork	Schedule workload flag structure
[in]	nbv	Non-bonded Verlet object
[in]	stateGpu	GPU state propagator object
[in]	gpuForceReduction	GPU force reduction object
[in]	pmePpCommGpu	PME-PP GPU communication object
[in]	pmedata	PME data object
[in]	dd	Domain decomposition object

std::vector< MtsLevel > gmx::setupMtsLevels	(	const GromppMtsOpts &	mtsOpts,
		std::vector< std::string > *	errorMessages
	)

Sets up and returns the MTS levels and checks requirements of MTS.

Appends errors about allowed input values ir to errorMessages, when not nullptr.

Parameters

[in]	mtsOpts	Options for setting the MTS levels
[in,out]	errorMessages	List of error messages, can be nullptr

static void gmx::setupNonLocalGpuForceReduction ( const MdrunScheduleWorkload &  runScheduleWork, nonbonded_verlet_t *  nbv, StatePropagatorDataGpu *  stateGpu, GpuForceReduction *  gpuForceReduction, const gmx_domdec_t *  dd  )

static

Setup for the non-local GPU force reduction: reinitialization plus the registration of forces and dependencies.

Parameters

[in]	runScheduleWork	Schedule workload flag structure
[in]	nbv	Non-bonded Verlet object
[in]	stateGpu	GPU state propagator object
[in]	gpuForceReduction	GPU force reduction object
[in]	dd	Domain decomposition object

StepWorkload gmx::setupStepWorkload	(	int	legacyFlags,
		ArrayRef< const gmx::MtsLevel >	mtsLevels,
		int64_t	step,
		std::optional< bool >	writeCheckpoint,
		const DomainLifetimeWorkload &	domainWork,
		const SimulationWorkload &	simulationWork,
		const t_inputrec &	inputrec
	)

Set up force flag struct from the force bitmask.

Parameters

[in]	legacyFlags	Force bitmask flags used to construct the new flags
[in]	mtsLevels	The multiple time-stepping levels, either empty or 2 levels
[in]	step	The current MD step
[in]	writeCheckpoint	Whether we will write a checkpoint file at the current step, a value is required when update is on GPU
[in]	domainWork	Domain lifetime workload description.
[in]	simulationWork	Simulation workload description.
[in]	inputrec	Input record, needed for access to output intervals.

Returns

New Stepworkload description.

static SimdSetZeroProxy gmx_simdcall gmx::setZero ( )

inlinestatic

Helper function to set any SIMD or scalar variable to zero.

Returns

Proxy object that will call the actual function to set a SIMD/scalar variable to zero based on the conversion function called when you assign the result.

void gmx::shiftAtoms	(	const RVec &	shift,
		ArrayRef< RVec >	x
	)

Shift all coordinates.

Shift coordinates by a previously calculated value.

Can be used to e.g. place particles in a box.

Parameters

[in]	shift	Translation that should be applied.
[in]	x	Coordinates to translate.

bool gmx::simdCheck	(	const CpuInfo &	cpuInfo,
		SimdType	wanted,
		FILE *	log,
		bool	warnToStdErr
	)

Check if binary was compiled with the provided SIMD type.

Parameters

cpuInfo	Information about the CPU we are running on
wanted	SIMD type to query. If this matches the suggested type for this cpu, the routine returns quietly.
log	If not nullptr, statistics will be printed to the file. If we do not have a match there will also be a warning.
warnToStdErr	If true, warnings will also be printed to stderr.

static void gmx_unused gmx::simdPrefetch ( void gmx_unused *  m )

inlinestatic

Prefetch memory at address m.

This typically prefetches one cache line of memory from address m, usually 64bytes or more, but the exact amount will depend on the implementation. On many platforms this is simply a no-op. Technically it might not be part of the SIMD instruction set, but since it is a hardware-specific function that is normally only used in tight loops where we also apply SIMD, it fits well here.

There are no guarantees about the level of cache or temporality, but usually we expect stuff to end up in level 2, and be used in a few hundred clock cycles, after which it stays in cache until evicted (normal caching).

Parameters

m	Pointer to location prefetch. There are no alignment requirements, but if the pointer is not aligned the prefetch might start at the lower cache line boundary (meaning fewer bytes are prefetched).

static float gmx::sin ( float  x )

inlinestatic

Float sin.

Parameters

x	The argument to evaluate sin for

Returns

Sin(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::sin ( double  x )

inlinestatic

Double sin.

Parameters

x	The argument to evaluate sin for

Returns

Sin(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::sincos ( float  x, float *  sinval, float *  cosval  )

inlinestatic

Float sin & cos.

Parameters

	x	The argument to evaluate sin/cos for
[out]	sinval	Sin(x)
[out]	cosval	Cos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::sincos ( double  x, double *  sinval, double *  cosval  )

inlinestatic

Double sin & cos.

Parameters

	x	The argument to evaluate sin/cos for
[out]	sinval	Sin(x)
[out]	cosval	Cos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::sincosSingleAccuracy ( double  x, double *  sinval, double *  cosval  )

inlinestatic

Double sin & cos, but with single accuracy.

Parameters

	x	The argument to evaluate sin/cos for
[out]	sinval	Sin(x)
[out]	cosval	Cos(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::sinSingleAccuracy ( double  x )

inlinestatic

Double sin, but with single accuracy.

Parameters

x	The argument to evaluate sin for

Returns

Sin(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::sixthroot ( float  x )

inlinestatic

Calculate sixth root of x in single precision.

Parameters

x	Argument, must be greater than or equal to zero.

Returns

x^(1/6)

This routine is typically faster than using std::pow().

static double gmx::sixthroot ( double  x )

inlinestatic

Calculate sixth root of x in double precision.

Parameters

x	Argument, must be greater than or equal to zero.

Returns

x^(1/6)

This routine is typically faster than using std::pow().

static double gmx::sixthroot ( int  x )

inlinestatic

Calculate sixth root of integer x, return double.

Parameters

x	Argument, must be greater than or equal to zero.

Returns

x^(1/6)

This routine is typically faster than using std::pow().

static std::vector<int> gmx::solventMoleculeIndices ( int  solventMoleculeNumber, int  numberAtomsPerSolventMolecule, ArrayRef< const int >  solventGroupIndex  )

static

Calculate the solvent molecule atom indices from molecule number.

Note

the solvent group index has to be continuous

Parameters

[in]	solventMoleculeNumber	the number of the solvent molecule
[in]	numberAtomsPerSolventMolecule	how many atoms each solvent molecule contains
[in]	solventGroupIndex	continuous index of solvent atoms

Returns

atom indices of the specified solvent molecule

static void gmx::sort_atoms ( int  dim, gmx_bool  Backwards, int gmx_unused  dd_zone, bool gmx_unused  relevantAtomsAreWithinGridBounds, int *  a, int  n, ArrayRef< const RVec >  x, real  h0, real  invh, int  n_per_h, ArrayRef< int >  sort  )

static

Sorts particle index a on coordinates x along dim.

Backwards tells if we want decreasing iso increasing coordinates. h0 is the minimum of the coordinate range. invh is the 1/length of the sorting range. n_per_h (>=n) is the expected average number of particles per 1/invh sort is the sorting work array. sort should have a size of at least n_per_h*c_sortGridRatio + n, or easier, allocate at least n*c_sortGridMaxSizeFactor elements.

static void gmx::sort_cluster_on_flag ( int  numAtomsInCluster, int  atomStart, int  atomEnd, ArrayRef< const int32_t >  atomInfo, ArrayRef< int >  order, int *  flags  )

static

Set non-bonded interaction flags for the current cluster.

Sorts atoms on LJ coefficients: !=0 first, ==0 at the end.

std::vector< bool > gmx::splitEmbeddedBlocks	(	gmx_mtop_t *	mtop,
		const std::set< int > &	embeddedIndices
	)

Splits embedded atom containing molecules out of MM blocks in topology.

Modifies molblocks in topology mtop

Parameters

[in,out]	mtop	topology to be modified
[in]	embeddedIndices	set with global indices of embedded atoms

Returns

vector of flags for embedded atom-containing blocks in modified mtop

std::vector< std::filesystem::path > gmx::splitPathEnvironment

(

const std::string &

pathEnv

)

Split PATH environment variable into search paths.

Parameters

[in]

pathEnv

String to split.

Returns

vector of filesystem paths to search.

IntegerBox gmx::spreadRangeWithinLattice	(	const IVec &	center,
		dynamicExtents3D	extent,
		IVec	range
	)

Construct a box that holds all indices that are not more than a given range remote from center coordinates and still within a given lattice extent.

Parameters

[in]	center	the coordinates of the center of the spread range
[in]	extent	the end of the lattice, number of lattice points in each dimension
[in]	range	the distance from the center

Returns

box describing the range of indices

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::sqrt ( float  x )

inlinestatic

Float sqrt(x). This is the square root.

Parameters

x	Argument, should be >= 0.

Returns

The square root of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::sqrt ( double  x )

inlinestatic

Double sqrt(x). This is the square root.

Parameters

x	Argument, should be >= 0.

Returns

The square root of x. Undefined if argument is invalid.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::sqrtSingleAccuracy ( double  x )

inlinestatic

Calculate sqrt(x) for double, but with single accuracy.

Parameters

x	Argument that must be >=0.

Returns

sqrt(x).

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<typename T >

T gmx::square

(

T

x

)

calculate x^2

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^2

void gmx::stats_add_point	(	stats_t	stats,
		double	x,
		double	y,
		double	dx,
		double	dy
	)

Add a point to the data set.

Parameters

[in]	stats	The data structure
[in]	x	The x value
[in]	y	The y value
[in]	dx	The error in the x value
[in]	dy	The error in the y value

void gmx::stats_free

(

stats_t

stats

)

Destroy a data structure.

Parameters

stats

The data structure

void gmx::stats_get_ab	(	stats_t	stats,
		int	weight,
		real *	a,
		real *	b,
		real *	da,
		real *	db,
		real *	chi2,
		real *	Rfit
	)

Fit the data to y = ax + b, possibly weighted, if uncertainties have been input. da and db may be NULL.

Parameters

[in]	stats	The data structure
[in]	weight	type of weighting
[out]	a	slope
[out]	b	intercept
[out]	da	sigma in a
[out]	db	sigma in b
[out]	chi2	normalized quality of fit
[out]	Rfit	correlation coefficient

std::tuple< real, real, real > gmx::stats_get_ase

(

stats_t

stats

)

Pointers may be null, in which case no assignment will be done.

Parameters

[in]

stats

The data structure

Returns

Tuple of (average value, its standard deviation, its standard error)

Exceptions

InconsistentInputError

if given no points to analyze

real gmx::stats_get_average

(

stats_t

stats

)

Computes and returns the average value.

Parameters

[in]

stats

The data structure

Returns

Average value

Exceptions

InconsistentInputError

if given no points to average

stats_t gmx::stats_init

(

)

Initiate a data structure.

Returns

the data structure

void gmx::stop_cm	(	const MDLogger &	logger,
		int	natoms,
		real	mass[],
		rvec	x[],
		rvec	v[]
	)

Remove the center of mass motion in a set of coordinates.

Parameters

[in]	logger	Handle to logging interface.
[in]	natoms	Number of atoms
[in]	mass	Atomic masses
[in]	x	Coordinates
[out]	v	Velocities

static void gmx::store ( float *  m, float  a  )

inlinestatic

Store contents of float variable to aligned memory m.

Parameters

[out]	m	Pointer to memory.
	a	float variable to store

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::store ( double *  m, double  a  )

inlinestatic

Store contents of double variable to aligned memory m.

Parameters

[out]	m	Pointer to memory.
	a	double variable to store

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::store ( std::int32_t *  m, std::int32_t  a  )

inlinestatic

Store contents of integer variable to aligned memory m.

Parameters

[out]	m	Pointer to memory.
	a	integer variable to store

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::storeU ( float *  m, float  a  )

inlinestatic

Store contents of float variable to unaligned memory m.

Parameters

[out]	m	Pointer to memory, no alignment requirement.
	a	float variable to store.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::storeU ( double *  m, double  a  )

inlinestatic

Store contents of double variable to unaligned memory m.

Parameters

[out]	m	Pointer to memory, no alignment requirement.
	a	double variable to store.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::storeU ( std::int32_t *  m, std::int32_t  a  )

inlinestatic

Store contents of integer variable to unaligned memory m.

Parameters

[out]	m	Pointer to memory, no alignment requirement.
	a	integer variable to store.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<typename ValueType , int NumExpectedValues>

static std::string gmx::stringIdentityTransformWithArrayCheck ( const std::string &  toConvert, const std::string &  errorContextMessage  )

inlinestatic

Returns the input string, throwing an exception if the demanded conversion to an array will not succeed.

Template Parameters

ValueType	array element type to convert into
NumExpectedValues	number of values of the array

Parameters

[in]	toConvert	the string to convert
[in]	errorContextMessage	the message to add to the thrown exceptions if conversion of the string is bound to fail at some point

Returns

the input string

Exceptions

InvalidInputError	if splitting the string at whitespaces does not result in NumExpectedValues or zero substrings
InvalidInputError	if conversion of any of the NumExpectedValues substrings of the splitted input string fails

A typical use of this function would be in .mdp string option parsing where information in the .mdp file is transformed into the data that is stored in the .tpr file.

template<typename T >

void gmx::sumOverSimulations	(	ArrayRef< T >	data,
		MPI_Comm	multiSimComm,
		const bool	broadcastWithinSimulation,
		const MpiComm &	mpiComm
	)

Sum an array over all simulations on main ranks or all ranks of each simulation.

This assumes the data is identical on all ranks within each simulation.

Parameters

[in,out]	data	The data to sum.
[in]	multiSimComm	Communicator for the main ranks of sharing simulations.
[in]	broadcastWithinSimulation	Broadcast the result to all ranks within the simulation
[in]	mpiComm	MPI communicator for intra-simulation communication.

static bool gmx::supportsDynamicPairlistGenerationInterval ( const t_inputrec &  ir )

static

Returns if we can (heuristically) change nstlist and rlist.

Parameters

[in]

ir

The input parameter record

template<typename CommandGroupFunc >

static void gmx::syclEnqueueCustomOp ( sycl::handler &  cgh, CommandGroupFunc &&  cgf  )

inlinestatic

Helper function to add a custom operation to the SYCL handler.

In ACpp, it relies on the ACPP_EXT_ENQUEUE_CUSTOM_OPERATION extension. Should not be called when the extension is not available.

template<typename Queue >

static void gmx::syclMemcpyWithoutEvent ( Queue &&  queue, void *  destination, const void *  source, size_t  numBytes  )

inlinestatic

Helper function to submit a SYCL async memcpy without returning an event (if possible).

See syclSubmitWithoutEvent() for general details.

static void gmx::syclMemsetWithoutEvent ( sycl::queue &&  queue, void *  pointer, int  value, size_t  numBytes  )

inlinestatic

Helper function to submit a SYCL async memset without returning an event (if possible).

See syclSubmitWithoutEvent() for general details.

template<typename KernelNameType , typename KernelFunctionBuilder , typename Queue , typename Range , class... Args>

static void gmx::syclSubmitWithoutCghOrEvent ( Queue &&  queue, KernelFunctionBuilder  kernelFunctionBuilder, Range &&  range, Args &&...  args  )

inlinestatic

Helper function to submit a SYCL operation without returning an event.

Differs from syclSubmitWithoutEvent() in that if the submission protocol must use a command-group handler, it is not passed to the kernelFunctionBuilder.

template<typename KernelNameType , typename KernelFunctionBuilder , typename Queue , typename Range , class... Args>

static void gmx::syclSubmitWithoutEvent ( Queue &&  queue, KernelFunctionBuilder  kernelFunctionBuilder, Range &&  range, Args &&...  args  )

inlinestatic

Helper function to submit a SYCL operation without returning an event (if possible).

Gives some nice performance optimizations, especially on AMD and NVIDIA devices.

Parameters

[in]	queue	The sycl::queue to use
[in]	kernelFunctionBuilder	A function that returns a device kernel as a lambda
[in]	range	The range over which the device kernel runs
[in]	args	Parameter pack of device-kernel arguments

In ACpp, it relies on the ACPP_EXT_CG_PROPERTY_* and ACPP_EXT_COARSE_GRAINED_EVENTS extensions.

Two implementations are provided for DPC++. Both rely (when explicitly enabled) on SYCL_EXT_ONEAPI_ENQUEUE_FUNCTIONS. The GMX_SYCL_ENABLE_EXPERIMENTAL_SUBMIT_API implementation continues to use a command-group-handler, but no longer returns a sycl::event. The GMX_SYCL_ENABLE_HANDLER_FREE_SUBMISSION implementation uses free functions to submit work on a queue, requiring no handler and permitting the caller to choose whether to receive a sycl::event as a return value.

Falls back to the default submit otherwise.

The function aims to avoid the overhead associated with creating/recording/destroying events and (depending on the chosen implementation) command-group handlers, while always permitting fallback standard execution if other capabilities are not available.

bool gmx::systemHasConstraintsOrVsites

(

const gmx_mtop_t &

mtop

)

Returns whether mtop contains any constraints and/or vsites.

When we have constraints and/or vsites, it is beneficial to use update groups (when possible) to allow independent update of groups.

static float gmx::tan ( float  x )

inlinestatic

Float tan.

Parameters

x	The argument to evaluate tan for

Returns

Tan(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::tan ( double  x )

inlinestatic

Double tan.

Parameters

x	The argument to evaluate tan for

Returns

Tan(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::tanSingleAccuracy ( double  x )

inlinestatic

Double tan, but with single accuracy.

Parameters

x	The argument to evaluate tan for

Returns

Tan(x)

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static bool gmx::testBits ( float  a )

inlinestatic

Return true if any bits are set in the float variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels. Note that it will return true even for -0.0f (sign bit set), so it is not identical to not-equal.

Parameters

a

value

Returns

True if any bit in a is nonzero.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static bool gmx::testBits ( double  a )

inlinestatic

Return true if any bits are set in the double variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels. Note that it will return true even for -0.0 (sign bit set), so it is not identical to not-equal.

Parameters

a

value

Returns

True if any bit in a is nonzero.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static bool gmx::testBits ( std::int32_t  a )

inlinestatic

Return true if any bits are set in the integer variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels.

Parameters

a

value

Returns

True if any bit in a is nonzero.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static void gmx::threadMpiMdrunnerAccessBarrier ( )

static

Barrier for safe simultaneous thread access to mdrunner data.

Used to ensure that the main thread does not modify mdrunner during copy on the spawned threads.

bool gmx::timesClose ( Time  time, Time  referenceTime  )

inline

Check whether two times are nearly equal.

Times are considered close if their absolute difference is smaller than c_timePrecision.

Parameters

time	The test time
referenceTime	The reference time

Returns

bool Whether the absolute difference is < c_timePrecision

template<int align>

static void gmx::transposeScatterDecrU ( float *  base, const std::int32_t  offset[], float  v0, float  v1, float  v2  )

inlinestatic

Subtract 3 floats from base/offset.

Template Parameters

align

Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.

Parameters

[out]	base	Pointer to the start of the memory area
	offset	Offset to the start of triplet.
	v0	1st value, subtracted from base[align*offset[0]].
	v1	2nd value, subtracted from base[align*offset[0] + 1].
	v2	3rd value, subtracted from base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::transposeScatterDecrU ( double *  base, const std::int32_t  offset[], double  v0, double  v1, double  v2  )

inlinestatic

Subtract 3 doubles from base/offset.

Template Parameters

align

Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.

Parameters

[out]	base	Pointer to the start of the memory area
	offset	Offset to the start of triplet.
	v0	1st value, subtracted from base[align*offset[0]].
	v1	2nd value, subtracted from base[align*offset[0] + 1].
	v2	3rd value, subtracted from base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::transposeScatterIncrU ( float *  base, const std::int32_t  offset[], float  v0, float  v1, float  v2  )

inlinestatic

Add 3 floats to base/offset.

Template Parameters

align

Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.

Parameters

[out]	base	Pointer to the start of the memory area
	offset	Offset to the start of triplet.
	v0	1st value, added to base[align*offset[0]].
	v1	2nd value, added to base[align*offset[0] + 1].
	v2	3rd value, added to base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::transposeScatterIncrU ( double *  base, const std::int32_t  offset[], double  v0, double  v1, double  v2  )

inlinestatic

Add 3 doubles to base/offset.

Template Parameters

align

Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.

Parameters

[out]	base	Pointer to the start of the memory area
	offset	Offset to the start of triplet.
	v0	1st value, added to base[align*offset[0]].
	v1	2nd value, added to base[align*offset[0] + 1].
	v2	3rd value, added to base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::transposeScatterStoreU ( float *  base, const std::int32_t  offset[], float  v0, float  v1, float  v2  )

inlinestatic

Store 3 floats to 3 to base/offset.

Template Parameters

align

Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.

Parameters

[out]	base	Pointer to the start of the memory area
	offset	Offset to the start of triplet.
	v0	1st value, written to base[align*offset[0]].
	v1	2nd value, written to base[align*offset[0] + 1].
	v2	3rd value, written to base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

template<int align>

static void gmx::transposeScatterStoreU ( double *  base, const std::int32_t  offset[], double  v0, double  v1, double  v2  )

inlinestatic

Store 3 doubles to 3 to base/offset.

Template Parameters

align

Alignment of the memory to which we write, i.e. distance (measured in elements, not bytes) between index points.

Parameters

[out]	base	Pointer to the start of the memory area
	offset	Offset to the start of triplet.
	v0	1st value, written to base[align*offset[0]].
	v1	2nd value, written to base[align*offset[0] + 1].
	v2	3rd value, written to base[align*offset[0] + 2].

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static float gmx::trunc ( float  a )

inlinestatic

Truncate float, i.e. round towards zero - common hardware instruction.

Parameters

a	Any floating-point value

Returns

Integer rounded towards zero, represented in floating-point format.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

static double gmx::trunc ( double  a )

inlinestatic

Truncate double, i.e. round towards zero - common hardware instruction.

Parameters

a	Any doubleing-point value

Returns

Integer rounded towards zero, represented in doubleing-point format.

Note

This function might be superficially meaningless, but it helps us to write templated SIMD/non-SIMD code. For clarity it should not be used outside such code.

const char * gmx::unitCellTypeNames

(

UnitCellType

type

)

Get names for the different unit cell representation types.

Parameters

[in]

type

What name needs to be provided.

template<bool accumulate>

static auto gmx::unpackRecvBufKernel ( Float3 *__restrict__  gm_data, const Float3 *__restrict__  gm_dataPacked, const int *__restrict__  gm_map, int  mapSize  )

static

unpack non-local force data buffer on the GPU using pre-populated "map" containing index information.

Parameters

[out]	gm_data	full array of force values
[in]	gm_dataPacked	packed array of force values to be transferred
[in]	gm_map	array of indices defining mapping from full to packed array
[in]	mapSize	number of elements in map array

void gmx::update_ekinstate	(	ekinstate_t *	ekinstate,
		const gmx_ekindata_t &	ekind,
		const MpiComm &	mpiComm,
		const gmx_domdec_t *	dd
	)

Updates ekinstate.

Should be called on all ranks as a global reduction might be required. This copies ekind->ekinh and ekind->dekindl, which are assumed to be computed from the velocities at step at time t-dt/2.

Parameters

[out]	ekinstate	The kinetic energy state to update
[in]	ekind	The kinetic energy data to store
[in]	mpiComm	Communication data for my group, needed when ekind.needToReduceEkinhOld==true
[in]	dd	Domain decomposition object, pass nullptr when DD is not in use

void gmx::update_pcouple_after_coordinates	(	FILE *	fplog,
		int64_t	step,
		const PressureCouplingOptions &	pressureCoupling,
		int64_t	ld_seed,
		real	ensembleTemperature,
		const ivec *	nFreeze,
		const tensor	deform,
		real	delta_t,
		int	homenr,
		ArrayRef< const unsigned short >	cFREEZE,
		const matrix	pressure,
		const matrix	forceVirial,
		const matrix	constraintVirial,
		Matrix3x3 *	pressureCouplingMu,
		t_state *	state,
		t_nrnb *	nrnb,
		BoxDeformation *	boxDeformation,
		bool	scaleCoordinates
	)

Implement aspects of pressure coupling.

Always called after the coordinate update due to forces. This ensures that when the coordinates should be updated by pressure coupling, the box and the shift vectors remained consistent at the time of the coordinate update.

For Berendsen and c-rescale, on pressure-coupling steps:

• recalculate the scaling matrix mu,
• use mu to scale coordinates iff scaleCoordinates, doing positions always and velocites iff c-rescale
• use mu to update box size

For Parrinello-Rahman, on the step one before pressure-coupling steps:

• update the box according to the new velocity computed in parrinellorahman_pcoupl
• use mu to scale positions iff scaleCoordinates

For MTTK, on pressure-coupling steps:

• update the box according to state->veta
• recalculate the box velocity according to state->veta and the new box
• the positions are NOT scaled, as they are already scaled during the integration

When box deformation is active, always applies it.

/param[out] pressureCouplingMu Used later by the GPU update to scale the coordinates to suit the new box size

void gmx::updateCorrelationGridHistory	(	CorrelationGridHistory *	corrGridHist,
		const CorrelationGrid &	corrGrid
	)

Update the correlation grid history for checkpointing.

Parameters

[in,out]	corrGridHist	Correlation grid history to set.
[in]	corrGrid	Correlation grid state to read.

static void gmx::updateGlobalState ( t_state *  globalState, const PaddedHostVector< RVec > &  x, const PaddedHostVector< RVec > &  v, const tensor  box, int  ddpCount, int  ddpCountCgGl, const std::vector< int > &  cgGl  )

static

Update the legacy global state.

When restoring from checkpoint, data will be distributed during domain decomposition at setup stage. Domain decomposition still uses the legacy global t_state object so make sure it's up-to-date.

template<StoreUpdatedVelocities storeUpdatedVelocities, NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, typename VelocityType >

std::enable_if_t<std::is_same_v<VelocityType, RVec> || std::is_same_v<VelocityType, const RVec>, void> gmx::updateMDLeapfrogSimple	(	int	start,
		int	nrend,
		real	dt,
		real	dtPressureCouple,
		const RVec *gmx_restrict	invMassPerDim,
		ArrayRef< const t_grp_tcstat >	tcstat,
		ArrayRef< const unsigned short >	cTC,
		const RVec	pRVScaleMatrixDiagonal,
		const RVec *gmx_restrict	x,
		RVec *gmx_restrict	xprime,
		VelocityType *gmx_restrict	v,
		const RVec *gmx_restrict	f
	)

Integrate using leap-frog with T-scaling and optionally diagonal Parrinello-Rahman p-coupling.

Template Parameters

storeUpdatedVelocities	Tells whether we should store the updated velocities
numTempScaleValues	The number of different T-couple values
parrinelloRahmanVelocityScaling	The properties of the Parrinello-Rahman velocity scaling matrix

Parameters

[in]	start	Index of first atom to update
[in]	nrend	Last atom to update: nrend - 1
[in]	dt	The time step
[in]	dtPressureCouple	Time step for pressure coupling
[in]	invMassPerDim	1/mass per atom and dimension
[in]	tcstat	Temperature coupling information
[in]	cTC	T-coupling group index per atom
[in]	pRVScaleMatrixDiagonal	Parrinello-Rahman v-scale matrix diagonal
[in]	x	Input coordinates
[out]	xprime	Updated coordinates
[in,out]	v	Velocities, type either RVec* or const RVec*
[in]	f	Forces

We expect this template to get good SIMD acceleration by most compilers, unlike the more complex general template. For this reason, all the arrays of RVec should be annotated with gmx_restrict so the compiler knows there is no aliasing, and for the same reason we do not use ArrayRef<RVec> for them. Note that we might get even better SIMD acceleration when we introduce aligned (and padded) memory, possibly with some hints for the compilers.

static void gmx::updatePositions ( int  a, real  dt, const RVec *gmx_restrict  x, RVec *gmx_restrict  xprime, const RVec *gmx_restrict  v  )

inlinestatic

Update positions.

To maximize the ability of the compiler to optimize, all the arrays of RVec should be annotated with gmx_restrict, so the compiler knows there is no aliasing, and for the same reason we do not use ArrayRef<RVec> for them.

template<NumVelocityScalingValues numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, NumVelocityScalingValues numEndVelocityScalingValues>

static void gmx::updateVelocities ( int  a, real  dt, real  lambdaStart, real  lambdaEnd, const RVec *gmx_restrict  invMassPerDim, RVec *gmx_restrict  v, const RVec *gmx_restrict  f, const RVec &  diagPR, const Matrix3x3 &  matrixPR  )

inlinestatic

Update velocities.

To maximize the ability of the compiler to optimize, all the arrays of RVec should be annotated with gmx_restrict, so the compiler knows there is no aliasing, and for the same reason we do not use ArrayRef<RVec> for them.

static bool gmx::useLjCombRule ( const enum VdwType  vdwType )

inlinestatic

Returns true if LJ combination rules are used in the non-bonded kernels.

Parameters

[in]

vdwType

The VdW interaction/implementation type as defined by VdwType enumeration.

Returns

Whether combination rules are used by the run.

double gmx::v_lj_ewald_lr	(	double	beta,
		double	r
	)

Return the real space grid contribution for LJ-Ewald.

Parameters

beta	Ewald splitting parameter
r	Distance for which to calculate the real-space contrib

Returns

Real space grid contribution for Ewald Lennard-Jones interaction

double gmx::v_q_ewald_lr	(	double	beta,
		double	r
	)

Return the real space grid contribution for Ewald.

Parameters

beta	Ewald splitting parameter
r	Distance for which to calculate the real-space contrib

Returns

Real space grid contribution for Ewald electrostatics

static bool gmx::valueIsInGrid ( const awh_dvec  value, ArrayRef< const GridAxis >  axis  )

static

Query if a value is in range of the grid.

Parameters

[in]	value	Value to check.
[in]	axis	The grid axes.

Returns

true if the value is in the grid.

static bool gmx::valueIsInInterval ( double  origin, double  end, double  period, double  value  )

static

Checks if a value is within an interval.

Parameters

[in]	origin	Start value of interval.
[in]	end	End value of interval.
[in]	period	Period (or 0 if not periodic).
[in]	value	Value to check.

Returns

true if the value is within the interval.

template<typename ValueType >

bool gmx::valueTypeIsDataType ( const hid_t  dataType )

noexcept

Return true if the template value type matches the HDF5 data type.

Template Parameters

ValueType

Type of value to check.

Parameters

[in]

dataType

Handle to HDF5 data type to check against.

Returns

True if the types match, otherwise false.

template<typename ValueType >

bool gmx::valueTypeIsDataType ( const hid_t  dataType, const ArrayRef< const ValueType > gmx_unused  valueBuffer  )

noexcept

Return true if the template value type matches the HDF5 data type.

Helper function to allow for ValueType inference from a buffer.

Template Parameters

ValueType

Type of value to check.

Parameters

[in]	dataType	Handle to HDF5 data type to check against.
[in]	valueBuffer	Unused buffer which allows the compiler to infer the value type.

Returns

True if the types match, otherwise false.

template<>

bool gmx::valueTypeIsDataType< char * > ( const hid_t  dataType )

inlinenoexcept

Return true if the template value type matches the HDF5 data type.

Template Parameters

ValueType

Type of value to check.

Parameters

[in]

dataType

Handle to HDF5 data type to check against.

Returns

True if the types match, otherwise false. Specialization of valueTypeIsDataType() for char* type.

template<>

bool gmx::valueTypeIsDataType< const char * > ( const hid_t  dataType )

inlinenoexcept

Return true if the template value type matches the HDF5 data type.

Template Parameters

ValueType

Type of value to check.

Parameters

[in]

dataType

Handle to HDF5 data type to check against.

Returns

True if the types match, otherwise false. Specialization of valueTypeIsDataType() for const char* type.

template<>

bool gmx::valueTypeIsDataType< std::string > ( const hid_t  dataType )

inlinenoexcept

Return true if the template value type matches the HDF5 data type.

Template Parameters

ValueType

Type of value to check.

Parameters

[in]

dataType

Handle to HDF5 data type to check against.

Returns

True if the types match, otherwise false. Specialization of valueTypeIsDataType() for std::string type.

real gmx::vrescale_resamplekin	(	real	kk,
		real	sigma,
		real	ndeg,
		real	taut,
		int64_t	step,
		int64_t	seed
	)

Generate a new kinetic energy for the v-rescale thermostat.

Generates a new value for the kinetic energy, according to Bussi et al JCP (2007), Eq. (A7)

This is used by update_tcoupl(), and by the VRescaleThermostat of the modular simulator.

Todo:

Move this to the VRescaleThermostat once the modular simulator becomes the default code path.

Parameters

[in]	kk	present value of the kinetic energy of the atoms to be thermalized (in arbitrary units)
[in]	sigma	target average value of the kinetic energy (ndeg k_b T/2) (in the same units as kk)
[in]	ndeg	number of degrees of freedom of the atoms to be thermalized
[in]	taut	relaxation time of the thermostat, in units of 'how often this routine is called'
[in]	step	the time step this routine is called on
[in]	seed	the random number generator seed

Returns

the new kinetic energy

static int gmx::vsiteIlistNrCount ( const gmx::EnumerationArray< InteractionFunction, InteractionList > &  ilists )

static

Returns the sum of the vsite ilist sizes over all vsite types.

Parameters

[in]

ilists

The interaction list

void gmx::write_IMDgroup_to_file	(	bool	bIMD,
		t_inputrec *	ir,
		const t_state *	state,
		const gmx_mtop_t &	sys,
		int	nfile,
		const t_filenm	fnm[]
	)

Writes out the group of atoms selected for interactive manipulation.

Called by grompp. The resulting file has to be read in by VMD if one wants it to connect to mdrun.

Parameters

bIMD	Only springs into action if bIMD is TRUE. Otherwise returns directly.
ir	Structure containing MD input parameters, among those the IMD data structure.
state	The current state of the MD system.
sys	The global, complete system topology.
nfile	Number of files.
fnm	Filename struct.

void gmx::writeAtomicProperties	(	AtomRange &	atomRange,
		hid_t	baseContainer,
		const std::optional< IndexMap > &	selectedAtomsIndexMap = std::nullopt
	)

Write atomic properties to the H5MD file.

The result atomic properties are directly stored in the baseContainer. Atomic information includes:

• attribute:particle_count: The number of particles in the group
• dataset:particle_id: The unique identifier for the particle
• dataset:particle_name: The name of the particle, stored as an index to a lookup table
• dataset:particle_name_table (string[numUniqueNames]): The lookup table for particle names
• dataset:particle_species: The atomic number of the particle
• dataset:charge: The partial charge of the particle
• dataset:mass: The mass of the particle

Parameters

[in]	atomRange	Atom range for iterating all atoms and accessing atomic properties.
[in]	baseContainer	The HDF5 container to write the atomic properties to.
[in]	selectedAtomsIndexMap	The index map of the selected atoms, not provided means considering all atoms. Providing an empty map throws an internal error.

void gmx::writeBonds	(	const gmx_mtop_t &	topology,
		hid_t	baseContainer,
		const std::optional< IndexMap > &	selectedAtomsIndexMap = std::nullopt
	)

Write the covalent connectivity to the H5MD file.

The result bond connectivity is stored in the group <baseContainer>/bonds. The connectivity information is deduced from the topology and written as an [numBonds x 2] dataset of int64_t. If a selection is applied, only the bonds where both bonded particles are within the selection are considered.

Parameters

[in]	topology	The topology of the simulation system.
[in]	baseContainer	The HDF5 container to write the connectivity to.
[in]	selectedAtomsIndexMap	The index map of the selected atoms, not provided means considering all atoms. Providing an empty map throws an internal error.

void gmx::writeDisulfideBonds	(	const gmx_mtop_t &	topology,
		hid_t	baseContainer,
		const std::optional< IndexMap > &	selectedAtomsIndexMap = std::nullopt
	)

Write the additional annotation of disulfide bonds to the H5MD file.

The result bond connectivity is stored in the group <baseContainer>/disulfide_bonds.

Parameters

[in]	topology	The topology of the simulation system.
[in]	baseContainer	The HDF5 container to write the connectivity to.
[in]	selectedAtomsIndexMap	The index map of the selected atoms, not provided means considering all atoms. Providing an empty map throws an internal error.

void gmx::writeHeader	(	TextWriter *	writer,
		const std::string &	text,
		const std::string &	section,
		bool	writeFormattedText
	)

Write appropiate Header to output stream.

Parameters

[in]	writer	TextWriter object for writing information.
[in]	text	String with the header before writing.
[in]	section	String with section text for header.
[in]	writeFormattedText	If we need to format the text for LaTeX output or not

void gmx::writeInformation	(	TextOutputFile *	outputStream,
		const t_inputrec &	ir,
		const gmx_mtop_t &	top,
		bool	writeFormattedText,
		bool	notStdout
	)

Wrapper for writing out information.

This function is actual called from within the run method to write the information to the terminal or to file. New write out methods should be added to it instead of adding them in run.

Parameters

[in]	outputStream	The filestream used to write the information to.
[in]	ir	Reference to inputrec of the run input.
[in]	top	Local topology used to derive the information to write out.
[in]	writeFormattedText	Decide if we want formatted text output or not.
[in]	notStdout	Bool to see if we can close the file after writing or not in case of stdout.

void gmx::writeKeyValueTreeAsMdp	(	TextWriter *	writer,
		const KeyValueTreeObject &	tree
	)

Write a flat key-value tree to writer in mdp style.

Sub-objects will output nothing, so they can be used to contain a special key-value pair to create a comment, as well as the normal key and value. The comment pair will have a key of "comment", and the value will be used as a comment (if non-empty).

template<typename ValueType >

void gmx::writeKvtCheckpointValue	(	const ValueType &	value,
		std::string_view	name,
		std::string_view	identifier,
		KeyValueTreeObjectBuilder	kvtBuilder
	)

Write to a key-value-tree used for checkpointing.

Template Parameters

ValueType

Parameters

[in]	value	name of the value to be checkpointed
[in]	name	the value to be checkpointed
[in]	identifier	uniquely identifies the module that is checkpointing typically the module name
[in]	kvtBuilder	the key-value-tree builder used to store the checkpoint values

template void gmx::writeKvtCheckpointValue	(	const std::int64_t &	value,
		std::string_view	name,
		std::string_view	identifier,
		KeyValueTreeObjectBuilder	kvtBuilder
	)

Write to a key-value-tree used for checkpointing.

Template Parameters

ValueType

Parameters

[in]	value	name of the value to be checkpointed
[in]	name	the value to be checkpointed
[in]	identifier	uniquely identifies the module that is checkpointing typically the module name
[in]	kvtBuilder	the key-value-tree builder used to store the checkpoint values

template void gmx::writeKvtCheckpointValue	(	const real &	value,
		std::string_view	name,
		std::string_view	identifier,
		KeyValueTreeObjectBuilder	kvtBuilder
	)

Write to a key-value-tree used for checkpointing.

Template Parameters

ValueType

Parameters

[in]	value	name of the value to be checkpointed
[in]	name	the value to be checkpointed
[in]	identifier	uniquely identifies the module that is checkpointing typically the module name
[in]	kvtBuilder	the key-value-tree builder used to store the checkpoint values

void gmx::writeMoleculeBlocks	(	hid_t	baseContainer,
		ArrayRef< const gmx_molblock_t >	molBlocks,
		ArrayRef< const gmx_moltype_t >	molTypes
	)

Write the molecule block information to the HDF5 container of GROMACS topology.

Note

The resulting names and counts of molecule blocks are stored in the base container as attributes.

Parameters

[in]	baseContainer	The HDF5 container to write the topology information to.
[in]	molBlocks	The molecule blocks to write.
[in]	molTypes	The molecule types corresponding to the molecule blocks, used for providing the name of each molecule block.

void gmx::writeMoleculeTypes	(	hid_t	baseContainer,
		ArrayRef< const gmx_moltype_t >	molTypes
	)

Write the internal representation of molecules molTypes to the HDF5 container baseContainer of GROMACS topology.

The hierarchy is as follows:

/h5md/modules/gromacs_topology (group (baseContainer) for the GROMACS topology) -- molecule1 (group for molecule 1, same group name as molecule_block_names[0] ) ++ particle_count (attribute for the number of particles in molecule 1) ++ residue_count (attribute for the number of residues in molecule 1) -- id (dataset for the atomic identifier in molecule 1) -- mass (dataset for the atomic masses in molecule 1) -- charge (dataset for the atomic charges in molecule 1) -- species (dataset for the atomic species (atomic number) in molecule 1) -- particle_name (dataset for the atomic names (indices into particle name table) in molecule 1) -- particle_name_table (dataset for the atomic name lookup table in molecule 1) -- residue_id (dataset for the residue identifier in molecule 1) -- sequence (dataset for the residue sequence (indices into residue name table) in molecule 1) -- residue_name (dataset for the residue names (indices into residue name table) in molecule 1) -- residue_name_table (dataset for the residue name lookup table in molecule 1)

Parameters

[in]	baseContainer	The HDF5 container to write to
[in]	molTypes	The molecule types to write

void gmx::writeNextFrame	(	H5md *	h5md,
		ArrayRef< const RVec >	positions,
		ArrayRef< const RVec >	velocities,
		ArrayRef< const RVec >	forces,
		const matrix	box,
		int64_t	step,
		double	time
	)

Write input data as the next frame of the trajectory.

Parameters

[out]	h5md	Handle to H5md object
[in]	positions	Position data to write (or empty if not to write).
[in]	velocities	Velocity data to write (or empty if not to write).
[in]	forces	Force data to write (or empty if not to write).
[in]	box	Simulation box for frame.
[in]	step	Simulation step for frame.
[in]	time	Simulation time for frame.

Exceptions

H5mdError

if position, velocity or force data is given but the corresponding data set has not been created, or if the size of the data buffers do not match the number of atoms of the system.

void gmx::writeParameterInformation	(	TextWriter *	writer,
		const t_inputrec &	ir,
		bool	writeFormattedText
	)

Write information about system parameters.

This method writes the basic information for the system parameters and simulation settings as reported in the ir.

Parameters

[in]	writer	TextWriter object for writing information.
[in]	ir	Reference to inputrec of the run input.
[in]	writeFormattedText	Decide if we want formatted text output or not.

void gmx::writeResidueInfo	(	AtomRange &	atomRange,
		hid_t	baseContainer,
		const std::optional< IndexMap > &	selectedAtomsIndexMap = std::nullopt
	)

Write residue and sequence information to the H5MD file.

The result residue-related information is stored in the group baseContainer/<groupName>. Including:

• residue_id: The unique identifier for the residue
• sequence: The sequence of residues, stored as indices to the lookup table residue_name_table
• residue_name: The name of the residue, stored as indices to the lookup table residue_name_table
• residue_name_table (string[numUniqueResidueNames]): The lookup table for residue names

Parameters

[in]	atomRange	Atom range for iterating all atoms and accessing atomic properties.
[in]	baseContainer	The HDF5 container to write the residue information to.
[in]	selectedAtomsIndexMap	The index map of the selected atoms, not provided means considering all atoms. Providing an empty map throws an internal error.

void gmx::writeSystemInformation	(	TextWriter *	writer,
		const gmx_mtop_t &	top,
		bool	writeFormattedText
	)

Write information about the molecules in the system.

This method should write all possible information about the molecular composition of the system.

Parameters

[in]	writer	TextWriter object for writing information.
[in]	top	Local topology used to derive the information to write out.
[in]	writeFormattedText	Decide if we want formatted text output or not.

Variable Documentation

const EnumerationArray<ActiveFmmBackend, const char*> gmx::c_activeFmmBackendNames

static

Initial value:

= {
    { "inactive", "exafmm", "fmsolvr" }
}

String names corresponding to ActiveFmmBackend enum values.

constexpr Architecture gmx::c_architecture

static

Initial value:

=













        Architecture::Unknown

Constant that tells what the architecture is.

const EnumerationArray<ChangeAtomsType, const char*> gmx::c_changeAtomsTypeNames

static

Initial value:

= {
    { "preserved-if-present", "always-from-structure", "never", "always" }
}

Mapping for enums from ChangeAtomsType.

const EnumerationArray<ChangeSettingType, const char*> gmx::c_changeSettingTypeNames

static

Initial value:

= {
    { "preserved-if-present", "always", "never" }
}

Mapping for enums from ChangeSettingType.

const EnumerationArray<DensityFittingAmplitudeMethod, const char*> gmx::c_densityFittingAmplitudeMethodNames

static

Initial value:

= {
    { "unity", "mass", "charge" }
}

The names of the methods to determine the amplitude of the atoms to be spread on a grid.

const EnumerationArray<DensitySimilarityMeasureMethod, const char*> gmx::c_densitySimilarityMeasureMethodNames

static

Initial value:

= {
    { "inner-product", "relative-entropy", "cross-correlation" }
}

Name the methods that may be used to evaluate similarity between densities.

constexpr double gmx::c_epsilon0

Initial value:

=
        ((c_epsilon0Si * c_nano * c_kilo) / (c_electronCharge * c_electronCharge * c_avogadro))

const EnumerationArray<ExaFmmTreeType, const char*> gmx::c_exaFmmTreeTypeNames

static

Initial value:

= {
    { "uniform", "adaptive" }
}

String names corresponding to ExaFmmTreeType enum values.

const EnumerationArray<FmmDirectProvider, const char*> gmx::c_fmmDirectProviderNames

static

Initial value:

= {
    { "GROMACS", "FMM" }
}

String names corresponding to FmmDirectProvider enum values.

const std::string gmx::c_fmmExaFmmMaxParticlesPerCellOptionName = "exafmm-max-particles-per-cell"

MDP option name to set the maximum number of particles per cell for ExaFMM.

• Used only when an adaptive tree is used
• Must not be set when using a uniform tree

const std::string gmx::c_fmmExaFmmTreeDepthOptionName = "exafmm-tree-depth"

MDP option name to set the tree depth for ExaFMM.

• Required when using a uniform tree and the direct provider is FMM
• When the direct provider is GROMACS, the tree depth is determined based on the domain decomposition grid and should not be set by the user.

const std::string gmx::c_fmmExaFmmTreeTypeOptionName = "exafmm-tree-type"

MDP option name to choose the tree type for ExaFMM (uniform or adaptive)

• Must be uniform when the direct provider is GROMACS
• If using an adaptive tree, maximum particles per cell must be specified

constexpr InteractionFunction gmx::c_ftypeVsiteEnd

static

Initial value:

=
        InteractionFunction::CenterOfMassPullingEnergy

The start and end value of the vsite indices in the ftype enum.

constexpr InteractionFunction gmx::c_ftypeVsiteStart = InteractionFunction::VirtualSite1

static

The start value of the vsite indices in the ftype enum.

The validity of the start and end values is checked in makeVirtualSitesHandler(). This is used to avoid loops over all ftypes just to get the vsite entries. (We should replace the fixed ilist array by only the used entries.)

constexpr real gmx::c_maxRInvSix = 1.0e15_real

Higher limit for r^-6 used for Lennard-Jones interactions.

This is needed to avoid overflow of LJ energy and force terms for excluded atoms and foreign energies of hard-core states of overlapping atoms. Note that in single precision this value leaves room for C12 coefficients up to 3.4e8.

const real gmx::c_maxSpacingScaling = 1.7

Scale the grid by a most at factor 1.7.

This still leaves room for about 4-4.5x decrease in grid spacing while limiting the cases where large imbalance leads to extreme cutoff scaling for marginal benefits.

This should help to avoid:

• large increase in power consumption for little performance gain
• increasing communication volume
• limiting DLB

constexpr real gmx::c_minDistanceSquared = 1.0e-12_real

Lower limit for square interaction distances in nonbonded kernels.

This is a minimum on r^2 to avoid overflows when computing r^6. This will only affect results for soft-cored interaction at distances smaller than 1e-6 and will limit extremely high foreign energies for overlapping atoms. Note that we could use a somewhat smaller minimum in double precision. But because invsqrt in double precision can use single precision, this number can not be much smaller, we use the same number for simplicity.

const int gmx::c_nbnxmCpuDynamicListPruningMinLifetime = 5

static

The minimum nstlist for dynamic pair list pruning on CPUs.

In most cases going lower than 5 will lead to a too high pruning cost.

constexpr int gmx::c_nbnxmGpuDynamicListPruningMinLifetime = 4

static

The minimum nstlist for dynamic pair list pruning om GPUs.

In most cases going lower than 4 will lead to a too high pruning cost. This value should be a multiple of c_nbnxmGpuRollingListPruningInterval

constexpr int gmx::c_nbnxmGpuRollingListPruningInterval = 2

static

The interval in steps at which we perform dynamic, rolling pruning on a GPU.

Ideally we should auto-tune this value. Not considering overheads, 1 would be the ideal value. But 2 seems a reasonable compromise that reduces GPU kernel launch overheads and also avoids inefficiency on large GPUs when pruning small lists. Because with domain decomposition we alternate local/non-local pruning at even/odd steps, which gives a period of 2, this value currenly needs to be 2, which is indirectly asserted when the GPU pruning is dispatched during the force evaluation.

constexpr float gmx::c_nbnxmMinDistanceSquared = 3.82e-07F

Lower limit for square interaction distances in nonbonded kernels.

For smaller values we will overflow when calculating r^-1 or r^-12, but to keep it simple we always apply the limit from the tougher r^-12 condition.

const EnumerationArray<QMMMElectrostaticCoupling, const char*> gmx::c_qmmmElectrostaticCouplingNames

static

Initial value:

= {
    { "point-charge", "gauss" }
}

Names of the supported QM/MM electrostatic coupling modes for tight-binding methods in CP2K.

const EnumerationArray<QMMMQMMethod, const char*> gmx::c_qmmmQMMethodNames

static

Initial value:

= { { "PBE",
                                                                                   "PBE-D3",
                                                                                   "BLYP",
                                                                                   "BLYP-D3",
                                                                                   "PBE0",
                                                                                   "PBE0-D3",
                                                                                   "B3LYP",
                                                                                   "B3LYP-D3",
                                                                                   "CAM-B3LYP",
                                                                                   "CAM-B3LYP-D3",
                                                                                   "WB97X",
                                                                                   "WB97X-D3",
                                                                                   "SCC-DFTB",
                                                                                   "GFN1-xTB",
                                                                                   "GFN2-xTB",
                                                                                   "INPUT" } }

The names of the supported QM methods.

const EnumerationArray<RotationType, const char*> gmx::c_rotationTypeNames

static

Initial value:

= {
    { "xyz", "z", "none" }
}

constexpr int gmx::c_sciHistogramSize = 8192

static

Number of separate bins used during sorting of plist on gpu.

Ideally this number would be increased for very large system sizes (the cpu version of sorting uses 2 x avg(num cjPacked) but as sorting has negligible impact for very large system sizes we use a constant here for simplicity. On H100 sorting begins to have negligible effect for system sizes greater than ~400k atoms.

constexpr int gmx::c_sciSortingThreadsPerBlock = 256

static

Number of threads per block used by the gpu sorting kernel.

TODO this is a reasonable default but the number has not been tuned

constexpr int gmx::c_syclPruneKernelJPackedConcurrency = c_pruneKernelJPackedConcurrency

static

Prune kernel's jPacked processing concurrency.

The GMX_NBNXM_PRUNE_KERNEL_JPACKED_CONCURRENCY macro allows compile-time override.

constexpr bool gmx::c_useDelayedWait = false

static

Block to wait for communication to PME ranks to complete.

This should be faster with a real non-blocking MPI implementation

const gmx::EnumerationArray<XvgFormat, const char*> gmx::c_xvgFormatNames

Initial value:

= {
    { "xmgrace", "xmgr", "none" }
}

Names for XvgFormat.

Technically this duplicates a definition in pargs.cpp for legacy support code, but as the latter will go away and the alternatives are ugly, the duplication is acceptable.

constexpr EnumerationArray<ChannelHistory, const char*> gmx::ChannelString

static

Initial value:

= { "none",
                                                                                 "channel0",
                                                                                 "channel1" }

Names for the channels.

const t_dirname gmx::ddb_dirnames[DDB_DIR_NR]

static

Initial value:

= { "CH3", "NH3",  "NH2",  "PHE", "TYR",
                                                    "TRP", "HISA", "HISB", "HISH" }

const int gmx::ddNonbondedZonePairRanges[sc_maxNumIZones][3]

static

Initial value:

= { { 0, 0, 8 },
                                                                   { 1, 3, 6 },
                                                                   { 2, 5, 6 },
                                                                   { 3, 5, 7 } }

The non-bonded zone-pair setup for domain decomposition.

The first number is the i-zone, the second number the first j-zone seen by this i-zone, the third number the last+1 j-zone seen by this i-zone. As is, this is for 3D decomposition, where there are 4 i-zones. With 2D decomposition use only the first 2 i-zones and a last+1 j-zone of 4. With 1D decomposition use only the first i-zone and a last+1 j-zone of 2.

constexpr EnumerationArray<Domain, const char*> gmx::DomainString

static

Initial value:

= { "not_assigned",
                                                                        "Domain_A",
                                                                        "Domain_B" }

Names for the domains.

gmx::dvdlElecForeign

Initial value:

{ hostAllocationPolicy }
{

    {
        const size_t newSize = nLambda.value() + 1;
        eLJForeign.resize(newSize);
        eElecForeign.resize(newSize);
        dvdlLJForeign.resize(newSize);
        dvdlElecForeign.resize(newSize);
    }
}

NbnxmGpu::NbnxmGpu(const DeviceStreamManager& deviceStreamManager, std::optional<size_t> nLambda) :
    deviceContext{ deviceStreamManager.context() }

const shift_consts_t const float const float const float const float const float float float* gmx::eLJ

Initial value:

{
    
    const float dispShiftV2 = dispersionShift.c2

gmx::else

Initial value:

{
        
        *f += -c6 * (dispShiftV2 + dispShiftV3 * rSwitch) * rSwitch * rSwitch * rInv
              + c12 * (repuShiftV2 + repuShiftV3 * rSwitch) * rSwitch * rSwitch * rInv

const float gmx::epsilon

Initial value:

{
    const float sigma2 = sigma * sigma

constexpr std::array<InteractionFunction, numFTypesOnGpu> gmx::fTypesOnGpu

Initial value:

= {
    InteractionFunction::Bonds,
    InteractionFunction::Angles,
    InteractionFunction::UreyBradleyPotential,
    InteractionFunction::ProperDihedrals,
    InteractionFunction::RyckaertBellemansDihedrals,
    InteractionFunction::ImproperDihedrals,
    InteractionFunction::PeriodicImproperDihedrals,
    InteractionFunction::LennardJones14
}

List of all bonded function types supported on GPUs.

Note

This list should be in sync with the actual GPU code.

Perturbed interactions are not supported on GPUs.

The function types in the list are ordered on increasing value.

Currently bonded are only supported with CUDA and SYCL, not with OpenCL.

BondedGpuKernelBuffers float4 float3 float3* gmx::gm_fShift

Initial value:

{
    assert( blockDim.y == 1 && blockDim.z == 1 )

unsigned int gmx::gpu_min_ci_balanced_factor = 50

static

This parameter should be determined heuristically from the kernel execution times.

This value is best for small systems on a single AMD Radeon R9 290X (and about 5% faster than 40, which is the default for CUDA devices). Larger simulation systems were quite insensitive to the value of this parameter.

constexpr gmx::EnumerationArray<PairlistType, int> gmx::IClusterSizePerListType

static

Initial value:

= {
    { 4, 4, 4, sc_gpuClusterSize(PairlistType::Hierarchical8x8x8), 1 }
}

Gives the i-cluster size for each pairlist type.

const char gmx::IMDstr[] = "IMD:"

static

Tag output from the IMD module with this string.

constexpr gmx::EnumerationArray<PairlistType, int> gmx::JClusterSizePerListType

static

Initial value:

= {
    { 2, 4, 8, sc_gpuClusterSize(PairlistType::Hierarchical8x8x8), 1 }
}

Gives the j-cluster size for each pairlist type.

const char* gmx::kernel_electrostatic_family_definitions[]

static

Initial value:

= {
    " -DEL_CUTOFF -DEELNAME=_ElecCut",
    " -DEL_RF -DEELNAME=_ElecRF",
    " -DEL_EWALD_TAB -DEELNAME=_ElecEwQSTab",
    " -DEL_EWALD_TAB -DVDW_CUTOFF_CHECK -DEELNAME=_ElecEwQSTabTwinCut",
    " -DEL_EWALD_ANA -DEELNAME=_ElecEw",
    " -DEL_EWALD_ANA -DVDW_CUTOFF_CHECK -DEELNAME=_ElecEwTwinCut"
}

Array of the defines needed to generate a specific eel flavour.

The twin-cutoff entries are not normally used, because those setups are not available to the user. FastGen takes care of generating both single- and twin-cutoff versions because PME tuning might need both.

const char* gmx::kernel_VdW_family_definitions[]

static

Initial value:

= {
    " -DVDWNAME=_VdwLJ",
    " -DLJ_COMB_GEOM -DVDWNAME=_VdwLJCombGeom",
    " -DLJ_COMB_LB -DVDWNAME=_VdwLJCombLB",
    " -DLJ_FORCE_SWITCH -DVDWNAME=_VdwLJFsw",
    " -DLJ_POT_SWITCH -DVDWNAME=_VdwLJPsw",
    " -DLJ_EWALD_COMB_GEOM -DVDWNAME=_VdwLJEwCombGeom",
    " -DLJ_EWALD_COMB_LB -DVDWNAME=_VdwLJEwCombLB"
}

Array of the defines needed to generate a specific vdw flavour.

const gmx::EnumerationArray<MtsForceGroups, std::string> gmx::mtsForceGroupNames

static

Initial value:

= {
    "longrange-nonbonded", "nonbonded", "pair", "dihedral", "angle", "pull", "awh"
}

Names for the MTS force groups.

constexpr unsigned int gmx::NBNXM_INTERACTION_MASK_ALL = 0xffffffffU

Cluster-pair Interaction masks.

Bit i*j-cluster-size + j tells if atom i and j interact.All interaction mask is the same for all kernels

const int gmx::nbnxmReferenceNstlist = 10

static

Cost of non-bonded kernels.

We determine the extra cost of the non-bonded kernels compared to a reference nstlist value of 10 (which is the default in grompp).

const std::vector<std::string> gmx::periodic_system

Initial value:

= {
    "X  ", "H  ", "He ", "Li ", "Be ", "B  ", "C  ", "N  ", "O  ", "F  ", "Ne ", "Na ",
    "Mg ", "Al ", "Si ", "P  ", "S  ", "Cl ", "Ar ", "K  ", "Ca ", "Sc ", "Ti ", "V  ",
    "Cr ", "Mn ", "Fe ", "Co ", "Ni ", "Cu ", "Zn ", "Ga ", "Ge ", "As ", "Se ", "Br ",
    "Kr ", "Rb ", "Sr ", "Y  ", "Zr ", "Nb ", "Mo ", "Tc ", "Ru ", "Rh ", "Pd ", "Ag ",
    "Cd ", "In ", "Sn ", "Sb ", "Te ", "I  ", "Xe ", "Cs ", "Ba ", "La ", "Ce ", "Pr ",
    "Nd ", "Pm ", "Sm ", "Eu ", "Gd ", "Tb ", "Dy ", "Ho ", "Er ", "Tm ", "Yb ", "Lu ",
    "Hf ", "Ta ", "W  ", "Re ", "Os ", "Ir ", "Pt ", "Au ", "Hg ", "Tl ", "Pb ", "Bi ",
    "Po ", "At ", "Rn ", "Fr ", "Ra ", "Ac ", "Th ", "Pa ", "U  ", "Np ", "Pu ", "Am ",
    "Cm ", "Bk ", "Cf ", "Es ", "Fm ", "Md ", "No ", "Lr ", "Rf ", "Db ", "Sg ", "Bh ",
    "Hs ", "Mt ", "Ds ", "Rg ", "Cn ", "Nh ", "Fl ", "Mc ", "Lv ", "Ts ", "Og "
}

symbols of the elements in periodic table

const EnumerationArray<IncompatibilityReasons, std::string> gmx::reasonStrings

static

Initial value:

= {
    "flexible constraints are present",
    "an incompatible virtual site type is used",
    "the construction atoms of a virtual site are only partly with a group of constrained atoms",
    "atoms that are (in)directly constrained together are interdispersed with other atoms",
    "there are three or more consecutively coupled constraints"
}

Strings explaining why the system is incompatible with update groups.

constexpr int32_t gmx::sc_atomInfo_FreeEnergyPerturbation = 1 << 8

static

Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo.

No bit should exceed 1 << 31, so that it fits into a 32-bit integer.

Since the tpx format support max 256 energy groups, we do the same here, reserving bits 0-7 for the energy-group ID.

const ivec gmx::sc_ddZoneOrder[sc_maxNumZones]

static

Initial value:

= { { 0, 0, 0 }, { 1, 0, 0 }, { 1, 1, 0 },
                                                     { 0, 1, 0 }, { 0, 1, 1 }, { 0, 0, 1 },
                                                     { 1, 0, 1 }, { 1, 1, 1 } }

The DD zone order.

constexpr auto gmx::sc_torchRealType = GMX_DOUBLE ? torch::kFloat64 : torch::kFloat32

static

Define the torch datatype according to GMX_DOUBLE.

Important for converting data types, as model inference is always done in float32.

const t_tab_props gmx::tprops[etabNR]

static

Initial value:

= {
    { "LJ6", FALSE },         { "LJ12", FALSE },      { "LJ6Shift", FALSE },
    { "LJ12Shift", FALSE },   { "Shift", TRUE },      { "RF", TRUE },
    { "RF-zero", TRUE },      { "COUL", TRUE },       { "Ewald", TRUE },
    { "Ewald-Switch", TRUE }, { "Ewald-User", TRUE }, { "Ewald-User-Switch", TRUE },
    { "LJ6Ewald", FALSE },    { "LJ6Switch", FALSE }, { "LJ12Switch", FALSE },
    { "COULSwitch", TRUE },   { "EXPMIN", FALSE },    { "USER", FALSE },
}

const std::array<InteractionFunction, numFtypes> gmx::vSiteFunctionTypes

Initial value:

= {
    InteractionFunction::VirtualSite1,
    InteractionFunction::VirtualSite2,
    InteractionFunction::VirtualSite2FlexibleDistance,
    InteractionFunction::VirtualSite3,
    InteractionFunction::VirtualSite3FlexibleDistance,
    InteractionFunction::VirtualSite3FlexibleAngleDistance,
    InteractionFunction::VirtualSite3Outside,
    InteractionFunction::VirtualSite4FlexibleDistance,
    InteractionFunction::VirtualSite4FlexibleDistanceNormalization,
    InteractionFunction::VirtualSiteN
}

const std::array<InteractionFunction, numFtypes> gmx::vSiteFunctionTypesReversed

Initial value:

= {
    InteractionFunction::VirtualSiteN,
    InteractionFunction::VirtualSite4FlexibleDistanceNormalization,
    InteractionFunction::VirtualSite4FlexibleDistance,
    InteractionFunction::VirtualSite3Outside,
    InteractionFunction::VirtualSite3FlexibleAngleDistance,
    InteractionFunction::VirtualSite3FlexibleDistance,
    InteractionFunction::VirtualSite3,
    InteractionFunction::VirtualSite2FlexibleDistance,
    InteractionFunction::VirtualSite2,
    InteractionFunction::VirtualSite1
}