Description

Generic GROMACS namespace.

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

Declares registerLegacyModules().

Declares the integrators for energy minimization and NMA.

Encapsulates membed methods.

Declares the simulator interface for mdrun.

Defines the dispatch function for the .mdp integrator field.

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

Author: David van der Spoel david.nosp@m..van.nosp@m.dersp.nosp@m.oel@.nosp@m.icm.u.nosp@m.u.se; Mark Abraham mark..nosp@m.j.ab.nosp@m.raham.nosp@m.@gma.nosp@m.il.co.nosp@m.m

Author: Joe Jordan ejjor.nosp@m.dan@.nosp@m.kth.s.nosp@m.e; David van der Spoel david.nosp@m..van.nosp@m.dersp.nosp@m.oel@.nosp@m.icm.u.nosp@m.u.se

Author: Teemu Murtola teemu.nosp@m..mur.nosp@m.tola@.nosp@m.gmai.nosp@m.l.com

Namespaces
	anonymous_namespace{alignedallocator.cpp}

	anonymous_namespace{analysismodule.cpp}

	anonymous_namespace{arrayref.cpp}

	anonymous_namespace{arrayrefwithpadding.cpp}

	anonymous_namespace{autocorr.cpp}

	anonymous_namespace{awh_history.cpp}

	anonymous_namespace{bench_system.cpp}

	anonymous_namespace{biasgrid.cpp}

	anonymous_namespace{biasparams.cpp}

	anonymous_namespace{biassharing.cpp}

	anonymous_namespace{biasstate.cpp}

	anonymous_namespace{biaswriter.cpp}

	anonymous_namespace{boxutilities.cpp}

	anonymous_namespace{calc_verletbuf.cpp}

	anonymous_namespace{clfftinitializer.cpp}

	anonymous_namespace{cmdlinehelpcontext.cpp}

	anonymous_namespace{cmdlinehelpmodule.cpp}

	anonymous_namespace{cmdlinehelpwriter.cpp}

	anonymous_namespace{cmdlineinit.cpp}

	anonymous_namespace{cmdlinemodulemanager.cpp}

	anonymous_namespace{cmdlineoptionsmodule.cpp}

	anonymous_namespace{cmdlineprogramcontext.cpp}

	anonymous_namespace{cmdlinerunner.cpp}

	anonymous_namespace{com.cpp}

	anonymous_namespace{computeglobalselement.cpp}

	anonymous_namespace{convert_tpr.cpp}

	anonymous_namespace{coolstuff.cpp}

	anonymous_namespace{coordstate.cpp}

	anonymous_namespace{correlationgrid.cpp}

	anonymous_namespace{correlationtensor.cpp}

	anonymous_namespace{cpuinfo.cpp}

	anonymous_namespace{cubicsplinetable.cpp}

	anonymous_namespace{decidegpuusage.cpp}

	anonymous_namespace{densityfit.cpp}

	anonymous_namespace{densityfitting.cpp}

	anonymous_namespace{densityfittingamplitudelookup.cpp}

	anonymous_namespace{densityfittingforceprovider.cpp}

	anonymous_namespace{densityfittingoptions.cpp}

	anonymous_namespace{devicetransfers_ocl.cpp}

	anonymous_namespace{dump.cpp}

	anonymous_namespace{electricfield.cpp}

	anonymous_namespace{energydata.cpp}

	anonymous_namespace{energydrifttracker.cpp}

	anonymous_namespace{entropy.cpp}

	anonymous_namespace{enumerationhelpers.cpp}

	anonymous_namespace{errorcodes.cpp}

	anonymous_namespace{exceptions.cpp}

	anonymous_namespace{exclusionblocks.cpp}

	anonymous_namespace{expandedensembleelement.cpp}

	anonymous_namespace{expfit.cpp}

	anonymous_namespace{exponentialdistribution.cpp}

	anonymous_namespace{filenameoption.cpp}

	anonymous_namespace{filenameoptionmanager.cpp}

	anonymous_namespace{fileredirector.cpp}

	anonymous_namespace{filestream.cpp}

	anonymous_namespace{findallgputasks.cpp}

	anonymous_namespace{firstorderpressurecoupling.cpp}

	anonymous_namespace{fixedcapacityvector.cpp}

	anonymous_namespace{freeenergyparameters.cpp}

	anonymous_namespace{freeenergyperturbationdata.cpp}

	anonymous_namespace{futil.cpp}

	anonymous_namespace{gammadistribution.cpp}

	anonymous_namespace{gausstransform.cpp}

	anonymous_namespace{gmx_covar.cpp}

	anonymous_namespace{gpp_atomtype.cpp}

	anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}

	anonymous_namespace{handlerestart.cpp}

	anonymous_namespace{hardwaretopology.cpp}

	anonymous_namespace{helpwritercontext.cpp}

	anonymous_namespace{histogram.cpp}

	anonymous_namespace{histogramsize.cpp}

	anonymous_namespace{idef.cpp}

	anonymous_namespace{identifyavx512fmaunits.cpp}

	anonymous_namespace{ikeyvaluetreeerror.cpp}

	anonymous_namespace{init.cpp}

	anonymous_namespace{inmemoryserializer.cpp}

	anonymous_namespace{insert_molecules.cpp}

	anonymous_namespace{keyvaluetree.cpp}

	anonymous_namespace{keyvaluetreeserializer.cpp}

	anonymous_namespace{keyvaluetreetransform.cpp}

	anonymous_namespace{listoflists.cpp}

	anonymous_namespace{logger.cpp}

	anonymous_namespace{manyautocorrelation.cpp}

	anonymous_namespace{mdmodulesnotifier.cpp}

	anonymous_namespace{mdspan.cpp}

	anonymous_namespace{message_string_collector.cpp}

	anonymous_namespace{modules.cpp}

	anonymous_namespace{mrcdensitymap.cpp}

	anonymous_namespace{mrcdensitymapheader.cpp}

	anonymous_namespace{mrcserializer.cpp}

	anonymous_namespace{mtop.cpp}

	anonymous_namespace{mttk.cpp}

	anonymous_namespace{multipletimestepping.cpp}

	anonymous_namespace{nbsearch.cpp}

	anonymous_namespace{neldermead.cpp}

	anonymous_namespace{nonbonded_bench.cpp}

	anonymous_namespace{normaldistribution.cpp}

	anonymous_namespace{nosehooverchains.cpp}

	anonymous_namespace{optionsection.cpp}

	anonymous_namespace{optionsvisitor.cpp}

	anonymous_namespace{pargs.cpp}

	anonymous_namespace{parrinellorahmanbarostat.cpp}

	anonymous_namespace{path.cpp}

	anonymous_namespace{pdb2gmx.cpp}

	anonymous_namespace{physicalnodecommunicator.cpp}

	anonymous_namespace{pointstate.cpp}

	anonymous_namespace{poscalc.cpp}

	anonymous_namespace{programcontext.cpp}

	anonymous_namespace{propagator.cpp}

	anonymous_namespace{pull.cpp}

	anonymous_namespace{pullelement.cpp}

	anonymous_namespace{qmmm.cpp}

	anonymous_namespace{qmmmforceprovider.cpp}

	anonymous_namespace{qmmmoptions.cpp}

	anonymous_namespace{quadraticsplinetable.cpp}

	anonymous_namespace{range.cpp}

	anonymous_namespace{read_params.cpp}

	anonymous_namespace{report_methods.cpp}

	anonymous_namespace{reportgpuusage.cpp}

	anonymous_namespace{rstparser.cpp}

	anonymous_namespace{seed.cpp}

	anonymous_namespace{selectioncollection.cpp}

	anonymous_namespace{selhelp.cpp}

	anonymous_namespace{shake.cpp}

	anonymous_namespace{shellcompletions.cpp}

	anonymous_namespace{simd_memory.cpp}

	anonymous_namespace{statepropagatordata.cpp}

	anonymous_namespace{stringtoenumvalueconverter.cpp}

	anonymous_namespace{stringutil.cpp}

	anonymous_namespace{tabulatednormaldistribution.cpp}

	anonymous_namespace{taskassignment.cpp}

	anonymous_namespace{template_mp.cpp}

	anonymous_namespace{threaded_force_buffer.cpp}

	anonymous_namespace{threefry.cpp}

	anonymous_namespace{timeunitmanager.cpp}

	anonymous_namespace{topologyinformation.cpp}

	anonymous_namespace{topsort.cpp}

	anonymous_namespace{transformationcoordinate.cpp}

	anonymous_namespace{treesupport.cpp}

	anonymous_namespace{uniformintdistribution.cpp}

	anonymous_namespace{uniformrealdistribution.cpp}

	anonymous_namespace{updategroups.cpp}

	anonymous_namespace{updategroupscog.cpp}

	anonymous_namespace{velocityscalingtemperaturecoupling.cpp}

	anonymous_namespace{wholemoleculetransform.cpp}

	compat
	Compatibility aliases for standard library features.

	detail

	internal
	Internal GROMACS namespace.

	test
	Testing utilities namespace.

Classes
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	AnalysisDataModuleManager
	Encapsulates handling of data modules attached to AbstractAnalysisData. More...

class	AnalysisDataProxy
	Internal implementation class used to implement column modules. 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	AnalysisDataFrameLocalDataSetHandle
	Handle to a single data set within frame-local data array. More...

class	AnalysisDataFrameLocalDataHandle
	Handle to a single frame data within frame-local data array. More...

class	AnalysisDataFrameLocalData
	Container for an array of frame-local values that supports parallel data processing. 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	AnalysisDataFrameAverager
	Helper class for modules that average values over frames. 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...

class	AnalysisDataParallelOptions
	Parallelization options for analysis data objects. More...

struct	BiasCoupledToSystem
	A bias and its coupling to the system. More...

class	Awh
	Coupling of the accelerated weight histogram method (AWH) with the system. More...

class	Bias
	A bias acting on a multidimensional coordinate. More...

class	GridAxis
	An axis, i.e. dimension, of the grid. More...

struct	GridPoint
	A point in the grid. More...

class	BiasGrid
	The grid for a single bias, generally multidimensional and periodic. More...

class	BiasParams
	Constant parameters for the bias. More...

class	BiasState
	The state of a bias. More...

class	AwhEnergyBlock
	AWH output data block that can be written to an energy file block. More...

class	BiasWriter
	Class organizing the output data storing and writing of an AWH bias. More...

class	CoordState
	Keeps track of the current coordinate value, grid index and umbrella location. More...

class	CorrelationGrid
	BiasGrid of local correlation tensors. More...

class	CorrelationBlockData
	Correlation block averaging weight-only data. More...

class	CorrelationTensor
	Correlation data for computing the correlation tensor of one grid point. More...

struct	DimParams
	Constant parameters for each dimension of the coordinate. More...

class	HistogramSize
	Tracks global size related properties of the bias histogram. More...

class	PointState
	The state of a coordinate point. More...

struct	DensityFittingModuleInfo
	Information about the density fitting module. More...

class	DensityFittingAmplitudeLookup
	Class that translates atom properties into amplitudes. More...

struct	DensityFittingForceProviderState
	Parameters defining the internal density fitting force provider state. More...

class	DensityFittingForceProvider
	Implements IForceProvider for density-fitting forces. More...

class	DensityFittingOptions
	Input data storage for density fitting. More...

class	DensityFittingOutputProvider
	Handle file output for density guided simulations. More...

struct	DensityFittingParameters
	Holding all directly user-provided parameters for density fitting. More...

struct	QMMMModuleInfo
	Information about the QM/MM module. More...

class	QMMMForceProvider
	Implements IForceProvider for QM/MM. More...

class	QMMMInputGenerator
	Class that takes QMMMParameters, Coordinates, Point charges, Box dimensions, pbcType. Generates QM/MM sample input parameters and pdb-style coordinates for CP2K. Input are generated as std::string objects which can be stored in tpr KVT and/or flushed into the files. More...

class	QMMMOptions
	Input data storage for QM/MM. More...

struct	QMMMTopologyInfo
	Contains various information about topology modifications Used for statistics during topology pre-processing within QMMMTopologyPreprocessor class. More...

class	QMMMTopologyPreprocessor
	Class implementing gmx_mtop_t QMMM modifications during preprocessing 1) Split QM-containing molecules from other molecules in blocks 2) Nullify charges on all virtual sites consisting of QM only atoms 3) Nullifies charges on all QM atoms 4) Excludes LJ interactions between QM atoms 5) Builds vector with atomic numbers of all atoms 6) Makes F_CONNBOND between atoms within QM region 7) Removes angles and settles containing 2 or more QM atoms 8) Removes dihedrals containing 3 or more QM atoms 9) Builds vector containing pairs of bonded QM - MM atoms (Link frontier) More...

struct	LinkFrontier
	Helper structure with indexes of broken bonds between QM and MM Used to determine and store pair of QM and MM atoms between which chemical bond is broken. More...

struct	QMMMParameters
	Holding all parameters needed for QM/MM simulation. Also used for setting all default parameter values. More...

class	CommandLineHelpContext
	Context information for writing out command-line help. More...

class	GlobalCommandLineHelpContext
	Helper for passing CommandLineHelpContext into parse_common_args(). More...

class	CommandLineHelpModule
	Command-line module for producing help. More...

class	CommandLineHelpWriter
	Writes help information for Options. More...

class	CommandLineModuleSettings
	Settings to pass information between a module and the general runner. 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	CommandLineModuleGroupData
	Internal data for a CommandLineModuleManager module group. More...

class	CommandLineCommonOptionsHolder
	Encapsulates some handling of common options to the wrapper binary. 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	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...

class	FixedCapacityVector
	Vector that behaves likes std::vector but has fixed capacity. More...

class	HashedMap
	Unordered key to value mapping. More...

class	GpuHaloExchange
	Manages GPU Halo Exchange object. 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	SeparatePmeRanksPermitted
	Class for managing usage of separate PME-only ranks. More...

struct	PpCommManager
	Object to manage communications with a specific PP rank. More...

class	PmeForceSenderGpu
	Manages sending forces from PME-only ranks to their PP ranks. More...

struct	CacheLineAlignedFlag
	Class with interfaces and data for CUDA version of PME Force sending functionality. More...

class	PmePpCommGpu
	Manages communication related to GPU buffers between this PME rank and its PP rank. More...

class	Gpu3dFft
	A 3D FFT class for performing R2C/C2R transforms. More...

struct	MDModulesCheckpointReadingDataOnMaster
	Provides the MDModules with the checkpointed data on the master 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...

class	FileIOXdrSerializer
	Serializer to read/write XDR data. 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...

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	ListOfLists
	A list of lists, optimized for performance. 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...

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...

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

class	HardwareTopology
	Information about packages, cores, processing units, numa, caches. More...

struct	IMDEnergyBlock
	IMD (interactive molecular dynamics) energy record. More...

struct	IMDHeader
	IMD (interactive molecular dynamics) communication structure. More...

class	InteractiveMolecularDynamics
	Implement interactive molecular dynamics. More...

struct	IMDSocket
	IMD (interactive molecular dynamics) socket structure. 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...

struct	HostInteractionList
	Version of InteractionList that supports pinning. 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...

class	GaussianOn1DLattice
	Provide result of Gaussian function evaluation on a one-dimensional lattice. More...

struct	GaussianSpreadKernelParameters
	Parameters for density spreading kernels. More...

class	GaussTransform3D
	Sums Gaussian values at three dimensional lattice coordinates. The Gaussian is defined as $A \frac{1}{\sigma^3 \sqrt(2^3\pi^3)} * \exp(-\frac{(x-x0)^2}{2 \sigma^2})$ . More...

class	IntegerBox
	A 3-orthotope over integer intervals. More...

class	OuterProductEvaluator
	Evaluate the outer product of two number ranges. Keeps the memory for the outer product allocated. More...

class	MultiDimArray
	Multidimensional array that manages its own memory. More...

struct	RealFunctionvalueAtCoordinate
	Tie together coordinate and function value at this coordinate. More...

class	NelderMeadSimplex
	The simplex for the Nelder-Mead algorithm. More...

struct	OptimisationResult
	Compiles results of an a function optimisation. 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...

class	EnergyDriftTracker
	Class for tracking and printing the drift in the conserved energy quantity. More...

struct	PTCouplingArrays
	Arrays connected to Pressure and Temperature coupling. More...

class	GpuForceReduction
	Manages the force reduction directly in GPU memory. More...

struct	cellInfo
	structure to hold cell information for any nbat-format forces More...

struct	AtomPair
	A pair of atoms indexes. More...

struct	Task
	Unit of work within LINCS. More...

class	Lincs
	Data for LINCS algorithm. More...

struct	LincsDeviations
	Status information about how well LINCS satisified the constraints in this domain. More...

struct	AtomsAdjacencyListElement
	Helper type for discovering coupled constraints. More...

class	LincsGpu
	Class with interfaces and data for GPU version of LINCS. 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...

class	SettleData
	Data for executing SETTLE constraining. More...

struct	WaterMolecule
	Indices of atoms in a water molecule. More...

class	SettleGpu
	Class with interfaces and data for GPU version of SETTLE. 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...

struct	ScalingMatrix
	Scaling matrix struct. More...

struct	AtomIndexExtremes
	Struct for returning an atom range. More...

class	UpdateGroups
	Owns the update grouping and related data. More...

class	UpdateGroupsCog
	Class for managing and computing centers of geometry of update groups. More...

struct	DomainInfo
	Information on PBC and domain decomposition for virtual sites. More...

struct	AtomIndex
	List of atom indices belonging to a task. More...

struct	InterdependentTask
	Data structure for thread tasks that use constructing atoms outside their own atom range. More...

struct	VsiteThread
	Vsite thread task data structure. More...

class	ThreadingInfo
	Information on how the virtual site work is divided over thread tasks. 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	ISimulator
	The Simulator interface. More...

class	LegacySimulatorData
	The legacy simulator data. More...

class	LegacyMdrunOptions
	This class provides the same command-line option functionality to both CLI and API sessions. More...

class	LegacySimulator
	Struct to handle setting up and running the different simulation types. More...

class	MDModules
	Manages the collection of all modules used for mdrun. More...

class	MembedHolder
	Membed SimulatorBuilder parameter type. More...

class	Mdrunner
	Runner object for supporting setup and execution of mdrun. More...

class	MdrunnerBuilder
	Build a gmx::Mdrunner. More...

class	SimulationContext
	Simulation environment and configuration. More...

class	SimulationInputHandle
	Owning handle to a SimulationInput object. 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	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...

struct	AtomInfoWithinMoleculeBlock
	Contains information about each atom in a molecule block of the global topology. More...

class	CheckpointData
	} More...

class	AwhParams
	Structure holding parameter information for AWH. More...

struct	IsSerializableType
	Struct allowing to check if data is serializable through the KeyValueTree serializer. More...

struct	IsSerializableEnum
	Struct allowing to check if enum has a serializable underlying type. 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	CheckpointOptions
	Options for writing checkpoint files. More...

struct	TimingOptions
	Options for timing (parts of) mdrun. More...

struct	ImdOptions
	Options for IMD. More...

struct	MdrunOptions
	Collection of all options of mdrun that are not processed separately. 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 paritioning. More...

class	SimulationWorkload
	Manage what computation is required during the simulation. More...

class	ThreadForceBuffer
	Object that holds force and energies buffers plus a mask for a thread. More...

class	ThreadedForceBuffer
	Class for accumulating and reducing forces and energies on threads in parallel. More...

class	MimicCommunicator
	Class-wrapper around MiMiC communication library It uses GROMACS' unit conversion to switch from GROMACS' units to a.u. More...

class	AndersenTemperatureCoupling
	Element implementing the Andersen thermostat. More...

class	CheckpointHelper
	Checkpoint helper. More...

class	CheckpointHelperBuilder
	Builder for the checkpoint helper. More...

class	CompositeSimulatorElement
	Composite simulator element. More...

class	ComputeGlobalsElement
	Encapsulate the calls to `compute_globals` More...

class	ConstraintsElement
	Constraints element. More...

class	DomDecHelper
	Infrastructure element responsible for domain decomposition. More...

class	DomDecHelperBuilder
	Builder for DomDecHelper. More...

class	EnergyData
	Data class managing energies. More...

class	ExpandedEnsembleElement
	The expanded ensemble element. More...

class	FirstOrderPressureCoupling
	Element performing first-order pressure coupling. More...

class	ForceElement
	Force element. More...

class	FreeEnergyPerturbationData
	The free energy perturbation data. More...

class	FepStateSetting
	Allows external clients to specify how to change the FEP state. More...

class	ModularSimulator
	The modular simulator. More...

class	SignallerBuilder
	Builder for signallers. More...

class	ISimulatorElement
	The general interface for elements of the modular simulator. More...

class	ISignaller
	The general Signaller interface. More...

class	INeighborSearchSignallerClient
	Interface for clients of the NeighborSearchSignaller. More...

class	ILastStepSignallerClient
	Interface for clients of the LastStepSignaller. More...

class	ILoggingSignallerClient
	Interface for clients of the LoggingSignaller. More...

class	IEnergySignallerClient
	Interface for clients of the EnergySignaller. More...

class	ITrajectorySignallerClient
	Interface for signaller clients of the TrajectoryElement. More...

class	ITrajectoryWriterClient
	Interface for writer clients of the TrajectoryElement. More...

class	ITopologyHolderClient
	Client requiring read access to the local topology. More...

class	ICheckpointHelperClient
	Client that needs to store data during checkpointing. 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...

struct	PropagatorTag
	Strong type used to name propagators. More...

struct	TimeStep
	Strong type used to denote propagation time steps. More...

struct	Offset
	Strong type used to denote scheduling offsets. More...

struct	PropagatorConnection
	Information needed to connect a propagator to a temperature and / or pressure coupling element. More...

class	IDomDecHelperClient
	Client interface of the DomDecHelper class. More...

struct	MttkPropagatorConnectionDetails
	Struct collecting the propagator tags and offsets used by the MTTK pressure coupling. More...

class	MttkData
	Class holding the extra dof and parameters used by the MTTK algorithm. More...

class	MttkPropagatorConnection
	Object holding the callbacks and scaling views for the connection of MTTKElement objects to propagators. More...

class	MttkElement
	Element propagating the MTTK degree of freedom. More...

class	MttkBoxScaling
	This element scales the box based on the MTTK dof. More...

class	NoseHooverGroup
	The current state of the Nose-Hoover chain degree of freedom for a temperature group. More...

class	NoseHooverChainsData
	Class holding data used by the Nose-Hoover chains. More...

class	NoseHooverChainsElement
	Element propagating the Nose-Hoover chains. More...

class	ParrinelloRahmanBarostat
	Element implementing the Parrinello-Rahman barostat. More...

class	PmeLoadBalanceHelper
	Infrastructure element responsible for PME load balancing. More...

class	Propagator
	Propagator element. More...

class	PullElement
	Element calling pull functionality. More...

class	ReferenceTemperatureManager
	Object managing reference temperature changes. More...

class	NeighborSearchSignaller
	Element signalling a neighbor search step. More...

class	LastStepSignaller
	Element signalling the last step. More...

class	LoggingSignaller
	Element signalling a logging step. More...

class	TrajectorySignaller
	Element signalling trajectory writing. More...

class	EnergySignaller
	Element signalling energy related special steps. More...

class	ModularSimulatorAlgorithm
	The modular simulator. More...

class	GlobalCommunicationHelper
	Helper container with data connected to global communication. More...

class	ModularSimulatorAlgorithmBuilderHelper
	Helper for element addition. More...

class	ModularSimulatorAlgorithmBuilder
	Builder for ModularSimulatorAlgorithm objects. More...

class	StatePropagatorData
	StatePropagatorData and associated data. More...

class	TopologyHolder
	Object holding the topology. More...

class	TrajectoryElement
	Trajectory element signals and handles trajectory writing. More...

class	TrajectoryElementBuilder
	Build the `TrajectoryElement` More...

struct	TemperatureCouplingData
	Data used by the concrete temperature coupling implementations. More...

class	ITemperatureCouplingImpl
	Interface for temperature coupling implementations. More...

class	VRescaleTemperatureCoupling
	Implements v-rescale temperature coupling. More...

class	BerendsenTemperatureCoupling
	Implements Berendsen temperature coupling. More...

class	NoseHooverTemperatureCoupling
	Implements the Nose-Hoover temperature coupling. More...

class	VelocityScalingTemperatureCoupling
	Element implementing the a velocity-scaling thermostat. More...

struct	BenchmarkSystem
	Description of the system used for benchmarking. More...

class	Range
	Defines a range of integer numbers and accompanying operations. 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	RstParagraphIterator
	Iterator over reStructuredText paragraphs. More...

class	OptionStorageTemplate
	Templated base class for constructing option value storage classes. 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	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	BooleanOption
	Specifies an option that provides boolean values. More...

class	IntegerOption
	Specifies an option that provides integer values. More...

class	Int64Option
	Specifies an option that provides 64-bit 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 integer option information. More...

class	Int64OptionInfo
	Wrapper class for accessing 64-bit 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	BooleanOptionStorage
	Converts, validates, and stores boolean values. More...

class	IntegerOptionStorage
	Converts, validates, and stores integer values. More...

class	Int64OptionStorage
	Converts, validates, and stores integer values. More...

class	DoubleOptionStorage
	Converts, validates, and stores floating-point (double) values. More...

class	FloatOptionStorage
	Converts, validates, and stores floating-point (float) values. More...

class	StringOptionStorage
	Converts, validates, and stores string values. More...

class	EnumOptionStorage
	Converts, validates, and stores enum values. More...

class	OptionsBehaviorCollection
	Container for IOptionsBehavior objects. 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	FileNameOptionStorage
	Converts, validates, and stores file names. 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	IOptionSectionStorage
	Provides behavior specific to a certain option section type. More...

class	IOptionValueStore
	Represents the final storage location of option values. More...

class	OptionManagerContainer
	Container to keep managers added with Options::addManager() and pass them to options. More...

class	IOptionManager
	Base class for option managers. More...

class	Options
	Collection of 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	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	RepeatingOptionSectionStorage
	Implements handling of the structures that stores per-section values. More...

class	RepeatingOptionSection
	Declares an option section that creates a structure for each instance. More...

class	TimeUnitManager
	Provides common functionality for time unit conversions. More...

class	TimeUnitBehavior
	Options behavior to add a time unit option. More...

class	OptionValueConverterSimple
	Helper for converting from Any to a given type. More...

class	OptionValueStoreNull
	Value storage that does not store anywhere. 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	ThreeFry2x64General
	General implementation class for ThreeFry counter-based random engines. More...

class	ThreeFry2x64
	ThreeFry2x64 random engine with 20 iteractions. More...

class	ThreeFry2x64Fast
	ThreeFry2x64 random engine with 13 iteractions. 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	RestraintForceProvider
	Provide IForceProvider for RestraintMDModuleImpl. More...

class	RestraintMDModuleImpl
	IMDModule implementation for RestraintMDModule. More...

class	IndexGroupsAndNames
	Bundle index groups with their names. 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	SelectionParserValue
	Describes a parsed value, possibly resulting from expression evaluation. More...

class	SelectionParserParameter
	Describes a parsed method parameter. More...

class	PositionCalculationCollection
	Collection of `gmx_ana_poscalc_t` structures for the same topology. 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...

class	SelectionEvaluator
	Implements selection evaluation. More...

struct	SelectionTopologyProperties
	Describes topology properties required for selection evaluation. 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	SelectionFileOptionStorage
	Implementation for a special option for reading selections from files. 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	SelectionOptionStorage
	Converts, validates, and stores selection values. More...

struct	SelectionLocation
	Stores the location of a selection element in the selection text. More...

class	SelectionTreeElement
	Represents an element of a selection expression. More...

struct	SelMethodEvalContext
	Evaluation context for selection methods. More...

class	SelectionParserSymbol
	Single symbol for the selection parser. More...

class	SelectionParserSymbolIterator
	Forward iterator for iterating symbols of a given type. More...

class	SelectionParserSymbolTable
	Symbol table for the selection parser. 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	SwapCoordinates
	Implement Computational Electrophysiology swapping. 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...

class	RangePartitioning
	Division of a range of indices into consecutive blocks. More...

struct	ExclusionBlock
	Describes exclusions for a single atom. More...

class	EnergyFrame
	Contains the content of an .edr frame read by an EnergyFrameReader. More...

class	TrajectoryFrame
	Contains a valid trajectory frame. 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	SurfaceAreaCalculator
	Computes surface areas for a group of atoms/spheres. 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	TrajectoryAnalysisRunnerCommon
	Implements common trajectory analysis runner functionality. More...

class	TopologyInformation
	Topology information available to a trajectory analysis module. 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...

class	BinaryInformationSettings
	Settings for printBinaryInformation(). 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	EnumerationIterator
	Allows iterating sequential enumerators. More...

class	EnumerationWrapper
	Allows constructing iterators for looping over sequential enumerators. 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	FlagsTemplate
	Template class for typesafe handling of combination of flags. More...

class	ISerializer
	Interface for types that convert standard data types into a form suitable for storage or transfer. 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	LogWriteHelper
	Helper class for implementing 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	MDModulesNotifier
	Organizes notifications about an event of interest to modules. More...

struct	BuildMDModulesNotifier
	Aide to avoid nested MDModulesNotifier definition. More...

struct	BuildMDModulesNotifier<>
	Template specialization to end parameter unpacking recursion. More...

struct	BuildMDModulesNotifier< CurrentCallParameter, CallParameter...>
	Template specialization to assemble MDModulesNotifier. 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...

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	QMInputFileName
	Notification for QM program input filename provided by user as command-line argument for grompp. More...

struct	MDModulesNotifiers
	Group of notifers to organize that MDModules can receive callbacks they subscribe to. More...

class	MessageStringCollector
	Helper class for collecting message strings, optionally with context. More...

class	MessageStringContext
	Convenience class for creating a message context. More...

struct	no_delete
	Deleter for std::shared_ptr that does nothing. More...

class	PhysicalNodeCommunicator
	Holds a communicator for the physical node of this rank. 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	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	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...

class	TextReader
	Reads text from a TextInputStream. More...

class	TextInputStream
	Interface for reading text. More...

class	TextOutputStream
	Interface for writing text. More...

class	TextWriter
	Writes text into a TextOutputStream. More...

struct	isIntegralConstant
	Is true if type is a std::integral_constant. More...

struct	functor_wrapper
	wrap function into functor to be used as deleter More...

class	NonbondedBenchmarkInfo
	Declares gmx nonbonded-bench. More...

class	BasicVector
	C++ class for 3D 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...

class	PotentialPointData
	Structure to hold the results of IRestraintPotential::evaluate(). More...

class	IRestraintPotential
	Interface for Restraint potentials. More...

class	ExceptionInfo
	Stores additional context information for exceptions. More...

struct	ThrowLocation
	Stores the location from which an exception was thrown. 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...

Typedefs
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 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.

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	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.

typedef struct gmx::CacheLineAlignedFlag	CacheLineAlignedFlag
	Class with interfaces and data for CUDA version of PME Force sending functionality. More...

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<class ElementType >
using	BasicMatrix3x3 = MultiDimArray< std::array< ElementType, 3 *3 >, extents< 3, 3 >>
	Three-by-three matrix of ElementType. More...

using	Matrix3x3 = BasicMatrix3x3< real >
	Three-by-three real number matrix. More...

using	Matrix3x3Span = Matrix3x3::view_type
	Convenience alias for a matrix view.

using	Matrix3x3ConstSpan = Matrix3x3::const_view_type
	Convenience alias for a const matrix view.

using	mode = sycl::access_mode

typedef std::array < SimulationSignal, eglsNR >	SimulationSignals
	Convenience typedef for the group of signals used.

using	VirialHandling = VirtualSitesHandler::VirialHandling
	VirialHandling is often used outside VirtualSitesHandler class members.

typedef std::array < std::vector< int > , c_ftypeVsiteEnd-c_ftypeVsiteStart >	VsitePbc
	Type for storing PBC atom information for all vsite types in the system.

using	SimulatorFunctionType ) = void(
	Function type for simulator code.

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 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 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 std::shared_ptr < IOptionsBehavior >	OptionsBehaviorPointer
	Smart pointer for behaviors stored in OptionsBehaviorCollection.

typedef FlagsTemplate< OptionFlag >	OptionFlags
	Holds a combination of OptionFlag values.

typedef std::random_device	RandomDevice
	Random device. More...

typedef ThreeFry2x64Fast	DefaultRandomEngine
	Default fast and accurate random engine in Gromacs. 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::vector< Selection >	SelectionList
	Container of selections used in public selection interfaces.

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 FlagsTemplate < SelectionFlag >	SelectionFlags
	Holds a collection of SelectionFlag values.

typedef std::shared_ptr < SelectionTreeElement >	SelectionTreeElementPointer
	Smart pointer type for selection tree element pointers.

typedef void(*	sel_evalfunc )(struct gmx_sel_evaluate_t data, const SelectionTreeElementPointer &sel, gmx_ana_index_t g)
	Function pointer for evaluating a gmx::SelectionTreeElement.

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.

using	BoxMatrix = std::array< std::array< real, DIM >, DIM >
	A 3x3 matrix data type useful for simulation boxes. More...

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.

template<class T >
using	AlignedAllocator = Allocator< T, AlignedAllocationPolicy >
	Aligned memory allocator. More...

template<class T >
using	PageAlignedAllocator = Allocator< T, PageAlignedAllocationPolicy >
	PageAligned memory allocator. More...

using	FilePtr = std::unique_ptr< FILE, functor_wrapper< FILE, fclose_wrapper >>
	Simple guard pointer which calls fclose. See unique_cptr for details.

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.

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	Vector = ::gmx::RVec
	Provide a vector type name with a more stable interface than RVec and a more stable implementation than vec3<>. More...

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	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::ForceCorrelationVolume, AwhOutputEntryType::FrictionTensor }
	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	QMMMQMMethod { QMMMQMMethod::PBE, QMMMQMMethod::BLYP, 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	ShellCompletionFormat { eShellCompletionFormat_Bash }
	Output format for ShellCompletionWriter. 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	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	FftBackend { Cufft, Ocl, HeFFTe_CUDA, SyclMkl, SyclRocfft, Sycl, Count }
	Enum specifying all GPU FFT backends supported by GROMACS Some of the backends support only single GPU, some only multi-node, multi-GPU. 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	DeviceStreamType : int { DeviceStreamType::NonBondedLocal, DeviceStreamType::NonBondedNonLocal, DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer, DeviceStreamType::UpdateAndConstraints, 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 { Unknown, Architecture::X86, Architecture::Arm, Architecture::PowerPC }
	Enum for GROMACS CPU hardware detection support. 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 }
	Sets the number of different temperature coupling values. More...

enum	VelocityScalingType { VelocityScalingType::None = 0, VelocityScalingType::Diagonal = 1, VelocityScalingType::Count = 2 }
	Different variants of the Parrinello-Rahman velocity scaling. More...

enum	ResetSignal { noSignal = 0, doResetCounters = 1 }
	Reset signals. More...

enum	StopSignal : int { noSignal = 0, stopAtNextNSStep = 1, stopImmediately = -1 }
	Stop signals. More...

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::Full, Count }
	Sets the type of Parrinello-Rahman pressure scaling. More...

enum	ReferenceTemperatureChangeAlgorithm
	The algorithm changing the reference temperature. More...

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	HelpOutputFormat { eHelpOutputFormat_Console, eHelpOutputFormat_Rst, eHelpOutputFormat_Other, eHelpOutputFormat_NR }
	Output format for help writing. More...

enum	OptionFileType : int { Topology, RunInput, Trajectory, Energy, PDB, Index, 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...

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	SelectionStringMatchType { eStringMatchType_Auto, eStringMatchType_Exact, eStringMatchType_Wildcard, eStringMatchType_RegularExpression }
	String matching mode for string keyword expressions. More...

enum	SelectionFlag : uint64_t { efSelection_OnlyStatic = 1 << 0, efSelection_OnlyAtoms = 1 << 1, efSelection_OnlySorted = 1 << 2, efSelection_DynamicMask = 1 << 3, efSelection_DisallowEmpty = 1 << 4, efSelection_EvaluateVelocities = 1 << 5, efSelection_EvaluateForces = 1 << 6 }
	Flags for options. 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::X86_Avx512Knl, SimdType::Arm_NeonAsimd, SimdType::Arm_Sve, SimdType::Ibm_Vsx }
	Enumerated options for SIMD architectures. 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	ErrorCode { eeOK, eeOutOfMemory, eeFileNotFound, eeFileIO, eeInvalidInput, eeInconsistentInput, eeTolerance, eeInstability, eeNotImplemented, eeInvalidValue, eeInvalidCall, eeInternalError, eeAPIError, eeRange, eeParallelConsistency, eeModularSimulator, eeUnknownError }
	Possible error return codes from Gromacs functions. More...

enum	EndianSwapBehavior : int { EndianSwapBehavior::DoNotSwap, EndianSwapBehavior::Swap, EndianSwapBehavior::SwapIfHostIsBigEndian, EndianSwapBehavior::SwapIfHostIsLittleEndian, EndianSwapBehavior::Count }
	Specify endian swapping behavoir. More...

enum	GpuAwareMpiStatus : int { GpuAwareMpiStatus::Supported, GpuAwareMpiStatus::NotSupported, GpuAwareMpiStatus::NotKnown, GpuAwareMpiStatus::Forced }
	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.

Functions

AnalysisHistogramSettingsInitializer histogramFromRange (real min, real max)

Initializes a histogram using a range and a bin width. More...

AnalysisHistogramSettingsInitializer histogramFromBins (real start, int nbins, real binwidth)

Initializes a histogram using bin width and the number of bins. More...

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...

std::unique_ptr< Awh > prepareAwhModule (FILE *fplog, const t_inputrec &inputRecord, t_state *stateGlobal, const t_commrec *commRecord, 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 double *const *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 t_commrec &commRecord)

Sum an array over all simulations on master 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 double *const *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...

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, warninp_t 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, warninp_t 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_grpopts *inputrecGroupOptions, real initLambda, const gmx_mtop_t &mtop, warninp_t wi)

Sets AWH parameters that need state parameters such as the box vectors. More...

void checkAwhParams (const AwhParams &awhParams, const t_inputrec &inputrec, warninp_t 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.

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::unique_ptr< IMDModule > createElectricFieldModule ()

Creates a module for an external electric field. More...

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::string &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::string &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::string &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.

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

Modify atoms information in coordinate frame to fit output selection. More...

static void flagInteractionsForType (const int 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 t_commrec *cr, 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 t_commrec *cr, 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 t_commrec *cr, 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 bool useUpdateGroups)

Compute the total bonded interaction count. More...

void mdAlgorithmsSetupAtomData (const t_commrec *cr, 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, gmx_shellfc_t *shellfc)

Sets atom data for several MD algorithms. More...

void make_local_shells (const t_commrec *cr, const t_mdatoms &md, gmx_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 (const t_commrec *cr, const t_inputrec &inputrec, FILE *fplog)

Print statistics for domain decomposition communication.

void dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, int64_t step, const t_commrec *cr, bool bMasterState, int nstglobalcomm, t_state *state_global, const gmx_mtop_t &top_global, const t_inputrec &inputrec, gmx::ImdSession *imdSession, pull_t *pull_work, t_state *state_local, 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 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 ()), complexGrid_(*complexGrid->buffer_.get()),{GMX_RELEASE_ASSERT(performOutOfPlaceFFT,"Only out-of-place FFT is implemented in hipSYCL"

GMX_RELEASE_ASSERT (allocateGrids==false,"Grids need to be pre-allocated")

GMX_RELEASE_ASSERT (gridSizesInXForEachRank.size()==1 &&gridSizesInYForEachRank.size()==1,"FFT decomposition not implemented with SYCL backend")

template<typename ValueType >

void readKvtCheckpointValue (compat::not_null< ValueType * > value, const std::string &name, const std::string &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, const std::string &name, const std::string &identifier, const KeyValueTreeObject &kvt)

Read to a key-value-tree value used for checkpointing. More...

template void readKvtCheckpointValue (compat::not_null< real * > value, const std::string &name, const std::string &identifier, const KeyValueTreeObject &kvt)

Read to a key-value-tree value used for checkpointing. More...

template<typename ValueType >

void writeKvtCheckpointValue (const ValueType &value, const std::string &name, const std::string &identifier, KeyValueTreeObjectBuilder kvtBuilder)

Write to a key-value-tree used for checkpointing. More...

template void writeKvtCheckpointValue (const std::int64_t &value, const std::string &name, const std::string &identifier, KeyValueTreeObjectBuilder kvtBuilder)

Write to a key-value-tree used for checkpointing. More...

template void writeKvtCheckpointValue (const real &value, const std::string &name, const std::string &identifier, KeyValueTreeObjectBuilder kvtBuilder)

Write to a key-value-tree used for checkpointing. 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...

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.

template<class T1 , class T2 >

bool operator== (const Allocator< T1, HostAllocationPolicy > &a, const Allocator< T2, HostAllocationPolicy > &b)

Return true if two allocators are identical. More...

template<typename PinnableVector >

void changePinningPolicy (PinnableVector *v, PinningPolicy pinningPolicy)

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

void pinBuffer (void *pointer, std::size_t numBytes) noexcept

Pin the allocation to physical memory. More...

void unpinBuffer (void *pointer) noexcept

Unpin the allocation. More...

void doDeviceTransfers (const DeviceInformation &deviceInfo, 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...

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)

Reduce the locally collected hardwareInfo over MPI ranks.

std::unique_ptr< gmx_hw_info_t > gmx_detect_hardware (const PhysicalNodeCommunicator &physicalNodeComm)

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 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...

int identifyAvx512FmaUnits ()

Test whether machine has dual AVX512 FMA units. More...

std::unique_ptr< IMDModule > createInteractiveMolecularDynamicsModule ()

Creates a module for interactive molecular dynamics.

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 t_commrec *cr)

Check for non-working integrator / parallel options.

std::unique_ptr< ImdSession > makeImdSession (const t_inputrec *ir, const t_commrec *cr, 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. More...

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 master 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...

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 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 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...

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...

Matrix3x3 transpose (Matrix3x3ConstSpan matrixView)

Calculate the transpose of a 3x3 matrix, from its view.

void matrixVectorMultiply (Matrix3x3ConstSpan matrix, RVec *v)

Multiply matrix with vector.

constexpr real determinant (Matrix3x3ConstSpan matrix)

Determinant of a 3x3 matrix.

constexpr real trace (Matrix3x3ConstSpan matrixView)

Calculates the trace of a 3x3 matrix view.

template<typename ElementType , int N, int M = N>

MultiDimArray< std::array
< ElementType, N *M >, extents
< N, M > > identityMatrix ()

Create an identity matrix of ElementType with N * M elements. More...

static Matrix3x3 createMatrix3x3FromLegacyMatrix (const matrix legacyMatrix)

Create new matrix type from legacy type.

static void fillLegacyMatrix (Matrix3x3ConstSpan newMatrix, matrix legacyMatrix)

Fill legacy matrix from new matrix type.

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 > prepareBoxDeformation (const matrix &initialBox, DDRole ddRole, NumRanks numRanks, MPI_Comm communicator, const t_inputrec &inputrec)

Factory function for box deformation module. 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 t_commrec *cr, 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 t_commrec *cr, 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, ArrayRef< const 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, ArrayRef< const 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...

int countFlexibleConstraints (ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams)

Return the number of flexible constraints in the ilist and iparams.

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...

void do_constrain_first (FILE *log, gmx::Constraints *constr, const t_inputrec *inputrec, int numAtoms, 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 do_log, bool do_ene, int64_t step, t_state *state, real *dvdlambda, bool computeVirial, tensor constraintsVirial)

Constrain velocities only. More...

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

Constraint 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 F_CONSTR and F_CONSTRNC constraints are concatenated.

bool inter_charge_group_constraints (const gmx_mtop_t &mtop)

Returns whether there are inter charge group constraints.

bool inter_charge_group_settles (const gmx_mtop_t &mtop)

Returns whether there are inter charge group settles.

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.

real calculateAcceptanceWeight (LambdaWeightCalculation calculationMode, real lambdaEnergyDifference)

Calculates the acceptance weight for a lambda state transition. More...

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, DeviceBuffer< Float3 > d_nbnxmForceToAdd, DeviceBuffer< Float3 > d_rvecForceToAdd, DeviceBuffer< Float3 > d_baseForce, DeviceBuffer< int > d_cell, const DeviceStream &deviceStream)

Backend-specific function to launch GPU Force Reduction kernel. More...

template<bool addRvecForce, bool accumulateForce>

static auto reduceKernel (sycl::handler &cgh, DeviceAccessor< Float3, mode::read > a_nbnxmForce, OptionalAccessor< Float3, mode::read, addRvecForce > a_rvecForceToAdd, DeviceAccessor< Float3, accumulateForce?mode::read_write:mode::write > a_forceTotal, DeviceAccessor< int, mode::read > a_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 > &b_nbnxmForce, const DeviceBuffer< Float3 > &b_rvecForceToAdd, DeviceBuffer< Float3 > &b_forceTotal, const DeviceBuffer< int > &b_cell, const DeviceStream &deviceStream)

Force reduction SYCL kernel launch code.

void launchLeapFrogKernel (int numAtoms, DeviceBuffer< Float3 > d_x, DeviceBuffer< Float3 > d_xp, 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, VelocityScalingType prVelocityScalingType, Float3 prVelocityScalingMatrixDiagonal, const DeviceStream &deviceStream)

Backend-specific function to launch GPU Leap Frog kernel. More...

template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>

auto leapFrogKernel (sycl::handler &cgh, DeviceAccessor< Float3, mode::read_write > a_x, DeviceAccessor< Float3, mode::discard_write > a_xp, DeviceAccessor< Float3, mode::read_write > a_v, DeviceAccessor< Float3, mode::read > a_f, DeviceAccessor< float, mode::read > a_inverseMasses, float dt, OptionalAccessor< float, mode::read, numTempScaleValues!=NumTempScaleValues::None > a_lambdas, OptionalAccessor< unsigned short, mode::read, numTempScaleValues==NumTempScaleValues::Multiple > a_tempScaleGroups, Float3 prVelocityScalingMatrixDiagonal)

Main kernel for the Leap-Frog integrator. More...

template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling, class... Args>

static sycl::event launchLeapFrogKernel (const DeviceStream &deviceStream, int numAtoms, Args &&...args)

Leap Frog SYCL kernel launch code.

static NumTempScaleValues getTempScalingType (bool doTemperatureScaling, int numTempScaleValues)

Convert doTemperatureScaling and numTempScaleValues to NumTempScaleValues.

template<class... Args>

static sycl::event launchLeapFrogKernel (NumTempScaleValues tempScalingType, VelocityScalingType prVelocityScalingType, 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.

template<int align>

static void gmx_simdcall gatherLoadUTransposeTSANSafe (const real *base, const std::int32_t *offset, SimdReal *v0, SimdReal *v1, SimdReal *v2)

Helper function so that we can run TSAN with SIMD support (where implemented).

static void gmx_simdcall calc_dr_x_f_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict x, const rvec *gmx_restrict f, const real *gmx_restrict blc, const real *pbc_simd, rvec *gmx_restrict r, real *gmx_restrict rhs, real *gmx_restrict sol)

Calculate the constraint distance vectors r to project on from x. More...

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 void gmx_simdcall calc_dr_x_xp_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict x, const rvec *gmx_restrict xp, const real *gmx_restrict bllen, const real *gmx_restrict blc, const real *pbc_simd, rvec *gmx_restrict r, real *gmx_restrict rhs, real *gmx_restrict sol)

Calculate the constraint distance vectors r to project on from x. More...

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 gmx_simdcall calc_dist_iter_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec *gmx_restrict x, const real *gmx_restrict bllen, const real *gmx_restrict blc, const real *pbc_simd, real wfac, real *gmx_restrict rhs, real *gmx_restrict sol, bool *bWarn)

As calc_dist_iter(), but using SIMD intrinsics.

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, const t_commrec *cr, bool bCalcDHDL, real wangle, bool *bWarn, real invdt, ArrayRef< RVec > vRef, bool bCalcVir, tensor vir_r_m_dr)

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.

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

Finds all triangles of atoms that share constraints to a central atom.

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 t_commrec *cr, 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, const t_commrec *cr, 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)

Applies LINCS constraints. More...

ArrayRef< real > lincs_rmsdData (Lincs *lincsd)

Return the data for determining constraint RMS relative deviations.

static std::vector
< std::vector
< AtomsAdjacencyListElement > > constructAtomsAdjacencyList (const int numAtoms, ArrayRef< const int > iatoms)

Constructs and returns an atom constraint adjacency list.

int countCoupled (int a, ArrayRef< int > numCoupledConstraints, ArrayRef< const std::vector< AtomsAdjacencyListElement >> atomsAdjacencyList)

Helper function to go through constraints recursively. More...

void addWithCoupled (ArrayRef< const int > iatoms, const int stride, ArrayRef< const std::vector< AtomsAdjacencyListElement >> atomsAdjacencyList, ArrayRef< int > splitMap, const int c, int *currentMapIndex)

Add constraint to splitMap with all constraints coupled to it. More...

static std::vector< int > countNumCoupledConstraints (ArrayRef< const int > iatoms, ArrayRef< const std::vector< AtomsAdjacencyListElement >> atomsAdjacencyList)

Computes and returns how many constraints are coupled to each constraint. 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>

auto lincsKernel (sycl::handler &cgh, const int numConstraintsThreads, DeviceAccessor< AtomPair, mode::read > a_constraints, DeviceAccessor< float, mode::read > a_constraintsTargetLengths, OptionalAccessor< int, mode::read, haveCoupledConstraints > a_coupledConstraintsCounts, OptionalAccessor< int, mode::read, haveCoupledConstraints > a_coupledConstraintsIndices, OptionalAccessor< float, mode::read, haveCoupledConstraints > a_massFactors, OptionalAccessor< float, mode::read_write, haveCoupledConstraints > a_matrixA, DeviceAccessor< float, mode::read > a_inverseMasses, const int numIterations, const int expansionOrder, DeviceAccessor< Float3, mode::read > a_x, DeviceAccessor< Float3, mode::read_write > a_xp, const float invdt, OptionalAccessor< Float3, mode::read_write, updateVelocities > a_v, OptionalAccessor< float, mode::read_write, computeVirial > a_virialScaled, PbcAiuc pbcAiuc)

Main kernel for LINCS constraints. More...

template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, class... Args>

static sycl::event launchLincsKernel (const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&...args)

template<class... Args>

static sycl::event 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 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)

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 dOH, real invmO, real invmH, real dHH)

Computes and returns settle parameters. More...

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 > virialScaled, const PbcAiuc &pbcAiuc, const DeviceStream &deviceStream)

Apply SETTLE. More...

template<bool updateVelocities, bool computeVirial>

auto settleKernel (sycl::handler &cgh, const int numSettles, DeviceAccessor< WaterMolecule, mode::read > a_settles, SettleParameters pars, DeviceAccessor< Float3, mode::read > a_x, DeviceAccessor< Float3, mode::read_write > a_xp, float invdt, OptionalAccessor< Float3, mode::read_write, updateVelocities > a_v, OptionalAccessor< float, mode::read_write, computeVirial > a_virialScaled, PbcAiuc pbcAiuc)

Function returning the SETTLE kernel lambda.

template<bool updateVelocities, bool computeVirial, class... Args>

static sycl::event launchSettleKernel (const DeviceStream &deviceStream, int numSettles, Args &&...args)

SETTLE SYCL kernel launch code.

template<class... Args>

static sycl::event 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, int nsb, 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 StopSignal convertToStopSignal (signed char sig)

Convert signed char (as used by SimulationSignal) to StopSignal enum. 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 (sycl::handler &cgh, DeviceAccessor< Float3, sycl::access_mode::read_write > a_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 int 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 0 when criteria (see updategroups.h) are not met.

static RangePartitioning makeUpdateGroupingsPerMoleculeType (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)

Returns a list of update groups for moltype.

std::vector< RangePartitioning > makeUpdateGroupingsPerMoleculeType (const gmx_mtop_t &mtop)

Returns a vector with update groups for each moleculetype in mtop or an empty vector 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...

real computeCutoffMargin (PbcType pbcType, matrix box, real rlist)

Return the margin required for successful domain decomposition. 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 useDomainDecomposition, bool systemHasConstraintsOrVsites, real cutoffMargin)

Builder for update groups. More...

static int vsiteIlistNrCount (ArrayRef< const InteractionList > ilist)

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, ArrayRef< const InteractionList > ilist, 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, ArrayRef< const InteractionList > ilist, 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, ArrayRef< const InteractionList > ilist)

Create positions of vsite atoms based for the local system. More...

static int vsite_count (ArrayRef< const InteractionList > ilist, int 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, ArrayRef< const InteractionList > ilist, 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, ArrayRef< const InteractionList > ilist, 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::unique_ptr
< VirtualSitesHandler > makeVirtualSitesHandler (const gmx_mtop_t &mtop, const t_commrec *cr, 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, int thread, int nthread, int natperthread, gmx::ArrayRef< int > taskIndex, ArrayRef< const 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, ArrayRef< const InteractionList > ilist, 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...

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 DevelopmentFeatureFlags manageDevelopmentFeatures (const gmx::MDLogger &mdlog, const bool useGpuForNonbonded, const PmeRunMode pmeRunMode, const int numRanksPerSimulation, const int numPmeRanksPerSimulation)

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 bool gpuAccelerationOfNonbondedIsUseful (const MDLogger &mdlog, const t_inputrec &ir, const bool issueWarning, const bool doRerun)

Return whether GPU acceleration of nonbondeds is supported with the given settings. More...

static gmx::LoggerOwner buildLogger (FILE *fplog, const bool isSimulationMasterRank)

Initializes the logger for mdrun.

static TaskTarget findTaskTarget (const char *optionString)

Make a TaskTarget from an mdrun argument string.

static void finish_run (FILE *fplog, const gmx::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 gmx_pme_t *pme, gmx_bool bWriteStat)

Finish run, aggregate data to print performance info.

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

Initialize local stateful simulation data. More...

SimulationInputHandle makeSimulationInput (const LegacyMdrunOptions &options)

Direct the construction of a SimulationInput. More...

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 isSimulationMaster, 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.

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
< T >::value, const typename
T::value_type, typename
T::value_type > > makeCheckpointArrayRef (T &container)

Get an ArrayRef whose const-ness is defined by the checkpointing operation. More...

template<CheckpointDataOperation operation, typename T >

ArrayRef< std::conditional_t
< operation==CheckpointDataOperation::Write||std::is_const
< T >::value, const T, T > > makeCheckpointArrayRefFromArray (T *begin, size_t size)

Get an ArrayRef to a C array whose const-ness is defined by the checkpointing operation. More...

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.

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...

bool needStateGpu (SimulationWorkload simulationWorkload)

If StatePropagatorDataGpu object is needed. 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_)))

template<typename... Ts>

auto checkUseModularSimulator (Ts &&...args) -> decltype(ModularSimulator::isInputCompatible(std::forward< Ts >(args)...))

Whether or not to use the ModularSimulator. More...

numDegreesOfFreedom_ (numDegreesOfFreedom)

simulationTimeStep_ (simulationTimeStep)

referenceTemperature_ (referenceTemperature)

mttkPropagatorConnection_ (mttkPropagatorConnection)

nextEnergyCalculationStep_ (-1)

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 matrix matrixPR)

Update velocities.

static void updatePositions (int a, real dt, const rvec *gmx_restrict x, rvec *gmx_restrict xprime, const rvec *gmx_restrict v)

Update positions.

template<NumVelocityScalingValues numStartVelocityScalingValues>

static void scaleVelocities (int a, real lambda, rvec *gmx_restrict v)

Scale velocities.

template<NumPositionScalingValues numPositionScalingValues>

static void scalePositions (int a, real lambda, rvec *gmx_restrict x)

Scale positions.

template<ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>

static bool diagonalizePRMatrix (matrix matrixPR, rvec diagPR)

Helper function diagonalizing the PR matrix if possible.

scalingStepPR_ (-1)

wcycle_ (wcycle)

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 > gmx_unused *propagator, const PropagatorTag &propagatorTag)

template<CheckpointDataOperation operation>

static void doCheckpointData (CheckpointData< operation > *checkpointData, ArrayRef< double > 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, Args &&...args)

Factory function for elements that can be added via ModularSimulatorAlgorithmBuilder: Get a pointer to an object of type Element to add to the call list. More...

template<typename Base , typename Element >

static std::enable_if_t
< std::is_base_of< Base,
Element >::value, 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< Base,
Element >::value, 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->nstxout, inputrec->nstvout, inputrec->nstfout, inputrec->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...

static void generateCoordinates (int multiplicationFactor, std::vector< gmx::RVec > *coordinates, matrix box)

Generates coordinates and a box for the base system scaled by multiplicationFactor.

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 int xyzToShiftIndex (int x, int y, int z)

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)

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)

Implements selection compilation. More...

void swap (SelectionCollection &lhs, SelectionCollection &rhs)

HelpTopicPointer createSelectionHelpTopic ()

*/ More...

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...

static SimdFloat gmx_simdcall invsqrtSingleAccuracy (SimdFloat x)

Calculate 1/sqrt(x) for SIMD float, only targeting single accuracy. More...

static SimdFloat maskzInvsqrtSingleAccuracy (SimdFloat x, SimdFBool m)

Calculate 1/sqrt(x) for masked SIMD floats, only targeting single accuracy. More...

static void gmx_simdcall invsqrtPairSingleAccuracy (SimdFloat x0, SimdFloat x1, SimdFloat *out0, SimdFloat *out1)

Calculate 1/sqrt(x) for two SIMD floats, only targeting single accuracy. More...

static SimdFloat gmx_simdcall invSingleAccuracy (SimdFloat x)

Calculate 1/x for SIMD float, only targeting single accuracy. More...

static SimdFloat maskzInvSingleAccuracy (SimdFloat x, SimdFBool m)

Calculate 1/x for masked SIMD floats, only targeting single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall sqrtSingleAccuracy (SimdFloat x)

Calculate sqrt(x) for SIMD float, always targeting single accuracy. More...

static SimdFloat gmx_simdcall cbrtSingleAccuracy (SimdFloat x)

Calculate cbrt(x) for SIMD float, always targeting single accuracy. More...

static SimdFloat gmx_simdcall invcbrtSingleAccuracy (SimdFloat x)

Calculate 1/cbrt(x) for SIMD float, always targeting single accuracy. More...

static SimdFloat gmx_simdcall log2SingleAccuracy (SimdFloat x)

SIMD float log2(x), only targeting single accuracy. This is the base-2 logarithm. More...

static SimdFloat gmx_simdcall logSingleAccuracy (SimdFloat x)

SIMD float log(x), only targeting single accuracy. This is the natural logarithm. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall exp2SingleAccuracy (SimdFloat x)

SIMD float 2^x, only targeting single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall expSingleAccuracy (SimdFloat x)

SIMD float e^x, only targeting single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall powSingleAccuracy (SimdFloat x, SimdFloat y)

SIMD pow(x,y), only targeting single accuracy. More...

static SimdFloat gmx_simdcall erfSingleAccuracy (SimdFloat x)

SIMD float erf(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall erfcSingleAccuracy (SimdFloat x)

SIMD float erfc(x), only targeting single accuracy. More...

static void gmx_simdcall sinCosSingleAccuracy (SimdFloat x, SimdFloat *sinval, SimdFloat *cosval)

SIMD float sin & cos, only targeting single accuracy. More...

static SimdFloat gmx_simdcall sinSingleAccuracy (SimdFloat x)

SIMD float sin(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall cosSingleAccuracy (SimdFloat x)

SIMD float cos(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall tanSingleAccuracy (SimdFloat x)

SIMD float tan(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall asinSingleAccuracy (SimdFloat x)

SIMD float asin(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall acosSingleAccuracy (SimdFloat x)

SIMD float acos(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall atanSingleAccuracy (SimdFloat x)

SIMD float atan(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall atan2SingleAccuracy (SimdFloat y, SimdFloat x)

SIMD float atan2(y,x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall pmeForceCorrectionSingleAccuracy (SimdFloat z2)

SIMD Analytic PME force correction, only targeting single accuracy. More...

static SimdFloat gmx_simdcall pmePotentialCorrectionSingleAccuracy (SimdFloat z2)

SIMD Analytic PME potential correction, only targeting single accuracy. More...

static Simd4Float gmx_simdcall invsqrtSingleAccuracy (Simd4Float x)

Calculate 1/sqrt(x) for SIMD4 float, only targeting single accuracy. More...

const std::string & simdString (SimdType s)

Return a string with the name of a SIMD type. More...

SimdType simdSuggested (const CpuInfo &c)

Return the SIMD type that would fit this hardware best.

SimdType simdCompiled ()

Return the SIMD type the library was compiled with.

bool simdCheck (SimdType s, FILE *log, bool warnToStdErr)

Check if binary was compiled with the provided SIMD type. More...

static SimdFloat gmx_simdcall iprod (SimdFloat ax, SimdFloat ay, SimdFloat az, SimdFloat bx, SimdFloat by, SimdFloat bz)

SIMD float inner product of multiple float vectors. More...

static SimdFloat gmx_simdcall norm2 (SimdFloat ax, SimdFloat ay, SimdFloat az)

SIMD float norm squared of multiple vectors. More...

static void gmx_simdcall cprod (SimdFloat ax, SimdFloat ay, SimdFloat az, SimdFloat bx, SimdFloat by, SimdFloat bz, SimdFloat *cx, SimdFloat *cy, SimdFloat *cz)

SIMD float cross-product of multiple vectors. More...

static SimdDouble gmx_simdcall iprod (SimdDouble ax, SimdDouble ay, SimdDouble az, SimdDouble bx, SimdDouble by, SimdDouble bz)

SIMD double inner product of multiple double vectors. More...

static SimdDouble gmx_simdcall norm2 (SimdDouble ax, SimdDouble ay, SimdDouble az)

SIMD double norm squared of multiple vectors. More...

static void gmx_simdcall cprod (SimdDouble ax, SimdDouble ay, SimdDouble az, SimdDouble bx, SimdDouble by, SimdDouble bz, SimdDouble *cx, SimdDouble *cy, SimdDouble *cz)

SIMD double cross-product of multiple vectors. More...

static Simd4Float gmx_simdcall norm2 (Simd4Float ax, Simd4Float ay, Simd4Float az)

SIMD4 float norm squared of multiple vectors. More...

static Simd4Double gmx_simdcall norm2 (Simd4Double ax, Simd4Double ay, Simd4Double az)

SIMD4 double norm squared of multiple vectors. More...

std::unique_ptr< IMDModule > createSwapCoordinatesModule ()

Creates a module for Computational Electrophysiology swapping.

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

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

static bool decideWhetherToUseGpusForPmeFft (const TaskTarget pmeFftTarget)

static bool canUseGpusForPme (const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const gmx_hw_info_t &hardwareInfo, const t_inputrec &inputrec, std::string *errorMessage)

bool decideWhetherToUseGpusForPmeWithThreadMpi (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, int numDevicesToUse, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, 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 buildSupportsNonbondedOnGpu, bool nonbondedOnGpuIsUseful, bool gpusWereDetected)

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

bool decideWhetherToUseGpusForPme (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, 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 doRerun, const DevelopmentFeatureFlags &devFlags, const gmx::MDLogger &mdlog)

Decide whether to use GPU for update. More...

bool decideWhetherDirectGpuCommunicationCanBeUsed (const DevelopmentFeatureFlags &devFlags, bool haveMts, bool haveSwapCoords, 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 t_inputrec &inputrec, bool disableNonbondedCalculation, const DevelopmentFeatureFlags &devFlags, bool havePpDomainDecomposition, bool haveSeparatePmeRank, bool useGpuForNonbonded, 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...

std::vector< GpuTask > findGpuTasksOnThisRank (bool haveGpusOnThisPhysicalNode, TaskTarget nonbondedTarget, 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...

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...

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.

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...

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 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...

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 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::size_t pageSize ()

Return the memory page size on this system. More...

std::string simpleValueToString (const Any &value)

Converts a Any value to a string. More...

void printBinaryInformation (FILE *fp, const IProgramContext &programContext)

Print basic information about the executable. 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...

std::string bromacs ()

Return a cool definition for the acronym GROMACS.

std::string getCoolQuote ()

Return a string with a cool quote.

std::string getCudaDriverVersionString ()

Returns a string of the CUDA driver version.

std::string getCudaRuntimeVersionString ()

Returns a string of the CUDA runtime version.

template<typename EnumerationArrayType >

EnumerationArrayType::EnumerationWrapperType keysOf (const EnumerationArrayType &)

Returns an object that provides iterators over the keys associated with EnumerationArrayType. More...

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...

void fclose_wrapper (FILE *fp)

fclose wrapper to be used as unique_ptr deleter

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::string findLibraryFile (const std::string &filename, bool bAddCWD=true, bool bFatal=true)

Finds full path for a library file. More...

std::string findLibraryFile (const char *filename, bool bAddCWD=true, bool bFatal=true)

Finds full path for a library file. More...

FilePtr openLibraryFile (const std::string &filename, bool bAddCWD=true, bool bFatal=true)

Opens a library file for reading in an RAII-style FILE handle. More...

FilePtr openLibraryFile (const char *filename, bool bAddCWD=true, bool bFatal=true)

Opens a library file for reading in an RAII-style FILE handle. More...

IKeyValueTreeErrorHandler * defaultKeyValueTreeErrorHandler ()

Returns a default IKeyValueTreeErrorHandler that throws on first exception.

void init (int *argc, char ***argv)

Initializes the GROMACS library. More...

void finalize ()

Deinitializes the GROMACS library. More...

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.

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().

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...

void serializeKeyValueTree (const KeyValueTreeObject &root, ISerializer *serializer)

Serializes a KeyValueTreeObject with given serializer.

KeyValueTreeObject deserializeKeyValueTree (ISerializer *serializer)

Deserializes a KeyValueTreeObject from a given serializer.

GpuAwareMpiStatus checkMpiCudaAwareSupport ()

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

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...

void MPI_Comm_free_wrapper (MPI_Comm *comm)

Wrapper function for RAII-style cleanup. More...

const IProgramContext & getProgramContext ()

Returns the global IProgramContext instance. More...

void setProgramContext (const IProgramContext *context)

Sets the global IProgramContext instance. 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...

int64_t int64FromString (const char *str)

Parses a 64-bit 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<>

int64_t fromString< int64_t > (const char *str)

Implementation for 64-bit 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 int64ToString (int64_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...

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 excpetion if the demanded conversion to an array will not succeed. 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 (const char *fmt,...)

Formats a string (snprintf() wrapper). More...

std::string formatStringV (const char *fmt, 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 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...

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...

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...

std::string getSyclCompilerVersion ()

Returns an internal version strings of the Intel DPC++ and hipSYCL compiler.

template<class Function >

auto dispatchTemplatedFunction (Function &&f)

Helper function to select appropriate template based on runtime values. 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.

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...

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<T>::value>>

static constexpr bool isPowerOfTwo (const T v)

Check whether v is an integer power of 2.

template<typename ValueType >

BasicVector< ValueType > operator* (const BasicVector< ValueType > &basicVector, const ValueType &scalar)

Allow vector scalar multiplication.

template<typename ValueType >

BasicVector< ValueType > operator* (const ValueType &scalar, const BasicVector< ValueType > &basicVector)

Allow scalar vector multiplication.

template<typename VectorType >

static VectorType unitVector (const VectorType &v)

unitv for gmx::BasicVector

template<typename ValueType >

static ValueType norm (BasicVector< ValueType > v)

norm for gmx::BasicVector

template<typename ValueType >

static ValueType norm2 (BasicVector< ValueType > v)

Square of the vector norm for gmx::BasicVector.

template<typename VectorType >

static VectorType cross (const VectorType &a, const VectorType &b)

cross product for gmx::BasicVector

template<typename ValueType >

static ValueType dot (BasicVector< ValueType > a, BasicVector< ValueType > b)

dot product for gmx::BasicVector

template<typename VectorType >

static VectorType scaleByVector (const VectorType &a, const VectorType &b)

Multiply two vectors element by element and return the result.

template<typename VectorType >

static VectorType elementWiseMin (const VectorType &a, const VectorType &b)

Return the element-wise minimum of two vectors.

template<typename VectorType >

static 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 T >

ArrayRef< std::conditional_t
< std::is_const< T >::value,
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)

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<class Exception , class Tag , class T >

std::enable_if_t
< std::is_base_of
< GromacsException, Exception >
::value, Exception > operator<< (Exception ex, const ExceptionInfo< Tag, T > &item)

Associates extra information with an exception. More...

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, 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...

Single precision SIMD math functions

Note: In most cases you should use the real-precision functions instead.

static SimdFloat gmx_simdcall copysign (SimdFloat x, SimdFloat y)

Composes floating point value with the magnitude of x and the sign of y. More...

static SimdFloat gmx_simdcall rsqrtIter (SimdFloat lu, SimdFloat x)

Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD float. More...

static SimdFloat gmx_simdcall invsqrt (SimdFloat x)

Calculate 1/sqrt(x) for SIMD float. More...

static void gmx_simdcall invsqrtPair (SimdFloat x0, SimdFloat x1, SimdFloat *out0, SimdFloat *out1)

Calculate 1/sqrt(x) for two SIMD floats. More...

static SimdFloat gmx_simdcall rcpIter (SimdFloat lu, SimdFloat x)

Perform one Newton-Raphson iteration to improve 1/x for SIMD float. More...

static SimdFloat gmx_simdcall inv (SimdFloat x)

Calculate 1/x for SIMD float. More...

static SimdFloat gmx_simdcall operator/ (SimdFloat nom, SimdFloat denom)

Division for SIMD floats. More...

static SimdFloat maskzInvsqrt (SimdFloat x, SimdFBool m)

Calculate 1/sqrt(x) for masked entries of SIMD float. More...

static SimdFloat gmx_simdcall maskzInv (SimdFloat x, SimdFBool m)

Calculate 1/x for SIMD float, masked version. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall sqrt (SimdFloat x)

Calculate sqrt(x) for SIMD floats. More...

static SimdFloat gmx_simdcall cbrt (SimdFloat x)

Cube root for SIMD floats. More...

static SimdFloat gmx_simdcall invcbrt (SimdFloat x)

Inverse cube root for SIMD floats. More...

static SimdFloat gmx_simdcall log2 (SimdFloat x)

SIMD float log2(x). This is the base-2 logarithm. More...

static SimdFloat gmx_simdcall log (SimdFloat x)

SIMD float log(x). This is the natural logarithm. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall exp2 (SimdFloat x)

SIMD float 2^x. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall exp (SimdFloat x)

SIMD float exp(x). More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdFloat gmx_simdcall pow (SimdFloat x, SimdFloat y)

SIMD float pow(x,y) More...

static SimdFloat gmx_simdcall erf (SimdFloat x)

SIMD float erf(x). More...

static SimdFloat gmx_simdcall erfc (SimdFloat x)

SIMD float erfc(x). More...

static void gmx_simdcall sincos (SimdFloat x, SimdFloat *sinval, SimdFloat *cosval)

SIMD float sin & cos. More...

static SimdFloat gmx_simdcall sin (SimdFloat x)

SIMD float sin(x). More...

static SimdFloat gmx_simdcall cos (SimdFloat x)

SIMD float cos(x). More...

static SimdFloat gmx_simdcall tan (SimdFloat x)

SIMD float tan(x). More...

static SimdFloat gmx_simdcall asin (SimdFloat x)

SIMD float asin(x). More...

static SimdFloat gmx_simdcall acos (SimdFloat x)

SIMD float acos(x). More...

static SimdFloat gmx_simdcall atan (SimdFloat x)

SIMD float asin(x). More...

static SimdFloat gmx_simdcall atan2 (SimdFloat y, SimdFloat x)

SIMD float atan2(y,x). More...

static SimdFloat gmx_simdcall pmeForceCorrection (SimdFloat z2)

Calculate the force correction due to PME analytically in SIMD float. More...

static SimdFloat gmx_simdcall pmePotentialCorrection (SimdFloat z2)

Calculate the potential correction due to PME analytically in SIMD float. More...

Double precision SIMD math functions

Note: In most cases you should use the real-precision functions instead.

static SimdDouble gmx_simdcall copysign (SimdDouble x, SimdDouble y)

Composes floating point value with the magnitude of x and the sign of y. More...

static SimdDouble gmx_simdcall rsqrtIter (SimdDouble lu, SimdDouble x)

Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD double. More...

static SimdDouble gmx_simdcall invsqrt (SimdDouble x)

Calculate 1/sqrt(x) for SIMD double. More...

static void gmx_simdcall invsqrtPair (SimdDouble x0, SimdDouble x1, SimdDouble *out0, SimdDouble *out1)

Calculate 1/sqrt(x) for two SIMD doubles. More...

static SimdDouble gmx_simdcall rcpIter (SimdDouble lu, SimdDouble x)

Perform one Newton-Raphson iteration to improve 1/x for SIMD double. More...

static SimdDouble gmx_simdcall inv (SimdDouble x)

Calculate 1/x for SIMD double. More...

static SimdDouble gmx_simdcall operator/ (SimdDouble nom, SimdDouble denom)

Division for SIMD doubles. More...

static SimdDouble maskzInvsqrt (SimdDouble x, SimdDBool m)

Calculate 1/sqrt(x) for masked entries of SIMD double. More...

static SimdDouble gmx_simdcall maskzInv (SimdDouble x, SimdDBool m)

Calculate 1/x for SIMD double, masked version. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall sqrt (SimdDouble x)

Calculate sqrt(x) for SIMD doubles. More...

static SimdDouble gmx_simdcall cbrt (SimdDouble x)

Cube root for SIMD doubles. More...

static SimdDouble gmx_simdcall invcbrt (SimdDouble x)

Inverse cube root for SIMD doubles. More...

static SimdDouble gmx_simdcall log2 (SimdDouble x)

SIMD double log2(x). This is the base-2 logarithm. More...

static SimdDouble gmx_simdcall log (SimdDouble x)

SIMD double log(x). This is the natural logarithm. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall exp2 (SimdDouble x)

SIMD double 2^x. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall exp (SimdDouble x)

SIMD double exp(x). More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall pow (SimdDouble x, SimdDouble y)

SIMD double pow(x,y) More...

static SimdDouble gmx_simdcall erf (SimdDouble x)

SIMD double erf(x). More...

static SimdDouble gmx_simdcall erfc (SimdDouble x)

SIMD double erfc(x). More...

static void gmx_simdcall sincos (SimdDouble x, SimdDouble *sinval, SimdDouble *cosval)

SIMD double sin & cos. More...

static SimdDouble gmx_simdcall sin (SimdDouble x)

SIMD double sin(x). More...

static SimdDouble gmx_simdcall cos (SimdDouble x)

SIMD double cos(x). More...

static SimdDouble gmx_simdcall tan (SimdDouble x)

SIMD double tan(x). More...

static SimdDouble gmx_simdcall asin (SimdDouble x)

SIMD double asin(x). More...

static SimdDouble gmx_simdcall acos (SimdDouble x)

SIMD double acos(x). More...

static SimdDouble gmx_simdcall atan (SimdDouble x)

SIMD double asin(x). More...

static SimdDouble gmx_simdcall atan2 (SimdDouble y, SimdDouble x)

SIMD double atan2(y,x). More...

static SimdDouble gmx_simdcall pmeForceCorrection (SimdDouble z2)

Calculate the force correction due to PME analytically in SIMD double. More...

static SimdDouble gmx_simdcall pmePotentialCorrection (SimdDouble z2)

Calculate the potential correction due to PME analytically in SIMD double. More...

SIMD math functions for double prec. data, single prec. accuracy

Note: In some cases we do not need full double accuracy of individual SIMD math functions, although the data is stored in double precision SIMD registers. This might be the case for special algorithms, or if the architecture does not support single precision. Since the full double precision evaluation of math functions typically require much more expensive polynomial approximations these functions implement the algorithms used in the single precision SIMD math functions, but they operate on double precision SIMD variables.

static SimdDouble gmx_simdcall invsqrtSingleAccuracy (SimdDouble x)

Calculate 1/sqrt(x) for SIMD double, but in single accuracy. More...

static SimdDouble maskzInvsqrtSingleAccuracy (SimdDouble x, SimdDBool m)

1/sqrt(x) for masked-in entries of SIMD double, but in single accuracy. More...

static void gmx_simdcall invsqrtPairSingleAccuracy (SimdDouble x0, SimdDouble x1, SimdDouble *out0, SimdDouble *out1)

Calculate 1/sqrt(x) for two SIMD doubles, but single accuracy. More...

static SimdDouble gmx_simdcall invSingleAccuracy (SimdDouble x)

Calculate 1/x for SIMD double, but in single accuracy. More...

static SimdDouble gmx_simdcall maskzInvSingleAccuracy (SimdDouble x, SimdDBool m)

1/x for masked entries of SIMD double, single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall sqrtSingleAccuracy (SimdDouble x)

Calculate sqrt(x) (correct for 0.0) for SIMD double, with single accuracy. More...

static SimdDouble gmx_simdcall cbrtSingleAccuracy (SimdDouble x)

Cube root for SIMD doubles, single accuracy. More...

static SimdDouble gmx_simdcall invcbrtSingleAccuracy (SimdDouble x)

Inverse cube root for SIMD doubles, single accuracy. More...

static SimdDouble gmx_simdcall log2SingleAccuracy (SimdDouble x)

SIMD log2(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall logSingleAccuracy (SimdDouble x)

SIMD log(x). Double precision SIMD data, single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall exp2SingleAccuracy (SimdDouble x)

SIMD 2^x. Double precision SIMD, single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall expSingleAccuracy (SimdDouble x)

SIMD exp(x). Double precision SIMD, single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>

static SimdDouble gmx_simdcall powSingleAccuracy (SimdDouble x, SimdDouble y)

SIMD pow(x,y). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall erfSingleAccuracy (SimdDouble x)

SIMD erf(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall erfcSingleAccuracy (SimdDouble x)

SIMD erfc(x). Double precision SIMD data, single accuracy. More...

static void gmx_simdcall sinCosSingleAccuracy (SimdDouble x, SimdDouble *sinval, SimdDouble *cosval)

SIMD sin & cos. Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall sinSingleAccuracy (SimdDouble x)

SIMD sin(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall cosSingleAccuracy (SimdDouble x)

SIMD cos(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall tanSingleAccuracy (SimdDouble x)

SIMD tan(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall asinSingleAccuracy (SimdDouble x)

SIMD asin(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall acosSingleAccuracy (SimdDouble x)

SIMD acos(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall atanSingleAccuracy (SimdDouble x)

SIMD asin(x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall atan2SingleAccuracy (SimdDouble y, SimdDouble x)

SIMD atan2(y,x). Double precision SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall pmeForceCorrectionSingleAccuracy (SimdDouble z2)

Analytical PME force correction, double SIMD data, single accuracy. More...

static SimdDouble gmx_simdcall pmePotentialCorrectionSingleAccuracy (SimdDouble z2)

Analytical PME potential correction, double SIMD data, single accuracy. More...

SIMD4 math functions

Note: Only a subset of the math functions are implemented for SIMD4.

static Simd4Float gmx_simdcall rsqrtIter (Simd4Float lu, Simd4Float x)

Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD4 float. More...

static Simd4Float gmx_simdcall invsqrt (Simd4Float x)

Calculate 1/sqrt(x) for SIMD4 float. More...

static Simd4Double gmx_simdcall rsqrtIter (Simd4Double lu, Simd4Double x)

Perform one Newton-Raphson iteration to improve 1/sqrt(x) for SIMD4 double. More...

static Simd4Double gmx_simdcall invsqrt (Simd4Double x)

Calculate 1/sqrt(x) for SIMD4 double. More...

static Simd4Double gmx_simdcall invsqrtSingleAccuracy (Simd4Double x)

Calculate 1/sqrt(x) for SIMD4 double, but in single accuracy. 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 (int64_t t)

static std::string toString (float t)

static std::string toString (double t)

static std::string toString (std::string t)

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_indent = 0
	Indent 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 const std::string	c_qmmmCP2KModuleName = "qmmm-cp2k"
	Tag with name of the QMMM with CP2K MDModule.

static const EnumerationArray < QMMMQMMethod, const char * >	c_qmmmQMMethodNames
	The names of the supported QM methods. 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...

	pmeStream

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< int, numFTypesOnGpu >	fTypesOnGpu
	List of all bonded function types supported on GPUs. More...

static const int	simd_width = 4
	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 constexpr int	c_ftypeVsiteStart = F_VSITE1
	The start value of the vsite indices in the ftype enum. More...

static constexpr int	c_ftypeVsiteEnd = F_VSITEN + 1
	The start and end value of the vsite indices in the ftype enum.

constexpr bool	BUGFREE_NOEXCEPT_STRING = std::is_nothrow_move_assignable<std::string>::value
	Work-around for GCC bug 58265 still present in CentOS 7 devtoolset-7.

static constexpr int64_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...

const std::array< RVec, 2 >	c_forces = { { { 0.5, 0.1, 1.2 }, { -2.1, 0.2, 0.3 } } }

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.

	boxRel_ { { 0 } }

static constexpr EnumerationArray< NhcUsage, const char * >	nhcUsageNames = { "System", "Barostat" }

	boxVelocity_ { { 0 } }

	previousBox_ { { 0 } }

constexpr int	c_centralShiftIndex = detail::c_numIvecs / 2

constexpr int	c_numShiftVectors = detail::c_numIvecs

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

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


static constexpr int64_t	sc_atomInfo_FreeEnergyPerturbation = 1 << 15
	Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo. More...

static constexpr int64_t	sc_atomInfo_HasPerturbedChargeIn14Interaction = 1 << 16

static constexpr int64_t	sc_atomInfo_Exclusion = 1 << 17

static constexpr int64_t	sc_atomInfo_Constraint = 1 << 20

static constexpr int64_t	sc_atomInfo_Settle = 1 << 21

static constexpr int64_t	sc_atomInfo_BondCommunication = 1 << 22

static constexpr int64_t	sc_atomInfo_HasVdw = 1 << 23

static constexpr int64_t	sc_atomInfo_HasCharge = 1 << 24


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.

template<class ElementType >

using gmx::BasicMatrix3x3 = typedef MultiDimArray<std::array<ElementType, 3 * 3>, extents<3, 3>>

Three-by-three matrix of ElementType.

Template Parameters

ElementType type of element to be stored in matrix

using gmx::BoxMatrix = typedef std::array<std::array<real, DIM>, DIM>

A 3x3 matrix data type useful for simulation boxes.

Todo:: Implement a full replacement for C-style real[DIM][DIM]

typedef struct gmx::CacheLineAlignedFlag gmx::CacheLineAlignedFlag

Class with interfaces and data for CUDA version of PME Force sending functionality.

typedef ThreeFry2x64Fast gmx::DefaultRandomEngine

Default fast and accurate random engine in Gromacs.

This engine will return 2*2^64 random results using the default gmx::RandomDomain::Other stream, and can be initialized with a single seed argument without having to remember empty template angle brackets.

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.

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 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

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

X86

Not one of the cases below.

Arm

X86.

PowerPC

ARM.

IBM PowerPC

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.
ForceCorrelationVolume	The volume of the force correlation tensor.
FrictionTensor	The full friction tensor.

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::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.

$\mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) = \frac{1}{N_\mathrm{voxel}}/\sum_{v=1}^{N_\mathrm{voxel}} \rho^v_{\mathrm{r}} \rho^v_{\mathrm{c}}$

relativeEntropy

Measure similarity between densities by negative relative entropy.

Note: Voxels with negative values are ignored.

$\mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) = \sum_{v=1}^{N_\mathrm{voxel}} \rho^v_{\mathrm{r}} (\log(\rho^v_{\mathrm{c}}) - \log(\rho^v_{\mathrm{r}}))$

crossCorrelation

Measure similarity between densities by cross correlation.

$\mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) = \frac{\sum_{v}\left((\rho_{\mathrm{r}} - \bar{\rho}_{\mathrm{r}})(\rho_{\mathrm{c}} - \bar{\rho}_{\mathrm{c}})\right)} {\sqrt{\sum_v(\rho_{\mathrm{r}} - \bar{\rho}_{\mathrm{r}})^2 \sum_v (\rho_{\mathrm{c}} - \bar{\rho}_{\mathrm{c}})^2}}$

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.
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::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

Enum specifying all GPU FFT backends supported by GROMACS Some of the backends support only single GPU, some only multi-node, multi-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::GpuAwareMpiStatus : int

strong

Enum describing GPU-aware support in underlying MPI library.

Enumerator
Supported	GPU-aware support available.
NotSupported	GPU-aware support NOT available.
NotKnown	GPU-aware support status not known.
Forced	GPU-aware support forced using env variable.

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::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::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::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::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.

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::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::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.
BLYP	DFT with BLYP functional.
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::ReferenceTemperatureChangeAlgorithm

strong

The algorithm changing the reference temperature.

In the legacy implementation, reference temperature changes by different algorithms are not handled identically. This enum is used to inform clients what algorithm caused the temperature change, allowing them to customize their response.

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::SelectionFlag : 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 the implementation of SelectionOption.

Enumerator
efSelection_DynamicMask	Whether POS_MASKONLY should be used for output position evaluation.
efSelection_DisallowEmpty	If set, unconditionally empty selections result in compilation errors.
efSelection_EvaluateVelocities	Whether velocities of output positions should be evaluated.
efSelection_EvaluateForces	Whether forces on output positions should be evaluated.

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.
X86_Avx512Knl	AVX_512_KNL.
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::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::VelocityScalingType

strong

Different variants of the Parrinello-Rahman velocity scaling.

This is needed to template the kernel

Todo:: Unify with similar enum in CPU update module

Enumerator
None	Do not apply velocity scaling (not a PR-coupling run or step)
Diagonal	Apply velocity scaling using a diagonal matrix.
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 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.

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,
		ArrayRef< const std::vector< 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 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::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 (SIMMASTER(cr)) { // Only the master 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 master-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 t_commrec *	cr,
		int *	dd_nc,
		t_inputrec *	ir,
		t_state *	state,
		ObservablesHistory *	observablesHistory,
		bool	reproducibilityRequested,
		const MDModulesNotifiers &	notifiers,
		gmx::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 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::assignVsitesToThread	(	VsiteThread *	tData,
		int	thread,
		int	nthread,
		int	natperthread,
		gmx::ArrayRef< int >	taskIndex,
		ArrayRef< const 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.ilist. taskIndex[] is set for all vsites in our range, either to our local tasks or to the single last task as taskIndex[]=2*nthreads.

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 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.

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::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 master 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.

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.

static void gmx_simdcall gmx::calc_dr_x_f_simd	(	int	b0,
		int	b1,
		gmx::ArrayRef< const AtomPair >	atoms,
		const rvec *gmx_restrict	x,
		const rvec *gmx_restrict	f,
		const real *gmx_restrict	blc,
		const real *	pbc_simd,
		rvec *gmx_restrict	r,
		real *gmx_restrict	rhs,
		real *gmx_restrict	sol
	)

static

Calculate the constraint distance vectors r to project on from x.

Determine the right-hand side of the matrix equation using quantity f. This function only differs from calc_dr_x_xp_simd below in that no constraint length is subtracted and no PBC is used for f.

static void gmx_simdcall gmx::calc_dr_x_xp_simd	(	int	b0,
		int	b1,
		gmx::ArrayRef< const AtomPair >	atoms,
		const rvec *gmx_restrict	x,
		const rvec *gmx_restrict	xp,
		const real *gmx_restrict	bllen,
		const real *gmx_restrict	blc,
		const real *	pbc_simd,
		rvec *gmx_restrict	r,
		real *gmx_restrict	rhs,
		real *gmx_restrict	sol
	)

static

Calculate the constraint distance vectors r to project on from x.

Determine the right-hand side of the matrix equation using coordinates xp.

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

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.

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).

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

Check the AWH parameters.

Parameters

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

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,
		warninp_t	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.

GpuAwareMpiStatus gmx::checkMpiCudaAwareSupport ( )

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

Returns: GPU-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

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 master 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

real gmx::computeCutoffMargin	(	PbcType	pbcType,
		matrix	box,
		real	rlist
	)

Return the margin required for successful domain decomposition.

Parameters

[in]	pbcType	The PBC type in use
[in]	box	The box in use
[in]	rlist	The list size in use

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 bool	useUpdateGroups
	)

static

Compute the total bonded interaction count.

Parameters

[in]	mtop	The global system topology
[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
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

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

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

Constraint coordinates.

The dvdlambda contribution has to be added to the bonded interactions

bool gmx::constrain_lincs	(	bool	computeRmsd,
		const t_inputrec &	ir,
		int64_t	step,
		Lincs *	lincsd,
		ArrayRef< const real >	invmass,
		const t_commrec *	cr,
		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
	)

Applies LINCS constraints.

Returns: true if the constraining succeeded.

void gmx::constrain_velocities	(	gmx::Constraints *	constr,
		bool	do_log,
		bool	do_ene,
		int64_t	step,
		t_state *	state,
		real *	dvdlambda,
		bool	computeVirial,
		tensor	constraintsVirial
	)

Constrain velocities only.

The dvdlambda contribution has to be added to the bonded interactions

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,
		ArrayRef< const InteractionList >	ilist,
		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]	ilist	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,
		ArrayRef< const InteractionList >	ilist,
		const t_pbc *	pbc_null
	)

static

Executes the vsite construction task for a single thread.

Template Parameters

operation Whether we are calculating positions, velocities, or both

Parameters

[in,out]	x	Coordinates to construct vsites for
[in,out]	v	Velocities are generated for virtual sites if `operation` requires it
[in]	ip	Interaction parameters for all interaction, only vsite parameters are used
[in]	ilist	The interaction lists, only vsites are usesd
[in]	pbc_null	PBC struct, used for PBC distance calculations when !=nullptr

void gmx::constructVirtualSites	(	ArrayRef< RVec >	x,
		ArrayRef< const t_iparams >	ip,
		ArrayRef< const InteractionList >	ilist
	)

Create positions of vsite atoms based for the local system.

Parameters

[in,out]	x	The coordinates
[in]	ip	Interaction parameters
[in]	ilist	The interaction list

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

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

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::countCoupled	(	int	a,
		ArrayRef< int >	numCoupledConstraints,
		ArrayRef< const std::vector< AtomsAdjacencyListElement >>	atomsAdjacencyList
	)

inline

Helper function to go through constraints recursively.

For each constraint, counts the number of coupled constraints and stores the value in numCoupledConstraints array. This information is used to split the array of constraints between thread blocks on a GPU so there is no coupling between constraints from different thread blocks. After the numCoupledConstraints array is filled, the value numCoupledConstraints[c] should be equal to the number of constraints that are coupled to c and located after it in the constraints array.

Parameters

[in]	a	Atom index.
[in,out]	numCoupledConstraints	Indicates if the constraint was already counted and stores the number of constraints (i) connected to it and (ii) located after it in memory. This array is filled by this recursive function. For a set of coupled constraints, only for the first one in this list the number of consecutive coupled constraints is needed: if there is not enough space for this set of constraints in the thread block, the group has to be moved to the next one.
[in]	atomsAdjacencyList	Stores information about connections between atoms.

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 std::vector<int> gmx::countNumCoupledConstraints	(	ArrayRef< const int >	iatoms,
		ArrayRef< const std::vector< AtomsAdjacencyListElement >>	atomsAdjacencyList
	)

static

Computes and returns how many constraints are coupled to each constraint.

Needed to introduce splits in data so that all coupled constraints will be computed in a single GPU block. The position c of the vector numCoupledConstraints should have the number of constraints that are coupled to a constraint c and are after c in the vector. Only first index of the connected group of the constraints is needed later in the code, hence the numCoupledConstraints vector is also used to keep track if the constrain was already counted.

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 double const	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.

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::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

std::unique_ptr< IMDModule > gmx::createElectricFieldModule ( )

Creates a module for an external electric field.

The returned class describes the time dependent electric field that can be applied to all charges in a simulation. The field is described by the following: E(t) = A cos(omega*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(sigma))); If sigma = 0 there is no pulse and we have instead E(t) = A cos(omega*t)

force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e

WARNING: There can be problems with the virial. Since the field is not self-consistent this is unavoidable. For neutral molecules the virial is correct within this approximation. For neutral systems with many charged molecules the error is small. But for systems with a net charge or a few charged molecules the error can be significant when the field is high. Solution: implement a self-consistent electric field into PME.

SimulationWorkload gmx::createSimulationWorkload	(	const t_inputrec &	inputrec,
		bool	disableNonbondedCalculation,
		const DevelopmentFeatureFlags &	devFlags,
		bool	havePpDomainDecomposition,
		bool	haveSeparatePmeRank,
		bool	useGpuForNonbonded,
		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]	inputrec	The input record
[in]	disableNonbondedCalculation	Disable calculation of nonbonded forces
[in]	devFlags	The development feature flags
[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 interactions calculations on GPU(s).
[in]	pmeRunMode	Run mode indicating what resource is PME execured 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::string &	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_partition_system	(	FILE *	fplog,
		const gmx::MDLogger &	mdlog,
		int64_t	step,
		const t_commrec *	cr,
		bool	bMasterState,
		int	nstglobalcomm,
		t_state *	state_global,
		const gmx_mtop_t &	top_global,
		const t_inputrec &	inputrec,
		gmx::ImdSession *	imdSession,
		pull_t *	pull_work,
		t_state *	state_local,
		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 bMasterState==TRUE then state_global from the master 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]	step	Current step
[in]	cr	Communication record
[in]	bMasterState	Is it a master state
[in]	nstglobalcomm	Will globals be computed on this step
[in]	state_global	Global state
[in]	top_global	Global topology
[in]	inputrec	Input record
[in]	imdSession	IMD handle
[in]	pull_work	Pulling data
[in]	state_local	Local state
[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	(	const DevelopmentFeatureFlags &	devFlags,
		bool	haveMts,
		bool	haveSwapCoords,
		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]	devFlags	GPU development / experimental feature flags.
[in]	haveMts	Whether the simulation uses multiple time stepping
[in]	haveSwapCoords	Whether the swap-coords functionality is active
[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	doRerun,
		const DevelopmentFeatureFlags &	devFlags,
		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]	doRerun	It this is a rerun.
[in]	devFlags	GPU development / experimental feature flags.
[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	buildSupportsNonbondedOnGpu,
		bool	nonbondedOnGpuIsUseful,
		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]	buildSupportsNonbondedOnGpu	Whether GROMACS was build with GPU support.
[in]	nonbondedOnGpuIsUseful	Whether computing nonbonded interactions on a GPU is useful for this calculation.
[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::decideWhetherToUseGpusForNonbondedWithThreadMpi	(	TaskTarget	nonbondedTarget,
		bool	haveAvailableDevices,
		const std::vector< int > &	userGpuTaskAssignment,
		EmulateGpuNonbonded	emulateGpuNonbonded,
		bool	buildSupportsNonbondedOnGpu,
		bool	nonbondedOnGpuIsUseful,
		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]	buildSupportsNonbondedOnGpu	Whether GROMACS was built with GPU support.
[in]	nonbondedOnGpuIsUseful	Whether computing nonbonded interactions on a GPU is useful for this calculation.
[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 gmx_hw_info_t &	hardwareInfo,
		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]	hardwareInfo	Hardware information
[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 gmx_hw_info_t &	hardwareInfo,
		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]	hardwareInfo	Hardware information
[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.

MrcDensityMapHeader gmx::deserializeMrcDensityMapHeader ( ISerializer * serializer )

Deserializes an MrcDensityMapHeader from a given serializer.

Parameters

[in] serializer the serializer

Returns: mrc density map header

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.

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<class Function >

auto gmx::dispatchTemplatedFunction ( Function && f )

Helper function to select appropriate template based on runtime values.

Can use enums or booleans for template parameters. These enums must have a member Count indicating the total number of valid values.

Example usage:

   enum class Options {
       Op1 = 0,
       Op2 = 1,
       Count = 2
   };
   template<bool p0, Options p1, Options p2>
   bool foo(int i);
   bool bar(bool p0, Options p1, Options p2, int i) {
       return dispatchTemplatedFunction(
           [=](auto p0, auto p1, auto p2) {
               return foo<p0, p1, p2>(i);
           },
           p0, p1, p2);
   }
* 

Template Parameters

Function Type of f.

Parameters

f	Function to call.

Returns: The result of calling f().

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`

void gmx::doDeviceTransfers	(	const DeviceInformation &	deviceInfo,
		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.

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.

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

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.

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.

std::vector< GpuTask > gmx::findGpuTasksOnThisRank	(	bool	haveGpusOnThisPhysicalNode,
		TaskTarget	nonbondedTarget,
		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]	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::string gmx::findLibraryFile	(	const std::string &	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.

std::string gmx::findLibraryFile	(	const char *	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 int	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.

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

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.

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.

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).

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

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.

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.

template<typename Element , typename... Args>

ISimulatorElement* gmx::getElementPointer	(	LegacySimulatorData *	legacySimulatorData,
		ModularSimulatorAlgorithmBuilderHelper *	builderHelper,
		StatePropagatorData *	statePropagatorData,
		EnergyData *	energyData,
		FreeEnergyPerturbationData *	freeEnergyPerturbationData,
		GlobalCommunicationHelper *	globalCommunicationHelper,
		ObservablesReducer *	observablesReducer,
		Args &&...	args
	)

Factory function for elements that can be added via ModularSimulatorAlgorithmBuilder: Get a pointer to an object of type Element to add to the call list.

This allows elements to be built via the templated ModularSimulatorAlgorithmBuilder::add<Element> method. Elements buildable throught this factor function are required to implement a static function with minimal signature

static ISimulatorElement* getElementPointerImpl(
        LegacySimulatorData*                    legacySimulatorData,
        ModularSimulatorAlgorithmBuilderHelper* builderHelper,
        StatePropagatorData*                    statePropagatorData,
        EnergyData*                             energyData,
        FreeEnergyPerturbationData*             freeEnergyPerturbationData,
        GlobalCommunicationHelper*              globalCommunicationHelper,
        ObservablesReducer*                     observablesReducer)

This function may also accept additional parameters which are passed using the variadic template parameter pack forwarded in getElementPointer.

This function returns a pointer to an object of the Element type. Note that the caller will check whether the returned object has previously been stored using the storeElement function, and throw an exception if the element is not found. The function can check whether a previously stored pointer is valid using the checkElementExistence function. Most implementing functions will simply want to create an object, store it using storeElement, and then use the return value of storeElement as a return value to the caller. However, this setup allows the function to store a created element (using a static pointer inside the function) and return it in case that the factory function is called repeatedly. This allows to create an element once, but have it called multiple times during the simulation run.

See Also: ModularSimulatorAlgorithmBuilder::add Function using this functionality; ComputeGlobalsElement<ComputeGlobalsAlgorithm::VelocityVerlet>::getElementPointerImpl Implementation using the single object / multiple call sites functionality

Template Parameters

Element	The type of the element
Args	Variable number of argument types allowing specific implementations to have additional arguments

Parameters

legacySimulatorData	Pointer allowing access to simulator level data
builderHelper	ModularSimulatorAlgorithmBuilder helper object
statePropagatorData	Pointer to the `StatePropagatorData` object
energyData	Pointer to the `EnergyData` object
freeEnergyPerturbationData	Pointer to the `FreeEnergyPerturbationData` object
globalCommunicationHelper	Pointer to the `GlobalCommunicationHelper` object
observablesReducer	Pointer to the `ObservablesReducer` object
args	Variable number of additional parameters to be forwarded

Returns: Pointer to the element to be added. Element needs to have been stored using storeElement

static int gmx::getFileType ( const std::string & 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 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

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.

double gmx::getTransformationPullCoordinateValue	(	pull_coord_work_t *	coord,
		ArrayRef< const pull_coord_work_t >	variableCoords
	)

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

Returns: Transformation value for pull coordinate.

Exceptions

InconsistentInputError when the expression uses coordinates with index equal to or larger than the index of coord.

std::unique_ptr< gmx_hw_info_t > gmx::gmx_detect_hardware ( const PhysicalNodeCommunicator & physicalNodeComm )

Run detection and make correct and consistent hardware information available on all ranks.

May do communication on MPI_COMM_WORLD 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.

Todo:: Replace the use of MPI_COMM_WORLD e.g. by using a libraryCommWorld argument. See https://gitlab.com/gromacs/gromacs/-/issues/3650

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.

static bool gmx::gpuAccelerationOfNonbondedIsUseful	(	const MDLogger &	mdlog,
		const t_inputrec &	ir,
		const bool	issueWarning,
		const bool	doRerun
	)

static

Return whether GPU acceleration of nonbondeds is supported with the given settings.

If not, and if a warning may be issued, logs a warning about falling back to CPU code. With thread-MPI, only the first call to this function should have issueWarning true.

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

std::tuple< StartingBehavior, LogFilePtr > gmx::handleRestart	(	bool	isSimulationMaster,
		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.

The routine also does communication to coordinate behaviour between all simulations, including for error conditions.

Exceptions

FileIOError	When the filesystem behavior prevents the user's choices being implemented.
InconsistentInputError	When the users's choices cannot be implemented.
GromacsException	On ranks upon which the error condition was not detected.

Parameters

[in]	isSimulationMaster	Whether this rank is the master rank of a simulation
[in]	communicator	MPI communicator
[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

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::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

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 , int N, int M = N>

MultiDimArray<std::array<ElementType, N * M>, extents<N, M> > gmx::identityMatrix ( )

Create an identity matrix of ElementType with N * M elements.

Template Parameters

ElementType	type of matrix elements
N	number of rows
M	number of columns, defaults to number of rows if not set

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 master 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_winsockinit ( )

Define a function to initialize winsock.

Function to initialize winsock.

Returns: 0 if successful.

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::initCorrelationGridHistory	(	CorrelationGridHistory *	correlationGridHistory,
		int	numCorrelationTensors,
		int	tensorSize,
		int	blockDataListSize
	)

Initialize correlation grid history, sets all sizes.

Parameters

[in,out]	correlationGridHistory	Correlation grid history for master 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().

void gmx::invertBoxMatrix	(	const matrix	src,
		matrix	dest
	)

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.

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 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::launchForceReductionKernel	(	int	numAtoms,
		int	atomStart,
		bool	addRvecForce,
		bool	accumulate,
		DeviceBuffer< Float3 >	d_nbnxmForceToAdd,
		DeviceBuffer< Float3 >	d_rvecForceToAdd,
		DeviceBuffer< Float3 >	d_baseForce,
		DeviceBuffer< int >	d_cell,
		const DeviceStream &	deviceStream
	)

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.

void gmx::launchLeapFrogKernel	(	int	numAtoms,
		DeviceBuffer< Float3 >	d_x,
		DeviceBuffer< Float3 >	d_xp,
		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,
		VelocityScalingType	prVelocityScalingType,
		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_xp	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).
	prVelocityScalingType	Type of Parrinello-Rahman velocity rescaling.
	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::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 >	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]	virialScaled	Scaled virial tensor to be updated.
[in]	pbcAiuc	PBC data.
[in]	deviceStream	Device stream to launch kernel in.

template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>

auto gmx::leapFrogKernel	(	sycl::handler &	cgh,
		DeviceAccessor< Float3, mode::read_write >	a_x,
		DeviceAccessor< Float3, mode::discard_write >	a_xp,
		DeviceAccessor< Float3, mode::read_write >	a_v,
		DeviceAccessor< Float3, mode::read >	a_f,
		DeviceAccessor< float, mode::read >	a_inverseMasses,
		float	dt,
		OptionalAccessor< float, mode::read, numTempScaleValues!=NumTempScaleValues::None >	a_lambdas,
		OptionalAccessor< unsigned short, mode::read, numTempScaleValues==NumTempScaleValues::Multiple >	a_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.
velocityScaling	Type of the Parrinello-Rahman velocity rescaling.

Parameters

	cgh	SYCL's command group handler.
[in,out]	a_x	Coordinates to update upon integration.
[out]	a_xp	A copy of the coordinates before the integration (for constraints).
[in,out]	a_v	Velocities to update.
[in]	a_f	Atomic forces.
[in]	a_inverseMasses	Reciprocal masses.
[in]	dt	Timestep.
[in]	a_lambdas	Temperature scaling factors (one per group).
[in]	a_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>

auto gmx::lincsKernel	(	sycl::handler &	cgh,
		const int	numConstraintsThreads,
		DeviceAccessor< AtomPair, mode::read >	a_constraints,
		DeviceAccessor< float, mode::read >	a_constraintsTargetLengths,
		OptionalAccessor< int, mode::read, haveCoupledConstraints >	a_coupledConstraintsCounts,
		OptionalAccessor< int, mode::read, haveCoupledConstraints >	a_coupledConstraintsIndices,
		OptionalAccessor< float, mode::read, haveCoupledConstraints >	a_massFactors,
		OptionalAccessor< float, mode::read_write, haveCoupledConstraints >	a_matrixA,
		DeviceAccessor< float, mode::read >	a_inverseMasses,
		const int	numIterations,
		const int	expansionOrder,
		DeviceAccessor< Float3, mode::read >	a_x,
		DeviceAccessor< Float3, mode::read_write >	a_xp,
		const float	invdt,
		OptionalAccessor< Float3, mode::read_write, updateVelocities >	a_v,
		OptionalAccessor< float, mode::read_write, computeVirial >	a_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:

Consider going to warp-level synchronization for the coupled constraints.
Move more data to local/shared memory and try to get rid of atomic operations (at least on the device level).
Use analytical solution for matrix A inversion.
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).

Parameters

[in]	cgh	SYCL handler.
[in]	numConstraintsThreads	Total number of threads.
[in]	a_constraints	List of constrained atoms.
[in]	a_constraintsTargetLengths	Equilibrium distances for the constraints.
[in]	a_coupledConstraintsCounts	Number of constraints, coupled with the current one.
[in]	a_coupledConstraintsIndices	List of coupled with the current one.
[in]	a_massFactors	Mass factors.
[in]	a_matrixA	Elements of the coupling matrix.
[in]	a_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]	a_x	Unconstrained positions.
[in,out]	a_xp	Positions at the previous step, will be updated.
[in]	invdt	Inverse timestep (needed to update velocities).
[in,out]	a_v	Velocities of atoms, will be updated if `updateVelocities`.
[in,out]	a_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.

ListOfLists< int > gmx::make_at2con	(	int	numAtoms,
		ArrayRef< const 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 F_CONSTR and higher indices matching the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.

Parameters

[in]	numAtoms	The number of atoms to construct the list for
[in]	ilist	Interaction list, size F_NRE
[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 F_CONSTR and higher indices matching the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.

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

void gmx::make_local_shells	(	const t_commrec *	cr,
		const t_mdatoms &	md,
		gmx_shellfc_t *	shfc
	)

Gets the local shell with domain decomposition.

Parameters

[in]	cr	Communication record
[in]	md	The MD atom data
[in,out]	shfc	The shell/flexible-constraint data

template<typename T >

ArrayRef<std::conditional_t<std::is_const<T>::value, const typename T::value_type, typename T::value_type> > gmx::makeArrayRef ( T & c )

Create ArrayRef from container with type deduction.

See Also: ArrayRef

Todo:: Use std::is_const_v when CUDA 11 is a requirement.

static ListOfLists<int> gmx::makeAtomsToConstraintsList	(	int	numAtoms,
		ArrayRef< const 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 F_CONSTR and higher indices matching the order in F_CONSTRNC offset by the number of constraints in F_CONSTR.

Parameters

[in]	numAtoms	The number of atoms to construct the list for
[in]	ilists	The interaction lists, size F_NRE
[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 paritioning of the atom range into atom groups

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	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.

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.

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.

std::unique_ptr< ImdSession > gmx::makeImdSession	(	const t_inputrec *	ir,
		const t_commrec *	cr,
		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
cr	Information structure for MPI communication.
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 accceptable (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
	)

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.

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::vector< RangePartitioning > gmx::makeUpdateGroupingsPerMoleculeType ( const gmx_mtop_t & mtop )

Returns a vector with update groups for each moleculetype in mtop or an empty vector when the criteria (see below) are not satisfied.

An empty vector 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	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.

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.

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,
		const t_commrec *	cr,
		PbcType	pbcType,
		ArrayRef< const RangePartitioning >	updateGroupingPerMoleculeType
	)

Create the virtual site handler.

Parameters

[in]	mtop	The global topology
[in]	cr	The communication record
[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 gmx::MDLogger &	mdlog,
		const bool	useGpuForNonbonded,
		const PmeRunMode	pmeRunMode,
		const int	numRanksPerSimulation,
		const int	numPmeRanksPerSimulation
	)

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]	useGpuForNonbonded	True if the nonbonded task is offloaded in this run.
[in]	pmeRunMode	Run mode indicating what resource is PME execured on.
[in]	numRanksPerSimulation	The number of ranks in each simulation.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation, can be -1

Returns: The object populated with development feature flags.

void gmx::mapGridToDataGrid	(	std::vector< int > *	gridpointToDatapoint,
		const double const	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.

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::mdAlgorithmsSetupAtomData	(	const t_commrec *	cr,
		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,
		gmx_shellfc_t *	shellfc
	)

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]	cr	Communication record
[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

static void gmx::mdrunner_start_fn ( const void * arg )

static

The callback used for running on spawned threads.

Obtains the pointer to the master 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::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::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.

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 $\mathbb{R}^N\to\mathbb{R}$ 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, $x_c = \frac1n \sum_{i=1}{N} x_i$ .

3 Reflect the worst simplex vertex (the one with the highest function value) at the centroid to obtain a reflection point $x_r = x_c + \alpha (x_c - x_{N+1})$ 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 $x_e = x_c + \gamma (x_r - x_c)$ . 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; $x_t = x_c + \rho (x_{N+1} - x_c)$ . 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 $x_i = x_1 + \sigma (x_i - x_1)$ 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.

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

FilePtr gmx::openLibraryFile	(	const std::string &	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.

FilePtr gmx::openLibraryFile	(	const char *	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.

static t_trxstatus* gmx::openTNG	(	const std::string &	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 T2 >

bool gmx::operator==	(	const Allocator< T1, HostAllocationPolicy > &	a,
		const Allocator< T2, HostAllocationPolicy > &	b
	)

Return true if two allocators are identical.

True if pinning policy is the same.

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.

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 accceptable (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 accceptable (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 accceptable (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 ',').

void gmx::pinBuffer	(	void *	pointer,
		std::size_t	numBytes
	)

noexcept

Pin the allocation to physical memory.

Requires that pointer is not nullptr.

Does not throw.

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 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 t_commrec *	commRecord,
		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]	commRecord	Struct for communication, can be nullptr.
[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.

std::unique_ptr< BoxDeformation > gmx::prepareBoxDeformation	(	const matrix &	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 SIMMASTER to other ranks, and constructs and returns an object to manage that update.

Exceptions

NotImplementedError if the inputrec specifies an unsupported combination.

void gmx::prepareLogAppending ( FILE * fplog )

Prepare to use the open log file when appending.

Does not throw.

void gmx::printBinaryInformation	(	FILE *	fp,
		const IProgramContext &	programContext
	)

Print basic information about the executable.

Parameters

	fp	Where to print the information to.
[in]	programContext	Program information object to use.

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 t_commrec *	cr,
		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)

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.

template<typename ValueType >

void gmx::readKvtCheckpointValue	(	compat::not_null< ValueType * >	value,
		const std::string &	name,
		const std::string &	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,
		const std::string &	name,
		const std::string &	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,
		const std::string &	name,
		const std::string &	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.

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.

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.

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.

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 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::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 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.

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.

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::setStateDependentAwhParams	(	AwhParams *	awhParams,
		const pull_params_t &	pull_params,
		pull_t *	pull_work,
		const matrix	box,
		PbcType	pbcType,
		const tensor &	compressibility,
		const t_grpopts *	inputrecGroupOptions,
		real	initLambda,
		const gmx_mtop_t &	mtop,
		warninp_t	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]	inputrecGroupOptions	Parameters for atom groups.
[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,
		warninp_t	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.

SettleParameters gmx::settleParameters	(	real	mO,
		real	mH,
		real	dOH,
		real	invmO,
		real	invmH,
		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

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 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	(	SimdType	s,
		FILE *	log,
		bool	warnToStdErr
	)

Check if binary was compiled with the provided SIMD type.

Parameters

s	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).

const std::string & gmx::simdString ( SimdType s )

Return a string with the name of a SIMD type.

Parameters

s	SIMD type to turn into string

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().

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

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 excpetion 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 t_commrec &	commRecord
	)

Sum an array over all simulations on master 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 master ranks of sharing simulations.
[in]	broadcastWithinSimulation	Broadcast the result to all ranks within the simulation
[in]	commRecord	Struct for intra-simulation communication.

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 master 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.

void gmx::unpinBuffer ( void * pointer )

noexcept

Unpin the allocation.

Requries that pointer is not nullptr and was previously pinned with pinBuffer().

Does not throw.

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.

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.

static int gmx::vsiteIlistNrCount ( ArrayRef< const InteractionList > ilist )

static

Returns the sum of the vsite ilist sizes over all vsite types.

Parameters

[in] ilist 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::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,
		const std::string &	name,
		const std::string &	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,
		const std::string &	name,
		const std::string &	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,
		const std::string &	name,
		const std::string &	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::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::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

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))

constexpr int gmx::c_ftypeVsiteStart = F_VSITE1

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.)

const EnumerationArray<QMMMQMMethod, const char*> gmx::c_qmmmQMMethodNames

static

Initial value:

= {
    { "PBE", "BLYP", "INPUT" }
}

The names of the supported QM methods.

constexpr double gmx::c_speedOfLight

Initial value:

=

2.99792458e05

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 std::array<int, numFTypesOnGpu> gmx::fTypesOnGpu

Initial value:

= { F_BONDS,  F_ANGLES, F_UREY_BRADLEY,
                                                          F_PDIHS,  F_RBDIHS, F_IDIHS,
                                                          F_PIDIHS, F_LJ14 }

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, not with OpenCL.

const char gmx::IMDstr[] = "IMD:"

static

Tag output from the IMD module with this string.

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.

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

constexpr int64_t gmx::sc_atomInfo_FreeEnergyPerturbation = 1 << 15

static

Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo.

No bit should exceed 1 << 63, so that it fits into a 64-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.

Description

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Higher-level SIMD utility functions, double precision.

Higher-level SIMD utility functions, single precision.

SIMD data types

High-level SIMD proxy objects to disambiguate load/set operations

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation