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().

Defines function for computing Lennard-Jones interaction using SIMD.

Defines a class for masking (sub-) diagonal interactions in an cluster pair.

Defines function for computing Coulomb interaction using SIMD.

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

The philosophy is as follows. The flavor of Coulomb interactions types is set using constexpr variables. This is then used to select the appropriate templated class with functions in this files through template specialization. Functions in this file take C-style arrays of SIMD of size nR registers as arguments, indicated by a suffix with the letter 'V', which are a list of registers with one for each i-particle (4xM kernels) or pair of i-particles (2xMM kernels) that have LJ interactions. Note that we do not use functions for single SIMD registers because this limits the instruction parallelism that compilers can extract.

Author: Berk Hess hess@.nosp@m.kth..nosp@m.se

Declares and defines a templated class DiagonalMasker with a maskArray function which sets diagonal and sub-diagonal entries of a cluster-pair mask array to false when the i- and j-cluster index combination falls on the diagonal.

Author: Berk Hess hess@.nosp@m.kth..nosp@m.se

The philosophy is as follows. The different flavors of LJ interactions types and calculating energies or not are set using constexpr variables. These are then used to select the appropriate templated functions in this files through template specialization. Functions in this file take C-style arrays of SIMD of size nR registers as arguments, indicated by a suffix with the letter 'V', which are a list of registers with one for each i-particle (4xM kernels) or pair of i-particles (2xMM kernels) that have LJ interactions. This can be half the number of total registers when only part of the i-atoms have LJ. Note that we do not use functions for single SIMD registers because this limits the instruction parallelism that compilers can extract.

A specialized templated LennardJonesCalculator class is used. For each cluster pair, forceC612() or forceSigmaEpsilon() is called, depending on the combination rule. Additionaly addLennardJonesEwaldCorrections() needs to be called when using Ewald for Lennard-Jones.

Note that when atoms can get very close to each other, which we assume only happens when atoms are excluded, the masking template parameter should be set to true to avoid overflows when calculating r^-6.

Note that only plain or potential-shifted LJ interactions are supported with Lorentz-Berthelot combination rules. For switched LJ interations choose no combination rule.

Author: Berk Hess hess@.nosp@m.kth..nosp@m.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{colvars.cpp}

	anonymous_namespace{colvarsMDModule.cpp}

	anonymous_namespace{colvarsMDModule_stub.cpp}

	anonymous_namespace{colvarsoptions.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{enerdata.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_heffte.cpp}

	anonymous_namespace{gpu_3dfft_ocl_vkfft.cpp}

	anonymous_namespace{gpu_3dfft_sycl_rocfft.cpp}

	anonymous_namespace{gpu_3dfft_sycl_vkfft.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{massrepartitioning.cpp}

	anonymous_namespace{mdmodulesnotifier.cpp}

	anonymous_namespace{mdspan.cpp}

	anonymous_namespace{message_string_collector.cpp}

	anonymous_namespace{modules.cpp}

	anonymous_namespace{mpiinfo.cpp}

	anonymous_namespace{mrcdensitymap.cpp}

	anonymous_namespace{mrcdensitymapheader.cpp}

	anonymous_namespace{mrcserializer.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{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{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	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	AnalysisDataFrameAverager
	Helper class for modules that average values over frames. 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...

class	ColvarProxyGromacs
	Implements a GROMACS version of colvarproxy. This class hold for the communication between colvars and GROMACS. 2 child class will inherit from this one: one during pre processing (ColvarsPreProcessor) and one during the simulation (ColvarsForceProvider). Most of the work needed for the communication will be implemented in this class. More...

struct	ColvarsForceProviderState
	Parameters defining the internal colvars force provider state. More...

class	ColvarsForceProvider
	Implements IForceProvider for colvars. Override the ColvarProxyGromacs generic class for the communication. More...

struct	ColvarsModuleInfo
	Information about the colvars module. More...

class	ColvarsOptions
	Input data storage for colvars. More...

class	ColvarsPreProcessor
	Class that read a colvars configuration file during pre-processing and retrieve the colvars atoms coordinates to be stored in tpr KVT. More...

class	ColvarsSimulationsParameters
	Collect colvars parameters only available during simulation setup. 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	ProcessFrameConversion
	ProcessFrameConversion class for handling the running of several analysis steps. More...

class	IFrameConverter
	IFrameConverter interface for manipulating coordinate information. More...

class	IOutputAdapter
	OutputAdapter class for handling trajectory file flag setting and processing. More...

class	OutputAdapterContainer
	Storage for output adapters that modify the state of a t_trxframe object. More...

class	OutputSelector
	OutputSelector class controls setting which coordinates are actually written. More...

class	SetAtoms
	SetAtoms class controls availability of atoms data. More...

class	SetBox
	Allows changing box information when writing a coordinate file. More...

class	SetForces
	SetForces class allows changing writing of forces to file. More...

class	SetPrecision
	SetPrecision class allows changing file writing precision. More...

class	SetStartTime
	SetStartTime class allows changing trajectory time information. More...

class	SetTimeStep
	SetTimeStep class allows changing trajectory time information. More...

class	SetVelocities
	SetVelocities class allows changing writing of velocities to file. More...

class	OutputRequirementOptionDirector
	Container for the user input values that will be used by the builder to determine which OutputAdapters should/could/will be registered to the coordinate file writer. More...

struct	OutputRequirements
	Finalized version of requirements after processing. More...

class	DomainDecompositionBuilder
	Builds a domain decomposition management object. More...

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	EnergyAnalysisFrame
	Class describing an energy frame, that is the all the data stored for one energy term at one time step in an energy file. More...

class	EnergyTerm
	Class describing the whole time series of an energy term. More...

struct	EnergyNameUnit
	Convenience structure for keeping energy name and unit together. More...

class	IEnergyAnalysis
	Interface class overloaded by the separate energy modules. More...

class	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...

struct	PpForceCommManager
	Object to manage communications with a specific PP rank. 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	MDModulesCheckpointReadingDataOnMain
	Provides the MDModules with the checkpointed data on the main rank. More...

struct	MDModulesCheckpointReadingBroadcast
	Provides the MDModules with the communication record to broadcast. More...

struct	MDModulesWriteCheckpointData
	Writing the MDModules data to a checkpoint file. More...

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...

class	Lincs
	Data for LINCS algorithm. More...

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

struct	AtomPair
	A pair of atoms indexes. 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...

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	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	MDModulesAtomsRedistributedSignal
	Notification that atoms may have been redistributed. 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	EdrOutputFilename
	Energy trajectory output filename from Mdrun. More...

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

struct	EnsembleTemperature
	Provides the constant ensemble temperature. More...

struct	MDModulesNotifiers
	Group of notifers to organize that MDModules can receive callbacks they subscribe to. 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 partitioning. 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	CoulombCalculator
	Base Coulomb calculator class, only specializations are used. More...

class	CoulombCalculator< KernelCoulombType::RF >
	Specialized calculator for RF. More...

class	CoulombCalculator< KernelCoulombType::EwaldAnalytical >
	Specialized calculator for Ewald using an analytic approximation. More...

class	CoulombCalculator< KernelCoulombType::EwaldTabulated >
	Specialized calculator for Ewald using tabulated functions. More...

class	DiagonalMasker
	Base Coulomb calculator class, only specializations are used. More...

class	DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeEqualsISize >
	Specialized masker for JSizeEqualsISize. More...

class	DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsDoubleISize >
	Specialized masker for JSizeIsDoubleISize. More...

class	DiagonalMasker< nR, kernelLayout, KernelLayoutClusterRatio::JSizeIsHalfISize >
	Specialized masker for JSizeIsHalfISize. More...

class	LennardJonesCalculator
	Base LJ calculator class, only specializations are used. More...

class	LennardJonesCalculator< false, InteractionModifiers::PotShift >
	Specialized calculator for LJ with potential shift and no energy calculation. More...

class	LennardJonesCalculator< true, InteractionModifiers::PotShift >
	Specialized calculator for LJ with potential shift and energy calculation. More...

class	LennardJonesCalculator< calculateEnergies, InteractionModifiers::ForceSwitch >
	Specialized calculator for LJ with force switch. More...

class	LennardJonesCalculator< calculateEnergies, InteractionModifiers::PotSwitch >
	Specialized calculator for LJ with potential switch. More...

class	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	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	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	FileNameOptionStorage
	Converts, validates, and stores file names. More...

class	IOptionSectionStorage
	Provides behavior specific to a certain option section type. More...

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

class	OptionsAssigner
	Decorator class for assigning values to Options. More...

class	OptionSection
	Declares a simple option section. More...

class	OptionSectionHandle
	Allows adding options to an OptionSection. More...

class	OptionStorageTemplate
	Templated base class for constructing option value storage classes. More...

class	OptionStorageTemplateSimple
	Simplified option storage template for options that have one-to-one value conversion. More...

class	OptionsVisitor
	Pure interface for visiting options in a Options object. More...

class	OptionsTypeVisitor
	Abstract base class for visiting options of a particular type. More...

class	OptionsIterator
	Decorator class for visiting options in a Options object. More...

class	OptionsModifyingVisitor
	Pure interface for visiting options in a Options object, allowing modifications. More...

class	OptionsModifyingTypeVisitor
	Abstract base class for visiting options of a particular type, allowing modifications. More...

class	OptionsModifyingIterator
	Decorator class for visiting options in a Options object, allowing changes. More...

class	RepeatingOptionSectionHandle
	Allows adding options to an RepeatingOptionSection. More...

class	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	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	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	SelectionEvaluator
	Implements 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	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...

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

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

class	SansDebye
	Derrived class for computing SANS scattering. More...

struct	pairHash
	Hash function to allow use of pair in unordered_map. More...

class	SaxsDebye
	Derrived class for computing neutron scattering. More...

struct	PairDistValue
	structure to store pair dist units More...

class	ComputeDebyeScattering
	Base class for computing SANS and SAXS using Debye Method. More...

struct	CromerMannParameters
	Cromer-Mann scattering factor parameters to compute structure factor dependent on Q. More...

struct	AtomicStructureFactor
	Neutron scattering factor parameters for an atom type. 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	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...

struct	BoolType
	A clone of a bool as a workaround on the template specialization of std::vector<bool> that is incompatible with ArrayRef. More...

class	DataFileOptions
	Search parameters for DataFileFinder. More...

struct	DataFileInfo
	Information about a data file found by DataFileFinder::enumerateFiles(). More...

class	DataFileFinder
	Searches data files from a set of paths. More...

class	DefaultInitializationAllocator
	Allocator adaptor that interposes construct() calls to convert value initialization into default initialization. More...

class	DirectoryEnumerator
	Lists files in a directory. More...

class	IFileInputRedirector
	Allows overriding file existence checks from code that supports it. More...

class	IFileOutputRedirector
	Allows capturing `stdout` and file output from code that supports it. More...

class	StandardInputStream
	Text input stream implementation for reading from `stdin`. More...

class	TextInputFile
	Text input stream implementation for reading from a file. More...

class	TextOutputFile
	Text output stream implementation for writing to a file. More...

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

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

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

class	StringCompare
	Compare object for std::string STL containers and algorithms that supports run-time decision on how to compare. More...

class	StringOutputStream
	Text output stream implementation for writing to an in-memory string. More...

class	StringInputStream
	Helper class to convert static string data to a stream. More...

class	StringToEnumValueConverter
	A class to convert a string to an enum value of type `EnumType`. More...

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

class	TextInputStream
	Interface for reading text. More...

class	TextOutputStream
	Interface for writing text. More...

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

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

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

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

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

class	AbstractAnalysisData
	Abstract base class for all objects that provide data. More...

class	AnalysisData
	Parallelizable data container for raw data. More...

class	AnalysisDataHandle
	Handle for inserting data into AnalysisData. More...

class	AbstractAnalysisArrayData
	Abstract base class for data objects that present in-memory data. More...

class	AnalysisArrayData
	Simple in-memory data array. More...

class	AnalysisDataValue
	Value type for representing a single value in analysis data objects. More...

class	AnalysisDataFrameHeader
	Value type for storing frame-level information for analysis data. More...

class	AnalysisDataPointSetRef
	Value type wrapper for non-mutable access to a set of data column values. More...

class	AnalysisDataFrameRef
	Value type wrapper for non-mutable access to a data frame. More...

class	IAnalysisDataModule
	Interface for a module that gets notified whenever data is added. More...

class	AnalysisDataModuleSerial
	Convenience base class for serial analysis data modules. More...

class	AnalysisDataModuleParallel
	Convenience base class for parallel analysis data modules. More...

class	AnalysisDataAverageModule
	Data module for independently averaging each column in input data. More...

class	AnalysisDataFrameAverageModule
	Data module for averaging of columns for each frame. More...

class	AnalysisDataDisplacementModule
	Data module for calculating displacements. More...

class	AnalysisHistogramSettingsInitializer
	Provides "named parameter" idiom for constructing histograms. More...

class	AnalysisHistogramSettings
	Contains parameters that specify histogram bin locations. More...

class	AbstractAverageHistogram
	Base class for representing histograms averaged over frames. More...

class	AnalysisDataSimpleHistogramModule
	Data module for per-frame histograms. More...

class	AnalysisDataWeightedHistogramModule
	Data module for per-frame weighted histograms. More...

class	AnalysisDataBinAverageModule
	Data module for bin averages. More...

class	AnalysisDataLifetimeModule
	Data module for computing lifetime histograms for columns in input data. More...

class	AnalysisDataPlotSettings
	Common settings for data plots. More...

class	AbstractPlotModule
	Abstract data module for writing data into a file. More...

class	AnalysisDataPlotModule
	Plotting module for straightforward plotting of data. More...

class	AnalysisDataVectorPlotModule
	Plotting module specifically for data consisting of vectors. More...

struct	StaticLog2
	Evaluate log2(n) for integer n statically at compile time. More...

struct	StaticLog2< 1 >
	Specialization of StaticLog2<n> for n==1. More...

struct	StaticLog2< 0 >
	Specialization of StaticLog2<n> for n==0. More...

class	AbstractOption
	Abstract base class for specifying option properties. More...

class	OptionTemplate
	Templated base class for constructing concrete option settings classes. More...

class	OptionInfo
	Gives information and allows modifications to an option after creation. More...

class	BooleanOption
	Specifies an option that provides boolean values. More...

class	IntegerOption
	Specifies an option that provides 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	FileNameOption
	Specifies an option that provides file names. More...

class	FileNameOptionInfo
	Wrapper class for accessing file name option information. More...

class	FileNameOptionManager
	Handles interaction of file name options with global options. More...

class	IOptionsBehavior
	Interface to provide extension points for options parsing. More...

class	IOptionsContainer
	Interface for adding input options. More...

class	IOptionsContainerWithSections
	Interface for adding input options with sections. More...

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

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

class	Options
	Collection of options. More...

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

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

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

class	IRestraintPotential
	Interface for Restraint potentials. More...

class	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	Selection
	Provides access to a single selection. More...

class	SelectionPosition
	Provides access to information about a single selected position. More...

class	SelectionCollection
	Collection of selections. More...

struct	SelectionTopologyProperties
	Describes topology properties required for selection evaluation. More...

class	SelectionOption
	Specifies an option that provides selection(s). More...

class	SelectionOptionInfo
	Wrapper class for accessing and modifying selection option information. More...

class	ITopologyProvider
	Provides topology information to SelectionOptionBehavior. More...

class	SelectionOptionBehavior
	Options behavior to allow using SelectionOptions. More...

class	SelectionOptionManager
	Handles interaction of selection options with other options and user input. More...

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

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

class	EnumerationIterator
	Allows iterating sequential enumerators. More...

class	EnumerationWrapper
	Allows constructing iterators for looping over sequential enumerators. More...

class	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...

class	FlagsTemplate
	Template class for typesafe handling of combination of flags. More...

struct	InstallationPrefixInfo
	Provides information about installation prefix (see IProgramContext::installationPrefix()). More...

class	IProgramContext
	Provides context information about the program that is calling the library. More...

class	StringFormatter
	Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms. More...

class	IdentityFormatter
	Function object to implement the same interface as `StringFormatter` to use with strings that should not be formatted further. More...

class	EqualCaseInsensitive
	Function object for comparisons with `equalCaseInsensitive`. More...

class	TextLineWrapperSettings
	Stores settings for line wrapping. More...

class	TextLineWrapper
	Wraps lines to a predefined length. More...

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

Typedefs
typedef double	awh_dvec [c_biasMaxNumDim]
	A real vector in AWH coordinate space.

typedef int	awh_ivec [c_biasMaxNumDim]
	An integer vector in AWH coordinate space.

typedef int	force_env_t
	Type for CP2K force environment handle.

typedef std::unique_ptr < ICommandLineModule >	CommandLineModulePointer
	Smart pointer type for managing a ICommandLineModule.

typedef std::map< std::string, CommandLineModulePointer >	CommandLineModuleMap
	Container type for mapping module names to module objects.

typedef std::unique_ptr < CommandLineModuleGroupData >	CommandLineModuleGroupDataPointer
	Smart pointer type for managing a CommandLineModuleGroup.

typedef std::vector < CommandLineModuleGroupDataPointer >	CommandLineModuleGroupList
	Container type for keeping a list of module groups.

typedef std::unique_ptr < ICommandLineOptionsModule >	ICommandLineOptionsModulePointer
	Smart pointer to manage an ICommandLineOptionsModule.

typedef std::unique_ptr < IExecutableEnvironment >	ExecutableEnvironmentPointer
	Shorthand for a smart pointer to IExecutableEnvironment.

using	TrajectoryFrameWriterPointer = std::unique_ptr< TrajectoryFrameWriter >
	Smart pointer to manage the TrajectoryFrameWriter object.

using	ProcessFrameConversionPointer = std::unique_ptr< ProcessFrameConversion >
	Smart pointer to manage the analyse object.

using	FrameConverterPointer = std::unique_ptr< IFrameConverter >
	Typedef to have direct access to the individual FrameConverter modules.

using	OutputAdapterPointer = std::unique_ptr< IOutputAdapter >
	Smart pointer to manage the frame adapter object.

using	OutputSelectorPointer = std::unique_ptr< OutputSelector >
	Smart pointer to manage the object.

using	SetAtomsPointer = std::unique_ptr< SetAtoms >
	Smart pointer to manage the object.

using	SetBoxPointer = std::unique_ptr< SetBox >
	Smart pointer to manage the object.

using	SetForcesPointer = std::unique_ptr< SetForces >
	Smart pointer to manage the object.

using	SetPrecisionPointer = std::unique_ptr< SetPrecision >
	Smart pointer to manage the outputselector object.

using	SetStartTimePointer = std::unique_ptr< SetStartTime >
	Smart pointer to manage the object.

using	SetTimeStepPointer = std::unique_ptr< SetTimeStep >
	Smart pointer to manage the object.

using	SetVelocitiesPointer = std::unique_ptr< SetVelocities >
	Smart pointer to manage the object.

using	EnergyAnalysisFrameIterator = std::vector< EnergyAnalysisFrame >::const_iterator
	Typedef for looping over EnergyFrame.

using	IEnergyAnalysisPointer = std::unique_ptr< IEnergyAnalysis >
	Pointer to the EnergyAnalysisModule classes.

typedef struct gmx::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.

using	mode = sycl::access_mode

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.

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 SimdReal	SimdBitMask
	Define SimdBitMask as a real SIMD register.

typedef std::unique_ptr < AbstractCompositeHelpTopic >	CompositeHelpTopicPointer
	Smart pointer type to manage a AbstractCompositeHelpTopic object.

typedef std::unique_ptr < IHelpTopic >	HelpTopicPointer
	Smart pointer type to manage a IHelpTopic object.

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

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

typedef 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::unique_ptr < internal::SelectionData >	SelectionDataPointer
	Smart pointer for managing an internal selection data object.

typedef std::vector < SelectionDataPointer >	SelectionDataList
	Container for storing a list of selections internally.

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

typedef 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.

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	MPI_Comm_ptr = gmx::unique_cptr< MPI_Comm, MPI_Comm_free_wrapper >
	Make a smart pointer for MPI communicators.

typedef std::shared_ptr < TextInputStream >	TextInputStreamPointer
	Shorthand for a smart pointer to a TextInputStream.

typedef std::shared_ptr < TextOutputStream >	TextOutputStreamPointer
	Shorthand for a smart pointer to a TextOutputStream.

typedef std::shared_ptr < IAnalysisDataModule >	AnalysisDataModulePointer
	Smart pointer for managing a generic analysis data module.

typedef ArrayRef< const AnalysisDataValue >	AnalysisDataValuesRef
	Shorthand for reference to an array of data values.

typedef std::shared_ptr < AnalysisDataAverageModule >	AnalysisDataAverageModulePointer
	Smart pointer to manage an AnalysisDataAverageModule object.

typedef std::shared_ptr < AnalysisDataFrameAverageModule >	AnalysisDataFrameAverageModulePointer
	Smart pointer to manage an AnalysisDataFrameAverageModule object.

typedef std::shared_ptr < AnalysisDataDisplacementModule >	AnalysisDataDisplacementModulePointer
	Smart pointer to manage an AnalysisDataDisplacementModule object.

typedef std::unique_ptr < AbstractAverageHistogram >	AverageHistogramPointer
	Smart pointer to manage an AbstractAverageHistogram object.

typedef std::shared_ptr < AnalysisDataSimpleHistogramModule >	AnalysisDataSimpleHistogramModulePointer
	Smart pointer to manage an AnalysisDataSimpleHistogramModule object.

typedef std::shared_ptr < AnalysisDataWeightedHistogramModule >	AnalysisDataWeightedHistogramModulePointer
	Smart pointer to manage an AnalysisDataWeightedHistogramModule object.

typedef std::shared_ptr < AnalysisDataBinAverageModule >	AnalysisDataBinAverageModulePointer
	Smart pointer to manage an AnalysisDataBinAverageModule object.

typedef std::shared_ptr < AnalysisDataLifetimeModule >	AnalysisDataLifetimeModulePointer
	Smart pointer to manage an AnalysisDataLifetimeModule object.

typedef std::shared_ptr < AnalysisDataPlotModule >	AnalysisDataPlotModulePointer
	Smart pointer to manage an AnalysisDataPlotModule object.

typedef std::shared_ptr < AnalysisDataVectorPlotModule >	AnalysisDataVectorPlotModulePointer
	Smart pointer to manage an AnalysisDataVectorPlotModule object.

typedef 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.

typedef FloatOption	RealOption
	Typedef for either DoubleOption or FloatOption, depending on precision. More...

typedef FloatOptionInfo	RealOptionInfo
	Typedef for either DoubleOptionInfo or FloatOptionInfo, depending on precision. More...

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

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

typedef std::vector< Selection >	SelectionList
	Container of selections used in public selection interfaces.

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

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.

using	Index = std::ptrdiff_t
	Integer type for indexing into arrays or vectors. More...

typedef ExceptionInfo< struct ExceptionInfoErrno_, int >	ExceptionInfoErrno
	Stores `errno` value that triggered the exception.

typedef ExceptionInfo< struct ExceptionInfoApiFunc_, const char * >	ExceptionInfoApiFunction
	Stores the function name that returned the `errno` in ExceptionInfoErrno.

typedef ExceptionInfo< struct ExceptionInfoLocation_, ThrowLocation >	ExceptionInfoLocation
	Stores the location where the exception was thrown.

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

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.


using	ClContext = ClHandle< cl_context >
	Convenience declarations.

using	ClCommandQueue = ClHandle< cl_command_queue >

using	ClProgram = ClHandle< cl_program >

using	ClKernel = ClHandle< cl_kernel >

Enumerations
enum	AwhOutputEntryType { AwhOutputEntryType::MetaData, AwhOutputEntryType::CoordValue, AwhOutputEntryType::Pmf, AwhOutputEntryType::Bias, AwhOutputEntryType::Visits, AwhOutputEntryType::Weights, AwhOutputEntryType::Target, AwhOutputEntryType::SharedForceCorrelationVolume, AwhOutputEntryType::SharedFrictionTensor }
	Enum with the AWH variables to write. More...

enum	AwhOutputMetaData { AwhOutputMetaData::NumBlock, AwhOutputMetaData::TargetError, AwhOutputMetaData::ScaledSampleWeight, AwhOutputMetaData::Count }
	Enum with the types of metadata to write. More...

enum	Normalization { Normalization::None, Normalization::Coordinate, Normalization::FreeEnergy, Normalization::Distribution }
	Enum with different ways of normalizing the output. More...

enum	DensityFittingAmplitudeMethod : int { DensityFittingAmplitudeMethod::Unity, DensityFittingAmplitudeMethod::Mass, DensityFittingAmplitudeMethod::Charge, Count }
	The methods that determine how amplitudes are spread on a grid in density guided simulations. More...

enum	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	FrameConverterFlags : unsigned long { FrameConverterFlags::NoGuarantee = 1 << 0, FrameConverterFlags::MoleculesAreWhole = 1 << 1, FrameConverterFlags::NoPBCJumps = 1 << 2, FrameConverterFlags::MoleculeCOMInBox = 1 << 3, FrameConverterFlags::ResidueCOMInBox = 1 << 4, FrameConverterFlags::AtomsInBox = 1 << 5, FrameConverterFlags::UnitCellIsRectangular = 1 << 6, FrameConverterFlags::UnitCellIsTriclinic = 1 << 7, FrameConverterFlags::UnitCellIsCompact = 1 << 8, FrameConverterFlags::SystemIsCenteredInBox = 1 << 9, FrameConverterFlags::FitToReferenceRotTrans = 1 << 10, FrameConverterFlags::FitToReferenceRotTransXY = 1 << 11, FrameConverterFlags::FitToReferenceTranslation = 1 << 12, FrameConverterFlags::FitToReferenceTranslationXY = 1 << 13, FrameConverterFlags::FitToReferenceProgressive = 1 << 14, FrameConverterFlags::NewSystemCenter = 1 << 15, FrameConverterFlags::Count }
	The enums here define the guarantees provided by frameconverters concerning the modifications they provide. More...

enum	HaloType { Coordinates, Forces }
	Whether the halo exchange is of coordinates or forces.

enum	DdRankOrder { DdRankOrder::select, DdRankOrder::interleave, DdRankOrder::pp_pme, DdRankOrder::cartesian, DdRankOrder::Count }
	The options for the domain decomposition MPI task ordering. More...

enum	DlbOption { DlbOption::select, DlbOption::turnOnWhenUseful, DlbOption::no, DlbOption::yes, DlbOption::Count }
	The options for the dynamic load balancing. More...

enum	DDBondedChecking : bool { DDBondedChecking::ExcludeZeroLimit = false, DDBondedChecking::All = true }
	Options for checking bonded interactions. More...

enum	DirectionX : int { Up = 0, Down, Center, Count }
	Direction of neighbouring rank in X-dimension relative to current rank. Used in GPU implementation of PME halo exchange.

enum	DirectionY : int { Left = 0, Right, Center, Count }
	Direction of neighbouring rank in Y-dimension relative to current rank. Used in GPU implementation of PME halo exchange.

enum	FftBackend { FftBackend::Cufft, FftBackend::OclVkfft, FftBackend::Ocl, FftBackend::CuFFTMp, FftBackend::HeFFTe_CUDA, FftBackend::HeFFTe_Sycl_OneMkl, FftBackend::HeFFTe_Sycl_Rocfft, FftBackend::HeFFTe_Sycl_cuFFT, FftBackend::SyclMkl, FftBackend::SyclRocfft, FftBackend::SyclVkfft, FftBackend::SyclBbfft, FftBackend::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 { Architecture::Unknown, Architecture::X86, Architecture::Arm, Architecture::PowerPC, Architecture::RiscV32, Architecture::RiscV64 }
	Enum for GROMACS CPU hardware detection support. More...

enum	SimdType { SimdType::None, SimdType::Reference, SimdType::Generic, SimdType::X86_Sse2, SimdType::X86_Sse4_1, SimdType::X86_Avx128Fma, SimdType::X86_Avx, SimdType::X86_Avx2, SimdType::X86_Avx2_128, SimdType::X86_Avx512, SimdType::X86_Avx512Knl, SimdType::Arm_NeonAsimd, SimdType::Arm_Sve, SimdType::Ibm_Vsx }
	Enumerated options for SIMD architectures. More...

enum	IMDMessageType : int { IMDMessageType::Disconnect, IMDMessageType::Energies, IMDMessageType::FCoords, IMDMessageType::Go, IMDMessageType::Handshake, IMDMessageType::Kill, IMDMessageType::Mdcomm, IMDMessageType::Pause, IMDMessageType::TRate, IMDMessageType::IOerror, IMDMessageType::Count }
	Enum for types of IMD messages. More...

enum	DensitySimilarityMeasureMethod : int { DensitySimilarityMeasureMethod::innerProduct, DensitySimilarityMeasureMethod::relativeEntropy, DensitySimilarityMeasureMethod::crossCorrelation, Count }
	The methods that determine how two densities are compared to one another. More...

enum	CheckpointSignal { noSignal = 0, doCheckpoint = 1 }
	Checkpoint signals. More...

enum	ConstraintVariable : int { Positions, Velocities, Derivative, Deriv_FlexCon, Force, ForceDispl }
	Describes supported flavours of constrained updates.

enum	FlexibleConstraintTreatment { FlexibleConstraintTreatment::Include, FlexibleConstraintTreatment::Exclude }
	Tells make_at2con how to treat flexible constraints. More...

enum	NumTempScaleValues { NumTempScaleValues::None = 0, NumTempScaleValues::Single = 1, NumTempScaleValues::Multiple = 2, NumTempScaleValues::Count = 3 }
	Sets the number of different temperature coupling values. More...

enum	GraphState : int { GraphState::Invalid, GraphState::Recording, GraphState::Recorded, GraphState::Instantiated, GraphState::Count }
	State of graph. More...

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

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

enum	IncompatibilityReasons { FlexibleConstraint, IncompatibleVsite, VsiteConstructingAtomsSplit, ConstrainedAtomOrder, NoCentralConstraintAtom, Count }
	Reasons why the system can be incompatible with update groups.

enum	VSiteCalculatePosition { Yes, No }
	Whether we're calculating the virtual site position.

enum	VSiteCalculateVelocity { Yes, No }
	Whether we're calculating the virtual site velocity.

enum	PbcMode { PbcMode::all, PbcMode::none }
	PBC modes for vsite construction and spreading. More...

enum	VSiteOperation { VSiteOperation::Positions, VSiteOperation::Velocities, VSiteOperation::PositionsAndVelocities, VSiteOperation::Count }
	Whether we calculate vsite positions, velocities, or both. More...

enum	VirtualSiteVirialHandling : int { VirtualSiteVirialHandling::None, VirtualSiteVirialHandling::Pbc, VirtualSiteVirialHandling::NonLinear }
	Tells how to handle virial contributions due to virtual sites. More...

enum	StartingBehavior : int { StartingBehavior::RestartWithAppending, StartingBehavior::RestartWithoutAppending, StartingBehavior::NewSimulation, StartingBehavior::Count }
	Enumeration for describing how mdrun is (re)starting. More...

enum	: std::ptrdiff_t { dynamic_extent = -1 }
	Define constant that signals dynamic extent.

enum	AwhTargetType : int { Constant, Cutoff, Boltzmann, LocalBoltzmann, Count, Default = Constant }
	Target distribution enum.

enum	AwhHistogramGrowthType : int { ExponentialLinear, Linear, Count, Default = ExponentialLinear }
	Weight histogram growth enum.

enum	AwhPotentialType : int { Convolved, Umbrella, Count, Default = Convolved }
	AWH potential type enum.

enum	AwhCoordinateProviderType : int { Pull, FreeEnergyLambda, Count, Default = Pull }
	AWH bias reaction coordinate provider.

enum	CheckpointDataOperation { Read, Write, Count }
	The operations on CheckpointData. More...

enum	AtomLocality : int { AtomLocality::Local = 0, AtomLocality::NonLocal = 1, AtomLocality::All = 2, AtomLocality::Count = 3 }
	Atom locality indicator: local, non-local, all. More...

enum	InteractionLocality : int { InteractionLocality::Local = 0, InteractionLocality::NonLocal = 1, InteractionLocality::Count = 2 }
	Interaction locality indicator: local, non-local, all. More...

enum	AppendingBehavior { AppendingBehavior::Auto, AppendingBehavior::Appending, AppendingBehavior::NoAppending }
	Enumeration for mdrun appending behavior. More...

enum	MtsForceGroups : int { MtsForceGroups::LongrangeNonbonded, MtsForceGroups::Nonbonded, MtsForceGroups::Pair, MtsForceGroups::Dihedral, MtsForceGroups::Angle, MtsForceGroups::Pull, MtsForceGroups::Awh, MtsForceGroups::Count }
	Force group available for selection for multiple time step integration. More...

enum	ReductionRequirement : int { ReductionRequirement::Soon, ReductionRequirement::Eventually }
	Control whether reduction is required soon. More...

enum	ObservablesReducerStatus : int { ObservablesReducerStatus::ReadyToReduce, ObservablesReducerStatus::AlreadyReducedThisStep }
	Report whether the reduction has happened this step. More...

enum	ComputeGlobalsAlgorithm { LeapFrog, VelocityVerlet }
	The different global reduction schemes we know about.

enum	EnergySignallerEvent { EnergyCalculationStep, VirialCalculationStep, FreeEnergyCalculationStep }
	The energy events signalled by the EnergySignaller.

enum	TrajectoryEvent { StateWritingStep, EnergyWritingStep }
	The trajectory writing events.

enum	ModularSimulatorBuilderState { AcceptingClientRegistrations, NotAcceptingClientRegistrations }
	Enum allowing builders to store whether they can accept client registrations.

enum	ReportPreviousStepConservedEnergy { Yes, No, Count }
	Enum describing whether an element is reporting conserved energy from the previous step.

enum	ScheduleOnInitStep { ScheduleOnInitStep::Yes, ScheduleOnInitStep::No, ScheduleOnInitStep::Count }
	Whether the element does schedule on the initial step. More...

enum	NhcUsage { NhcUsage::System, NhcUsage::Barostat, NhcUsage::Count }
	The usages of Nose-Hoover chains. More...

enum	ScaleVelocities { PreStepOnly, PreStepAndPostStep }
	Which velocities the thermostat scales.

enum	IntegrationStage { IntegrationStage::PositionsOnly, IntegrationStage::VelocitiesOnly, IntegrationStage::LeapFrog, IntegrationStage::VelocityVerletPositionsAndVelocities, IntegrationStage::ScaleVelocities, IntegrationStage::ScalePositions, IntegrationStage::Count }
	The different integration types we know about. More...

enum	NumPositionScalingValues { NumPositionScalingValues::None, NumPositionScalingValues::Single, NumPositionScalingValues::Multiple, NumPositionScalingValues::Count }
	Sets the number of different position scaling values. More...

enum	NumVelocityScalingValues { NumVelocityScalingValues::None, NumVelocityScalingValues::Single, NumVelocityScalingValues::Multiple, Count }
	Sets the number of different velocity scaling values. More...

enum	ParrinelloRahmanVelocityScaling { ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Anisotropic, Count }
	Describes the properties of the Parrinello-Rahman pressure scaling matrix. 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	KernelCoulombType { KernelCoulombType::RF, KernelCoulombType::EwaldAnalytical, KernelCoulombType::EwaldTabulated }
	List of type of Nbnxm kernel coulomb type implementations. More...

enum	ILJInteractions { ILJInteractions::All, ILJInteractions::Half, ILJInteractions::None }
	The fraction of i-particles for which LJ interactions need to be computed. More...

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

enum	COMShiftType : int { Residue, Molecule, Count }
	How COM shifting should be applied.

enum	CenteringType : int { Triclinic, Rectangular, Zero, Count }
	Helper enum class to define centering types.

enum	UnitCellType : int { Triclinic, Rectangular, Compact, Count }
	Helper enum class to define Unit cell representation types.

enum	RandomDomain { RandomDomain::Other = 0x00000000, RandomDomain::MaxwellVelocities = 0x00001000, RandomDomain::TestParticleInsertion = 0x00002000, RandomDomain::UpdateCoordinates = 0x00003000, RandomDomain::UpdateConstraints = 0x00004000, RandomDomain::Thermostat = 0x00005000, RandomDomain::Barostat = 0x00006000, RandomDomain::ReplicaExchange = 0x00007000, RandomDomain::ExpandedEnsemble = 0x00008000, RandomDomain::AwhBiasing = 0x00009000 }
	Enumerated values for fixed part of random seed (domain) More...

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

enum	TaskTarget : int { Auto, Cpu, Gpu }
	Record where a compute task is targetted.

enum	EmulateGpuNonbonded : bool { EmulateGpuNonbonded::No, EmulateGpuNonbonded::Yes }
	Help pass GPU-emulation parameters with type safety. More...

enum	GpuTask : int { GpuTask::Nonbonded, GpuTask::Pme, GpuTask::Count }
	Types of compute tasks that can be run on a GPU. More...

enum	Isotope { H, D, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt, Count }
	isotopes

enum	ErrorCode { eeOK, eeOutOfMemory, eeFileNotFound, eeFileIO, eeInvalidInput, eeInconsistentInput, eeTolerance, eeInstability, eeNotImplemented, eeInvalidValue, eeInvalidCall, eeInternalError, eeAPIError, eeRange, eeParallelConsistency, eeModularSimulator, 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::NotSupported = 0, GpuAwareMpiStatus::Forced, GpuAwareMpiStatus::Supported }
	Enum describing GPU-aware support in underlying MPI library. More...

enum	StringCompareType { StringCompareType::Exact, StringCompareType::CaseInsensitive, StringCompareType::CaseAndDashInsensitive }
	Specifies how strings should be compared in various contexts. More...

enum	StripStrings : int { StripStrings::No, StripStrings::Yes }
	Enum class for whether StringToEnumValueConverter will strip strings of leading and trailing whitespace before comparison. More...

enum	TimeUnit : int { Femtoseconds, Picoseconds, Nanoseconds, Microseconds, Milliseconds, Seconds, Count, Default = Picoseconds }
	Time values for TimeUnitManager and legacy oenv module.

enum	OptionFileType : int { Topology, RunInput, Trajectory, Energy, PDB, AtomIndex, Plot, GenericData, Csv, QMInput, Count }
	Purpose of file(s) provided through an option.

enum	OptionFlag : uint64_t { efOption_Set = 1 << 0, efOption_HasDefaultValue = 1 << 1, efOption_ExplicitDefaultValue = 1 << 2, efOption_ClearOnNextSet = 1 << 3, efOption_Required = 1 << 4, efOption_MultipleTimes = 1 << 5, efOption_Hidden = 1 << 6, efOption_Vector = 1 << 8, efOption_DefaultValueIfSetExists = 1 << 11, efOption_NoDefaultValue = 1 << 9, efOption_DontCheckMinimumCount = 1 << 10 }
	Flags for options. More...

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...

Functions
static bool	anyDimUsesProvider (const AwhBiasParams &awhBiasParams, const AwhCoordinateProviderType awhCoordProvider)
	Checks whether any dimension uses the given coordinate provider type. More...

static bool	anyDimUsesProvider (const AwhParams &awhParams, const AwhCoordinateProviderType awhCoordProvider)
	Checks whether any dimension uses the given coordinate provider type. More...

static bool	anyBiasIsScaledByMetric (const AwhParams &awhParams)
	Checks whether any bias scales the target distribution based on the AWH friction metric. More...

std::unique_ptr< Awh >	prepareAwhModule (FILE fplog, const t_inputrec &inputRecord, t_state stateGlobal, const 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 MultiDimArray< std::vector< double >, dynamicExtents2D > &data, int numDataPoints, const std::string &dataFilename, const BiasGrid &grid, const std::string &correctFormatMessage)
	Maps each point in the grid to a point in the data grid. More...

template<typename T >
void	sumOverSimulations (ArrayRef< T > data, MPI_Comm multiSimComm, const bool broadcastWithinSimulation, const t_commrec &commRecord)
	Sum an array over all simulations on main ranks or all ranks of each simulation. More...

bool	haveBiasSharingWithinSimulation (const AwhParams &awhParams)
	Returns if any bias is sharing within a simulation. More...

void	biasesAreCompatibleForSharingBetweenSimulations (const AwhParams &awhParams, ArrayRef< const size_t > pointSize, const BiasSharing &biasSharing)
	Checks whether biases are compatible for sharing between simulations, throws when not. More...

static void	normalizeFreeEnergyAndPmfSum (std::vector< PointState > *pointState)
	Normalizes the free energy and PMF sum. More...

static int	countTrailingZeroRows (const MultiDimArray< std::vector< double >, dynamicExtents2D > &data, int numRows, int numColumns)
	Count trailing data rows containing only zeros. More...

static void	readUserPmfAndTargetDistribution (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const std::string &filename, int numBias, int biasIndex, std::vector< PointState > *pointState)
	Initializes the PMF and target with data read from an input table. More...

static void	normalizeBlock (AwhEnergyBlock *block, const Bias &bias)
	Normalizes block data for output. More...

void	initCorrelationGridHistory (CorrelationGridHistory *correlationGridHistory, int numCorrelationTensors, int tensorSize, int blockDataListSize)
	Initialize correlation grid history, sets all sizes. More...

CorrelationGridHistory	initCorrelationGridHistoryFromState (const CorrelationGrid &corrGrid)
	Allocate a correlation grid history with the same structure as the given correlation grid. More...

void	updateCorrelationGridHistory (CorrelationGridHistory *corrGridHist, const CorrelationGrid &corrGrid)
	Update the correlation grid history for checkpointing. More...

void	restoreCorrelationGridStateFromHistory (const CorrelationGridHistory &corrGridHist, CorrelationGrid *corrGrid)
	Restores the correlation grid state from the correlation grid history. More...

double	getSqrtDeterminant (gmx::ArrayRef< const double > correlationIntegral)
	Returns the volume element of the correlation metric. More...

const char *	enumValueToString (AwhTargetType enumValue)
	String for target distribution.

const char *	enumValueToString (AwhHistogramGrowthType enumValue)
	String for weight histogram growth.

const char *	enumValueToString (AwhPotentialType enumValue)
	String for AWH potential type.

const char *	enumValueToString (AwhCoordinateProviderType enumValue)
	String for AWH bias reaction coordinate provider.

static double	get_pull_coord_period (const t_pull_coord &pullCoordParams, const t_pbc &pbc, const real intervalLength)
	Gets the period of a pull coordinate. More...

static bool	intervalIsInPeriodicInterval (double origin, double end, double period)
	Checks if the given interval is defined in the correct periodic interval. More...

static bool	valueIsInInterval (double origin, double end, double period, double value)
	Checks if a value is within an interval. More...

static void	checkInputConsistencyInterval (const AwhParams &awhParams, WarningHandler *wi)
	Check if the starting configuration is consistent with the given interval. More...

static void	setStateDependentAwhPullDimParams (AwhDimParams dimParams, const int biasIndex, const int dimIndex, const pull_params_t &pull_params, pull_t pull_work, const t_pbc &pbc, const tensor &compressibility, WarningHandler *wi)
	Sets AWH parameters, for one AWH pull dimension. More...

void	setStateDependentAwhParams (AwhParams awhParams, const pull_params_t &pull_params, pull_t pull_work, const matrix box, PbcType pbcType, const tensor &compressibility, const t_inputrec &inputrec, real initLambda, const gmx_mtop_t &mtop, WarningHandler *wi)
	Sets AWH parameters that need state parameters such as the box vectors. More...

void	checkAwhParams (const AwhParams &awhParams, const t_inputrec &inputrec, WarningHandler *wi)
	Check the AWH parameters. More...

bool	awhHasFepLambdaDimension (const AwhParams &awhParams)
	Returns true when AWH has a bias with a free energy lambda state dimension.

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.

unsigned long	convertFlag (FrameConverterFlags flag)
	Conversion of flag to its corresponding unsigned long value.

static void	adjustAtomInformation (t_atoms atoms, t_atoms selectionAtoms, const Selection &sel)
	Modify atoms information in coordinate frame to fit output selection. More...

template<bool usePbc>
static auto	packSendBufKernel (Float3 __restrict__ gm_dataPacked, const Float3 __restrict__ gm_data, const int *__restrict__ gm_map, int mapSize, Float3 coordinateShift)

template<bool accumulate>
static auto	unpackRecvBufKernel (Float3 __restrict__ gm_data, const Float3 __restrict__ gm_dataPacked, const int *__restrict__ gm_map, int mapSize)
	unpack non-local force data buffer on the GPU using pre-populated "map" containing index information. More...

template<bool usePbc, class... Args>
static void	launchPackSendBufKernel (const DeviceStream &deviceStream, int xSendSize, Args &&...args)

template<bool accumulateForces, class... Args>
static void	launchUnpackRecvBufKernel (const DeviceStream &deviceStream, int fRecvSize, Args &&...args)

static void	flagInteractionsForType (const 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 DDBondedChecking ddBondedChecking, 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 bMainState, t_state state_global, const gmx_mtop_t &top_global, const t_inputrec &inputrec, const MDModulesNotifiers &mdModulesNotifiers, gmx::ImdSession imdSession, pull_t pull_work, t_state state_local, 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	handleCufftError (cufftResult_t status, const char *msg)

static void	handleClfftError (clfftStatus status, const char *msg)
	Throws the exception on clFFT error.

	makePlan ("complex-to-real", rocfft_transform_type_real_inverse, PlanSetupData{rocfft_array_type_hermitian_interleaved, makeComplexStrides(complexGridSizePadded), computeTotalSize(complexGridSizePadded)}, PlanSetupData{rocfft_array_type_real, makeRealStrides(realGridSizePadded), computeTotalSize(realGridSizePadded)}, std::vector< size_t >{size_t(realGridSize[ZZ]), size_t(realGridSize[YY]), size_t(realGridSize[XX])}, pmeStream)

realGrid_ *	realGrid ()),{GMX_RELEASE_ASSERT(performOutOfPlaceFFT,"Only out-of-place FFT is implemented in hipSYCL"

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

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

template<typename NativeQueue >
static void	launchVkFft (const DeviceBuffer< float > &realGrid, const DeviceBuffer< float > &complexGrid, NativeQueue queue, gmx_fft_direction fftDirection, VkFFTApplication application, VkFFTLaunchParams launchParams)

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...

static real	smallestAtomMass (const gmx_mtop_t &mtop)

void	repartitionAtomMasses (gmx_mtop_t mtop, bool useFep, real massFactor, WarningHandler wi)
	Scales the smallest masses in the system by up to `massFactor`. More...

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	doDeviceTransfers (const DeviceContext &deviceContext, 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, [[maybe_unused]] MPI_Comm world)
	Reduce the locally collected `hardwareInfo` over MPI ranks.

std::unique_ptr< gmx_hw_info_t >	gmx_detect_hardware (const PhysicalNodeCommunicator &physicalNodeComm, MPI_Comm libraryCommWorld)
	Run detection and make correct and consistent hardware information available on all ranks. More...

void	logHardwareDetectionWarnings (const gmx::MDLogger &mdlog, const gmx_hw_info_t &hardwareInformation)
	Issue warnings to mdlog that were decided during detection. More...

static bool	runningOnCompatibleOSForAmd ()
	Return true if executing on compatible OS for AMD OpenCL. More...

static bool	runningOnCompatibleHWForNvidia (const DeviceInformation &deviceInfo)
	Return true if executing on compatible GPU for NVIDIA OpenCL. More...

static int	fillSupportedSubGroupSizes (const cl_device_id devId, const DeviceVendor deviceVendor, int resultCapacity, int *result)
	Return the list of sub-group sizes supported by the device. More...

static bool	runningOnCompatibleHWForAmd (const DeviceInformation &deviceInfo)
	Return true if executing on compatible GPU for AMD OpenCL. More...

static DeviceStatus	isDeviceFunctional (const DeviceInformation &deviceInfo)
	Checks that device `deviceInfo` is compatible with GROMACS. More...

std::string	makeOpenClInternalErrorString (const char *message, cl_int status)
	Make an error string following an OpenCL API call. More...

static bool	isDeviceFunctional (const DeviceInformation &deviceInfo, std::string *errorMessage)
	Checks that device `deviceInfo` is sane (ie can run a kernel). More...

static DeviceStatus	checkGpu (size_t deviceId, const DeviceInformation &deviceInfo)
	Check whether the `ocl_gpu_device` is suitable for use by mdrun. More...

int	identifyAvx512FmaUnits ()
	Test whether machine has dual AVX512 FMA units. More...

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

SimdType	simdSuggested (const CpuInfo &c)
	Return the SIMD type that would fit this hardware best.

static SimdType	simdCompiled ()

bool	simdCheck (const CpuInfo &cpuInfo, SimdType wanted, FILE *log, bool warnToStdErr)
	Check if binary was compiled with the provided SIMD type. More...

std::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 main socket. More...

void	imd_sleep (unsigned int seconds)
	Portability wrapper around sleep function.

int	imdsock_bind (IMDSocket *sock, int port)
	Bind the IMD socket to address and port. More...

int	imd_sock_listen (IMDSocket *sock)
	Set socket to listening state. More...

IMDSocket *	imdsock_accept (IMDSocket *sock)
	Accept incoming connection and redirect to client socket. More...

int	imdsock_getport (IMDSocket sock, int port)
	Get the port number used for IMD connection. More...

int	imd_htonl (int src)
	Portability wrapper around system htonl function.

int	imd_ntohl (int src)
	Portability wrapper around system ntohl function.

int	imdsock_write (IMDSocket sock, const char buffer, int length)
	Write to socket. More...

int	imdsock_read (IMDSocket sock, char buffer, int length)
	Read from socket. More...

void	imdsock_shutdown (IMDSocket *sock)
	Shutdown the socket. More...

int	imdsock_destroy (IMDSocket *sock)
	Close the socket and free the sock struct memory. More...

int	imdsock_tryread (IMDSocket *sock, int timeoutsec, int timeoutusec)
	Try to read from the socket. More...

bool	buildSupportsListedForcesGpu (std::string *error)
	Checks whether the GROMACS build allows to compute bonded interactions on a GPU. More...

bool	inputSupportsListedForcesGpu (const t_inputrec &ir, const gmx_mtop_t &mtop, std::string *error)
	Checks whether the input system allows to compute bonded interactions on a GPU. More...

static bool	someInteractionsCanRunOnGpu (const InteractionLists &ilists)
	Returns whether there are any interactions in ilists suitable for a GPU.

static bool	bondedInteractionsCanRunOnGpu (const gmx_mtop_t &mtop)
	Returns whether there are any bonded interactions in the global topology suitable for a GPU.

static int	chooseSubGroupSizeForDevice (const DeviceInformation &deviceInfo)

static bool	fTypeHasPerturbedEntries (const InteractionDefinitions &idef, int fType)
	Return whether function type `fType` in `idef` has perturbed interactions.

static void	convertIlistToNbnxnOrder (const InteractionList &src, HostInteractionList *dest, int numAtomsPerInteraction, ArrayRef< const int > nbnxnAtomOrder)
	Converts `src` with atom indices in state order to `dest` in nbnxn order.

static int	roundUpToFactor (const int input, const int factor)
	Returns `input` rounded up to the closest multiple of `factor`.

template<bool calcVir, bool calcEner>
auto	bondedKernel (sycl::handler &cgh, const BondedGpuKernelParameters &kernelParams, const DeviceBuffer< t_iatom > gm_iatoms_[numFTypesOnGpu], float __restrict__ gm_vTot, const t_iparams __restrict__ gm_forceParams_, const sycl::float4 __restrict__ gm_xq_, Float3 __restrict__ gm_f_, Float3 *__restrict__ gm_fShift_)

static void	PrintTo (const RVec &value, std::ostream *os)
	Print an RVec to `os`.

static void	PrintTo (const PaddedVector< RVec > &vector, std::ostream *os)
	Print a padded vector of RVec to `os`.

void	normalizeSumPositiveValuesToUnity (ArrayRef< float > data)
	Divide all values of a view by a constant so that the sum of all its positive values is one. More...

void	exponentialMovingAverageStateAsKeyValueTree (KeyValueTreeObjectBuilder builder, const ExponentialMovingAverageState &state)
	Convert the exponential moving average state as key-value-tree object.

ExponentialMovingAverageState	exponentialMovingAverageStateFromKeyValueTree (const KeyValueTreeObject &object)
	Sets the exponential moving average state from a key-value-tree object. More...

unsigned int	log2I (std::uint32_t x)
	Compute floor of logarithm to base 2, 32 bit unsigned argument. More...

unsigned int	log2I (std::uint64_t x)
	Compute floor of logarithm to base 2, 64 bit unsigned argument. More...

unsigned int	log2I (std::int32_t x)
	Compute floor of logarithm to base 2, 32 bit signed argument. More...

unsigned int	log2I (std::int64_t x)
	Compute floor of logarithm to base 2, 64 bit signed argument. More...

std::int64_t	greatestCommonDivisor (std::int64_t p, std::int64_t q)
	Find greatest common divisor of two numbers. More...

double	erfinv (double x)
	Inverse error function, double precision. More...

float	erfinv (float x)
	Inverse error function, single precision. More...

IntegerBox	spreadRangeWithinLattice (const IVec &center, dynamicExtents3D extent, IVec range)
	Construct a box that holds all indices that are not more than a given range remote from center coordinates and still within a given lattice extent. More...

static void	assertMatrixIsBoxMatrix (const Matrix3x3 gmx_used_in_debug &m)
	Assert that the matrix `m` describes a simulation box. More...

static void	assertMatrixIsBoxMatrix (const matrix gmx_used_in_debug m)
	Assert that the matrix `m` describes a simulation box. More...

static void	multiplyVectorByTransposeOfBoxMatrix (const Matrix3x3 &m, const rvec v, rvec result)
	Multiply vector `v` by the transpose of the box matrix `m`, relying on the fact that the upper triangle of the matrix is zero.

static RVec	multiplyVectorByTransposeOfBoxMatrix (const Matrix3x3 &m, const RVec &v)
	Multiply vector `v` by the transpose of the box matrix `m`, relying on the fact that the upper triangle of the matrix is zero.

static Matrix3x3	multiplyBoxMatrices (const Matrix3x3 &a, const Matrix3x3 &b)
	Multiply box matrices, relying on the fact that their upper triangle is zero.

static Matrix3x3	multiplyBoxMatrices (const Matrix3x3 &a, const matrix b)
	Multiply box matrices, relying on the fact that their upper triangle is zero.

static Matrix3x3	invertBoxMatrix (const Matrix3x3 &src)
	Invert a simulation-box matrix. More...

static void	invertBoxMatrix (const matrix src, matrix dest)
	Invert a simulation-box matrix in `src`, return in `dest`. More...

void	invertMatrix (const matrix src, matrix dest)
	Invert a general 3x3 matrix in `src`, return in `dest`. More...

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 > >	diagonalMatrix (const ElementType value)
	Create a diagonal matrix of ElementType with N * M elements. More...

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...

Matrix3x3	transpose (Matrix3x3ConstSpan matrixView)
	Calculate the transpose of a 3x3 matrix, from its view.

void	matrixVectorMultiply (Matrix3x3ConstSpan matrix, RVec *v)
	Multiply matrix with vector.

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<typename ElementType >
BasicVector< ElementType >	multiplyVectorByMatrix (const BasicMatrix3x3< ElementType > &m, const rvec v)
	Return the product of multiplying the vector `v` by the 3x3 matrix `m`.

template<typename ElementType >
BasicMatrix3x3< ElementType >	operator+ (const BasicMatrix3x3< ElementType > &a, const BasicMatrix3x3< ElementType > &b)
	Return the sum of two 3x3 matrices `a` and `b`.

template<typename ElementType >
BasicMatrix3x3< ElementType >	operator* (const BasicMatrix3x3< ElementType > &m, const ElementType s)
	Return the product of multiplying the 3x3 matrix `m` by the scalar `s`.

template<typename ElementType >
BasicMatrix3x3< ElementType >	operator* (const ElementType s, const BasicMatrix3x3< ElementType > &m)
	Return the product of multiplying the 3x3 matrix `m` by the scalar `s`.

template<typename ElementType >
BasicVector< ElementType >	diagonal (const BasicMatrix3x3< ElementType > &m)
	Return a vector that is the diagonal of the 3x3 matrix `m`.

template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::const_iterator	begin (const MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray begin function addressing its contiguous memory.

template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::iterator	begin (MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray begin function addressing its contiguous memory.

template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::const_iterator	end (const MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray end function addressing its contiguous memory.

template<class TContainer , class Extents >
constexpr MultiDimArray < TContainer, Extents > ::iterator	end (MultiDimArray< TContainer, Extents > &multiDimArray)
	Free MultiDimArray end function addressing its contiguous memory.

template<class TContainer , class Extents >
void	swap (MultiDimArray< TContainer, Extents > &a, MultiDimArray< TContainer, Extents > &b) noexcept
	Swap function.

OptimisationResult	nelderMead (const std::function< real(ArrayRef< const real >)> &functionToMinimize, ArrayRef< const real > initialGuess, real minimumRelativeSimplexLength=1e-8, int maxSteps=10'000)
	Derivative-free downhill simplex optimisation. More...

std::unique_ptr< BoxDeformation >	buildBoxDeformation (const Matrix3x3 &initialBox, DDRole ddRole, NumRanks numRanks, MPI_Comm communicator, const t_inputrec &inputrec)
	Factory function for box deformation module. More...

void	setBoxDeformationFlowMatrix (const matrix boxDeformationVelocity, const matrix box, matrix flowMatrix)
	Set a matrix for computing the flow velocity at coordinates. More...

static CheckpointSignal	convertToCheckpointSignal (signed char sig)
	Convert signed char (as used by SimulationSignal) to CheckpointSignal enum. More...

static void	clear_constraint_quantity_nonlocal (const gmx_domdec_t &dd, ArrayRef< RVec > q)
	Clears constraint quantities for atoms in nonlocal region.

void	too_many_constraint_warnings (ConstraintAlgorithm eConstrAlg, int warncount)
	Generate a fatal error because of too many LINCS/SETTLE warnings.

static void	write_constr_pdb (const char fn, const char title, const gmx_mtop_t &mtop, int start, int homenr, const 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...

bool	hasTriangleConstraints (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns True if there is at least one triangular constraint.

void	do_constrain_first (FILE log, gmx::Constraints constr, const t_inputrec *inputrec, int 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.

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, const DeviceBuffer< Float3 > d_nbnxmForceToAdd, const DeviceBuffer< Float3 > d_rvecForceToAdd, DeviceBuffer< Float3 > d_baseForce, DeviceBuffer< int > d_cell, const DeviceStream &deviceStream, DeviceBuffer< uint64_t > d_forcesReadyNvshmemFlags, const uint64_t forcesReadyNvshmemFlagsCounter)
	Backend-specific function to launch GPU Force Reduction kernel. More...

template<bool addRvecForce, bool accumulateForce>
static auto	reduceKernel (const Float3 __restrict__ gm_nbnxmForce, const Float3 __restrict__ gm_rvecForceToAdd, Float3 __restrict__ gm_forceTotal, const int __restrict__ gm_cell, const int atomStart)
	Function returning the force reduction kernel lambda.

template<bool addRvecForce, bool accumulateForce>
static void	launchReductionKernel_ (const int numAtoms, const int atomStart, const DeviceBuffer< Float3 > &d_nbnxmForce, const DeviceBuffer< Float3 > &d_rvecForceToAdd, DeviceBuffer< Float3 > &d_forceTotal, const DeviceBuffer< int > &d_cell, const DeviceStream &deviceStream)
	Force reduction SYCL kernel launch code.

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, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, Float3 prVelocityScalingMatrixDiagonal, const DeviceStream &deviceStream)
	Backend-specific function to launch GPU Leap Frog kernel. More...

template<NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
auto	leapFrogKernel (Float3 __restrict__ gm_x, Float3 __restrict__ gm_xp, Float3 __restrict__ gm_v, const Float3 __restrict__ gm_f, const float __restrict__ gm_inverseMasses, float dt, const float __restrict__ gm_lambdas, const unsigned short *__restrict__ gm_tempScaleGroups, Float3 prVelocityScalingMatrixDiagonal)
	Main kernel for the Leap-Frog integrator. More...

template<NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, class... Args>
static void	launchLeapFrogKernel (const DeviceStream &deviceStream, int numAtoms, Args &&...args)
	Leap Frog SYCL kernel launch code.

static NumTempScaleValues	getTempScalingType (bool doTemperatureScaling, int numTempScaleValues)
	Convert `doTemperatureScaling` and `numTempScaleValues` to NumTempScaleValues.

template<class... Args>
static void	launchLeapFrogKernel (NumTempScaleValues tempScalingType, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, Args &&...args)
	Select templated kernel and launch it.

real	lincs_rmsd (const Lincs *lincsd)
	Return the RMSD of the constraint.

static void	lincs_matrix_expand (const Lincs &lincsd, const Task &li_task, gmx::ArrayRef< const real > blcc, gmx::ArrayRef< real > rhs1, gmx::ArrayRef< real > rhs2, gmx::ArrayRef< real > sol)
	Do a set of nrec LINCS matrix multiplications. More...

static void	lincs_update_atoms_noind (int ncons, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update atomic coordinates when an index is not required.

static void	lincs_update_atoms_ind (gmx::ArrayRef< const int > ind, gmx::ArrayRef< const AtomPair > atoms, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec *x)
	Update atomic coordinates when an index is required.

static void	lincs_update_atoms (Lincs li, int th, real preFactor, gmx::ArrayRef< const real > fac, gmx::ArrayRef< const gmx::RVec > r, gmx::ArrayRef< const real > invmass, rvec x)
	Update coordinates for atoms.

static void	do_lincsp (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > fPadded, ArrayRef< RVec > fp, t_pbc pbc, Lincs lincsd, int th, ArrayRef< const real > invmass, ConstraintVariable econq, bool bCalcDHDL, bool bCalcVir, tensor rmdf)
	LINCS projection, works on derivatives of the coordinates.

static gmx_unused void	calc_dist_iter (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec gmx_restrict xp, const real gmx_restrict bllen, const real gmx_restrict blc, const t_pbc pbc, real wfac, real gmx_restrict rhs, real gmx_restrict sol, bool *bWarn)
	Determine the distances and right-hand side for the next iteration.

static void	do_lincs (ArrayRefWithPadding< const RVec > xPadded, ArrayRefWithPadding< RVec > xpPadded, const matrix box, t_pbc pbc, Lincs lincsd, int th, ArrayRef< const real > invmass, const t_commrec cr, bool bCalcDHDL, real wangle, bool bWarn, real invdt, ArrayRef< RVec > vRef, bool bCalcVir, tensor vir_r_m_dr, gmx_wallcycle *wcycle)
	Implements LINCS constraining.

static void	set_lincs_matrix_task (Lincs li, Task li_task, ArrayRef< const real > invmass, int ncc_triangle, int nCrossTaskTriangles)
	Sets the elements in the LINCS matrix for task task.

static void	set_lincs_matrix (Lincs *li, ArrayRef< const real > invmass, real lambda)
	Sets the elements in the LINCS matrix.

int	count_triangle_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Counts the number of constraint triangles, i.e. triplets of atoms connected by three constraints. More...

static bool	more_than_two_sequential_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Finds sequences of sequential constraints.

Lincs *	init_lincs (FILE fplog, const gmx_mtop_t &mtop, int nflexcon_global, ArrayRef< const ListOfLists< int >> atomsToConstraintsPerMolType, bool bPLINCS, int nIter, int nProjOrder, ObservablesReducerBuilder observablesReducerBuilder)
	Initializes and returns the lincs data struct.

void	done_lincs (Lincs *li)
	Destructs the lincs object when it is not nullptr.

static void	lincs_thread_setup (Lincs *li, int natoms)
	Sets up the work division over the threads.

static void	assign_constraint (Lincs *li, int constraint_index, int a1, int a2, real lenA, real lenB, const ListOfLists< int > &at2con)
	Assign a constraint.

static void	check_assign_connected (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is connected to other constraints, and if so add those connected constraints to our task.

static void	check_assign_triangle (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int constraint_index, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is involved in a constraint triangle, and if so add the other two constraints in the triangle to our task.

static void	set_matrix_indices (Lincs *li, const Task &li_task, const ListOfLists< int > &at2con, bool bSortMatrix)
	Sets matrix indices.

void	set_lincs (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass, real lambda, bool bDynamics, const 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, gmx_wallcycle wcycle)
	Applies LINCS constraints. 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...

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, const AtomPair __restrict__ gm_constraints, const float __restrict__ gm_constraintsTargetLengths, const int __restrict__ gm_coupledConstraintsCounts, const int __restrict__ gm_coupledConstraintsIndices, const float __restrict__ gm_massFactors, float __restrict__ gm_matrixA, const float __restrict__ gm_inverseMasses, const int numIterations, const int expansionOrder, const Float3 __restrict__ gm_x, Float3 __restrict__ gm_xp, const float invdt, Float3 __restrict__ gm_v, float *__restrict__ gm_virialScaled, PbcAiuc pbcAiuc)
	Main kernel for LINCS constraints. More...

template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, class... Args>
static void	launchLincsKernel (const DeviceStream &deviceStream, const int numConstraintsThreads, Args &&...args)

template<class... Args>
static void	launchLincsKernel (bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, Args &&...args)
	Select templated kernel and launch it.

template<typename... Args>
std::unique_ptr< Constraints >	makeConstraints (const gmx_mtop_t &mtop, const t_inputrec &ir, pull_t *pull_work, bool havePullConstraintsWork, bool doEssentialDynamics, Args &&...args)
	Factory function for Constraints. More...

std::unique_ptr< MDAtoms >	makeMDAtoms (FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir, bool useGpuForPme)
	Builder function for MdAtomsWrapper. More...

static ResetSignal	convertToResetSignal (signed char sig)
	Convert signed char (as used by SimulationSignal) to ResetSignal enum. More...

static void	initializeProjectionMatrix (const real invmO, const real invmH, const real dOH, const real dHH, matrix inverseCouplingMatrix)
	Initializes a projection matrix. More...

SettleParameters	settleParameters (real mO, real mH, real invmO, real invmH, real dOH, real dHH)
	Computes and returns settle parameters. More...

void	settle_proj (const SettleData &settled, ConstraintVariable econq, int nsettle, const int iatoms[], const t_pbc *pbc,ArrayRef< const RVec > x, ArrayRef< RVec > der, ArrayRef< RVec > derp, int CalcVirAtomEnd, tensor vir_r_m_dder)
	Analytical algorithm to subtract the components of derivatives of coordinates working on settle type constraint.

template<typename T , typename TypeBool , int packSize, typename TypePbc , bool bCorrectVelocity, bool bCalcVirial>
static void	settleTemplate (const SettleData &settled, int settleStart, int settleEnd, const TypePbc pbc, const real x, real xprime, real invdt, real gmx_restrict v, tensor vir_r_m_dr, bool bErrorHasOccurred)
	The actual settle code, templated for real/SimdReal and for optimization.

template<typename T , typename TypeBool , int packSize, typename TypePbc >
static void	settleTemplateWrapper (const SettleData &settled, int nthread, int thread, TypePbc pbc, const real x[], real xprime[], real invdt, real v, bool bCalcVirial, tensor vir_r_m_dr, bool bErrorHasOccurred)
	Wrapper template function that divides the settles over threads and instantiates the core template with instantiated booleans.

void	csettle (const SettleData &settled,int nthread,int thread,const t_pbc pbc,ArrayRefWithPadding< const RVec > x,ArrayRefWithPadding< RVec > xprime,real invdt,ArrayRefWithPadding< RVec > v,bool bCalcVirial,tensor vir_r_m_dr,bool bErrorHasOccurred)
	Constrain coordinates using SETTLE. Can be called on any number of threads.

void	launchSettleGpuKernel (int numSettles, const DeviceBuffer< WaterMolecule > &d_atomIds, const SettleParameters &settleParameters, const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, DeviceBuffer< float > d_virialScaled, const PbcAiuc &pbcAiuc, const DeviceStream &deviceStream)
	Apply SETTLE. More...

template<bool updateVelocities, bool computeVirial>
auto	settleKernel (sycl::handler &cgh, const int numSettles, const WaterMolecule __restrict__ gm_settles, SettleParameters pars, const Float3 __restrict__ gm_x, Float3 __restrict__ gm_xp, float invdt, Float3 __restrict__ gm_v, float *__restrict__ gm_virialScaled, PbcAiuc pbcAiuc)
	Function returning the SETTLE kernel lambda.

template<bool updateVelocities, bool computeVirial, class... Args>
static void	launchSettleKernel (const DeviceStream &deviceStream, int numSettles, Args &&...args)
	SETTLE SYCL kernel launch code.

template<class... Args>
static void	launchSettleKernel (bool updateVelocities, bool computeVirial, Args &&...args)
	Select templated kernel and launch it.

static int	pcomp (const void p1, const void p2)
	Compares sort blocks.

static void	pr_sortblock (FILE fp, const char title, gmx::ArrayRef< const t_sortblock > sb)
	Prints sortblocks.

static void	resizeLagrangianData (shakedata *shaked, int ncons)
	Reallocates a vector.

void	make_shake_sblock_serial (shakedata shaked, InteractionDefinitions idef, int numAtoms)
	Make SHAKE blocks when not using DD.

void	make_shake_sblock_dd (shakedata *shaked, const InteractionList &ilcon)
	Make SHAKE blocks when using DD.

void	cshake (const int iatom[], int ncon, int nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > positions, const t_pbc pbc, ArrayRef< const RVec > initial_displacements, ArrayRef< const real > half_of_reduced_mass, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int *nerror)
	Inner kernel for SHAKE constraints. More...

static void	crattle (const int iatom[], int ncon, int nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > vp, ArrayRef< const RVec > rij, ArrayRef< const real > m2, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int nerror, real invdt)
	Implements RATTLE (ie. SHAKE for velocity verlet integrators)

static int	vec_shakef (FILE fplog, shakedata shaked, ArrayRef< const real > invmass, int ncon, ArrayRef< const t_iparams > ip, const int iatom, real tol, ArrayRef< const RVec > x, ArrayRef< RVec > prime, const t_pbc pbc, real omega, bool bFEP, real lambda, ArrayRef< real > scaled_lagrange_multiplier, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq)
	Applies SHAKE.

static void	check_cons (FILE log, int nc, ArrayRef< const RVec > x, ArrayRef< const RVec > prime, ArrayRef< const RVec > v, const t_pbc pbc, ArrayRef< const t_iparams > ip, const int *iatom, ArrayRef< const real > invmass, ConstraintVariable econq)
	Check that constraints are satisfied.

static bool	bshakef (FILE log, shakedata shaked, ArrayRef< const real > invmass, const InteractionDefinitions &idef, const t_inputrec &ir, ArrayRef< const RVec > x_s, ArrayRef< RVec > prime, const t_pbc pbc, t_nrnb nrnb, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, bool bDumpOnError, ConstraintVariable econq)
	Applies SHAKE.

bool	constrain_shake (FILE log,shakedata shaked,gmx::ArrayRef< const real > invmass,const InteractionDefinitions &idef,const t_inputrec &ir,ArrayRef< const RVec > x_s,ArrayRef< RVec > xprime,ArrayRef< RVec > vprime,const t_pbc pbc,t_nrnb nrnb,real lambda,real *dvdlambda,real invdt,ArrayRef< RVec > v,bool bCalcVir,tensor vir_r_m_dr,bool bDumpOnError,ConstraintVariable econq)
	Shake all the atoms blockwise. It is assumed that all the constraints in the idef->shakes field are sorted, to ascending block nr. The sblock array points into the idef->shakes.iatoms field, with block 0 starting at sblock[0] and running to ( < ) sblock[1], block n running from sblock[n] to sblock[n+1]. Array sblock should be large enough. Return TRUE when OK, FALSE when shake-error.

static 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 (Float3 *gm_x, const ScalingMatrix scalingMatrix)
	Function returning the scaling kernel lambda.

static bool	hasFlexibleConstraints (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns whether `moltype` contains flexible constraints.

static bool	hasIncompatibleVsites (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns whether moltype has incompatible vsites. More...

static InteractionList	jointConstraintList (const gmx_moltype_t &moltype)
	Returns a merged list with constraints of all types.

static AtomIndexExtremes	vsiteConstructRange (int a, const gmx_moltype_t &moltype)
	Returns the range of constructing atom for vsite with atom index `a`.

static AtomIndexExtremes	constraintAtomRange (int a, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
	Returns the range of atoms constrained to atom `a` (including `a` itself)

static std::vector< bool >	buildIsParticleVsite (const gmx_moltype_t &moltype)
	Returns a list that tells whether atoms in `moltype` are vsites.

static std::variant< int, IncompatibilityReasons >	detectGroup (int firstAtom, const gmx_moltype_t &moltype, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
	Returns the size of the update group starting at `firstAtom` or an incompatibility reason.

static std::variant < RangePartitioning, IncompatibilityReasons >	makeUpdateGroupingsPerMoleculeType (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns a list of update groups for `moltype` or an incompatibility reason.

std::variant< std::vector < RangePartitioning > , std::string >	makeUpdateGroupingsPerMoleculeType (const gmx_mtop_t &mtop)
	Returns a vector with update groups for each moleculetype in `mtop` or an error string when the criteria (see below) are not satisfied. More...

static std::unordered_multimap < int, int >	getAngleIndices (const gmx_moltype_t &moltype)
	Returns a map of angles ilist.iatoms indices with the middle atom as key.

template<int numPartnerAtoms>
static real	constraintGroupRadius (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, const int centralAtom, const ListOfLists< int > &at2con, const std::unordered_multimap< int, int > &angleIndices, const real constraintLength, const real temperature)
	When possible, computes the maximum radius of constrained atom in an update group. More...

static real	computeMaxUpdateGroupRadius (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, const RangePartitioning &updateGrouping, real temperature)
	Returns the maximum update group radius for `moltype`.

real	computeMaxUpdateGroupRadius (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType, real temperature)
	Returns the maximum update group radius. More...

bool	systemHasConstraintsOrVsites (const gmx_mtop_t &mtop)
	Returns whether mtop contains any constraints and/or vsites. More...

UpdateGroups	makeUpdateGroups (const gmx::MDLogger &mdlog, std::vector< RangePartitioning > &&updateGroupingPerMoleculeType, real maxUpdateGroupRadius, bool doRerun, bool useDomainDecomposition, bool systemHasConstraintsOrVsites, real cutoffMargin)
	Builder for update groups. More...

static int	vsiteIlistNrCount (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, gmx::GpuAwareMpiStatus gpuAwareMpiStatus)
	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 isSimulationMainRank)
	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 isSimulationMain, MPI_Comm communicator, const gmx_multisim_t *ms, AppendingBehavior appendingBehavior, int nfile, t_filenm fnm[])
	Handle startup of mdrun, particularly regarding -cpi and -append. More...

static void	prepareLogFile (BinaryInformationSettings settings, FILE *fplog)
	Implements aspects of logfile handling common to opening either for writing or appending.

LogFilePtr	openLogFile (const char *lognm, bool appendFiles)
	Open the log file for writing/appending. More...

void	prepareLogAppending (FILE *fplog)
	Prepare to use the open log file when appending. More...

void	closeLogFile (t_fileio *logfio)
	Close the log file.

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)

	ensembleTemperature_ (ensembleTemperature)

	mttkPropagatorConnection_ (mttkPropagatorConnection)

	nextEnergyCalculationStep_ (-1)

	mdlog_ (mdlog)

template<NumVelocityScalingValues numStartVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, NumVelocityScalingValues numEndVelocityScalingValues>
static void	updateVelocities (int a, real dt, real lambdaStart, real lambdaEnd, const ArrayRef< const RVec > invMassPerDim, rvec gmx_restrict v, const rvec gmx_restrict f, const RVec &diagPR, const Matrix3x3 &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	canTreatPRScalingMatrixAsDiagonal (const Matrix3x3 &matrixPR)
	Is the PR matrix diagonal?

	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`.

template<KernelLayout kernelLayout, KernelCoulombType coulombType, VdwCutoffCheck vdwCutoffCheck, LJCombinationRule ljCombinationRule, InteractionModifiers vdwModifier, LJEwald ljEwald, EnergyOutput energyOutput>
void	nbnxmKernelSimd (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)
	The actual NBNxM SIMD kernel. More...

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::None > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::System > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::RF, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldTabulated, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::ForceSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotSwitch, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::No, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::CombGeometric, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::Geometric, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::LorentzBerthelot, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnPairlistCpu nbl, const nbnxn_atomdata_t nbat, const interaction_const_t ic, const rvec shift_vec, nbnxn_atomdata_output_t *out)

template void	nbnxmKernelSimd< KernelLayout::r2xMM, KernelCoulombType::EwaldAnalytical, VdwCutoffCheck::Yes, LJCombinationRule::None, InteractionModifiers::PotShift, LJEwald::None, EnergyOutput::GroupPairs > (const NbnxnP

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