gmx Namespace Reference

Description

Generic GROMACS namespace.

Declares the integrators for energy minimization and NMA.

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

Classes
class	ArrayRef
	STL-like interface to a C array of T (or part of a std container of T). 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	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	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	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	FixedCapacityVector
	Vector that behaves likes std::vector but has fixed capacity. 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	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...
struct	AtomPair
	A pair of atoms indexes. 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	MembedHolder
	Membed SimulatorBuilder parameter type. 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	CheckpointData
	} More...
struct	IsSerializableEnum
	{ 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	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	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, DiagonalMaskType::JSizeEqualsISize >
	Specialized masker for JSizeEqualsISize. More...
class	DiagonalMasker< nR, kernelLayout, DiagonalMaskType::JSizeIsDoubleISize >
	Specialized masker for JSizeIsDoubleISize. More...
class	DiagonalMasker< nR, kernelLayout, DiagonalMaskType::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	AbstractOptionSection
	Base class for specifying option section properties. More...
class	AbstractOptionSectionHandle
	Base class for handles to option sections. More...
class	OptionSection
	Declares a simple option section. More...
class	OptionSectionHandle
	Allows adding options to an OptionSection. More...
class	RepeatingOptionSectionHandle
	Allows adding options to an RepeatingOptionSection. More...
class	RepeatingOptionSection
	Declares an option section that creates a structure for each instance. More...
class	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	ConvertTprInfo
	Declares gmx convert-tpr. 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	StringToEnumValueConverter
	A class to convert a string to an enum value of type EnumType. 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	IOptionManager
	Base class for option managers. More...
class	Options
	Collection of options. More...
class	TimeUnitManager
	Provides common functionality for time unit conversions. More...
class	TimeUnitBehavior
	Options behavior to add a time unit option. More...
class	PotentialPointData
	Structure to hold the results of IRestraintPotential::evaluate(). More...
class	IRestraintPotential
	Interface for Restraint potentials. More...
class	AnalysisNeighborhoodPositions
	Input positions for neighborhood searching. More...
class	AnalysisNeighborhood
	Neighborhood searching for analysis tools. More...
class	AnalysisNeighborhoodPair
	Value type to represent a pair of positions found in neighborhood searching. More...
class	AnalysisNeighborhoodSearch
	Initialized neighborhood search with a fixed set of reference positions. More...
class	AnalysisNeighborhoodPairSearch
	Initialized neighborhood pair search with a fixed set of positions. More...
class	Selection
	Provides access to a single selection. More...
class	SelectionPosition
	Provides access to information about a single selected position. More...
class	SelectionCollection
	Collection of selections. More...
struct	SelectionTopologyProperties
	Describes topology properties required for selection evaluation. More...
class	SelectionOption
	Specifies an option that provides selection(s). More...
class	SelectionOptionInfo
	Wrapper class for accessing and modifying selection option information. More...
class	ITopologyProvider
	Provides topology information to SelectionOptionBehavior. More...
class	SelectionOptionBehavior
	Options behavior to allow using SelectionOptions. More...
class	SelectionOptionManager
	Handles interaction of selection options with other options and user input. More...
class	RangePartitioning
	Division of a range of indices into consecutive blocks. More...
class	TrajectoryAnalysisModuleData
	Base class for thread-local data storage during trajectory analysis. More...
class	TrajectoryAnalysisModule
	Base class for trajectory analysis modules. More...
class	TrajectoryAnalysisSettings
	Trajectory analysis module configuration object. More...
class	TrajectoryAnalysisCommandLineRunner
	Runner for command-line trajectory analysis tools. More...
class	ExceptionInfo
	Stores additional context information for exceptions. More...
class	ExceptionInitializer
	Provides information for Gromacs exception constructors. More...
class	GromacsException
	Base class for all exception objects in Gromacs. More...
class	FileIOError
	Exception class for file I/O errors. More...
class	UserInputError
	Exception class for user input errors. More...
class	InvalidInputError
	Exception class for situations where user input cannot be parsed/understood. More...
class	InconsistentInputError
	Exception class for situations where user input is inconsistent. More...
class	ToleranceError
	Exception class when a specified tolerance cannot be achieved. More...
class	SimulationInstabilityError
	Exception class for simulation instabilities. More...
class	InternalError
	Exception class for internal errors. More...
class	APIError
	Exception class for incorrect use of an API. More...
class	RangeError
	Exception class for out-of-range values or indices. More...
class	NotImplementedError
	Exception class for use of an unimplemented feature. More...
class	ParallelConsistencyError
	Exception class for use when ensuring that MPI ranks to throw in a coordinated fashion. More...
class	ModularSimulatorError
	Exception class for modular simulator. More...
class	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...

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.
typedef struct gmx::CacheLineAlignedFlag	CacheLineAlignedFlag
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 < 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.
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...
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.
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	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	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::SyclDbfft,   FftBackend::Sycl, Count }
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	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 }
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
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	DiagonalMaskType { DiagonalMaskType::JSizeEqualsISize, DiagonalMaskType::JSizeIsDoubleISize, DiagonalMaskType::JSizeIsHalfISize }
	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	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	TaskTarget : int { Auto, Cpu, Gpu }
	Record where a compute task is targetted.
enum	EmulateGpuNonbonded : bool { EmulateGpuNonbonded::No, EmulateGpuNonbonded::Yes }
	Help pass GPU-emulation parameters with type safety. More...
enum	GpuTask : int { GpuTask::Nonbonded, GpuTask::Pme, GpuTask::Count }
	Types of compute tasks that can be run on a GPU. More...
enum	ErrorCode {   eeOK, eeOutOfMemory, eeFileNotFound, eeFileIO,   eeInvalidInput, eeInconsistentInput, eeTolerance, eeInstability,   eeNotImplemented, eeInvalidValue, eeInvalidCall, eeInternalError,   eeAPIError, eeRange, eeParallelConsistency, eeModularSimulator,   eeUnknownError }
	Possible error return codes from Gromacs functions. More...
enum	EndianSwapBehavior : int {   EndianSwapBehavior::DoNotSwap, EndianSwapBehavior::Swap, EndianSwapBehavior::SwapIfHostIsBigEndian, EndianSwapBehavior::SwapIfHostIsLittleEndian,   EndianSwapBehavior::Count }
	Specify endian swapping behavoir. More...
enum	GpuAwareMpiStatus : int { GpuAwareMpiStatus::Supported, GpuAwareMpiStatus::NotSupported, GpuAwareMpiStatus::NotKnown, GpuAwareMpiStatus::Forced }
	Enum describing GPU-aware support in underlying MPI library. More...
enum	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, Index, Plot, GenericData,   Csv, QMInput, Count }
	Purpose of file(s) provided through an option.

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...
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...
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>
auto	packSendBufKernel (sycl::handler &cgh, DeviceAccessor< Float3, sycl::access_mode::read_write > a_dataPacked, DeviceAccessor< Float3, sycl::access_mode::read > a_data, DeviceAccessor< int, sycl::access_mode::read > a_map, int mapSize, Float3 coordinateShift)
template<bool accumulate>
auto	unpackRecvBufKernel (sycl::handler &cgh, DeviceAccessor< Float3, sycl::access_mode::read_write > a_data, DeviceAccessor< Float3, sycl::access_mode::read > a_dataPacked, DeviceAccessor< int, sycl::access_mode::read > a_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, 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...
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...
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.
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 > d_iatoms[numFTypesOnGpu], DeviceAccessor< float, sycl::access_mode::read_write > a_vTot, DeviceAccessor< t_iparams, sycl::access_mode::read > a_forceParams, DeviceAccessor< sycl::float4, sycl::access_mode::read > a_xq, DeviceAccessor< Float3, sycl::access_mode::read_write > a_f, DeviceAccessor< Float3, sycl::access_mode::read_write > a_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...
static CheckpointSignal	convertToCheckpointSignal (signed char sig)
	Convert signed char (as used by SimulationSignal) to CheckpointSignal enum. More...
static void	clear_constraint_quantity_nonlocal (const gmx_domdec_t &dd, ArrayRef< RVec > q)
	Clears constraint quantities for atoms in nonlocal region.
void	too_many_constraint_warnings (ConstraintAlgorithm eConstrAlg, int warncount)
	Generate a fatal error because of too many LINCS/SETTLE warnings.
static void	write_constr_pdb (const char *fn, const char *title, const gmx_mtop_t &mtop, int start, int homenr, const t_commrec *cr, ArrayRef< const RVec > x, const matrix box)
	Writes out coordinates.
static void	dump_confs (FILE *log, int64_t step, const gmx_mtop_t &mtop, int start, int homenr, const t_commrec *cr, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, const matrix box)
	Writes out domain contents to help diagnose crashes.
FlexibleConstraintTreatment	flexibleConstraintTreatment (bool haveDynamicsIntegrator)
	Returns the flexible constraint treatment depending on whether the integrator is dynamic.
static ListOfLists< int >	makeAtomsToConstraintsList (int numAtoms, ArrayRef< const InteractionList > ilists, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a block struct to go from atoms to constraints. More...
ListOfLists< int >	make_at2con (int numAtoms, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
ListOfLists< int >	make_at2con (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Returns a ListOfLists object to go from atoms to constraints. More...
int	countFlexibleConstraints (ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > iparams)
	Return the number of flexible constraints in the ilist and iparams.
static std::vector< int >	make_at2settle (int natoms, const InteractionList &ilist)
	Returns the index of the settle to which each atom belongs.
static std::vector < ListOfLists< int > >	makeAtomToConstraintMappings (const gmx_mtop_t &mtop, FlexibleConstraintTreatment flexibleConstraintTreatment)
	Makes a per-moleculetype container of mappings from atom indices to constraint indices. More...
void	do_constrain_first (FILE *log, gmx::Constraints *constr, const t_inputrec *inputrec, int numAtoms, int numHomeAtoms, ArrayRefWithPadding< RVec > x, ArrayRefWithPadding< RVec > v, const matrix box, real lambda)
	Constrain the initial coordinates and velocities.
void	constrain_velocities (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
	Constrain velocities only. More...
void	constrain_coordinates (gmx::Constraints *constr, bool do_log, bool do_ene, int64_t step, t_state *state, ArrayRefWithPadding< RVec > xp, real *dvdlambda, bool computeVirial, tensor constraintsVirial)
	Constraint coordinates. More...
static bool	isConstraintFlexible (ArrayRef< const t_iparams > iparams, int iparamsIndex)
	Returns whether constraint with parameter iparamsIndex is a flexible constraint.
const int *	constr_iatomptr (gmx::ArrayRef< const int > iatom_constr, gmx::ArrayRef< const int > iatom_constrnc, int con)
	Returns the constraint iatoms for a constraint number con which comes from a list where F_CONSTR and F_CONSTRNC constraints are concatenated.
static void	constr_recur (const ListOfLists< int > &at2con, const InteractionLists &ilist, gmx::ArrayRef< const t_iparams > iparams, gmx_bool bTopB, int at, int depth, int nc, ArrayRef< int > path, real r0, real r1, real *r2max, int *count)
	Recursing function to help find all adjacent constraints.
static real	constr_r_max_moltype (const gmx_moltype_t *molt, gmx::ArrayRef< const t_iparams > iparams, const t_inputrec *ir)
	Find the interaction radius needed for constraints for this molecule type.
real	constr_r_max (const MDLogger &mdlog, const gmx_mtop_t *mtop, const t_inputrec *ir)
	Returns an estimate of the maximum distance between atoms required for LINCS.
real	calculateAcceptanceWeight (LambdaWeightCalculation calculationMode, real lambdaEnergyDifference)
	Calculates the acceptance weight for a lambda state transition. More...
gmx::EnumerationArray < FreeEnergyPerturbationCouplingType, real >	currentLambdas (int64_t step, const t_lambda &fepvals, int currentLambdaState)
	Evaluate the current lambdas. More...
void	launchForceReductionKernel (int numAtoms, int atomStart, bool addRvecForce, bool accumulate, DeviceBuffer< Float3 > d_nbnxmForceToAdd, DeviceBuffer< Float3 > d_rvecForceToAdd, DeviceBuffer< Float3 > d_baseForce, DeviceBuffer< int > d_cell, const DeviceStream &deviceStream)
	Backend-specific function to launch GPU Force Reduction kernel. More...
template<bool addRvecForce, bool accumulateForce>
static auto	reduceKernel (sycl::handler &cgh, DeviceAccessor< Float3, mode::read > a_nbnxmForce, OptionalAccessor< Float3, mode::read, addRvecForce > a_rvecForceToAdd, DeviceAccessor< Float3, accumulateForce?mode::read_write:mode::write > a_forceTotal, DeviceAccessor< int, mode::read > a_cell, const int atomStart)
	Function returning the force reduction kernel lambda.
template<bool addRvecForce, bool accumulateForce>
static void	launchReductionKernel_ (const int numAtoms, const int atomStart, const DeviceBuffer< Float3 > &b_nbnxmForce, const DeviceBuffer< Float3 > &b_rvecForceToAdd, DeviceBuffer< Float3 > &b_forceTotal, const DeviceBuffer< int > &b_cell, const DeviceStream &deviceStream)
	Force reduction SYCL kernel launch code.
void	launchLeapFrogKernel (int numAtoms, DeviceBuffer< Float3 > d_x, DeviceBuffer< Float3 > d_xp, DeviceBuffer< Float3 > d_v, DeviceBuffer< Float3 > d_f, DeviceBuffer< float > d_inverseMasses, float dt, bool doTemperatureScaling, int numTempScaleValues, DeviceBuffer< unsigned short > d_tempScaleGroups, DeviceBuffer< float > d_lambdas, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling, Float3 prVelocityScalingMatrixDiagonal, const DeviceStream &deviceStream)
	Backend-specific function to launch GPU Leap Frog kernel. More...
template<NumTempScaleValues numTempScaleValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
auto	leapFrogKernel (sycl::handler &cgh, DeviceAccessor< Float3, mode::read_write > a_x, DeviceAccessor< Float3, mode::discard_write > a_xp, DeviceAccessor< Float3, mode::read_write > a_v, DeviceAccessor< Float3, mode::read > a_f, DeviceAccessor< float, mode::read > a_inverseMasses, float dt, OptionalAccessor< float, mode::read, numTempScaleValues!=NumTempScaleValues::None > a_lambdas, OptionalAccessor< unsigned short, mode::read, numTempScaleValues==NumTempScaleValues::Multiple > a_tempScaleGroups, Float3 prVelocityScalingMatrixDiagonal)
	Main kernel for the Leap-Frog integrator. More...
template<NumTempScaleValues numTempScaleValues, 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.
static int	count_triangle_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Finds all triangles of atoms that share constraints to a central atom.
static bool	more_than_two_sequential_constraints (const InteractionLists &ilist, const ListOfLists< int > &at2con)
	Finds sequences of sequential constraints.
Lincs *	init_lincs (FILE *fplog, const gmx_mtop_t &mtop, int nflexcon_global, ArrayRef< const ListOfLists< int >> atomsToConstraintsPerMolType, bool bPLINCS, int nIter, int nProjOrder, ObservablesReducerBuilder *observablesReducerBuilder)
	Initializes and returns the lincs data struct.
void	done_lincs (Lincs *li)
	Destructs the lincs object when it is not nullptr.
static void	lincs_thread_setup (Lincs *li, int natoms)
	Sets up the work division over the threads.
static void	assign_constraint (Lincs *li, int constraint_index, int a1, int a2, real lenA, real lenB, const ListOfLists< int > &at2con)
	Assign a constraint.
static void	check_assign_connected (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is connected to other constraints, and if so add those connected constraints to our task.
static void	check_assign_triangle (Lincs *li, gmx::ArrayRef< const int > iatom, const InteractionDefinitions &idef, bool bDynamics, int constraint_index, int a1, int a2, const ListOfLists< int > &at2con)
	Check if constraint with topology index constraint_index is involved in a constraint triangle, and if so add the other two constraints in the triangle to our task.
static void	set_matrix_indices (Lincs *li, const Task &li_task, const ListOfLists< int > &at2con, bool bSortMatrix)
	Sets matrix indices.
void	set_lincs (const InteractionDefinitions &idef, int numAtoms, ArrayRef< const real > invmass, real lambda, bool bDynamics, const t_commrec *cr, Lincs *li)
	Initialize lincs stuff.
static void	lincs_warning (gmx_domdec_t *dd, ArrayRef< const RVec > x, ArrayRef< const RVec > xprime, t_pbc *pbc, int ncons, gmx::ArrayRef< const AtomPair > atoms, gmx::ArrayRef< const real > bllen, real wangle, int maxwarn, int *warncount)
	Issues a warning when LINCS constraints cannot be satisfied.
static LincsDeviations	makeLincsDeviations (const Lincs &lincsd, ArrayRef< const RVec > x, const t_pbc *pbc)
	Determine how well the constraints have been satisfied.
bool	constrain_lincs (bool computeRmsd, const t_inputrec &ir, int64_t step, Lincs *lincsd, ArrayRef< const real > invmass, const t_commrec *cr, const gmx_multisim_t *ms, ArrayRefWithPadding< const RVec > x, ArrayRefWithPadding< RVec > xprime, ArrayRef< RVec > min_proj, const matrix box, t_pbc *pbc, bool hasMassPerturbed, real lambda, real *dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq, t_nrnb *nrnb, int maxwarn, int *warncount, 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, DeviceAccessor< AtomPair, mode::read > a_constraints, DeviceAccessor< float, mode::read > a_constraintsTargetLengths, OptionalAccessor< int, mode::read, haveCoupledConstraints > a_coupledConstraintsCounts, OptionalAccessor< int, mode::read, haveCoupledConstraints > a_coupledConstraintsIndices, OptionalAccessor< float, mode::read, haveCoupledConstraints > a_massFactors, OptionalAccessor< float, mode::read_write, haveCoupledConstraints > a_matrixA, DeviceAccessor< float, mode::read > a_inverseMasses, const int numIterations, const int expansionOrder, DeviceAccessor< Float3, mode::read > a_x, DeviceAccessor< Float3, mode::read_write > a_xp, const float invdt, OptionalAccessor< Float3, mode::read_write, updateVelocities > a_v, OptionalAccessor< float, mode::read_write, computeVirial > a_virialScaled, PbcAiuc pbcAiuc)
	Main kernel for LINCS constraints. More...
template<bool updateVelocities, bool computeVirial, bool haveCoupledConstraints, class... Args>
static 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 dOH, real invmO, real invmH, real dHH)
	Computes and returns settle parameters. More...
void	settle_proj (const SettleData &settled, ConstraintVariable econq, int nsettle, const int iatoms[], const t_pbc *pbc,ArrayRef< const RVec > x, ArrayRef< RVec > der, ArrayRef< RVec > derp, int CalcVirAtomEnd, tensor vir_r_m_dder)
	Analytical algorithm to subtract the components of derivatives of coordinates working on settle type constraint.
template<typename T , typename TypeBool , int packSize, typename TypePbc , bool bCorrectVelocity, bool bCalcVirial>
static void	settleTemplate (const SettleData &settled, int settleStart, int settleEnd, const TypePbc pbc, const real *x, real *xprime, real invdt, real *gmx_restrict v, tensor vir_r_m_dr, bool *bErrorHasOccurred)
	The actual settle code, templated for real/SimdReal and for optimization.
template<typename T , typename TypeBool , int packSize, typename TypePbc >
static void	settleTemplateWrapper (const SettleData &settled, int nthread, int thread, TypePbc pbc, const real x[], real xprime[], real invdt, real *v, bool bCalcVirial, tensor vir_r_m_dr, bool *bErrorHasOccurred)
	Wrapper template function that divides the settles over threads and instantiates the core template with instantiated booleans.
void	csettle (const SettleData &settled,int nthread,int thread,const t_pbc *pbc,ArrayRefWithPadding< const RVec > x,ArrayRefWithPadding< RVec > xprime,real invdt,ArrayRefWithPadding< RVec > v,bool bCalcVirial,tensor vir_r_m_dr,bool *bErrorHasOccurred)
	Constrain coordinates using SETTLE. Can be called on any number of threads.
void	launchSettleGpuKernel (int numSettles, const DeviceBuffer< WaterMolecule > &d_atomIds, const SettleParameters &settleParameters, const DeviceBuffer< Float3 > &d_x, DeviceBuffer< Float3 > d_xp, bool updateVelocities, DeviceBuffer< Float3 > d_v, real invdt, bool computeVirial, DeviceBuffer< float > virialScaled, const PbcAiuc &pbcAiuc, const DeviceStream &deviceStream)
	Apply SETTLE. More...
template<bool updateVelocities, bool computeVirial>
auto	settleKernel (sycl::handler &cgh, const int numSettles, DeviceAccessor< WaterMolecule, mode::read > a_settles, SettleParameters pars, DeviceAccessor< Float3, mode::read > a_x, DeviceAccessor< Float3, mode::read_write > a_xp, float invdt, OptionalAccessor< Float3, mode::read_write, updateVelocities > a_v, OptionalAccessor< float, mode::read_write, computeVirial > a_virialScaled, PbcAiuc pbcAiuc)
	Function returning the SETTLE kernel lambda.
template<bool updateVelocities, bool computeVirial, class... Args>
static 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 (sycl::handler &cgh, DeviceAccessor< Float3, sycl::access_mode::read_write > a_x, const ScalingMatrix scalingMatrix)
	Function returning the scaling kernel lambda.
static bool	hasFlexibleConstraints (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns whether moltype contains flexible constraints.
static bool	hasIncompatibleVsites (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns whether moltype has incompatible vsites. More...
static InteractionList	jointConstraintList (const gmx_moltype_t &moltype)
	Returns a merged list with constraints of all types.
static AtomIndexExtremes	vsiteConstructRange (int a, const gmx_moltype_t &moltype)
	Returns the range of constructing atom for vsite with atom index a.
static AtomIndexExtremes	constraintAtomRange (int a, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
	Returns the range of atoms constrained to atom a (including a itself)
static std::vector< bool >	buildIsParticleVsite (const gmx_moltype_t &moltype)
	Returns a list that tells whether atoms in moltype are vsites.
static 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 useDomainDecomposition, bool systemHasConstraintsOrVsites, real cutoffMargin)
	Builder for update groups. More...
static int	vsiteIlistNrCount (ArrayRef< const InteractionList > ilist)
	Returns the sum of the vsite ilist sizes over all vsite types. More...
static int	pbc_rvec_sub (const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
	Computes the distance between xi and xj, pbc is used when pbc!=nullptr.
static real	inverseNorm (const rvec x)
	Returns the 1/norm(x)
static PbcMode	getPbcMode (const t_pbc *pbcPtr)
	Returns the PBC mode based on the system PBC and vsite properties. More...
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void	construct_vsites_thread (ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
	Executes the vsite construction task for a single thread. More...
template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
static void	construct_vsites (const ThreadingInfo *threadingInfo, ArrayRef< RVec > x, ArrayRef< RVec > v, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const DomainInfo &domainInfo, const matrix box)
	Dispatch the vsite construction tasks for all threads. More...
void	constructVirtualSites (ArrayRef< RVec > x, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist)
	Create positions of vsite atoms based for the local system. More...
static int	vsite_count (ArrayRef< const InteractionList > ilist, int ftype)
	Returns the number of virtual sites in the interaction list, for VSITEN the number of atoms.
template<VirialHandling virialHandling>
static void	spreadForceForThread (ArrayRef< const RVec > x, ArrayRef< RVec > f, ArrayRef< RVec > fshift, matrix dxdf, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
	Executes the force spreading task for a single thread.
static void	spreadForceWrapper (ArrayRef< const RVec > x, ArrayRef< RVec > f, const VirialHandling virialHandling, ArrayRef< RVec > fshift, matrix dxdf, const bool clearDxdf, ArrayRef< const t_iparams > ip, ArrayRef< const InteractionList > ilist, const t_pbc *pbc_null)
	Wrapper function for calling the templated thread-local spread function.
static void	clearTaskForceBufferUsedElements (InterdependentTask *idTask)
	Clears the task force buffer elements that are written by task idTask.
static std::vector< int >	makeAtomToGroupMapping (const gmx::RangePartitioning &grouping)
	Returns the an array with group indices for each atom. More...
int	countNonlinearVsites (const gmx_mtop_t &mtop)
	Return the number of non-linear virtual site constructions in the system.
int	countInterUpdategroupVsites (const gmx_mtop_t &mtop, ArrayRef< const RangePartitioning > updateGroupingsPerMoleculeType)
	Return the number of virtual sites that cross update groups. More...
std::unique_ptr < VirtualSitesHandler >	makeVirtualSitesHandler (const gmx_mtop_t &mtop, const t_commrec *cr, PbcType pbcType, ArrayRef< const RangePartitioning > updateGroupingPerMoleculeType)
	Create the virtual site handler. More...
	iparams_ (mtop.ffparams.iparams)
static void	flagAtom (InterdependentTask *idTask, const int atom, const int numThreads, const int numAtomsPerThread)
	Flag that atom atom which is home in another task, if it has not already been added before.
static void	assignVsitesToThread (VsiteThread *tData, int thread, int nthread, int natperthread, gmx::ArrayRef< int > taskIndex, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > ip, ArrayRef< const ParticleType > ptype)
	Here we try to assign all vsites that are in our local range. More...
static void	assignVsitesToSingleTask (VsiteThread *tData, int task, gmx::ArrayRef< const int > taskIndex, ArrayRef< const InteractionList > ilist, ArrayRef< const t_iparams > ip)
	Assign all vsites with taskIndex[]==task to task tData.
void	constructVirtualSitesGlobal (const gmx_mtop_t &mtop, ArrayRef< RVec > x)
	Create positions of vsite atoms for the whole system assuming all molecules are wholex. More...
static bool	is_multisim_option_set (int argc, const char *const argv[])
	Return whether the command-line parameter that will trigger a multi-simulation is set.
static DevelopmentFeatureFlags	manageDevelopmentFeatures (const gmx::MDLogger &mdlog, const bool useGpuForNonbonded, const PmeRunMode pmeRunMode, const int numRanksPerSimulation, const int numPmeRanksPerSimulation)
	Manage any development feature flag variables encountered. More...
static void	threadMpiMdrunnerAccessBarrier ()
	Barrier for safe simultaneous thread access to mdrunner data. More...
static void	mdrunner_start_fn (const void *arg)
	The callback used for running on spawned threads. More...
static bool	gpuAccelerationOfNonbondedIsUseful (const MDLogger &mdlog, const t_inputrec &ir, const bool issueWarning, const bool doRerun)
	Return whether GPU acceleration of nonbondeds is supported with the given settings. More...
static gmx::LoggerOwner	buildLogger (FILE *fplog, const bool 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)
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)
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)
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)
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<int iClusterSize, int jClusterSize>
static constexpr DiagonalMaskType	getDiagonalMaskType ()
	Returns the diagonal mask type corresponding to the cluster sizes.
template<int nR, KernelLayout kernelLayout, DiagonalMaskType diagonalMaskType>
std::array< std::array < SimdBool, nR > , diagonalMaskType==DiagonalMaskType::JSizeEqualsISize?1:2 >	generateDiagonalMasks (const nbnxn_atomdata_t::SimdMasks &simdMasks)
	Returns the diagonal filter masks.
template<int nR, bool maskInteractions, std::size_t inputSize, std::size_t interactSize>
void	rInvSixAndRInvTwelve (const std::array< SimdReal, inputSize > &rInvSquaredV, const std::array< SimdBool, interactSize > &interactV, std::array< SimdReal, nR > &rInvSixV, std::array< SimdReal, nR > &rInvTwelveV)
	Computes r^-6 and r^-12, masked when requested.
template<int nR, bool maskInteractions, bool haveCutoffCheck, bool calculateEnergies, std::size_t inputSize, std::size_t interactSize, std::size_t vljvSize>
void	lennardJonesInteractionsSigmaEpsilon (const std::array< SimdReal, inputSize > &rInvV, const std::array< SimdBool, interactSize > &interactV, const SimdBool *const withinCutoffV, const std::array< SimdReal, nR > &sigmaV, const std::array< SimdReal, nR > &epsilonV, const SimdReal dispersionShift, const SimdReal repulsionShift, const SimdReal sixth, const SimdReal twelfth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV)
	Returns F*r and optionally the potential for LJ with (un)shifted potential with sigma/epsilon.
template<int nR, std::size_t inputSize>
void	computeForceSwitchVariables (const std::array< SimdReal, inputSize > &rSquaredV, const std::array< SimdReal, inputSize > &rInvV, SimdReal rSwitch, std::array< SimdReal, nR > &rSwitchedV, std::array< SimdReal, nR > &rSwitchedSquaredV, std::array< SimdReal, nR > &rSwitchedSquaredTimesRV)
	Computes (r - r_switch), (r - r_switch)^2 and (r - r_switch)^2 * r.
SimdReal	addLJForceSwitch (SimdReal force, SimdReal rSwitched, SimdReal rSwitchedSquaredTimesR, SimdReal c2, SimdReal c3)
	Adds the force switch term to force.
SimdReal	ljForceSwitchPotential (SimdReal rSwitched, SimdReal rSwitchedSquaredTimesR, SimdReal c0, SimdReal c3, SimdReal c4)
	Returns the LJ force switch function for the potential.
template<int nR, std::size_t inputSize>
void	computePotentialSwitchVariables (const std::array< SimdReal, inputSize > &rSquaredV, const std::array< SimdReal, inputSize > &rInvV, SimdReal rSwitch, std::array< SimdReal, nR > &rSwitchedV, std::array< SimdReal, nR > &rSwitchedSquaredV)
	Computes (r - r_switch) and (r - r_switch)^2.
SimdReal	potentialSwitchFunction (SimdReal rsw, SimdReal rsw2, SimdReal c3, SimdReal c4, SimdReal c5)
	Returns the potential switch function.
SimdReal	potentialSwitchFunctionDerivative (SimdReal rsw, SimdReal rsw2, SimdReal c2, SimdReal c3, SimdReal c4)
	Returns the derivative of the potential switch function.
template<int nR, bool maskInteractions, bool calculateEnergies, std::size_t inputSize, std::size_t interactSize, std::size_t ljepSize, std::size_t vljvSize>
void	addLennardJonesEwaldCorrections (const std::array< SimdReal, inputSize > &rSquaredV, const std::array< SimdReal, inputSize > &rInvSquaredV, const std::array< SimdBool, interactSize > &interactV, const SimdBool *withinCutoffV, const std::array< SimdReal, nR > &c6GridV, const std::array< SimdReal, ljepSize > &ljEwaldParams, SimdReal sixth, std::array< SimdReal, nR > &frLJV, std::array< SimdReal, vljvSize > &vLJV)
	Adds the Ewald long-range correction for r^-6.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r4xM, SimdReal >	loadIAtomData (const real *ptr, const int offset, const int iRegister)
	Load a single real for an i-atom into iRegister.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r2xMM, SimdReal >	loadIAtomData (const real *ptr, const int offset, const int iRegister)
	Load a pair of consecutive reals for two i-atom into the respective halves of iRegister.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r4xM, SimdReal >	loadJAtomData (const real *ptr, const int offset)
	Returns a SIMD register containing GMX_SIMD_REAL_WIDTH reals loaded from ptr + offset.
template<KernelLayout kernelLayout>
std::enable_if_t< kernelLayout==KernelLayout::r2xMM, SimdReal >	loadJAtomData (const real *ptr, const int offset)
	Returns a SIMD register containing a duplicate sequence of GMX_SIMD_REAL_WIDTH/2 reals loaded from ptr + offset.
template<bool loadMasks, KernelLayout kernelLayout>
std::enable_if_t<!loadMasks, std::array< SimdBool, 0 > >	loadSimdPairInteractionMasks (const int excl, SimdBitMask *filterBitMasksV)
	Loads no interaction masks, returns an empty array.
template<bool loadMasks, KernelLayout kernelLayout>
std::enable_if_t< loadMasks &&kernelLayout==KernelLayout::r4xM, std::array< SimdBool, c_nbnxnCpuIClusterSize > >	loadSimdPairInteractionMasks (const int excl, SimdBitMask *filterBitMasksV)
	Loads interaction masks for a cluster pair for 4xM kernel layout.
template<bool loadMasks, KernelLayout kernelLayout>
std::enable_if_t< loadMasks &&kernelLayout==KernelLayout::r2xMM, std::array< SimdBool, c_nbnxnCpuIClusterSize/2 > >	loadSimdPairInteractionMasks (const int excl, SimdBitMask *filterBitMasksV)
	Loads interaction masks for a cluster pair for 2xMM kernel layout.
template<KernelLayout kernelLayout, std::size_t offsetJJSize>
void	accumulateGroupPairEnergies4xM (SimdReal energies, real *groupPairEnergyBuffersPtr, const std::array< int, offsetJJSize > &offsetJJ)
	Adds energies to temporary energy group pair buffers for the 4xM kernel layout.
template<KernelLayout kernelLayout, std::size_t offsetJJSize>
void	accumulateGroupPairEnergies2xMM (SimdReal energies, real *groupPairEnergyBuffersPtr0, real *groupPairEnergyBuffersPtr1, const std::array< int, offsetJJSize > &offsetJJ)
	Adds energies to temporary energy group pair buffers for the 2xMM kernel layout.
template<int nR>
int	pairCountWithinCutoff (SimdReal rSquaredV[nR], SimdReal cutoffSquared)
	Return the number of atoms pairs that are within the cut-off distance.
bool	boxesAreEqual (const matrix box1, const matrix box2)
	Returns whether two boxes are of equal size and shape (within reasonable tolerance).
bool	boxIsZero (const matrix box)
	Returns whether a box is only initialised to zero or not.
void	shiftAtoms (const RVec &shift, ArrayRef< RVec > x)
	Shift all coordinates. More...
void	placeCoordinatesWithCOMInBox (const PbcType &pbcType, UnitCellType unitCellType, CenteringType centerType, const matrix box, ArrayRef< RVec > x, const gmx_mtop_t &mtop, COMShiftType comShiftType)
	Moves collection of atoms along the center of mass into a box. More...
static int	xyzToShiftIndex (int x, int y, int z)
	Convert grid coordinates to shift index.
static int	ivecToShiftIndex (ivec iv)
	Convert grid coordinates to shift index.
static int	shiftIndexToXDim (int iv)
	Return the shift in the X dimension of grid space corresponding to iv.
const char *	centerTypeNames (CenteringType type)
	Get names for the different centering types. More...
const char *	unitCellTypeNames (UnitCellType type)
	Get names for the different unit cell representation types. More...
double	getTransformationPullCoordinateValue (pull_coord_work_t *coord, ArrayRef< const pull_coord_work_t > variableCoords, double t)
	Calculates pull->coord[coord_ind].spatialData.value for a transformation pull coordinate. More...
static double	computeDerivativeForTransformationPullCoord (pull_coord_work_t *coord, const int variablePcrdIndex)
	Calculates and returns the derivative of a transformation pull coordinate from a dependent coordinate. More...
void	distributeTransformationPullCoordForce (pull_coord_work_t *pcrd, gmx::ArrayRef< pull_coord_work_t > variableCoords)
	Distributes the force on a transformation pull coordinates to the involved coordinates of lower rank. More...
static bool	checkIfRandomDeviceIsFunctional ()
	Check if the RDRAND random device functioning correctly. More...
template<typename GeneratorType >
static uint64_t	makeRandomSeedInternal (GeneratorType &gen)
	Get the next pure or pseudo-random number. More...
uint64_t	makeRandomSeed ()
	Return 64 random bits from the random device, suitable as seed. More...
template<class RealType = real, unsigned int Bits, class Rng >
RealType	generateCanonical (Rng &g)
	Generate a floating-point value with specified number of random bits. More...
void	compileSelection (SelectionCollection *coll)
void	swap (SelectionCollection &lhs, SelectionCollection &rhs)
static void gmx_unused	simdPrefetch (void gmx_unused *m)
	Prefetch memory at address m. More...
static void	store (float *m, float a)
	Store contents of float variable to aligned memory m. More...
static void	storeU (float *m, float a)
	Store contents of float variable to unaligned memory m. More...
static float	fma (float a, float b, float c)
	Float Fused-multiply-add. Result is a*b + c. More...
static float	fms (float a, float b, float c)
	Float Fused-multiply-subtract. Result is a*b - c. More...
static float	fnma (float a, float b, float c)
	Float Fused-negated-multiply-add. Result is -a*b + c. More...
static float	fnms (float a, float b, float c)
	Float Fused-negated-multiply-subtract. Result is -a*b - c. More...
static float	maskAdd (float a, float b, float m)
	Add two float variables, masked version. More...
static float	maskzMul (float a, float b, float m)
	Multiply two float variables, masked version. More...
static float	maskzFma (float a, float b, float c, float m)
	Float fused multiply-add, masked version. More...
static float gmx_simdcall	maskzRcp (float x, float m)
	Float 1.0/x, masked version. More...
static float	abs (float a)
	Float Floating-point abs(). More...
static float	max (float a, float b)
	Set each float element to the largest from two variables. More...
static float	min (float a, float b)
	Set each float element to the smallest from two variables. More...
static float	round (float a)
	Float round to nearest integer value (in floating-point format). More...
static float	trunc (float a)
	Truncate float, i.e. round towards zero - common hardware instruction. More...
static float	reduce (float a)
	Return sum of all elements in float variable (i.e., the variable itself). More...
static float	andNot (float a, float b)
	Bitwise andnot for two scalar float variables. More...
static bool	testBits (float a)
	Return true if any bits are set in the float variable. More...
static bool	anyTrue (bool a)
	Returns if the boolean is true. More...
static float	selectByMask (float a, bool mask)
	Select from single precision variable where boolean is true. More...
static float	selectByNotMask (float a, bool mask)
	Select from single precision variable where boolean is false. More...
static float	blend (float a, float b, bool sel)
	Blend float selection. More...
static std::int32_t	cvtR2I (float a)
	Round single precision floating point to integer. More...
static std::int32_t	cvttR2I (float a)
	Truncate single precision floating point to integer. More...
static std::int32_t	cvtI2R (std::int32_t a)
	Return integer. More...
static void	store (double *m, double a)
	Store contents of double variable to aligned memory m. More...
static void	storeU (double *m, double a)
	Store contents of double variable to unaligned memory m. More...
static double	fma (double a, double b, double c)
	double Fused-multiply-add. Result is a*b + c. More...
static double	fms (double a, double b, double c)
	double Fused-multiply-subtract. Result is a*b - c. More...
static double	fnma (double a, double b, double c)
	double Fused-negated-multiply-add. Result is - a*b + c. More...
static double	fnms (double a, double b, double c)
	double Fused-negated-multiply-subtract. Result is -a*b - c. More...
static double	maskAdd (double a, double b, double m)
	Add two double variables, masked version. More...
static double	maskzMul (double a, double b, double m)
	Multiply two double variables, masked version. More...
static double	maskzFma (double a, double b, double c, double m)
	double fused multiply-add, masked version. More...
static double gmx_simdcall	maskzRcp (double x, double m)
	Double 1.0/x, masked version. More...
static double	abs (double a)
	double doubleing-point abs(). More...
static double	max (double a, double b)
	Set each double element to the largest from two variables. More...
static double	min (double a, double b)
	Set each double element to the smallest from two variables. More...
static double	round (double a)
	double round to nearest integer value (in doubleing-point format). More...
static double	trunc (double a)
	Truncate double, i.e. round towards zero - common hardware instruction. More...
static double	reduce (double a)
	Return sum of all elements in double variable (i.e., the variable itself). More...
static double	andNot (double a, double b)
	Bitwise andnot for two scalar double variables. More...
static bool	testBits (double a)
	Return true if any bits are set in the double variable. More...
static double	selectByMask (double a, bool mask)
	Select from double precision variable where boolean is true. More...
static double	selectByNotMask (double a, bool mask)
	Select from double precision variable where boolean is false. More...
static double	blend (double a, double b, bool sel)
	Blend double selection. More...
static std::int32_t	cvtR2I (double a)
	Round single precision doubleing point to integer. More...
static std::int32_t	cvttR2I (double a)
	Truncate single precision doubleing point to integer. More...
static double	cvtF2D (float a)
	Convert float to double (mimicks SIMD conversion) More...
static float	cvtD2F (double a)
	Convert double to float (mimicks SIMD conversion) More...
static void	store (std::int32_t *m, std::int32_t a)
	Store contents of integer variable to aligned memory m. More...
static void	storeU (std::int32_t *m, std::int32_t a)
	Store contents of integer variable to unaligned memory m. More...
static std::int32_t	andNot (std::int32_t a, std::int32_t b)
	Bitwise andnot for two scalar integer variables. More...
static bool	testBits (std::int32_t a)
	Return true if any bits are set in the integer variable. More...
static std::int32_t	selectByMask (std::int32_t a, bool mask)
	Select from integer variable where boolean is true. More...
static std::int32_t	selectByNotMask (std::int32_t a, bool mask)
	Select from integer variable where boolean is false. More...
static std::int32_t	blend (std::int32_t a, std::int32_t b, bool sel)
	Blend integer selection. More...
static bool	cvtB2IB (bool a)
	Just return a boolean (mimicks SIMD real-to-int bool conversions) More...
static bool	cvtIB2B (bool a)
	Just return a boolean (mimicks SIMD int-to-real bool conversions) More...
static float	copysign (float x, float y)
	Composes single value with the magnitude of x and the sign of y. More...
static void	invsqrtPair (float x0, float x1, float *out0, float *out1)
	Calculate 1/sqrt(x) for two floats. More...
static float	inv (float x)
	Calculate 1/x for float. More...
static float	maskzInvsqrt (float x, bool m)
	Calculate 1/sqrt(x) for masked entry of float. More...
static float	maskzInv (float x, bool m)
	Calculate 1/x for masked entry of float. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	sqrt (float x)
	Float sqrt(x). This is the square root. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	cbrt (float x)
	Float cbrt(x). This is the cubic root. More...
static float	log (float x)
	Float log(x). This is the natural logarithm. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	exp2 (float x)
	Float 2^x. More...
template<MathOptimization opt = MathOptimization::Safe>
static float	exp (float x)
	Float exp(x). More...
static float	erf (float x)
	Float erf(x). More...
static float	erfc (float x)
	Float erfc(x). More...
static void	sincos (float x, float *sinval, float *cosval)
	Float sin & cos. More...
static float	sin (float x)
	Float sin. More...
static float	cos (float x)
	Float cos. More...
static float	tan (float x)
	Float tan. More...
static float	asin (float x)
	float asin. More...
static float	acos (float x)
	Float acos. More...
static float	atan (float x)
	Float atan. More...
static float	atan2 (float y, float x)
	Float atan2(y,x). More...
static float	pmeForceCorrection (float z2)
	Calculate the force correction due to PME analytically in float. More...
static float	pmePotentialCorrection (float z2)
	Calculate the potential correction due to PME analytically in float. More...
static double	copysign (double x, double y)
	Composes double value with the magnitude of x and the sign of y. More...
static void	invsqrtPair (double x0, double x1, double *out0, double *out1)
	Calculate 1/sqrt(x) for two doubles. More...
static double	inv (double x)
	Calculate 1/x for double. More...
static double	maskzInvsqrt (double x, bool m)
	Calculate 1/sqrt(x) for masked entry of double. More...
static double	maskzInv (double x, bool m)
	Calculate 1/x for masked entry of double. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	sqrt (double x)
	Double sqrt(x). This is the square root. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	cbrt (double x)
	Double cbrt(x). This is the cubic root. More...
static double	log (double x)
	Double log(x). This is the natural logarithm. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	exp2 (double x)
	Double 2^x. More...
template<MathOptimization opt = MathOptimization::Safe>
static double	exp (double x)
	Double exp(x). More...
static double	erf (double x)
	Double erf(x). More...
static double	erfc (double x)
	Double erfc(x). More...
static void	sincos (double x, double *sinval, double *cosval)
	Double sin & cos. More...
static double	sin (double x)
	Double sin. More...
static double	cos (double x)
	Double cos. More...
static double	tan (double x)
	Double tan. More...
static double	asin (double x)
	Double asin. More...
static double	acos (double x)
	Double acos. More...
static double	atan (double x)
	Double atan. More...
static double	atan2 (double y, double x)
	Double atan2(y,x). More...
static double	pmeForceCorrection (double z2)
	Calculate the force correction due to PME analytically in double. More...
static double	pmePotentialCorrection (double z2)
	Calculate the potential correction due to PME analytically in double. More...
static double	invsqrtSingleAccuracy (double x)
	Calculate 1/sqrt(x) for double, but with single accuracy. More...
static void	invsqrtPairSingleAccuracy (double x0, double x1, double *out0, double *out1)
	Calculate 1/sqrt(x) for two doubles, but with single accuracy. More...
static double	invSingleAccuracy (double x)
	Calculate 1/x for double, but with single accuracy. More...
static double	maskzInvsqrtSingleAccuracy (double x, bool m)
	Calculate 1/sqrt(x) for masked entry of double, but with single accuracy. More...
static double	maskzInvSingleAccuracy (double x, bool m)
	Calculate 1/x for masked entry of double, but with single accuracy. More...
static double	sqrtSingleAccuracy (double x)
	Calculate sqrt(x) for double, but with single accuracy. More...
static double	logSingleAccuracy (double x)
	Double log(x), but with single accuracy. This is the natural logarithm. More...
static double	exp2SingleAccuracy (double x)
	Double 2^x, but with single accuracy. More...
static double	expSingleAccuracy (double x)
	Double exp(x), but with single accuracy. More...
static double	erfSingleAccuracy (double x)
	Double erf(x), but with single accuracy. More...
static double	erfcSingleAccuracy (double x)
	Double erfc(x), but with single accuracy. More...
static void	sincosSingleAccuracy (double x, double *sinval, double *cosval)
	Double sin & cos, but with single accuracy. More...
static double	sinSingleAccuracy (double x)
	Double sin, but with single accuracy. More...
static double	cosSingleAccuracy (double x)
	Double cos, but with single accuracy. More...
static double	tanSingleAccuracy (double x)
	Double tan, but with single accuracy. More...
static double	asinSingleAccuracy (double x)
	Double asin, but with single accuracy. More...
static double	acosSingleAccuracy (double x)
	Double acos, but with single accuracy. More...
static double	atanSingleAccuracy (double x)
	Double atan, but with single accuracy. More...
static double	atan2SingleAccuracy (double y, double x)
	Double atan2(y,x), but with single accuracy. More...
static double	pmeForceCorrectionSingleAccuracy (double z2)
	Force correction due to PME in double, but with single accuracy. More...
static double	pmePotentialCorrectionSingleAccuracy (double z2)
	Potential correction due to PME in double, but with single accuracy. More...
template<int align>
static void	gatherLoadTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1, float *v2, float *v3)
	Load 4 consecutive floats from base/offset into four variables. More...
template<int align>
static void	gatherLoadTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1)
	Load 2 consecutive floats from base/offset into four variables. More...
template<int align>
static void	gatherLoadUTranspose (const float *base, const std::int32_t offset[], float *v0, float *v1, float *v2)
	Load 3 consecutive floats from base/offsets, store into three vars. More...
template<int align>
static void	transposeScatterStoreU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Store 3 floats to 3 to base/offset. More...
template<int align>
static void	transposeScatterIncrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Add 3 floats to base/offset. More...
template<int align>
static void	transposeScatterDecrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Subtract 3 floats from base/offset. More...
static void	expandScalarsToTriplets (float scalar, float *triplets0, float *triplets1, float *triplets2)
	Copy single float to three variables. More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1, float *v2, float *v3)
	Load 4 floats from base/offsets and store into variables. More...
template<int align>
static void	gatherLoadUBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1)
	Load 2 floats from base/offsets and store into variables (unaligned). More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const float *base, std::int32_t offset, float *v0, float *v1)
	Load 2 floats from base/offsets and store into variables (aligned). More...
static float	reduceIncr4ReturnSum (float *m, float v0, float v1, float v2, float v3)
	Add each float to four consecutive memory locations, return sum. More...
template<int align>
static void	gatherLoadTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1, double *v2, double *v3)
	Load 4 consecutive doubles from base/offset into four variables. More...
template<int align>
static void	gatherLoadTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1)
	Load 2 consecutive doubles from base/offset into four variables. More...
template<int align>
static void	gatherLoadUTranspose (const double *base, const std::int32_t offset[], double *v0, double *v1, double *v2)
	Load 3 consecutive doubles from base/offsets, store into three vars. More...
template<int align>
static void	transposeScatterStoreU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Store 3 doubles to 3 to base/offset. More...
template<int align>
static void	transposeScatterIncrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Add 3 doubles to base/offset. More...
template<int align>
static void	transposeScatterDecrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Subtract 3 doubles from base/offset. More...
static void	expandScalarsToTriplets (double scalar, double *triplets0, double *triplets1, double *triplets2)
	Copy single double to three variables. More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1, double *v2, double *v3)
	Load 4 doubles from base/offsets and store into variables. More...
template<int align>
static void	gatherLoadUBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1)
	Load 2 doubles from base/offsets and store into variables (unaligned). More...
template<int align>
static void	gatherLoadBySimdIntTranspose (const double *base, std::int32_t offset, double *v0, double *v1)
	Load 2 doubles from base/offsets and store into variables (aligned). More...
static double	reduceIncr4ReturnSum (double *m, double v0, double v1, double v2, double v3)
	Add each double to four consecutive memory locations, return sum. More...
std::unique_ptr< IMDModule >	createSwapCoordinatesModule ()
	Creates a module for Computational Electrophysiology swapping.
bool	decideWhetherToUseGpusForNonbondedWithThreadMpi (TaskTarget nonbondedTarget, bool haveAvailableDevices, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool buildSupportsNonbondedOnGpu, bool nonbondedOnGpuIsUseful, int numRanksPerSimulation)
	Decide whether this thread-MPI simulation will run nonbonded tasks on GPUs. More...
static bool	decideWhetherToUseGpusForPmeFft (const TaskTarget pmeFftTarget)
static bool	canUseGpusForPme (const bool useGpuForNonbonded, const TaskTarget pmeTarget, const TaskTarget pmeFftTarget, const t_inputrec &inputrec, std::string *errorMessage)
bool	decideWhetherToUseGpusForPmeWithThreadMpi (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, int numDevicesToUse, const std::vector< int > &userGpuTaskAssignment, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation)
	Decide whether this thread-MPI simulation will run PME tasks on GPUs. More...
bool	decideWhetherToUseGpusForNonbonded (TaskTarget nonbondedTarget, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool buildSupportsNonbondedOnGpu, bool nonbondedOnGpuIsUseful, bool gpusWereDetected)
	Decide whether the simulation will try to run nonbonded tasks on GPUs. More...
bool	decideWhetherToUseGpusForPme (bool useGpuForNonbonded, TaskTarget pmeTarget, TaskTarget pmeFftTarget, const std::vector< int > &userGpuTaskAssignment, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation, bool gpusWereDetected)
	Decide whether the simulation will try to run tasks of different types on GPUs. More...
PmeRunMode	determinePmeRunMode (bool useGpuForPme, const TaskTarget &pmeFftTarget, const t_inputrec &inputrec)
	Determine PME run mode. More...
bool	decideWhetherToUseGpusForBonded (bool useGpuForNonbonded, bool useGpuForPme, TaskTarget bondedTarget, const t_inputrec &inputrec, const gmx_mtop_t &mtop, int numPmeRanksPerSimulation, bool gpusWereDetected)
	Decide whether the simulation will try to run bonded tasks on GPUs. More...
bool	decideWhetherToUseGpuForUpdate (bool isDomainDecomposition, bool useUpdateGroups, PmeRunMode pmeRunMode, bool havePmeOnlyRank, bool useGpuForNonbonded, TaskTarget updateTarget, bool gpusWereDetected, const t_inputrec &inputrec, const gmx_mtop_t &mtop, bool useEssentialDynamics, bool doOrientationRestraints, bool haveFrozenAtoms, bool useModularSimulator, bool doRerun, const gmx::MDLogger &mdlog)
	Decide whether to use GPU for update. More...
bool	decideWhetherDirectGpuCommunicationCanBeUsed (const DevelopmentFeatureFlags &devFlags, bool haveMts, bool haveSwapCoords, const gmx::MDLogger &mdlog)
	Decide whether direct GPU communication can be used. More...
bool	decideWhetherToUseGpuForHalo (bool havePPDomainDecomposition, bool useGpuForNonbonded, bool canUseDirectGpuComm, bool useModularSimulator, bool doRerun, bool haveEnergyMinimization, const gmx::MDLogger &mdlog)
	Decide whether to use GPU for halo exchange. More...
SimulationWorkload	createSimulationWorkload (const t_inputrec &inputrec, bool disableNonbondedCalculation, const DevelopmentFeatureFlags &devFlags, bool havePpDomainDecomposition, bool haveSeparatePmeRank, bool useGpuForNonbonded, PmeRunMode pmeRunMode, bool useGpuForBonded, bool useGpuForUpdate, bool useGpuDirectHalo, bool canUseDirectGpuComm, bool useGpuPmeDecomposition)
	Build datastructure that contains decisions whether to run different workload task on GPUs. More...
std::vector< GpuTask >	findGpuTasksOnThisRank (bool haveGpusOnThisPhysicalNode, TaskTarget nonbondedTarget, TaskTarget pmeTarget, TaskTarget bondedTarget, TaskTarget updateTarget, bool useGpuForNonbonded, bool useGpuForPme, bool rankHasPpTask, bool rankHasPmeTask)
	Returns container of all tasks on this rank that are eligible for GPU execution. More...
GpuTasksOnRanks	findAllGpuTasksOnThisNode (ArrayRef< const GpuTask > gpuTasksOnThisRank, const PhysicalNodeCommunicator &physicalNodeComm)
	Returns container of all tasks on all ranks of this node that are eligible for GPU execution. More...
void	checkHardwareOversubscription (int numThreadsOnThisRank, int rank, const HardwareTopology &hwTop, const PhysicalNodeCommunicator &comm, const MDLogger &mdlog)
	Warns for oversubscribing the hardware threads, when that is the case.
std::vector< int >	parseUserGpuIdString (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container describing device IDs exposed to the run. More...
std::vector< int >	makeListOfAvailableDevices (gmx::ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, const std::string &devicesSelectedByUserString)
	Implement GPU ID selection by returning the available GPU IDs on this physical node that are compatible. More...
std::vector< int >	parseUserTaskAssignmentString (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container describing device ID to task mapping. More...
std::vector< int >	makeGpuIds (ArrayRef< const int > compatibleGpus, size_t numGpuTasks)
	Make a vector containing numGpuTasks IDs of the IDs found in compatibleGpus. More...
std::string	makeGpuIdString (const std::vector< int > &gpuIds, int totalNumberOfTasks)
	Convert a container of GPU deviced IDs to a string that can be used by gmx tune_pme as input to mdrun -gputasks. More...
void	checkUserGpuIds (ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, ArrayRef< const int > compatibleGpus, ArrayRef< const int > gpuIds)
	Check that all user-selected GPUs are compatible. More...
void	reportGpuUsage (const MDLogger &mdlog, ArrayRef< const GpuTaskAssignment > gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool printHostName, PmeRunMode pmeRunMode, const SimulationWorkload &simulationWork)
	Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation. More...
template<GpuTask TaskType>
static bool	hasTaskType (const GpuTaskMapping &mapping)
	Function for whether the task of mapping has value TaskType. More...
static bool	hasPmeOrNonbondedTask (const GpuTaskMapping &mapping)
	Function for whether the mapping has the GPU PME or Nonbonded task. More...
static std::vector< int >	parseGpuDeviceIdentifierList (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container. More...
void	writeHeader (TextWriter *writer, const std::string &text, const std::string &section, bool writeFormattedText)
	Write appropiate Header to output stream. More...
void	writeSystemInformation (TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
	Write information about the molecules in the system. More...
void	writeParameterInformation (TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
	Write information about system parameters. More...
void	writeInformation (TextOutputFile *outputStream, const t_inputrec &ir, const gmx_mtop_t &top, bool writeFormattedText, bool notStdout)
	Wrapper for writing out information. More...
void	blockaToExclusionBlocks (const t_blocka *b, gmx::ArrayRef< ExclusionBlock > b2)
	Convert the exclusions. More...
void	exclusionBlocksToBlocka (gmx::ArrayRef< const ExclusionBlock > b2, t_blocka *b)
	Convert the exclusions expressed in b into t_blocka form.
void	mergeExclusions (ListOfLists< int > *excl, gmx::ArrayRef< ExclusionBlock > b2)
	Merge the contents of b2 into excl. More...
gmx_rmpbc_t	gmx_rmpbc_init (const gmx::TopologyInformation &topInfo)
	Convenience overload useful for implementing legacy tools.
static std::size_t	getPageSize ()
	Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes). More...
void	printBinaryInformation (FILE *fp, const IProgramContext &programContext)
	Print basic information about the executable. More...
void	printBinaryInformation (FILE *fp, const IProgramContext &programContext, const BinaryInformationSettings &settings)
	Print basic information about the executable with custom settings. More...
void	printBinaryInformation (TextWriter *writer, const IProgramContext &programContext, const BinaryInformationSettings &settings)
	Print basic information about the executable with custom settings. More...
ArrayRef< bool >	makeArrayRef (std::vector< BoolType > &boolVector)
	Create ArrayRef to bool from reference to std::vector<BoolType>. More...
ArrayRef< const bool >	makeConstArrayRef (const std::vector< BoolType > &boolVector)
	Create ArrayRef to const bool from reference to std::vector<BoolType>. More...
std::string	bromacs ()
	Return a cool definition for the acronym GROMACS.
std::string	getCoolQuote ()
	Return a string with a cool quote.
std::string	getCudaDriverVersionString ()
	Returns a string of the CUDA driver version.
std::string	getCudaRuntimeVersionString ()
	Returns a string of the CUDA runtime version.
const char *	getErrorCodeString (int errorcode)
	Returns a short string description of an error code. More...
void	printFatalErrorMessage (FILE *fp, const std::exception &ex)
	Formats a standard fatal error message for reporting an exception. More...
std::string	formatExceptionMessageToString (const std::exception &ex)
	Formats an error message for reporting an exception. More...
void	formatExceptionMessageToFile (FILE *fp, const std::exception &ex)
	Formats an error message for reporting an exception. More...
void	formatExceptionMessageToWriter (TextWriter *writer, const std::exception &ex)
	Formats an error message for reporting an exception. More...
int	processExceptionAtExit (const std::exception &ex)
	Handles an exception that is causing the program to terminate. More...
void	processExceptionAsFatalError (const std::exception &ex)
	Helper function for terminating the program on an exception. More...
const DataFileFinder &	getLibraryFileFinder ()
	Gets a finder for locating data files from share/top/. More...
void	setLibraryFileFinder (const DataFileFinder *finder)
	Sets a finder for location data files from share/top/. More...
std::filesystem::path	findLibraryFile (const std::filesystem::path &filename, bool bAddCWD=true, bool bFatal=true)
	Finds full path for a library file. More...
FilePtr	openLibraryFile (const std::filesystem::path &filename, bool bAddCWD=true, bool bFatal=true)
	Opens a library file for reading in an RAII-style FILE handle. More...
std::size_t	pageSize ()
	Return the memory page size on this system. More...
void	init (int *argc, char ***argv)
	Initializes the GROMACS library. More...
void	finalize ()
	Deinitializes the GROMACS library. More...
void	writeKeyValueTreeAsMdp (TextWriter *writer, const KeyValueTreeObject &tree)
	Write a flat key-value tree to writer in mdp style. More...
GpuAwareMpiStatus	checkMpiCudaAwareSupport ()
	Wrapper on top of MPIX_Query_cuda_support() For MPI implementations which don't support this function, it returns NotKnown Even when an MPI implementation does support this function, MPI library might not be robust enough to detect CUDA-aware support at runtime correctly e.g. when UCX PML is used or CUDA is disabled at runtime. More...
GpuAwareMpiStatus	checkMpiHipAwareSupport ()
	Wrapper on top of MPIX_Query_hip_support() or MPIX_Query_rocm_support(). For MPI implementations which don't support this function, it returns NotKnown. More...
GpuAwareMpiStatus	checkMpiZEAwareSupport ()
	Wrapper on top of MPIX_Query_ze_support() For MPI implementations which don't support this function, it returns NotKnown. More...
void	niceHeader (TextWriter *writer, const char *fn, char commentChar)
	Prints creation time stamp and user information into a string as comments, and returns it. More...
std::vector < std::filesystem::path >	splitPathEnvironment (const std::string &pathEnv)
	Split PATH environment variable into search paths. More...
std::vector < std::filesystem::path >	getSystemExecutablePaths ()
	Get collection of possible executable paths.
std::string	stripSourcePrefix (const char *path)
	Strip source prefix from path.
std::filesystem::path	concatenateBeforeExtension (const std::filesystem::path &path, const std::string &addition)
	Concatenate before extension.
std::filesystem::path	stripExtension (const std::filesystem::path &path)
	Remove extension from file path.
bool	extensionMatches (const std::filesystem::path &path, std::string_view extension)
	Check if file extension of path without final '.' matches extension.
void	MPI_Comm_free_wrapper (MPI_Comm *comm)
	Wrapper function for RAII-style cleanup. More...
template<typename ValueType , int NumExpectedValues>
static std::optional < std::array< ValueType, NumExpectedValues > >	parsedArrayFromInputString (const std::string &str)
	Convert a string into an array of values. More...
template<typename ValueType , int NumExpectedValues>
static std::string	stringIdentityTransformWithArrayCheck (const std::string &toConvert, const std::string &errorContextMessage)
	Returns the input string, throwing an exception if the demanded conversion to an array will not succeed. More...
template<class Function >
auto	dispatchTemplatedFunction (Function &&f)
const IProgramContext &	getProgramContext ()
	Returns the global IProgramContext instance. More...
void	setProgramContext (const IProgramContext *context)
	Sets the global IProgramContext instance. More...
std::size_t	countWords (const char *s)
	Returns number of space-separated words in zero-terminated char ptr. More...
std::size_t	countWords (const std::string &str)
	Returns the number of space-separated words in a string object. More...
bool	endsWith (const char *str, const char *suffix)
	Tests whether a string ends with another string. More...
std::string	stripSuffixIfPresent (const std::string &str, const char *suffix)
	Removes a suffix from a string. More...
std::string	stripString (const std::string &str)
	Removes leading and trailing whitespace from a string. More...
std::string	formatString (gmx_fmtstr const char *fmt,...)
std::string	formatStringV (const char *fmt, va_list ap)
	Formats a string (vsnprintf() wrapper). More...
std::vector< std::string >	splitString (const std::string &str)
	Splits a string to whitespace separated tokens. More...
std::vector< std::string >	splitDelimitedString (const std::string &str, char delim)
	Splits a string to tokens separated by a given delimiter. More...
std::vector< std::string >	splitAndTrimDelimitedString (const std::string &str, char delim)
	Splits str to tokens separated by delimiter delim. Removes leading and trailing whitespace from those strings with std::isspace. More...
std::string	replaceAll (const std::string &input, const char *from, const char *to)
	Replace all occurrences of a string with another string. More...
std::string	replaceAll (const std::string &input, const std::string &from, const std::string &to)
	Replace all occurrences of a string with another string. More...
std::string	replaceAllWords (const std::string &input, const char *from, const char *to)
	Replace whole words with others. More...
std::string	replaceAllWords (const std::string &input, const std::string &from, const std::string &to)
	Replace whole words with others. More...
bool	equalCaseInsensitive (const std::string &source, const std::string &target)
	Return whether two strings are equal, ignoring case. More...
bool	equalCaseInsensitive (const std::string &source, const std::string &target, size_t maxLengthOfComparison)
	Checks if at most maxLengthOfComparison characters of two strings match case insensitive. More...
std::string	toUpperCase (const std::string &text)
	Makes the string uppercase. More...
std::string	toLowerCase (const std::string &text)
	Makes the string lowercase. More...
std::string	getSyclCompilerVersion ()
	Returns an internal version strings of the Intel DPC++ and hipSYCL compiler.
int	gmx_mdrun (int argc, char *argv[])
	Implements C-style main function for mdrun. More...
int	gmx_mdrun (MPI_Comm communicator, const gmx_hw_info_t &hwinfo, int argc, char *argv[])
	Implements C-style main function for mdrun. More...
AnalysisHistogramSettingsInitializer	histogramFromRange (real min, real max)
	Initializes a histogram using a range and a bin width. More...
AnalysisHistogramSettingsInitializer	histogramFromBins (real start, int nbins, real binwidth)
	Initializes a histogram using bin width and the number of bins. More...
static float	invsqrt (float x)
	Calculate 1.0/sqrt(x) in single precision. More...
static double	invsqrt (double x)
	Calculate 1.0/sqrt(x) in double precision, but single range. More...
static double	invsqrt (int x)
	Calculate 1.0/sqrt(x) for integer x in double precision. More...
static float	invcbrt (float x)
	Calculate inverse cube root of x in single precision. More...
static double	invcbrt (double x)
	Calculate inverse sixth root of x in double precision. More...
static double	invcbrt (int x)
	Calculate inverse sixth root of integer x in double precision. More...
static float	sixthroot (float x)
	Calculate sixth root of x in single precision. More...
static double	sixthroot (double x)
	Calculate sixth root of x in double precision. More...
static double	sixthroot (int x)
	Calculate sixth root of integer x, return double. More...
static float	invsixthroot (float x)
	Calculate inverse sixth root of x in single precision. More...
static double	invsixthroot (double x)
	Calculate inverse sixth root of x in double precision. More...
static double	invsixthroot (int x)
	Calculate inverse sixth root of integer x in double precision. More...
template<typename T >
T	square (T x)
	calculate x^2 More...
template<typename T >
T	power3 (T x)
	calculate x^3 More...
template<typename T >
T	power4 (T x)
	calculate x^4 More...
template<typename T >
T	power5 (T x)
	calculate x^5 More...
template<typename T >
T	power6 (T x)
	calculate x^6 More...
template<typename T >
T	power12 (T x)
	calculate x^12 More...
static real	series_sinhx (real x)
	Maclaurin series for sinh(x)/x. More...
constexpr int32_t	exactDiv (int32_t a, int32_t b)
	Exact integer division, 32bit. More...
constexpr int64_t	exactDiv (int64_t a, int64_t b)
	Exact integer division, 64bit.
static int	roundToInt (float x)
	Round float to int. More...
static int	roundToInt (double x)
	Round double to int.
static int64_t	roundToInt64 (float x)
	Round float to int64_t.
static int64_t	roundToInt64 (double x)
	Round double to int64_t.
template<typename T , typename = std::enable_if_t<std::is_integral<T>::value>>
static constexpr bool	isPowerOfTwo (const T v)
	Check whether v is an integer power of 2.
template<typename ValueType >
BasicVector< ValueType >	operator* (const BasicVector< ValueType > &basicVector, const ValueType &scalar)
	Allow vector scalar multiplication.
template<typename ValueType >
BasicVector< ValueType >	operator* (const ValueType &scalar, const BasicVector< ValueType > &basicVector)
	Allow scalar vector multiplication.
template<typename VectorType >
static VectorType	unitVector (const VectorType &v)
	unitv for gmx::BasicVector
template<typename ValueType >
static ValueType	norm (BasicVector< ValueType > v)
	norm for gmx::BasicVector
template<typename ValueType >
static ValueType	norm2 (BasicVector< ValueType > v)
	Square of the vector norm for gmx::BasicVector.
template<typename VectorType >
static VectorType	cross (const VectorType &a, const VectorType &b)
	cross product for gmx::BasicVector
template<typename ValueType >
static ValueType	dot (BasicVector< ValueType > a, BasicVector< ValueType > b)
	dot product for gmx::BasicVector
template<typename VectorType >
static VectorType	scaleByVector (const VectorType &a, const VectorType &b)
	Multiply two vectors element by element and return the result.
template<typename VectorType >
static VectorType	elementWiseMin (const VectorType &a, const VectorType &b)
	Return the element-wise minimum of two vectors.
template<typename VectorType >
static VectorType	elementWiseMax (const VectorType &a, const VectorType &b)
	Return the element-wise maximum of two vectors.
template<typename ValueType >
static BasicVector< ValueType > ::RawArray *	as_vec_array (BasicVector< ValueType > *x)
	Casts a gmx::BasicVector array into an equivalent raw C array.
template<typename ValueType >
static const BasicVector < ValueType >::RawArray *	as_vec_array (const BasicVector< ValueType > *x)
	Casts a gmx::BasicVector array into an equivalent raw C array.
static rvec *	as_rvec_array (RVec *x)
	Casts a gmx::RVec array into an rvec array.
static const rvec *	as_rvec_array (const RVec *x)
	Casts a gmx::RVec array into an rvec array.
static dvec *	as_dvec_array (DVec *x)
	Casts a gmx::DVec array into an Dvec array.
static ivec *	as_ivec_array (IVec *x)
	Casts a gmx::IVec array into an ivec array.
static const dvec *	as_dvec_array (const DVec *x)
	Casts a gmx::DVec array into an dvec array.
static const ivec *	as_ivec_array (const IVec *x)
	Casts a gmx::IVec array into an ivec array.
template<typename T >
ArrayRef< std::conditional_t < std::is_const< T >::value, const typename T::value_type, typename T::value_type > >	makeArrayRef (T &c)
	Create ArrayRef from container with type deduction. More...
template<typename T >
ArrayRef< const typename T::value_type >	makeConstArrayRef (const T &c)
	Create ArrayRef to const T from container with type deduction. More...
template<typename T >
void	swap (ArrayRef< T > &a, ArrayRef< T > &b)
	Simple swap method for ArrayRef objects. More...
template<typename T >
std::vector< T >	copyOf (const ArrayRef< const T > &arrayRef)
	Return a vector that is a copy of an ArrayRef. More...
template<typename T >
index	ssize (const T &t)
	Return signed size of container.
template<typename EnumerationArrayType >
EnumerationArrayType::EnumerationWrapperType	keysOf (const EnumerationArrayType &)
	Returns an object that provides iterators over the keys associated with EnumerationArrayType. More...
template<class Exception , class Tag , class T >
std::enable_if_t < std::is_base_of < GromacsException, Exception > ::value, Exception >	operator<< (Exception ex, const ExceptionInfo< Tag, T > &item)
	Associates extra information with an exception. More...
void	fclose_wrapper (FILE *fp)
	fclose wrapper to be used as unique_ptr deleter
static bool	isNullOrEmpty (const char *str)
	Tests whether a string is null or empty. More...
static bool	startsWith (const std::string &str, const std::string &prefix)
	Tests whether a string starts with another string. More...
static bool	startsWith (const char *str, const char *prefix)
	Tests whether a string starts with another string. More...
static bool	endsWith (const std::string &str, const char *suffix)
	Tests whether a string ends with another string. More...
static bool	contains (const std::string &str, const char *substr)
	Tests whether a string contains another as a substring. More...
static bool	contains (const std::string &str, const std::string &substr)
	Tests whether a string contains another as a substring. More...
static bool	endsWith (const std::string &str, const std::string &suffix)
	Tests whether a string ends with another string. More...
std::string	formatString (const char *fmt,...)
	Formats a string (snprintf() wrapper). More...
template<typename InputIterator , typename FormatterType >
std::string	formatAndJoin (InputIterator begin, InputIterator end, const char *separator, const FormatterType &formatter)
	Formats all the range as strings, and then joins them with a separator in between. More...
template<typename ContainerType , typename FormatterType >
std::string	formatAndJoin (const ContainerType &container, const char *separator, const FormatterType &formatter)
	Formats all elements of the container as strings, and then joins them with a separator in between. More...
template<typename InputIterator >
std::string	joinStrings (InputIterator begin, InputIterator end, const char *separator)
	Joins strings from a range with a separator in between. More...
template<typename ContainerType >
std::string	joinStrings (const ContainerType &container, const char *separator)
	Joins strings from a container with a separator in between. More...
template<size_t count>
std::string	joinStrings (const char *const (&array)[count], const char *separator)
	Joins strings from an array with a separator in between. More...
template<class T >
void	free_wrapper (T *p)
	Wrapper of standard library free(), to be used as unique_cptr deleter for memory allocated by malloc, e.g. by an external library such as TNG.
template<class T >
void	sfree_wrapper (T *p)
	sfree wrapper to be used as unique_cptr deleter
template<typename T , typename D >
std::unique_ptr< T, D >	create_unique_with_deleter (T *t, D d)
	Create unique_ptr with any deleter function or lambda.
void	applyGlobalSimulationState (const SimulationInput &simulationInput, PartialDeserializedTprFile *partialDeserializedTpr, t_state *globalState, t_inputrec *inputrec, gmx_mtop_t *globalTopology)
	Get the global simulation input. More...
std::unique_ptr< t_state >	globalSimulationState (const SimulationInput &)
void	applyGlobalInputRecord (const SimulationInput &, t_inputrec *)
void	applyGlobalTopology (const SimulationInput &, gmx_mtop_t *)
template<typename T >
std::remove_const_t< T >	norm (T *v)
	Forward operations on C Array style vectors to C implementations. More...
template<typename T >
std::remove_const_t< T >	norm2 (T *v)

Variables
const gmx::EnumerationArray < XvgFormat, const char * >	c_xvgFormatNames
	Names for XvgFormat. More...
static const int	c_linewidth = 80 - 2
	Linewidth used for warning output.
static const int	c_biasMaxNumDim = 4
	The maximum dimensionality of the AWH coordinate.
static const EnumerationArray < DensitySimilarityMeasureMethod, const char * >	c_densitySimilarityMeasureMethodNames
	Name the methods that may be used to evaluate similarity between densities. More...
static const EnumerationArray < DensityFittingAmplitudeMethod, const char * >	c_densityFittingAmplitudeMethodNames
	The names of the methods to determine the amplitude of the atoms to be spread on a grid. More...
static const std::string	c_qmmmCP2KModuleName = "qmmm-cp2k"
	Tag with name of the QMMM with CP2K MDModule.
static const EnumerationArray < QMMMQMMethod, const char * >	c_qmmmQMMethodNames
	The names of the supported QM methods. More...
const std::vector< std::string >	periodic_system
	symbols of the elements in periodic table More...
static const EnumerationArray < ChangeSettingType, const char * >	c_changeSettingTypeNames
	Mapping for enums from ChangeSettingType. More...
static const EnumerationArray < ChangeAtomsType, const char * >	c_changeAtomsTypeNames
	Mapping for enums from ChangeAtomsType. More...
	pmeStream
static constexpr int64_t	sc_checkpointMaxAtomCount = std::numeric_limits<unsigned int>::max() / 3
	The maximum number of atoms that can be stored in a checkpoint file.
static constexpr Architecture	c_architecture
	Constant that tells what the architecture is. More...
constexpr int	c_loopWait = 1
	How long shall we wait in seconds until we check for a connection again?
constexpr int	c_connectWait = 1
	How long shall we check for the IMD_GO?
constexpr int	c_headerSize = 8
	IMD Header Size.
constexpr int	c_protocolVersion = 2
	IMD Protocol Version.
static const char	IMDstr [] = "IMD:"
	Tag output from the IMD module with this string. More...
constexpr int	c_maxConnections = 1
	Currently only 1 client connection is supported.
static constexpr int	numFTypesOnGpu = 8
	The number on bonded function types supported on GPUs.
constexpr std::array< int, numFTypesOnGpu >	fTypesOnGpu
	List of all bonded function types supported on GPUs. More...
static const int	simd_width = 1
	Define simd_width for memory allocation used for SIMD code.
static constexpr int	c_threadsPerBlock = 256
	Number of threads in a GPU block.
static constexpr int	sc_workGroupSize = 256
	Number of work-items in a work-group.
static const EnumerationArray < IncompatibilityReasons, std::string >	reasonStrings
	Strings explaining why the system is incompatible with update groups. More...
static constexpr int	c_ftypeVsiteStart = F_VSITE1
	The start value of the vsite indices in the ftype enum. More...
static constexpr int	c_ftypeVsiteEnd = F_VSITEN + 1
	The start and end value of the vsite indices in the ftype enum.
static constexpr int64_t	sc_atomInfo_EnergyGroupIdMask = 0b11111111
	The first 8 bits are reserved for energy-group ID.
static const gmx::EnumerationArray < MtsForceGroups, std::string >	mtsForceGroupNames
	Names for the MTS force groups. More...
const std::array< RVec, 2 >	c_forces = { { { 0.5, 0.1, 1.2 }, { -2.1, 0.2, 0.3 } } }
static constexpr int	s_maxNumThreadsForReduction = 256
	The max thread number is arbitrary, we used a fixed number to avoid memory management. Using more than 16 threads is probably never useful performance wise.
	boxRel_ { { 0 } }
static constexpr EnumerationArray< NhcUsage, const char * >	nhcUsageNames = { "System", "Barostat" }
	boxVelocity_ { { 0 } }
	previousBox_ { { 0 } }
constexpr int	c_centralShiftIndex = detail::c_numIvecs / 2
constexpr int	c_numShiftVectors = detail::c_numIvecs
constexpr bool	c_gpuBuildSyclWithoutGpuFft
constexpr double	c_angstrom = 1e-10
constexpr double	c_kilo = 1e3
constexpr double	c_nano = 1e-9
constexpr double	c_pico = 1e-12
constexpr double	c_nm2A = c_nano / c_angstrom
constexpr double	c_cal2Joule = 4.184
constexpr double	c_electronCharge = 1.602176634e-19
constexpr double	c_amu = 1.66053906660e-27
constexpr double	c_boltzmann = 1.380649e-23
constexpr double	c_avogadro = 6.02214076e23
constexpr double	c_universalGasConstant = c_boltzmann * c_avogadro
constexpr double	c_boltz = c_universalGasConstant / c_kilo
constexpr double	c_faraday = c_electronCharge * c_avogadro
constexpr double	c_planck1 = 6.62607015e-34
constexpr double	c_planck = (c_planck1 * c_avogadro / (c_pico * c_kilo))
constexpr double	c_epsilon0Si = 8.8541878128e-12
constexpr double	c_epsilon0
constexpr double	c_speedOfLight
constexpr double	c_rydberg = 1.0973731568160e-02
constexpr double	c_one4PiEps0 = (1.0 / (4.0 * 3.14159265358979323846 * c_epsilon0))
constexpr double	c_barMdunits = (1e5 * c_nano * c_pico * c_pico / c_amu)
constexpr double	c_presfac = 1.0 / c_barMdunits
constexpr double	c_debye2Enm = (1e-15 / (c_speedOfLight * c_electronCharge))
constexpr double	c_enm2Debye = 1.0 / c_debye2Enm
constexpr double	c_fieldfac = c_faraday / c_kilo
constexpr double	c_hartree2Kj = ((2.0 * c_rydberg * c_planck * c_speedOfLight) / c_avogadro)
constexpr double	c_bohr2Nm = 0.0529177210903
constexpr double	c_hartreeBohr2Md = (c_hartree2Kj * c_avogadro / c_bohr2Nm)
constexpr double	c_rad2Deg = 180.0 / 3.14159265358979323846
constexpr double	c_deg2Rad = 3.14159265358979323846 / 180.0
static constexpr int64_t	sc_atomInfo_FreeEnergyPerturbation = 1 << 15
	Constants whose bit describes a property of an atom in AtomInfoWithinMoleculeBlock.atomInfo. More...
static constexpr int64_t	sc_atomInfo_HasPerturbedCharge = 1 << 16
static constexpr int64_t	sc_atomInfo_Exclusion = 1 << 17
static constexpr int64_t	sc_atomInfo_Constraint = 1 << 20
static constexpr int64_t	sc_atomInfo_Settle = 1 << 21
static constexpr int64_t	sc_atomInfo_BondCommunication = 1 << 22
static constexpr int64_t	sc_atomInfo_HasVdw = 1 << 23
static constexpr int64_t	sc_atomInfo_HasCharge = 1 << 24
constexpr int	c_dBoxZ = 1
	Maximum dimensions of grid expressing shifts across PBC.
constexpr int	c_dBoxY = 1
constexpr int	c_dBoxX = 2

Typedef Documentation

template<class T >

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

Aligned memory allocator.

Template Parameters

T	Type of objects to allocate

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

template<class ElementType >

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

Three-by-three matrix of ElementType.

Template Parameters

ElementType

type of element to be stored in matrix

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

A 3x3 matrix data type useful for simulation boxes.

Todo:

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

typedef ThreeFry2x64Fast gmx::DefaultRandomEngine

Default fast and accurate random engine in Gromacs.

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

template<class T >

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

Memory allocator that uses HostAllocationPolicy.

Template Parameters

T	Type of objects to allocate

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

using gmx::index = typedef std::ptrdiff_t

Integer type for indexing into arrays or vectors.

Same as ptrdiff_t.

using gmx::Matrix3x3 = typedef BasicMatrix3x3<real>

Three-by-three real number matrix.

Note

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

template<class T >

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

PageAligned memory allocator.

Template Parameters

T	Type of objects to allocate

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

typedef std::random_device gmx::RandomDevice

Random device.

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

Enumeration Type Documentation

enum gmx::AppendingBehavior

strong

Enumeration for mdrun appending behavior.

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

enum gmx::Architecture

strong

Enum for GROMACS CPU hardware detection support.

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

enum gmx::AtomLocality : int

strong

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

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

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

enum gmx::AwhOutputEntryType

strong

Enum with the AWH variables to write.

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

enum gmx::AwhOutputMetaData

strong

Enum with the types of metadata to write.

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

enum gmx::CheckpointSignal

strong

Checkpoint signals.

Signals set and read by CheckpointHandler. Possible signals include

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

enum gmx::CoordinateFileFlags : unsigned long

strong

The enums here define the flags specifying the requirements of different outputadapter modules.

When building the object for deciding on the output to a new coordinate file, the CoordinateFile object needs to be able to validate that the dependencies of attached IOutputAdapters are fulfilled. Classes and interfaces that use the enum can check their dependencies against the information encoded in the flags and can then perform an appropriate reaction if there is a mismatch.

Todo:

Use std::bitset<16> for the entries.

Enumerator
Base	Base setting that says that the module has no requirements. Sets the flags to default setting to make sure all output methods are supported.
RequireForceOutput	Requires output method to support force output. If set, only output methods supporting writing of forces will work, others will generate an invalid input error.
RequireVelocityOutput	Requires output method to support velocity output. If set, only writing to files that support velocity output will succeed. Other writing methods will generate an error.
RequireAtomConnections	Requires support for connection information in output format. If set, only file output that supports writing of connection information will succeed. This means for now that only PDB and TNG files can be written. Other file writing methods will fail.
RequireAtomInformation	Requires that output format supports the writing of atom information to the file. If set, files will only be written if they can output the information from t_atoms and otherwise create an error while writing.
RequireChangedOutputPrecision	Requires that output format supports writing user-specified output precision. If set, output will only be written if the format supports the writing of custom precision of the included data.
RequireNewFrameStartTime	Requires that output format supports writing time to the file.
RequireNewFrameTimeStep	Requires that output format supports writing time to the file.
RequireNewBox	Requires that output format supports writing box information.
RequireCoordinateSelection	Requires output to support changes to selection of coordinates. Default for most methods, will need to be able to write coordinates to output file or generate an error.
Count	Needed for enumeration array.

enum gmx::DDBondedChecking : bool

strong

Options for checking bonded interactions.

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

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

enum gmx::DdRankOrder

strong

The options for the domain decomposition MPI task ordering.

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

enum gmx::DensityFittingAmplitudeMethod : int

strong

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

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

enum gmx::DensitySimilarityMeasureMethod : int

strong

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

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

enum gmx::DeviceStreamType : int

strong

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

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

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

enum gmx::DiagonalMaskType

strong

List of type of Nbnxm kernel coulomb type implementations.

Enumerator
JSizeEqualsISize	j-cluster size = i-cluster size
JSizeIsDoubleISize	j-cluster size = 2 * i-cluster size
JSizeIsHalfISize	j-cluster size = i-cluster size / 2

enum gmx::DlbOption

strong

The options for the dynamic load balancing.

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

enum gmx::EmulateGpuNonbonded : bool

strong

Help pass GPU-emulation parameters with type safety.

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

enum gmx::EndianSwapBehavior : int

strong

Specify endian swapping behavoir.

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

enum gmx::EnergySignallerVirialMode

strong

When we calculate virial.

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

enum gmx::FftBackend

strong

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

enum gmx::FlexibleConstraintTreatment

strong

Tells make_at2con how to treat flexible constraints.

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

enum gmx::FrameConverterFlags : unsigned long

strong

The enums here define the guarantees provided by frameconverters concerning the modifications they provide.

A method can specify different kind of guarantees for the operation, and aggregate methods can combine those flags to provide an overview about what has happened to a coordinate frame during processing.

Enumerator
NoGuarantee	Base setting means no guarantee is done by a module.
MoleculesAreWhole	Tells us that molecules have been made whole.
NoPBCJumps	Tells us that no jumps over periodic boundary are present. Implies molecules are made whole.
MoleculeCOMInBox	Tells us that COM of all molecules is in the box.
ResidueCOMInBox	Tells us that COM of residues is in the box.
AtomsInBox	Tells us that all atoms are in the box.
UnitCellIsRectangular	Tells us a converter changed the unit cell to rectangular.
UnitCellIsTriclinic	Tells us a converter changed the unit cell to triclinic.
UnitCellIsCompact	Tells us a converter changed the unit cell to compact.
SystemIsCenteredInBox	Tells us that converter centered system in a box. Invalidated by calling a method that changes the type of box.
FitToReferenceRotTrans	Tells us that converter has fit coordinate data to reference. Specific for rotational and translational fit.
FitToReferenceRotTransXY	Tells us that converter fit coordinate data to reference. Specific for rotation and translation in XY plane.
FitToReferenceTranslation	Tells us that converter fit coordinate data to reference. Specific for translational fit.
FitToReferenceTranslationXY	Tells us that converter fit coordinate data to reference. Specific for translational fit in XY plane.
FitToReferenceProgressive	Tells us that converter fit coordinate data to reference. Specific for progressive fit.
NewSystemCenter	Tells us that converter has set a new center for the system. This affects the routines that place atoms in the box and the unit cell changing routines, so they have to be invalidated by any method setting this flag.
Count	Final entry to get number of operations.

enum gmx::GpuAwareMpiStatus : int

strong

Enum describing GPU-aware support in underlying MPI library.

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

enum gmx::GpuTask : int

strong

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

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

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

enum gmx::GraphState : int

strong

State of graph.

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

enum gmx::ILJInteractions

strong

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

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

enum gmx::IMDMessageType : int

strong

Enum for types of IMD messages.

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

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

enum gmx::InteractionLocality : int

strong

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

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

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

enum gmx::KernelCoulombType

strong

List of type of Nbnxm kernel coulomb type implementations.

Enumerator
RF	Reaction-field, also used for plain cut-off.
EwaldAnalytical	Ewald with analytical reciprocal contribution correction.
EwaldTabulated	Ewald with tabulated reciprocal contribution correction.

enum gmx::MrcDataMode : int32_t

strong

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

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

enum gmx::MtsForceGroups : int

strong

Force group available for selection for multiple time step integration.

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

enum gmx::NhcUsage

strong

The usages of Nose-Hoover chains.

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

enum gmx::Normalization

strong

Enum with different ways of normalizing the output.

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

enum gmx::NumTempScaleValues

strong

Sets the number of different temperature coupling values.

This is needed to template the kernel

Todo:

Unify with similar enum in CPU update module

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

enum gmx::ObservablesReducerStatus : int

strong

Report whether the reduction has happened this step.

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

enum gmx::PbcMode

strong

PBC modes for vsite construction and spreading.

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

enum gmx::PinningPolicy : int

strong

Helper enum for pinning policy of the allocation of HostAllocationPolicy.

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

enum gmx::QMMMQMMethod

strong

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

Enumerator
PBE	DFT with PBE functional.
BLYP	DFT with BLYP functional.
INPUT	User provides suitable input file for QM package.

enum gmx::RandomDomain

strong

Enumerated values for fixed part of random seed (domain)

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

Note

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

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

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

enum gmx::ReductionRequirement : int

strong

Control whether reduction is required soon.

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

enum gmx::ResetSignal

strong

Reset signals.

Signals set and read by ResetHandler. Possible signals include

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

enum gmx::ScheduleOnInitStep

strong

Whether the element does schedule on the initial step.

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

enum gmx::SpaceGroup : int32_t

strong

Space group in three dimensions.

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

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

Enumerator
P1	no symmetry

enum gmx::StartingBehavior : int

strong

Enumeration for describing how mdrun is (re)starting.

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

enum gmx::StopSignal : int

strong

Stop signals.

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

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

enum gmx::StripStrings : int

strong

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

Enumerator
No	Do not strip strings.
Yes	Strip strings.

enum gmx::VirtualSiteVirialHandling : int

strong

Tells how to handle virial contributions due to virtual sites.

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

enum gmx::VSiteOperation

strong

Whether we calculate vsite positions, velocities, or both.

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

Function Documentation

static float gmx::abs ( float  a )

inlinestatic

Float Floating-point abs().

Parameters

a	any floating point values

Returns

abs(a) for each element.

Note

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

static double gmx::abs ( double  a )

inlinestatic

double doubleing-point abs().

Parameters

a	any doubleing point values

Returns

abs(a) for each element.

Note

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

static float gmx::acos ( float  x )

inlinestatic

Float acos.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

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

static double gmx::acos ( double  x )

inlinestatic

Double acos.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

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

static double gmx::acosSingleAccuracy ( double  x )

inlinestatic

Double acos, but with single accuracy.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

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

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

static

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

Parameters

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

Returns

New container for IoutputAdapter derived methods.

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

inline

Add constraint to splitMap with all constraints coupled to it.

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

Parameters

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

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

static

Modify atoms information in coordinate frame to fit output selection.

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

Parameters

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

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

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

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

Parameters

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

Returns

true if the grid point was updated.

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

inlinestatic

Bitwise andnot for two scalar float variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

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

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

inlinestatic

Bitwise andnot for two scalar double variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

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

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

inlinestatic

Bitwise andnot for two scalar integer variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

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

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

static

Checks whether any dimension uses the given coordinate provider type.

Parameters

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

Returns

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

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

static

Checks whether any dimension uses the given coordinate provider type.

Parameters

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

Returns

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

static bool gmx::anyTrue ( bool  a )

inlinestatic

Returns if the boolean is true.

Parameters

a	Logical variable.

Returns

true if a is true, otherwise false.

Note

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

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

Get the global simulation input.

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

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

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

Todo:

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

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

Initialize local stateful simulation data.

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

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

Warning

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

Todo:

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

Todo:

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

Warning

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

See Also

globalSimulationState()

applyGlobalInputRecord()

applyGlobalTopology()

static float gmx::asin ( float  x )

inlinestatic

float asin.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

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

static double gmx::asin ( double  x )

inlinestatic

Double asin.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

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

static double gmx::asinSingleAccuracy ( double  x )

inlinestatic

Double asin, but with single accuracy.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

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

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

inlinestatic

Assert that the matrix m describes a simulation box.

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

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

inlinestatic

Assert that the matrix m describes a simulation box.

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

static void gmx::assignVsitesToThread ( VsiteThread *  tData, int  thread, int  nthread, int  natperthread, gmx::ArrayRef< int >  taskIndex, ArrayRef< const InteractionList >  ilist, ArrayRef< const t_iparams >  ip, ArrayRef< const ParticleType >  ptype  )

static

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

Our task local atom range is tData->rangeStart - tData->rangeEnd. Vsites that depend only on local atoms, as indicated by taskIndex[]==thread, are assigned to task tData->ilist. Vsites