Description

Generic GROMACS namespace.

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

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

Namespaces
	compat
	Compatibility aliases for standard library features.

	test
	Testing utilities namespace.

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

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

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

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

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

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

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

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

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

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

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

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

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

class	AnalysisDataStorageFrame
	Allows assigning values for a data frame in AnalysisDataStorage. More...

class	AnalysisDataStorage
	Helper class that implements storage of data. More...

class	ArrayRef
	STL-like interface to a C array of T (or part of a std container of T). More...

class	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...

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

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

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

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

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

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

class	CommandLineModuleSettings
	Settings to pass information between a module and the general runner. More...

class	ICommandLineModule
	Module that can be run from command line using CommandLineModuleManager. More...

class	CommandLineModuleManager
	Implements a wrapper command-line interface for multiple modules. More...

class	CommandLineModuleGroup
	Handle to add content to a group added with CommandLineModuleManager::addModuleGroup(). More...

class	ICommandLineOptionsModuleSettings
	Settings to pass information between a CommandLineOptionsModule and generic code that runs it. More...

class	ICommandLineOptionsModule
	Module that can be run from a command line and uses gmx::Options for argument processing. More...

class	CommandLineParser
	Implements command-line parsing for Options objects. More...

class	IExecutableEnvironment
	Allows customization of the way various directories are found by CommandLineProgramContext. More...

class	CommandLineProgramContext
	Program context implementation for command line programs. More...

class	TrajectoryFileOpener
	Low level method to take care of only file opening and closing. More...

class	TrajectoryFrameWriter
	Writes coordinate frames to a sink, e.g. a trajectory file. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

class	GpuHaloExchange
	Manages GPU Halo Exchange object. More...

class	LocalAtomSet
	A local atom set collects local, global and collective indices of the home atoms on a rank. The indices of the home atoms are automatically updated during domain decomposition, thus gmx::LocalAtomSet::localIndex enables iteration over local atoms properties like coordinates or forces. TODO: add a LocalAtomSet iterator. More...

class	LocalAtomSetManager
	Hands out handles to local atom set indices and triggers index recalculation for all sets upon domain decomposition if run in parallel. More...

struct	DomdecOptions
	Structure containing all (command line) options for the domain decomposition. More...

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

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

struct	MdModulesCheckpointReadingDataOnMaster
	Provides the MdModules with the checkpointed data on the master rank. More...

struct	MdModulesCheckpointReadingBroadcast
	Provides the MdModules with the communication record to broadcast. More...

struct	MdModulesWriteCheckpointData
	Writing the MdModules data to a checkpoint file. More...

class	MrcDensityMapOfFloatReader
	Read an mrc/ccp4 file that contains float values. More...

class	MrcDensityMapOfFloatFromFileReader
	Read an mrc density map from a given file. More...

class	MrcDensityMapOfFloatWriter
	Write an mrc/ccp4 file that contains float values. More...

struct	MrcDataStatistics
	Statistics about mrc data arrays. More...

struct	MrcDensitySkewData
	Skew matrix and translation. As named in "EMDB Map Distribution Format Description Version 1.01 (c) emdatabank.org 2014". More...

struct	CrystallographicLabels
	Crystallographic labels for mrc data. More...

struct	MrcDensityMapHeader
	A container for the data in mrc density map file formats. More...

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

class	ClfftInitializer
	Handle clFFT library init and tear down in RAII style also with mutual exclusion. More...

class	DeviceStreamManager
	Device stream and context manager. More...

class	HostAllocationPolicy
	Policy class for configuring gmx::Allocator, to manage allocations of memory that may be needed for e.g. GPU transfers. More...

struct	OpenClTraits
	Stub for OpenCL type traits. More...

struct	OpenClTraitsBase
	Implements common trait infrastructure for OpenCL types. More...

struct	OpenClTraits< cl_context >
	Implements traits for cl_context. More...

struct	OpenClTraits< cl_command_queue >
	Implements traits for cl_command_queue. More...

struct	OpenClTraits< cl_program >
	Implements traits for cl_program. More...

struct	OpenClTraits< cl_kernel >
	Implements traits for cl_kernel. More...

class	ClHandle
	Wrapper of OpenCL type `cl_type` to implement RAII. More...

class	CpuInfo
	Detect CPU capabilities and basic logical processor info. More...

class	HardwareTopology
	Information about sockets, cores, threads, numa, caches. More...

struct	EnumerationArray
	Wrapper for a C-style array with size and indexing defined by an enum. Useful for declaring arrays of enum names for debug or other printing. An ArrayRef<DataType> may be constructed from an object of this type. More...

class	ArrayRefWithPadding
	Interface to a C array of T (or part of a std container of T), that includes padding that is suitable for the kinds of SIMD operations GROMACS uses. More...

class	TranslateAndScale
	Transform coordinates in three dimensions by first translating, then scaling them. More...

class	AffineTransformation
	Affine transformation of three-dimensional coordinates. More...

class	DensitySimilarityMeasure
	Measure similarity and gradient between densities. More...

class	DensityFittingForce
	Manages evaluation of density-fitting forces for particles that were spread with a kernel. More...

struct	ExponentialMovingAverageState
	Store the state of exponential moving averages. More...

class	ExponentialMovingAverage
	Evaluate the exponential moving average with bias correction. More...

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

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

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

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

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

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

class	PaddedVector
	PaddedVector is a container of elements in contiguous storage that allocates extra memory for safe SIMD-style loads for operations used in GROMACS. More...

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

class	CheckpointHandler
	Class handling the checkpoint signal. More...

class	Constraints
	Handles constraints. More...

class	MDAtoms
	Contains a C-style t_mdatoms while managing some of its memory with C++ vectors with allocators. More...

class	ResetHandler
	Class handling the reset of counters. More...

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

struct	shakedata
	Working data for the SHAKE algorithm. More...

class	SimulationSignal
	POD-style object used by mdrun ranks to set and receive signals within and between simulations. More...

class	SimulationSignaller
	Object used by mdrun ranks to signal to each other at this step. More...

class	StopHandler
	Class handling the stop signal. More...

class	StopConditionSignal
	Class setting the stop signal based on gmx_get_stop_condition() More...

class	StopConditionTime
	Class setting the stop signal based on maximal run time. More...

class	StopHandlerBuilder
	Class preparing the creation of a StopHandler. More...

class	Update
	Contains data for update phase. More...

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

class	VirtualSitesHandler
	Class that handles construction of vsites and spreading of vsite forces. More...

class	WholeMoleculeTransform
	This class manages a coordinate buffer with molecules not split over periodic boundary conditions for use in force calculations which require whole molecules. More...

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

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

class	MembedHolder
	Membed SimulatorBuilder parameter type. More...

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

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

class	SimulationContext
	Simulation environment and configuration. More...

struct	SimulatorConfig
	Simulation configuation settings. More...

struct	SimulatorStateData
	Data for a specific simulation state. More...

class	SimulatorEnv
	Collection of environmental information for a simulation. More...

class	Profiling
	Collection of profiling information. More...

class	ConstraintsParam
	Collection of constraint parameters. More...

class	LegacyInput
	Collection of legacy input information. More...

class	InteractiveMD
	SimulatorBuilder parameter type for InteractiveMD. More...

class	IonSwapping
	Parameter type for IonSwapping SimulatorBuilder component. More...

class	TopologyData
	Collection of handles to topology information. More...

class	BoxDeformationHandle
	Handle to information about the box. More...

class	SimulatorBuilder
	Class preparing the creation of Simulator objects. More...

class	accessor_basic
	The most basic memory access model for mdspan. More...

class	extents
	Multidimensional extents with static and dynamic dimensions. More...

class	layout_right
	Right-aligned array layout indexer. Carries the mapping class performing the translation from multidimensional index to one-dimensional number. More...

class	basic_mdspan
	Multidimensional array indexing and memory access with flexible mapping and access model. More...

struct	IsSerializableEnum
	{ More...

class	CheckpointData
	} More...

class	ReadCheckpointDataHolder
	Holder for read checkpoint data. More...

class	WriteCheckpointDataHolder
	Holder for write checkpoint data. More...

class	ForceBuffersView
	A view of the force buffer. More...

class	ForceBuffers
	Object that holds the force buffers. More...

class	ForceWithShiftForces
	Container for force and virial for algorithms that compute shift forces for virial calculation. More...

class	ForceWithVirial
	Container for force and virial for algorithms that provide their own virial tensor contribution. More...

class	ForceOutputs
	Force and virial output buffers for use in force computation. More...

class	ForceProviderInput
	Helper struct that bundles data for passing it over to the force providers. More...

class	ForceProviderOutput
	Helper struct bundling the output data of a force provider. More...

class	IForceProvider
	Interface for a component that provides forces during MD. More...

class	ForceProviders
	Evaluates forces from a collection of gmx::IForceProvider. More...

class	IMDModule
	Extension module for GROMACS simulations. More...

class	IMDOutputProvider
	Interface for handling additional output files during a simulation. More...

class	IMdpOptionProvider
	Interface for handling mdp/tpr input to a mdrun module. More...

struct	MtsLevel
	Setting for a single level for multiple time step integration. More...

class	StepWorkload
	Describes work done on this domain that may change per-step. More...

class	DomainLifetimeWorkload
	Describes work done on this domain on every step of its lifetime, but which might change after the next domain paritioning. More...

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

class	ModularSimulator
	The modular simulator. More...

class	ElementNotFoundError
	Exception class signalling that a requested element was not found. More...

class	MissingElementConnectionError
	Exception class signalling that elements were not connected properly. More...

class	SimulationAlgorithmSetupError
	Exception class signalling that the ModularSimulatorAlgorithm was set up in an incompatible way. More...

class	CheckpointError
	Exception class signalling an error in reading or writing modular checkpoints. More...

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

class	Range
	Defines a range of integer numbers and accompanying operations. More...

class	TextTableFormatter
	Formats rows of a table for text output. More...

class	HelpManager
	Helper for providing interactive online help. More...

class	AbstractSimpleHelpTopic
	Abstract base class for help topics that have simple text and no subtopics. More...

class	AbstractCompositeHelpTopic
	Abstract base class for help topics that have simple text and subtopics. More...

class	SimpleHelpTopic
	Template for simple implementation of AbstractSimpleHelpTopic. More...

class	CompositeHelpTopic
	Template for simple implementation of AbstractCompositeHelpTopic. More...

class	HelpLinks
	Hyperlink data for writing out help. More...

class	HelpWriterContext
	Context information for writing out help. More...

class	IHelpTopic
	Provides a single online help topic. More...

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

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

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

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

class	AbstractOptionStorage
	Abstract base class for converting, validating, and storing option values. More...

class	AbstractOptionSection
	Base class for specifying option section properties. More...

class	AbstractOptionSectionHandle
	Base class for handles to option sections. More...

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

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

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

class	DoubleOption
	Specifies an option that provides floating-point (double) values. More...

class	FloatOption
	Specifies an option that provides floating-point (float) values. More...

class	StringOption
	Specifies an option that provides string values. More...

class	EnumOption
	Specifies an option that accepts an EnumerationArray of string values and writes the selected index into an `enum` variable. More...

class	LegacyEnumOption
	Specifies an option that accepts enumerated string values and writes the selected index into an `enum` variable. More...

class	BooleanOptionInfo
	Wrapper class for accessing boolean option information. More...

class	IntegerOptionInfo
	Wrapper class for accessing integer option information. More...

class	Int64OptionInfo
	Wrapper class for accessing 64-bit integer option information. More...

class	DoubleOptionInfo
	Wrapper class for accessing floating-point option information. More...

class	FloatOptionInfo
	Wrapper class for accessing floating-point option information. More...

class	StringOptionInfo
	Wrapper class for accessing string option information. More...

class	EnumOptionInfo
	Wrapper class for accessing enum option information. More...

class	OptionsBehaviorCollection
	Container for IOptionsBehavior objects. More...

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

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

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

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

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

class	Options
	Collection of options. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

class	ExponentialDistribution
	Exponential distribution. More...

class	GammaDistribution
	Gamma distribution. More...

class	NormalDistribution
	Normal distribution. More...

class	TabulatedNormalDistribution
	Tabulated normal random distribution. More...

class	ThreeFry2x64General
	General implementation class for ThreeFry counter-based random engines. More...

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

class	ThreeFry2x64Fast
	ThreeFry2x64 random engine with 13 iteractions. More...

class	UniformIntDistribution
	Uniform integer distribution. More...

class	UniformRealDistribution
	Uniform real distribution. More...

class	RestraintManager
	Manage the Restraint potentials available for Molecular Dynamics. More...

class	RestraintMDModule
	MDModule wrapper for Restraint implementations. More...

class	Site
	Abstraction for a restraint interaction site. More...

class	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	SelectionFileOption
	Specifies a special option that provides selections from a file. More...

class	SelectionFileOptionInfo
	Wrapper class for accessing and modifying selection file option information. More...

class	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	Simd4Double
	SIMD4 double type. More...

class	Simd4DBool
	SIMD4 variable type to use for logical comparisons on doubles. More...

class	Simd4Float
	SIMD4 float type. More...

class	Simd4FBool
	SIMD4 variable type to use for logical comparisons on floats. More...

class	SimdDouble
	Double SIMD variable. Available if GMX_SIMD_HAVE_DOUBLE is 1. More...

class	SimdDInt32
	Integer SIMD variable type to use for conversions to/from double. More...

class	SimdDBool
	Boolean type for double SIMD data. More...

class	SimdDIBool
	Boolean type for integer datatypes corresponding to double SIMD. More...

class	SimdFloat
	Float SIMD variable. Available if GMX_SIMD_HAVE_FLOAT is 1. More...

class	SimdFInt32
	Integer SIMD variable type to use for conversions to/from float. More...

class	SimdFBool
	Boolean type for float SIMD data. More...

class	SimdFIBool
	Boolean type for integer datatypes corresponding to float SIMD. More...

struct	SimdFloatTag
	Tag type to select to load SimdFloat with simdLoad(U) More...

struct	SimdDoubleTag
	Tag type to select to load SimdDouble with simdLoad(U) More...

struct	SimdFInt32Tag
	Tag type to select to load SimdFInt32 with simdLoad(U) More...

struct	SimdDInt32Tag
	Tag type to select to load SimdDInt32 with simdLoad(U) More...

struct	AlignedArray< float, N >
	Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual). More...

struct	AlignedArray< double, N >
	Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment. Should not be deleted through base pointer (destructor is non-virtual). More...

class	SimdSetZeroProxy
	Proxy object to enable setZero() for SIMD and real types. More...

class	CubicSplineTable
	Cubic spline interpolation table. More...

class	QuadraticSplineTable
	Quadratic spline interpolation table. More...

struct	AnalyticalSplineTableInput
	Specification for analytical table function (name, function, derivative) More...

struct	NumericalSplineTableInput
	Specification for vector table function (name, function, derivative, spacing) More...

struct	DevelopmentFeatureFlags
	Structure that holds boolean flags corresponding to the development features present enabled through environment variables. More...

struct	GpuTaskMapping
	Specifies the GPU deviceID_ available for task_ to use. More...

class	GpuTaskAssignmentsBuilder
	Builder for the GpuTaskAssignments for all ranks on this node. More...

class	GpuTaskAssignments
	Contains the GPU task assignment for all ranks on this physical node. More...

class	ConvertTprInfo
	Declares gmx convert-tpr. More...

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

struct	ExclusionBlock
	Describes exclusions for a single atom. 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	UnionFinder
	Union-find data structure for keeping track of disjoint sets. More...

class	MappedUnionFinder
	Extension of UnionFind that supports non-consecutive integer indices as items. More...

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

class	AlignedAllocationPolicy
	Policy class for configuring gmx::Allocator, to manage allocations of aligned memory for SIMD code. More...

class	PageAlignedAllocationPolicy
	Policy class for configuring gmx::Allocator, to manage allocations of page-aligned memory that can be locked for asynchronous transfer to GPU devices. More...

class	Allocator
	Policy-based memory allocator. More...

class	Any
	Represents a dynamically typed value of an arbitrary type. More...

class	BinaryInformationSettings
	Settings for printBinaryInformation(). More...

class	PrivateImplPointer
	Helper class to manage a pointer to a private implementation class. More...

class	DataFileOptions
	Search parameters for DataFileFinder. More...

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

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

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

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

class	EnumerationIterator
	Allows iterating sequential enumerators. More...

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

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

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

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

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

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

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

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

class	ISerializer
	Interface for types that convert standard data types into a form suitable for storage or transfer. More...

class	KeyValueTreePath
	Identifies an entry in a key-value tree. More...

class	KeyValueTreeBuilder
	Root builder for creating trees that have an object at the root. More...

class	KeyValueTreeValueBuilder
	Builder for KeyValueTreeValue objects. More...

class	KeyValueTreeUniformArrayBuilder
	Builder for KeyValueTreeArray objects where all elements are of type `T`. More...

class	KeyValueTreeObjectArrayBuilder
	Builder for KeyValueTreeArray objects where all elements are KeyValueTreeObject objects. More...

class	KeyValueTreeObjectBuilder
	Builder for KeyValueTreeObject objects. More...

class	IKeyValueTreeTransformRules
	Interface to declare rules for transforming key-value trees. More...

class	KeyValueTreeTransformRulesScoped
	Helper object returned from IKeyValueTreeTransformRules::scopedTransform(). More...

class	KeyValueTreeTransformRuleBuilder
	Provides methods to specify one transformation rule. More...

class	ILogTarget
	Target where log output can be written. More...

class	LogEntryWriter
	Helper class for creating log entries with GMX_LOG. More...

class	LogLevelHelper
	Represents a single logging level. More...

class	MDLogger
	Declares a logging interface. More...

class	LoggerBuilder
	Initializes loggers. More...

class	LoggerOwner
	Manages memory for a logger built with LoggerBuilder. More...

class	MdModuleNotification
	Subscribe and trigger notification functions. More...

struct	registerMdModuleNotification< CurrentCallParameter, CallParameter...>
	Template specialization to assemble MdModuleNotification. More...

struct	MdModulesEnergyOutputToDensityFittingRequestChecker
	Check if module outputs energy to a specific field. More...

class	EnergyCalculationFrequencyErrors
	Collect errors for the energy calculation frequency. More...

struct	SimulationTimeStep
	Provides the simulation time step in ps. More...

struct	MdModulesNotifier
	Collection of callbacks to MDModules at differnt run-times. More...

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

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

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

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

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

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

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

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

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

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

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

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

class	TextInputStream
	Interface for reading text. More...

class	TextOutputStream
	Interface for writing text. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

typedef enum gmx::IMDType_t	IMDMessageType
	Enum for types of IMD messages. More...

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 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 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.

typedef std::function< void()>	CheckBondedInteractionsCallback
	The function type allowing to request a check of the number of bonded interactions.

using	Step = int64_t
	Step number.

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)>	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.

using	TemperatureCouplingType = int
	Typedef to match current use of ints as types.

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

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

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

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

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

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

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

typedef ThreeFry2x64Fast	DefaultRandomEngine
	Default fast and accurate random engine in Gromacs. More...

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

typedef std::list < SelectionParserValue >	SelectionParserValueList
	Container for a list of SelectionParserValue objects.

typedef std::unique_ptr < SelectionParserValueList >	SelectionParserValueListPointer
	Smart pointer type for managing a SelectionParserValueList.

typedef std::list < SelectionParserParameter >	SelectionParserParameterList
	Container for a list of SelectionParserParameter objects.

typedef std::unique_ptr < SelectionParserParameterList >	SelectionParserParameterListPointer
	Smart pointer type for managing a SelectionParserParameterList.

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

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

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

typedef 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.

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

typedef std::unique_ptr < TrajectoryAnalysisModuleData >	TrajectoryAnalysisModuleDataPointer
	Smart pointer to manage a TrajectoryAnalysisModuleData object.

typedef std::unique_ptr < TrajectoryAnalysisModule >	TrajectoryAnalysisModulePointer
	Smart pointer to manage a TrajectoryAnalysisModule.

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

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

using	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.

typedef tMPI::mutex	Mutex
	C++11-compatible basic mutex.

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

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

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

template<typename T , void D = sfree_wrapper>
using	unique_cptr = std::unique_ptr< T, functor_wrapper< T, D >>
	unique_ptr which takes function pointer (has to return void) as template argument

typedef unique_cptr< void >	sfree_guard
	Simple guard which calls sfree. See unique_cptr for details.


using	ClContext = ClHandle< cl_context >
	Convenience declarations.

using	ClCommandQueue = ClHandle< cl_command_queue >

using	ClProgram = ClHandle< cl_program >

using	ClKernel = ClHandle< cl_kernel >

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

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

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

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

enum	CoordinateFileFlags : unsigned long { CoordinateFileFlags::Base = 1 << 0, CoordinateFileFlags::RequireForceOutput = 1 << 1, CoordinateFileFlags::RequireVelocityOutput = 1 << 2, CoordinateFileFlags::RequireAtomConnections = 1 << 3, CoordinateFileFlags::RequireAtomInformation = 1 << 4, CoordinateFileFlags::RequireChangedOutputPrecision = 1 << 5, CoordinateFileFlags::RequireNewFrameStartTime = 1 << 6, CoordinateFileFlags::RequireNewFrameTimeStep = 1 << 7, CoordinateFileFlags::RequireNewBox = 1 << 8, CoordinateFileFlags::RequireCoordinateSelection = 1 << 9, CoordinateFileFlags::Count }
	The enums here define the flags specifying the requirements of different outputadapter modules. More...

enum	ChangeSettingType : int { PreservedIfPresent, Always, Never, Count }
	Enum class for setting basic flags in a t_trxframe.

enum	ChangeAtomsType { PreservedIfPresent, AlwaysFromStructure, Never, Always, Count }
	Enum class for t_atoms settings.

enum	ChangeFrameInfoType { PreservedIfPresent, Always, Count }
	Enum class for setting fields new or not.

enum	ChangeFrameTimeType { PreservedIfPresent, StartTime, TimeStep, Both, Count }
	Enum class for setting frame time from user input.

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

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

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

enum	DeviceStreamType : int { DeviceStreamType::NonBondedLocal, DeviceStreamType::NonBondedNonLocal, DeviceStreamType::Pme, DeviceStreamType::PmePpTransfer, DeviceStreamType::UpdateAndConstraints, DeviceStreamType::Count }
	Class enum to describe the different logical streams used for GPU work. More...

enum	PinningPolicy : int { CannotBePinned, PinnedIfSupported }
	Helper enum for pinning policy of the allocation of HostAllocationPolicy. More...

enum	Architecture { Unknown, Architecture::X86, Architecture::Arm, Architecture::PowerPC }
	Enum for GROMACS CPU hardware detection support. More...

enum	IMDType_t { IMD_DISCONNECT, IMD_ENERGIES, IMD_FCOORDS, IMD_GO, IMD_HANDSHAKE, IMD_KILL, IMD_MDCOMM, IMD_PAUSE, IMD_TRATE, IMD_IOERROR, IMD_NR }
	Enum for types of IMD messages. More...

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

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

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

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

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

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

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

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

enum	PbcMode { PbcMode::all, PbcMode::none }
	PBC modes for vsite construction and spreading. 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	{ eawhtargetCONSTANT, eawhtargetCUTOFF, eawhtargetBOLTZMANN, eawhtargetLOCALBOLTZMANN, eawhtargetNR }
	Target distribution enum.

enum	{ eawhgrowthEXP_LINEAR, eawhgrowthLINEAR, eawhgrowthNR }
	Weight histogram growth enum.

enum	{ eawhpotentialCONVOLVED, eawhpotentialUMBRELLA, eawhpotentialNR }
	AWH potential type enum.

enum	{ eawhcoordproviderPULL, eawhcoordproviderFREE_ENERGY_LAMBDA, eawhcoordproviderNR }
	AWH bias reaction coordinate provider.

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

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

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

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

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

enum	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	RegisterWithThermostat { True, False }
	Whether built propagator should be registered with thermostat.

enum	RegisterWithBarostat { True, False }
	Whether built propagator should be registered with barostat.

enum	IntegrationStep { PositionsOnly, VelocitiesOnly, LeapFrog, VelocityVerletPositionsAndVelocities, Count }
	The different integration types we know about. More...

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

enum	ParrinelloRahmanVelocityScaling { ParrinelloRahmanVelocityScaling::No, ParrinelloRahmanVelocityScaling::Diagonal, ParrinelloRahmanVelocityScaling::Full, Count }
	Sets the type of Parrinello-Rahman pressure scaling. More...

enum	UseFullStepKE { Yes, No, Count }
	Enum describing whether the thermostat is using full or half step kinetic energy.

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

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

enum	OptionFileType { eftUnknown, eftTopology, eftRunInput, eftTrajectory, eftEnergy, eftPDB, eftIndex, eftPlot, eftGenericData, eftCsv, eftOptionFileType_NR }
	Purpose of file(s) provided through an option.

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

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

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

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

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

enum	SimdType { SimdType::None, SimdType::Reference, SimdType::Generic, SimdType::X86_Sse2, SimdType::X86_Sse4_1, SimdType::X86_Avx128Fma, SimdType::X86_Avx, SimdType::X86_Avx2, SimdType::X86_Avx2_128, SimdType::X86_Avx512, SimdType::X86_Avx512Knl, SimdType::X86_Mic, SimdType::Arm_Neon, SimdType::Arm_NeonAsimd, SimdType::Arm_Sve, SimdType::Ibm_Vmx, SimdType::Ibm_Vsx, SimdType::Fujitsu_HpcAce }
	Enumerated options for SIMD architectures. More...

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

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

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

enum	ErrorCode { eeOK, eeOutOfMemory, eeFileNotFound, eeFileIO, eeInvalidInput, eeInconsistentInput, eeTolerance, eeInstability, eeNotImplemented, eeInvalidValue, eeInvalidCall, eeInternalError, eeAPIError, eeRange, eeParallelConsistency, eeModularSimulator, eeUnknownError }
	Possible error return codes from Gromacs functions. More...

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

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

Functions
AnalysisHistogramSettingsInitializer	histogramFromRange (real min, real max)
	Initializes a histogram using a range and a bin width. More...

AnalysisHistogramSettingsInitializer	histogramFromBins (real start, int nbins, real binwidth)
	Initializes a histogram using bin width and the number of bins. More...

static bool	anyDimUsesPull (const AwhBiasParams &awhBiasParams)
	Checks whether any dimension uses pulling as a coordinate provider. More...

static bool	anyDimUsesPull (const AwhParams &awhParams)
	Checks whether any dimension uses pulling as a coordinate provider. More...

static bool	anyDimUsesPull (const ArrayRef< BiasCoupledToSystem > biasCoupledToSystem)
	Checks whether any dimension uses pulling as a coordinate provider. 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 (const std::vector< 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, const std::vector< GridAxis > &axis)
	Query if a value is in range of the grid. More...

static int	getNearestIndexInGrid (const awh_dvec value, const std::vector< GridAxis > &axis)
	Map a value to the nearest point in the grid. More...

void	mapGridToDataGrid (std::vector< int > gridpointToDatapoint, const double const *data, int numDataPoints, const std::string &dataFilename, const BiasGrid &grid, const std::string &correctFormatMessage)
	Maps each point in the grid to a point in the data grid. More...

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

void	biasesAreCompatibleForSharingBetweenSimulations (const AwhParams &awhParams, const std::vector< size_t > &pointSize, const gmx_multisim_t *multiSimComm)
	Checks if biases are compatible for sharing between simulations, throws if not. More...

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

static int	countTrailingZeroRows (const double const data, int numRows, int numColumns)
	Count trailing data rows containing only zeros. More...

static void	readUserPmfAndTargetDistribution (const std::vector< 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...

AwhParams *	readAwhParams (std::vector< t_inpfile > *inp, warninp_t wi)
	Allocate and initialize the AWH parameters with values from the input file. More...

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

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

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

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

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

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

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

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...

CommandLineProgramContext &	initForCommandLine (int argc, char **argv)
	Initializes the GROMACS library for command-line use. More...

void	finalizeForCommandLine ()
	Deinitializes the GROMACS library after initForCommandLine(). More...

int	processExceptionAtExitForCommandLine (const std::exception &ex)
	Handles an exception and deinitializes after initForCommandLine. More...

int	runCommandLineModule (int argc, char argv[], ICommandLineModule module)
	Implements a main() method that runs a single module. More...

int	runCommandLineModule (int argc, char argv[], const char name, const char *description, std::function< std::unique_ptr< ICommandLineOptionsModule >()> factory)
	Implements a main() method that runs a single module. More...

void	writeCommandLineHelpCMain (const CommandLineHelpContext &context, const char name, int(mainFunction)(int argc, char *argv[]))
	Helper to implement ICommandLineModule::writeHelp() with a C-like main() function that calls parse_common_args(). More...

static int	getFileType (const std::string &filename)
	Get the internal file type from the `filename`. More...

static unsigned long	getSupportedOutputAdapters (int filetype)
	Get the flag representing the requirements for a given file output. More...

static OutputAdapterContainer	addOutputAdapters (const OutputRequirements &requirements, AtomsDataPtr atoms, const Selection &sel, unsigned long abilities)
	Creates a new container object with the user requested IOutputAdapter derived methods attached to it. More...

std::unique_ptr < TrajectoryFrameWriter >	createTrajectoryFrameWriter (const gmx_mtop_t *top, const Selection &sel, const std::string &filename, AtomsDataPtr atoms, OutputRequirements requirements)
	Factory function for TrajectoryFrameWriter. More...

static void	deepCopy_t_trxframe (const t_trxframe &input, t_trxframe copy, RVec xvec, RVec vvec, RVec fvec, int *indexvec)
	Create a deep copy of a t_trxframe `input` into `copy`. More...

static t_trxstatus *	openTNG (const std::string &name, const Selection &sel, const gmx_mtop_t *mtop)
	Method to open TNG file. More...

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

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

void	mdAlgorithmsSetupAtomData (const t_commrec cr, const t_inputrec ir, 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...

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<class T1 , class T2 >
bool	operator== (const Allocator< T1, HostAllocationPolicy > &a, const Allocator< T2, HostAllocationPolicy > &b)
	Return true if two allocators are identical. More...

template<typename PinnableVector >
void	changePinningPolicy (PinnableVector *v, PinningPolicy pinningPolicy)
	Helper function for changing the pinning policy of a pinnable vector. More...

void	pinBuffer (void *pointer, std::size_t numBytes) noexcept
	Pin the allocation to physical memory. More...

void	unpinBuffer (void *pointer) noexcept
	Unpin the allocation. More...

void	doDeviceTransfers (const DeviceInformation &deviceInfo, ArrayRef< const char > input, ArrayRef< char > output)
	Helper function for GPU test code to be platform agnostic. More...

bool	cpuIsX86Nehalem (const CpuInfo &cpuInfo)
	Return true if the CPU is an Intel x86 Nehalem. More...

static DeviceDetectionResult	detectAllDeviceInformation (const PhysicalNodeCommunicator &physicalNodeComm)
	Detect GPUs when that makes sense to attempt. More...

static void	gmx_collect_hardware_mpi (const gmx::CpuInfo &cpuInfo, const PhysicalNodeCommunicator &physicalNodeComm, gmx_hw_info_t *hardwareInfo)
	Reduce the locally collected `hardwareInfo` over MPI ranks.

void	hardwareTopologyDoubleCheckDetection (const gmx::MDLogger &mdlog, const gmx::HardwareTopology &hardwareTopology)
	Sanity check hardware topology and print some notes to log. More...

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

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

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

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

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

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

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

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

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

static void	spinUpCore ()
	Utility that does dummy computing for max 2 seconds to spin up cores. More...

void	hardwareTopologyPrepareDetection ()
	Prepare the system before hardware topology detection. More...

std::unique_ptr< IMDModule >	createInteractiveMolecularDynamicsModule ()
	Creates a module for interactive molecular dynamics.

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, const rvec x[], 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 master socket. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

bool	inputSupportsGpuBondeds (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 bool	addMessageIfNotSupported (ArrayRef< const std::string > errorReasons, std::string *error)
	Help build a descriptive message in `error` if there are `errorReasons` why bondeds on a GPU are not supported. More...

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

constexpr real	determinant (Matrix3x3ConstSpan matrix)
	Determinant of a 3x3 matrix.

constexpr real	trace (Matrix3x3ConstSpan matrixView)
	Calculates the trace of a 3x3 matrix view.

template<typename ElementType , int N, int M = N>
MultiDimArray< std::array < ElementType, N *M >, extents < N, M > >	identityMatrix ()
	Create an identity matrix of ElementType with N * M elements. More...

static Matrix3x3	createMatrix3x3FromLegacyMatrix (const matrix legacyMatrix)
	Create new matrix type from legacy type.

static void	fillLegacyMatrix (Matrix3x3ConstSpan newMatrix, matrix legacyMatrix)
	Fill legacy matrix from new matrix type.

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

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

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

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

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

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

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.

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

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

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

void	too_many_constraint_warnings (int 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, gmx_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, gmx_bool computeVirial, tensor constraintsVirial)
	Constraint coordinates. More...

static bool	isConstraintFlexible (ArrayRef< const t_iparams > iparams, int iparamsIndex)
	Returns whether constraint with parameter `iparamsIndex` is a flexible constraint.

const int *	constr_iatomptr (gmx::ArrayRef< const int > iatom_constr, gmx::ArrayRef< const int > iatom_constrnc, int con)
	Returns the constraint iatoms for a constraint number con which comes from a list where F_CONSTR and F_CONSTRNC constraints are concatenated.

bool	inter_charge_group_constraints (const gmx_mtop_t &mtop)
	Returns whether there are inter charge group constraints.

bool	inter_charge_group_settles (const gmx_mtop_t &mtop)
	Returns whether there are inter charge group settles.

static void	constr_recur (const ListOfLists< int > &at2con, const InteractionLists &ilist, gmx::ArrayRef< const t_iparams > iparams, gmx_bool bTopB, int at, int depth, int nc, ArrayRef< int > path, real r0, real r1, real r2max, int count)
	Recursing function to help find all adjacent constraints.

static real	constr_r_max_moltype (const gmx_moltype_t molt, gmx::ArrayRef< const t_iparams > iparams, const t_inputrec ir)
	Find the interaction radius needed for constraints for this molecule type.

real	constr_r_max (const MDLogger &mdlog, const gmx_mtop_t mtop, const t_inputrec ir)
	Returns an estimate of the maximum distance between atoms required for LINCS.

real	calculateAcceptanceWeight (int calculationMode, real lambdaEnergyDifference)
	Calculates the acceptance weight for a lambda state transition. More...

std::array< real, efptNR >	currentLambdas (int64_t step, const t_lambda &fepvals, int currentLambdaState)
	Evaluate the current lambdas. More...

template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>
auto	leapFrogKernel (cl::sycl::handler &cgh, DeviceAccessor< float3, mode::read_write > a_x, DeviceAccessor< float3, mode::discard_write > a_xp, DeviceAccessor< float3, mode::read_write > a_v, DeviceAccessor< float3, mode::read > a_f, DeviceAccessor< float, mode::read > a_inverseMasses, float dt, OptionalAccessor< float, mode::read, numTempScaleValues!=NumTempScaleValues::None > a_lambdas, OptionalAccessor< unsigned short, mode::read, numTempScaleValues==NumTempScaleValues::Multiple > a_tempScaleGroups, float3 prVelocityScalingMatrixDiagonal)
	Main kernel for the Leap-Frog integrator. More...

template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling, class... Args>
static cl::sycl::event	launchLeapFrogKernel (const DeviceStream &deviceStream, int numAtoms, Args &&...args)

static NumTempScaleValues	getTempScalingType (bool doTemperatureScaling, int numTempScaleValues)

template<class... Args>
static cl::sycl::event	launchLeapFrogKernel (NumTempScaleValues tempScalingType, VelocityScalingType prVelocityScalingType, Args &&...args)
	Select templated kernel and launch it.

ArrayRef< real >	lincs_rmsdData (Lincs *lincsd)
	Return the data for determining constraint RMS relative deviations.

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, 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, 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, const real invmass, rvec *x)
	Update coordinates for atoms.

template<int align>
static void gmx_simdcall	gatherLoadUTransposeTSANSafe (const real base, const std::int32_t offset, SimdReal v0, SimdReal v1, SimdReal *v2)
	Helper function so that we can run TSAN with SIMD support (where implemented).

static void gmx_simdcall	calc_dr_x_f_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec __restrict x, const rvec __restrict f, const real __restrict blc, const real pbc_simd, rvec __restrict r, real __restrict rhs, real *__restrict sol)
	Calculate the constraint distance vectors r to project on from x. More...

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

static void gmx_simdcall	calc_dr_x_xp_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec __restrict x, const rvec __restrict xp, const real __restrict bllen, const real __restrict blc, const real pbc_simd, rvec __restrict r, real __restrict rhs, real __restrict sol)
	Calculate the constraint distance vectors r to project on from x. More...

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

static void gmx_simdcall	calc_dist_iter_simd (int b0, int b1, gmx::ArrayRef< const AtomPair > atoms, const rvec __restrict x, const real __restrict bllen, const real __restrict blc, const real pbc_simd, real wfac, real __restrict rhs, real __restrict sol, bool *bWarn)
	As calc_dist_iter(), but using SIMD intrinsics.

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

static void	set_lincs_matrix_task (Lincs li, Task li_task, 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, 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)
	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, 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, const real invmass, const t_commrec cr, const gmx_multisim_t ms, ArrayRefWithPadding< const RVec > x, ArrayRefWithPadding< RVec > xprime, ArrayRef< RVec > min_proj, const matrix box, t_pbc pbc, bool hasMassPerturbed, real lambda, real dvdlambda, real invdt, ArrayRef< RVec > v, bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq, t_nrnb nrnb, int maxwarn, int warncount)
	Applies LINCS constraints. More...

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

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

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

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

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

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

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

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

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

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

static void	pr_sortblock (FILE fp, const char title, int nsb, t_sortblock sb[])
	Prints sortblocks.

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

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

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

void	cshake (const int iatom[], int ncon, int nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > positions, const t_pbc pbc, ArrayRef< const RVec > initial_displacements, ArrayRef< const real > half_of_reduced_mass, real omega, 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, 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, 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, const real invmass[], ConstraintVariable econq)
	Check that constraints are satisfied.

static bool	bshakef (FILE log, shakedata shaked, 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,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...

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

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

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

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

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

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

static int	detectGroup (int firstAtom, const gmx_moltype_t &moltype, const ListOfLists< int > &at2con, const InteractionList &ilistConstraints)
	Returns the size of the update group starting at `firstAtom` or 0 when criteria (see updategroups.h) are not met.

static RangePartitioning	makeUpdateGroups (const gmx_moltype_t &moltype, gmx::ArrayRef< const t_iparams > iparams)
	Returns a list of update groups for `moltype`.

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

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

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

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

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

static void	construct_vsites_thread (ArrayRef< RVec > x, const real dt, 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...

static void	construct_vsites (const ThreadingInfo *threadingInfo, ArrayRef< RVec > x, real dt, 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 > updateGroupingPerMoleculetype)
	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)
	Create the virtual site handler. More...

static int	getNumInterUpdategroupVsites (const gmx_mtop_t &mtop, const gmx_domdec_t *domdec)
	Returns the number of inter update-group vsites.

	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, const unsigned short 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)
	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, bool issueWarning)
	Return whether GPU acceleration of nonbondeds is supported with the given settings. More...

static gmx::LoggerOwner	buildLogger (FILE *fplog, const bool isSimulationMasterRank)
	Initializes the logger for mdrun.

static TaskTarget	findTaskTarget (const char *optionString)
	Make a TaskTarget from an mdrun argument string.

static void	finish_run (FILE fplog, const gmx::MDLogger &mdlog, const t_commrec cr, const t_inputrec inputrec, t_nrnb nrnb[], gmx_wallcycle_t 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 MdModulesNotifier &notifier, gmx::ReadCheckpointDataHolder *modularSimulatorCheckpointData, bool useModularSimulator)
	Initialize local stateful simulation data. More...

SimulationInputHandle	makeSimulationInput (const LegacyMdrunOptions &options)

std::tuple< StartingBehavior, LogFilePtr >	handleRestart (bool isSimulationMaster, MPI_Comm communicator, const gmx_multisim_t *ms, AppendingBehavior appendingBehavior, int nfile, t_filenm fnm[])
	Handle startup of mdrun, particularly regarding -cpi and -append. More...

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

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

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

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

template<class BasicMdspan >
constexpr std::enable_if_t < BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer >	begin (const BasicMdspan &basicMdspan)
	Free begin function addressing memory of a contiguously laid out basic_mdspan. More...

template<class BasicMdspan >
constexpr std::enable_if_t < BasicMdspan::is_always_contiguous(), typename BasicMdspan::pointer >	end (const BasicMdspan &basicMdspan)
	Free end function addressing memory of a contiguously laid out basic_mdspan. More...

template<class BasicMdspan >
constexpr BasicMdspan	addElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise addition.

template<class BasicMdspan >
constexpr BasicMdspan	subtractElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise subtraction - left minus right.

template<class BasicMdspan >
constexpr BasicMdspan	multiplyElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise multiplication.

template<class BasicMdspan >
constexpr BasicMdspan	divideElementwise (const BasicMdspan &span1, const BasicMdspan &span2)
	Elementwise division - left / right.

template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool	operator== (const extents< LHS...> &lhs, const extents< RHS...> &rhs) noexcept
	Comparison operator. More...

template<std::ptrdiff_t... LHS, std::ptrdiff_t... RHS>
constexpr bool	operator!= (const extents< LHS...> &lhs, const extents< RHS...> &rhs) noexcept
	Check for non-equality. More...

template<CheckpointDataOperation operation, typename T >
ArrayRef< std::conditional_t < operation==CheckpointDataOperation::Write\|\|std::is_const < T >::value, const typename T::value_type, typename T::value_type > >	makeCheckpointArrayRef (T &container)

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.

int	nonbondedMtsFactor (const t_inputrec &ir)
	Returns the interval in steps at which the non-bonded pair forces are calculated. More...

void	assertMtsRequirements (const t_inputrec &ir)
	(Release) Asserts that all multiple time-stepping requirements on `ir` are fulfilled

static int	forceGroupMtsLevel (ArrayRef< const MtsLevel > mtsLevels, const MtsForceGroups mtsForceGroup)
	Returns the MTS level at which a force group is to be computed. More...

template<typename... Ts>
auto	checkUseModularSimulator (Ts &&...args) -> decltype(ModularSimulator::isInputCompatible(std::forward< Ts >(args)...))
	Whether or not to use the ModularSimulator. More...

	statePropagatorData_ (statePropagatorData)

	energyData_ (energyData)

	fplog_ (fplog)

	inputrec_ (inputrec)

	mdAtoms_ (mdAtoms)

template<NumVelocityScalingValues numVelocityScalingValues, ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
static void	updateVelocities (int a, real dt, real lambda, const rvec __restrict invMassPerDim, rvec __restrict v, const rvec *__restrict f, const rvec diagPR, const matrix matrixPR)
	Update velocities.

static void	updatePositions (int a, real dt, const rvec __restrict x, rvec __restrict xprime, const rvec *__restrict v)
	Update positions.

template<ParrinelloRahmanVelocityScaling parrinelloRahmanVelocityScaling>
static bool	diagonalizePRMatrix (matrix matrixPR, rvec diagPR)
	Helper function diagonalizing the PR matrix if possible.

	scalingStepPR_ (-1)

	wcycle_ (wcycle)

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, 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 *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))

	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...

static void	generateCoordinates (int multiplicationFactor, std::vector< gmx::RVec > *coordinates, matrix box)
	Generates coordinates and a box for the base system scaled by `multiplicationFactor`.

void	assignOptionsFromKeyValueTree (Options options, const KeyValueTreeObject &tree, IKeyValueTreeErrorHandler errorHandler)
	Assigns option values from a given KeyValueTreeObject. More...

void	checkForUnknownOptionsInKeyValueTree (const KeyValueTreeObject &tree, const Options &options)
	Checks that a given KeyValueTreeObject can be assigned to given Options. More...

KeyValueTreeObject	adjustKeyValueTreeFromOptions (const KeyValueTreeObject &tree, const Options &options)
	Adjusts a KeyValueTreeObject to the structure of given Options. More...

bool	boxesAreEqual (const matrix box1, const matrix box2)
	Returns whether two boxes are of equal size and shape (within reasonable tolerance).

bool	boxIsZero (const matrix box)
	Returns whether a box is only initialised to zero or not.

void	shiftAtoms (const RVec &shift, ArrayRef< RVec > x)
	Shift all coordinates. More...

void	placeCoordinatesWithCOMInBox (const PbcType &pbcType, UnitCellType unitCellType, CenteringType centerType, const matrix box, ArrayRef< RVec > x, const gmx_mtop_t &mtop, COMShiftType comShiftType)
	Moves collection of atoms along the center of mass into a box. More...

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...

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)

HelpTopicPointer	createSelectionHelpTopic ()
	*/ More...

static void	simdPrefetch (void *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	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	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...

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...

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

template<MathOptimization opt = MathOptimization::Safe>
static double	exp2 (double x)
	Double 2^x. More...

template<MathOptimization opt = MathOptimization::Safe>
static double	exp (double x)
	Double exp(x). More...

static double	erf (double x)
	Double erf(x). More...

static double	erfc (double x)
	Double erfc(x). More...

static void	sincos (double x, double sinval, double cosval)
	Double sin & cos. More...

static double	sin (double x)
	Double sin. More...

static double	cos (double x)
	Double cos. More...

static double	tan (double x)
	Double tan. More...

static double	asin (double x)
	Double asin. More...

static double	acos (double x)
	Double acos. More...

static double	atan (double x)
	Double atan. More...

static double	atan2 (double y, double x)
	Double atan2(y,x). More...

static double	pmeForceCorrection (double z2)
	Calculate the force correction due to PME analytically in double. More...

static double	pmePotentialCorrection (double z2)
	Calculate the potential correction due to PME analytically in double. More...

static double	invsqrtSingleAccuracy (double x)
	Calculate 1/sqrt(x) for double, but with single accuracy. More...

static void	invsqrtPairSingleAccuracy (double x0, double x1, double out0, double out1)
	Calculate 1/sqrt(x) for two doubles, but with single accuracy. More...

static double	invSingleAccuracy (double x)
	Calculate 1/x for double, but with single accuracy. More...

static double	maskzInvsqrtSingleAccuracy (double x, bool m)
	Calculate 1/sqrt(x) for masked entry of double, but with single accuracy. More...

static double	maskzInvSingleAccuracy (double x, bool m)
	Calculate 1/x for masked entry of double, but with single accuracy. More...

static double	sqrtSingleAccuracy (double x)
	Calculate sqrt(x) for double, but with single accuracy. More...

static double	logSingleAccuracy (double x)
	Double log(x), but with single accuracy. This is the natural logarithm. More...

static double	exp2SingleAccuracy (double x)
	Double 2^x, but with single accuracy. More...

static double	expSingleAccuracy (double x)
	Double exp(x), but with single accuracy. More...

static double	erfSingleAccuracy (double x)
	Double erf(x), but with single accuracy. More...

static double	erfcSingleAccuracy (double x)
	Double erfc(x), but with single accuracy. More...

static void	sincosSingleAccuracy (double x, double sinval, double cosval)
	Double sin & cos, but with single accuracy. More...

static double	sinSingleAccuracy (double x)
	Double sin, but with single accuracy. More...

static double	cosSingleAccuracy (double x)
	Double cos, but with single accuracy. More...

static double	tanSingleAccuracy (double x)
	Double tan, but with single accuracy. More...

static double	asinSingleAccuracy (double x)
	Double asin, but with single accuracy. More...

static double	acosSingleAccuracy (double x)
	Double acos, but with single accuracy. More...

static double	atanSingleAccuracy (double x)
	Double atan, but with single accuracy. More...

static double	atan2SingleAccuracy (double y, double x)
	Double atan2(y,x), but with single accuracy. More...

static double	pmeForceCorrectionSingleAccuracy (double z2)
	Force correction due to PME in double, but with single accuracy. More...

static double	pmePotentialCorrectionSingleAccuracy (double z2)
	Potential correction due to PME in double, but with single accuracy. More...

template<int align>
static void	gatherLoadTranspose (const float base, const std::int32_t offset[], float v0, float v1, float v2, float *v3)
	Load 4 consecutive floats from base/offset into four variables. More...

template<int align>
static void	gatherLoadTranspose (const float base, const std::int32_t offset[], float v0, float *v1)
	Load 2 consecutive floats from base/offset into four variables. More...

template<int align>
static void	gatherLoadUTranspose (const float base, const std::int32_t offset[], float v0, float v1, float v2)
	Load 3 consecutive floats from base/offsets, store into three vars. More...

template<int align>
static void	transposeScatterStoreU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Store 3 floats to 3 to base/offset. More...

template<int align>
static void	transposeScatterIncrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Add 3 floats to base/offset. More...

template<int align>
static void	transposeScatterDecrU (float *base, const std::int32_t offset[], float v0, float v1, float v2)
	Subtract 3 floats from base/offset. More...

static void	expandScalarsToTriplets (float scalar, float triplets0, float triplets1, float *triplets2)
	Copy single float to three variables. More...

template<int align>
static void	gatherLoadBySimdIntTranspose (const float base, std::int32_t offset, float v0, float v1, float v2, float *v3)
	Load 4 floats from base/offsets and store into variables. More...

template<int align>
static void	gatherLoadUBySimdIntTranspose (const float base, std::int32_t offset, float v0, float *v1)
	Load 2 floats from base/offsets and store into variables (unaligned). More...

template<int align>
static void	gatherLoadBySimdIntTranspose (const float base, std::int32_t offset, float v0, float *v1)
	Load 2 floats from base/offsets and store into variables (aligned). More...

static float	reduceIncr4ReturnSum (float *m, float v0, float v1, float v2, float v3)
	Add each float to four consecutive memory locations, return sum. More...

template<int align>
static void	gatherLoadTranspose (const double base, const std::int32_t offset[], double v0, double v1, double v2, double *v3)
	Load 4 consecutive doubles from base/offset into four variables. More...

template<int align>
static void	gatherLoadTranspose (const double base, const std::int32_t offset[], double v0, double *v1)
	Load 2 consecutive doubles from base/offset into four variables. More...

template<int align>
static void	gatherLoadUTranspose (const double base, const std::int32_t offset[], double v0, double v1, double v2)
	Load 3 consecutive doubles from base/offsets, store into three vars. More...

template<int align>
static void	transposeScatterStoreU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Store 3 doubles to 3 to base/offset. More...

template<int align>
static void	transposeScatterIncrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Add 3 doubles to base/offset. More...

template<int align>
static void	transposeScatterDecrU (double *base, const std::int32_t offset[], double v0, double v1, double v2)
	Subtract 3 doubles from base/offset. More...

static void	expandScalarsToTriplets (double scalar, double triplets0, double triplets1, double *triplets2)
	Copy single double to three variables. More...

template<int align>
static void	gatherLoadBySimdIntTranspose (const double base, std::int32_t offset, double v0, double v1, double v2, double *v3)
	Load 4 doubles from base/offsets and store into variables. More...

template<int align>
static void	gatherLoadUBySimdIntTranspose (const double base, std::int32_t offset, double v0, double *v1)
	Load 2 doubles from base/offsets and store into variables (unaligned). More...

template<int align>
static void	gatherLoadBySimdIntTranspose (const double base, std::int32_t offset, double v0, double *v1)
	Load 2 doubles from base/offsets and store into variables (aligned). More...

static double	reduceIncr4ReturnSum (double *m, double v0, double v1, double v2, double v3)
	Add each double to four consecutive memory locations, return sum. More...

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

static SimdFloat	maskzInvsqrtSingleAccuracy (SimdFloat x, SimdFBool m)
	Calculate 1/sqrt(x) for masked SIMD floats, only targeting single accuracy. More...

static void gmx_simdcall	invsqrtPairSingleAccuracy (SimdFloat x0, SimdFloat x1, SimdFloat out0, SimdFloat out1)
	Calculate 1/sqrt(x) for two SIMD floats, only targeting single accuracy. More...

static SimdFloat gmx_simdcall	invSingleAccuracy (SimdFloat x)
	Calculate 1/x for SIMD float, only targeting single accuracy. More...

static SimdFloat	maskzInvSingleAccuracy (SimdFloat x, SimdFBool m)
	Calculate 1/x for masked SIMD floats, only targeting single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall	sqrtSingleAccuracy (SimdFloat x)
	Calculate sqrt(x) for SIMD float, always targeting single accuracy. More...

static SimdFloat gmx_simdcall	cbrtSingleAccuracy (SimdFloat x)
	Calculate cbrt(x) for SIMD float, always targeting single accuracy. More...

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

static SimdFloat gmx_simdcall	log2SingleAccuracy (SimdFloat x)
	SIMD float log2(x), only targeting single accuracy. This is the base-2 logarithm. More...

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

template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall	exp2SingleAccuracy (SimdFloat x)
	SIMD float 2^x, only targeting single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall	expSingleAccuracy (SimdFloat x)
	SIMD float e^x, only targeting single accuracy. More...

template<MathOptimization opt = MathOptimization::Safe>
static SimdFloat gmx_simdcall	powSingleAccuracy (SimdFloat x, SimdFloat y)
	SIMD pow(x,y), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	erfSingleAccuracy (SimdFloat x)
	SIMD float erf(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	erfcSingleAccuracy (SimdFloat x)
	SIMD float erfc(x), only targeting single accuracy. More...

static void gmx_simdcall	sinCosSingleAccuracy (SimdFloat x, SimdFloat sinval, SimdFloat cosval)
	SIMD float sin & cos, only targeting single accuracy. More...

static SimdFloat gmx_simdcall	sinSingleAccuracy (SimdFloat x)
	SIMD float sin(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	cosSingleAccuracy (SimdFloat x)
	SIMD float cos(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	tanSingleAccuracy (SimdFloat x)
	SIMD float tan(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	asinSingleAccuracy (SimdFloat x)
	SIMD float asin(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	acosSingleAccuracy (SimdFloat x)
	SIMD float acos(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	atanSingleAccuracy (SimdFloat x)
	SIMD float atan(x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	atan2SingleAccuracy (SimdFloat y, SimdFloat x)
	SIMD float atan2(y,x), only targeting single accuracy. More...

static SimdFloat gmx_simdcall	pmeForceCorrectionSingleAccuracy (SimdFloat z2)
	SIMD Analytic PME force correction, only targeting single accuracy. More...

static SimdFloat gmx_simdcall	pmePotentialCorrectionSingleAccuracy (SimdFloat z2)
	SIMD Analytic PME potential correction, only targeting single accuracy. More...

static Simd4Float gmx_simdcall	invsqrtSingleAccuracy (Simd4Float x)
	Calculate 1/sqrt(x) for SIMD4 float, only targeting single accuracy. More...

const std::string &	simdString (SimdType s)
	Return a string with the name of a SIMD type. More...

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

SimdType	simdCompiled ()
	Return the SIMD type the library was compiled with.

bool	simdCheck (SimdType s, FILE *log, bool warnToStdErr)
	Check if binary was compiled with the provided SIMD type. More...

static SimdFloat gmx_simdcall	iprod (SimdFloat ax, SimdFloat ay, SimdFloat az, SimdFloat bx, SimdFloat by, SimdFloat bz)
	SIMD float inner product of multiple float vectors. More...

static SimdFloat gmx_simdcall	norm2 (SimdFloat ax, SimdFloat ay, SimdFloat az)
	SIMD float norm squared of multiple vectors. More...

static void gmx_simdcall	cprod (SimdFloat ax, SimdFloat ay, SimdFloat az, SimdFloat bx, SimdFloat by, SimdFloat bz, SimdFloat cx, SimdFloat cy, SimdFloat *cz)
	SIMD float cross-product of multiple vectors. More...

static SimdDouble gmx_simdcall	iprod (SimdDouble ax, SimdDouble ay, SimdDouble az, SimdDouble bx, SimdDouble by, SimdDouble bz)
	SIMD double inner product of multiple double vectors. More...

static SimdDouble gmx_simdcall	norm2 (SimdDouble ax, SimdDouble ay, SimdDouble az)
	SIMD double norm squared of multiple vectors. More...

static void gmx_simdcall	cprod (SimdDouble ax, SimdDouble ay, SimdDouble az, SimdDouble bx, SimdDouble by, SimdDouble bz, SimdDouble cx, SimdDouble cy, SimdDouble *cz)
	SIMD double cross-product of multiple vectors. More...

static Simd4Float gmx_simdcall	norm2 (Simd4Float ax, Simd4Float ay, Simd4Float az)
	SIMD4 float norm squared of multiple vectors. More...

static Simd4Double gmx_simdcall	norm2 (Simd4Double ax, Simd4Double ay, Simd4Double az)
	SIMD4 double norm squared of multiple vectors. More...

std::unique_ptr< IMDModule >	createSwapCoordinatesModule ()
	Creates a module for Computational Electrophysiology swapping.

bool	decideWhetherToUseGpusForNonbondedWithThreadMpi (TaskTarget nonbondedTarget, int numDevicesToUse, 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...

bool	decideWhetherToUseGpusForPmeWithThreadMpi (bool useGpuForNonbonded, TaskTarget pmeTarget, int numDevicesToUse, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation)
	Decide whether this thread-MPI simulation will run PME tasks on GPUs. More...

bool	decideWhetherToUseGpusForNonbonded (TaskTarget nonbondedTarget, const std::vector< int > &userGpuTaskAssignment, EmulateGpuNonbonded emulateGpuNonbonded, bool buildSupportsNonbondedOnGpu, bool nonbondedOnGpuIsUseful, bool gpusWereDetected)
	Decide whether the simulation will try to run nonbonded tasks on GPUs. More...

bool	decideWhetherToUseGpusForPme (bool useGpuForNonbonded, TaskTarget pmeTarget, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, const t_inputrec &inputrec, int numRanksPerSimulation, int numPmeRanksPerSimulation, bool gpusWereDetected)
	Decide whether the simulation will try to run tasks of different types on GPUs. More...

PmeRunMode	determinePmeRunMode (bool useGpuForPme, const TaskTarget &pmeFftTarget, const t_inputrec &inputrec)
	Determine PME run mode. More...

bool	decideWhetherToUseGpusForBonded (bool useGpuForNonbonded, bool useGpuForPme, TaskTarget bondedTarget, const t_inputrec &inputrec, const gmx_mtop_t &mtop, int numPmeRanksPerSimulation, bool gpusWereDetected)
	Decide whether the simulation will try to run bonded tasks on GPUs. More...

bool	decideWhetherToUseGpuForUpdate (bool isDomainDecomposition, bool useUpdateGroups, PmeRunMode pmeRunMode, bool havePmeOnlyRank, bool useGpuForNonbonded, TaskTarget updateTarget, bool gpusWereDetected, const t_inputrec &inputrec, const gmx_mtop_t &mtop, bool useEssentialDynamics, bool doOrientationRestraints, bool useReplicaExchange, bool haveFrozenAtoms, bool doRerun, const DevelopmentFeatureFlags &devFlags, const gmx::MDLogger &mdlog)
	Decide whether to use GPU for update. More...

bool	decideWhetherToUseGpuForHalo (const DevelopmentFeatureFlags &devFlags, bool havePPDomainDecomposition, bool useGpuForNonbonded, bool useModularSimulator, bool doRerun, bool haveEnergyMinimization)
	Decide whether to use GPU for halo exchange. More...

SimulationWorkload	createSimulationWorkload (const t_inputrec &inputrec, bool disableNonbondedCalculation, const DevelopmentFeatureFlags &devFlags, bool useGpuForNonbonded, PmeRunMode pmeRunMode, bool useGpuForBonded, bool useGpuForUpdate, bool useGpuDirectHalo)
	Build datastructure that contains decisions whether to run different workload task on GPUs. More...

std::vector< GpuTask >	findGpuTasksOnThisRank (bool haveGpusOnThisPhysicalNode, TaskTarget nonbondedTarget, TaskTarget pmeTarget, TaskTarget bondedTarget, TaskTarget updateTarget, bool useGpuForNonbonded, bool useGpuForPme, bool rankHasPpTask, bool rankHasPmeTask)
	Returns container of all tasks on this rank that are eligible for GPU execution. More...

GpuTasksOnRanks	findAllGpuTasksOnThisNode (ArrayRef< const GpuTask > gpuTasksOnThisRank, const PhysicalNodeCommunicator &physicalNodeComm)
	Returns container of all tasks on all ranks of this node that are eligible for GPU execution. More...

void	reportGpuUsage (const MDLogger &mdlog, ArrayRef< const GpuTaskAssignment > gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool printHostName, bool useGpuForBonded, PmeRunMode pmeRunMode, bool useGpuForUpdate)
	Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation. More...

void	checkHardwareOversubscription (int numThreadsOnThisRank, int rank, const HardwareTopology &hwTop, const PhysicalNodeCommunicator &comm, const MDLogger &mdlog)
	Warns for oversubscribing the hardware threads, when that is the case.

template<GpuTask TaskType>
static bool	hasTaskType (const GpuTaskMapping &mapping)
	Function for whether the task of `mapping` has value `TaskType`. More...

static bool	hasPmeOrNonbondedTask (const GpuTaskMapping &mapping)
	Function for whether the `mapping` has the GPU PME or Nonbonded task. More...

static std::vector< int >	parseGpuDeviceIdentifierList (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container. More...

std::vector< int >	parseUserGpuIdString (const std::string &gpuIdString)
	Parse a GPU ID specifier string into a container describing device IDs exposed to the run. More...

std::vector< int >	makeGpuIdsToUse (const std::vector< std::unique_ptr< DeviceInformation >> &deviceInfoList, const std::string &gpuIdsAvailableString)
	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 (const std::vector< std::unique_ptr< DeviceInformation >> &deviceInfoList, const std::vector< int > &compatibleGpus, const std::vector< int > &gpuIds)
	Check that all user-selected GPUs are compatible. More...

void	writeHeader (TextWriter *writer, const std::string &text, const std::string &section, bool writeFormattedText)
	Write appropiate Header to output stream. More...

void	writeSystemInformation (TextWriter *writer, const gmx_mtop_t &top, bool writeFormattedText)
	Write information about the molecules in the system. More...

void	writeParameterInformation (TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
	Write information about system parameters. More...

void	writeInformation (TextOutputFile *outputStream, const t_inputrec &ir, const gmx_mtop_t &top, bool writeFormattedText, bool notStdout)
	Wrapper for writing out information. More...

void	blockaToExclusionBlocks (const t_blocka *b, gmx::ArrayRef< ExclusionBlock > b2)
	Convert the exclusions. More...

void	exclusionBlocksToBlocka (gmx::ArrayRef< const ExclusionBlock > b2, t_blocka *b)
	Convert the exclusions expressed in `b` into t_blocka form.

void	mergeExclusions (ListOfLists< int > *excl, gmx::ArrayRef< ExclusionBlock > b2)
	Merge the contents of `b2` into `excl`. More...

void	registerTrajectoryAnalysisModules (CommandLineModuleManager *manager)
	Registers all trajectory analysis command-line modules. More...

gmx_rmpbc_t	gmx_rmpbc_init (const gmx::TopologyInformation &topInfo)
	Convenience overload useful for implementing legacy tools.

static std::size_t	getPageSize ()
	Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes). More...

std::size_t	pageSize ()
	Return the memory page size on this system. More...

std::string	simpleValueToString (const Any &value)
	Converts a Any value to a string. More...

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.

void	printBinaryInformation (FILE *fp, const IProgramContext &programContext)
	Print basic information about the executable. More...

void	printBinaryInformation (FILE *fp, const IProgramContext &programContext, const BinaryInformationSettings &settings)
	Print basic information about the executable with custom settings. More...

void	printBinaryInformation (TextWriter *writer, const IProgramContext &programContext, const BinaryInformationSettings &settings)
	Print basic information about the executable with custom settings. More...

std::string	bromacs ()
	Return a cool definition for the acronym GROMACS.

std::string	getCoolQuote ()
	Return a string with a cool quote.

std::string	getCudaDriverVersionString ()
	Returns a string of the CUDA driver version.

std::string	getCudaRuntimeVersionString ()
	Returns a string of the CUDA runtime version.

template<typename EnumerationArrayType >
EnumerationArrayType::EnumerationWrapperType	keysOf (const EnumerationArrayType &)
	Returns an object that provides iterators over the keys associated with `EnumerationArrayType`. More...

const char *	getErrorCodeString (int errorcode)
	Returns a short string description of an error code. More...

void	printFatalErrorMessage (FILE *fp, const std::exception &ex)
	Formats a standard fatal error message for reporting an exception. More...

std::string	formatExceptionMessageToString (const std::exception &ex)
	Formats an error message for reporting an exception. More...

void	formatExceptionMessageToFile (FILE *fp, const std::exception &ex)
	Formats an error message for reporting an exception. More...

void	formatExceptionMessageToWriter (TextWriter *writer, const std::exception &ex)
	Formats an error message for reporting an exception. More...

int	processExceptionAtExit (const std::exception &ex)
	Handles an exception that is causing the program to terminate. More...

void	processExceptionAsFatalError (const std::exception &ex)
	Helper function for terminating the program on an exception. More...

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

IFileInputRedirector &	defaultFileInputRedirector ()
	Returns default implementation for IFileInputRedirector. More...

IFileOutputRedirector &	defaultFileOutputRedirector ()
	Returns default implementation for IFileOutputRedirector. More...

const DataFileFinder &	getLibraryFileFinder ()
	Gets a finder for locating data files from share/top/. More...

void	setLibraryFileFinder (const DataFileFinder *finder)
	Sets a finder for location data files from share/top/. More...

std::string	findLibraryFile (const std::string &filename, bool bAddCWD=true, bool bFatal=true)
	Finds full path for a library file. More...

std::string	findLibraryFile (const char *filename, bool bAddCWD=true, bool bFatal=true)
	Finds full path for a library file. More...

FilePtr	openLibraryFile (const std::string &filename, bool bAddCWD=true, bool bFatal=true)
	Opens a library file for reading in an RAII-style `FILE` handle. More...

FilePtr	openLibraryFile (const char *filename, bool bAddCWD=true, bool bFatal=true)
	Opens a library file for reading in an RAII-style `FILE` handle. More...

IKeyValueTreeErrorHandler *	defaultKeyValueTreeErrorHandler ()
	Returns a default IKeyValueTreeErrorHandler that throws on first exception.

void	init (int argc, char **argv)
	Initializes the GROMACS library. More...

void	finalize ()
	Deinitializes the GROMACS library. More...

void	dumpKeyValueTree (TextWriter *writer, const KeyValueTreeObject &tree)
	Writes a human-readable representation of the tree with given writer. More...

void	compareKeyValueTrees (TextWriter *writer, const KeyValueTreeObject &tree1, const KeyValueTreeObject &tree2, real ftol, real abstol)
	Compares two KeyValueTrees and prints any differences.

KeyValueTreePath	operator+ (const KeyValueTreePath &a, const KeyValueTreePath &b)
	Combines two paths as with KeyValueTreePath::append().

KeyValueTreePath	operator+ (const KeyValueTreePath &a, const std::string &b)
	Combines an element to a path as with KeyValueTreePath::append().

static std::string	simpleValueToString (const KeyValueTreeValue &value)
	Helper function to format a simple KeyValueTreeValue.

void	writeKeyValueTreeAsMdp (TextWriter *writer, const KeyValueTreeObject &tree)
	Write a flat key-value `tree` to `writer` in mdp style. More...

void	serializeKeyValueTree (const KeyValueTreeObject &root, ISerializer *serializer)
	Serializes a KeyValueTreeObject with given serializer.

KeyValueTreeObject	deserializeKeyValueTree (ISerializer *serializer)
	Deserializes a KeyValueTreeObject from a given serializer.

void	niceHeader (TextWriter writer, const char fn, char commentChar)
	Prints creation time stamp and user information into a string as comments, and returns it. More...

void	MPI_Comm_free_wrapper (MPI_Comm *comm)
	Wrapper function for RAII-style cleanup. More...

const IProgramContext &	getProgramContext ()
	Returns the global IProgramContext instance. More...

void	setProgramContext (const IProgramContext *context)
	Sets the global IProgramContext instance. More...

bool	boolFromString (const char *str)
	Parses a boolean from a string. More...

int	intFromString (const char *str)
	Parses an integer from a string. More...

int64_t	int64FromString (const char *str)
	Parses a 64-bit integer from a string. More...

float	floatFromString (const char *str)
	Parses a float value from a string. More...

double	doubleFromString (const char *str)
	Parses a double value from a string. More...

template<typename T >
static T	fromString (const char *str)
	Parses a value from a string to a given type. More...

template<typename T >
static T	fromString (const std::string &str)
	Parses a value from a string to a given type. More...

template<typename T >
static T	fromStdString (const std::string &str)
	Parses a value from a string to a given type. More...

template<>
bool	fromString< bool > (const char *str)
	Implementation for boolean values.

template<>
int	fromString< int > (const char *str)
	Implementation for integer values.

template<>
int64_t	fromString< int64_t > (const char *str)
	Implementation for 64-bit integer values.

template<>
float	fromString< float > (const char *str)
	Implementation for float values.

template<>
double	fromString< double > (const char *str)
	Implementation for double values.

static const char *	boolToString (bool value)
	Converts a boolean to a "true"/"false" string. More...

static std::string	intToString (int t)
	Returns a string containing the value of `t`. More...

static std::string	int64ToString (int64_t t)
	Returns a string containing the value of `t`. More...

static std::string	doubleToString (double t)
	Returns a string containing the value of `t`. More...

template<typename ValueType , int NumExpectedValues>
static std::optional < std::array< ValueType, NumExpectedValues > >	parsedArrayFromInputString (const std::string &str)
	Convert a string into an array of values. More...

template<typename ValueType , int NumExpectedValues>
static std::string	stringIdentityTransformWithArrayCheck (const std::string &toConvert, const std::string &errorContextMessage)
	Returns the input string, throwing an excpetion if the demanded conversion to an array will not succeed. More...

std::size_t	countWords (const char *s)
	Returns number of space-separated words in zero-terminated char ptr. More...

std::size_t	countWords (const std::string &str)
	Returns the number of space-separated words in a string object. More...

bool	endsWith (const char str, const char suffix)
	Tests whether a string ends with another string. More...

std::string	stripSuffixIfPresent (const std::string &str, const char *suffix)
	Removes a suffix from a string. More...

std::string	stripString (const std::string &str)
	Removes leading and trailing whitespace from a string. More...

std::string	formatString (const char *fmt,...)
	Formats a string (snprintf() wrapper). More...

std::string	formatStringV (const char *fmt, va_list ap)
	Formats a string (vsnprintf() wrapper). More...

std::vector< std::string >	splitString (const std::string &str)
	Splits a string to whitespace separated tokens. More...

std::vector< std::string >	splitDelimitedString (const std::string &str, char delim)
	Splits a string to tokens separated by a given delimiter. More...

std::vector< std::string >	splitAndTrimDelimitedString (const std::string &str, char delim)
	Splits `str` to tokens separated by delimiter `delim`. Removes leading and trailing whitespace from those strings with std::isspace. More...

std::string	replaceAll (const std::string &input, const char from, const char to)
	Replace all occurrences of a string with another string. More...

std::string	replaceAll (const std::string &input, const std::string &from, const std::string &to)
	Replace all occurrences of a string with another string. More...

std::string	replaceAllWords (const std::string &input, const char from, const char to)
	Replace whole words with others. More...

std::string	replaceAllWords (const std::string &input, const std::string &from, const std::string &to)
	Replace whole words with others. More...

bool	equalCaseInsensitive (const std::string &source, const std::string &target)
	Return whether two strings are equal, ignoring case. More...

bool	equalCaseInsensitive (const std::string &source, const std::string &target, size_t maxLengthOfComparison)
	Checks if at most `maxLengthOfComparison` characters of two strings match case insensitive. More...

static bool	isNullOrEmpty (const char *str)
	Tests whether a string is null or empty. More...

static bool	startsWith (const std::string &str, const std::string &prefix)
	Tests whether a string starts with another string. More...

static bool	startsWith (const char str, const char prefix)
	Tests whether a string starts with another string. More...

static bool	endsWith (const std::string &str, const char *suffix)
	Tests whether a string ends with another string. More...

static bool	contains (const std::string &str, const char *substr)
	Tests whether a string contains another as a substring. More...

static bool	contains (const std::string &str, const std::string &substr)
	Tests whether a string contains another as a substring. More...

static bool	endsWith (const std::string &str, const std::string &suffix)
	Tests whether a string ends with another string. More...

template<typename InputIterator , typename FormatterType >
std::string	formatAndJoin (InputIterator begin, InputIterator end, const char *separator, const FormatterType &formatter)
	Formats all the range as strings, and then joins them with a separator in between. More...

template<typename ContainerType , typename FormatterType >
std::string	formatAndJoin (const ContainerType &container, const char *separator, const FormatterType &formatter)
	Formats all elements of the container as strings, and then joins them with a separator in between. More...

template<typename InputIterator >
std::string	joinStrings (InputIterator begin, InputIterator end, const char *separator)
	Joins strings from a range with a separator in between. More...

template<typename ContainerType >
std::string	joinStrings (const ContainerType &container, const char *separator)
	Joins strings from a container with a separator in between. More...

template<size_t count>
std::string	joinStrings (const char const (&array)[count], const char separator)
	Joins strings from an array with a separator in between. More...

template<class Function >
auto	dispatchTemplatedFunction (Function &&f)

template<class Function , class Enum , class... Enums>
auto	dispatchTemplatedFunction (Function &&f, Enum e, Enums...es)

template<class T >
void	free_wrapper (T *p)
	Wrapper of standard library free(), to be used as unique_cptr deleter for memory allocated by malloc, e.g. by an external library such as TNG.

template<class T >
void	sfree_wrapper (T *p)
	sfree wrapper to be used as unique_cptr deleter

template<typename T , typename D >
std::unique_ptr< T, D >	create_unique_with_deleter (T *t, D d)
	Create unique_ptr with any deleter function or lambda.

int	gmx_mdrun (int argc, char *argv[])
	Implements C-style main function for mdrun. More...

int	gmx_mdrun (MPI_Comm communicator, const gmx_hw_info_t &hwinfo, int argc, char *argv[])
	Implements C-style main function for mdrun. More...


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)


void	applyGlobalSimulationState (const SimulationInput &simulationInput, PartialDeserializedTprFile partialDeserializedTpr, t_state globalState, t_inputrec inputrec, gmx_mtop_t globalTopology)
	Get the global simulation input. More...

std::unique_ptr< t_state >	globalSimulationState (const SimulationInput &)

void	applyGlobalInputRecord (const SimulationInput &, t_inputrec *)

void	applyGlobalTopology (const SimulationInput &, gmx_mtop_t *)

Constant width-4 double precision SIMD types and instructions
static Simd4Double gmx_simdcall	load4 (const double *m)
	Load 4 double values from aligned memory into SIMD4 variable. More...

static void gmx_simdcall	store4 (double *m, Simd4Double a)
	Store the contents of SIMD4 double to aligned memory m. More...

static Simd4Double gmx_simdcall	load4U (const double *m)
	Load SIMD4 double from unaligned memory. More...

static void gmx_simdcall	store4U (double *m, Simd4Double a)
	Store SIMD4 double to unaligned memory. More...

static Simd4Double gmx_simdcall	simd4SetZeroD ()
	Set all SIMD4 double elements to 0. More...

static Simd4Double gmx_simdcall	operator& (Simd4Double a, Simd4Double b)
	Bitwise and for two SIMD4 double variables. More...

static Simd4Double gmx_simdcall	andNot (Simd4Double a, Simd4Double b)
	Bitwise andnot for two SIMD4 double variables. c=(~a) & b. More...

static Simd4Double gmx_simdcall	operator\| (Simd4Double a, Simd4Double b)
	Bitwise or for two SIMD4 doubles. More...

static Simd4Double gmx_simdcall	operator^ (Simd4Double a, Simd4Double b)
	Bitwise xor for two SIMD4 double variables. More...

static Simd4Double gmx_simdcall	operator+ (Simd4Double a, Simd4Double b)
	Add two double SIMD4 variables. More...

static Simd4Double gmx_simdcall	operator- (Simd4Double a, Simd4Double b)
	Subtract two SIMD4 variables. More...

static Simd4Double gmx_simdcall	operator- (Simd4Double a)
	SIMD4 floating-point negate. More...

static Simd4Double gmx_simdcall	operator* (Simd4Double a, Simd4Double b)
	Multiply two SIMD4 variables. More...

static Simd4Double gmx_simdcall	fma (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-multiply-add. Result is a*b+c. More...

static Simd4Double gmx_simdcall	fms (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-multiply-subtract. Result is a*b-c. More...

static Simd4Double gmx_simdcall	fnma (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-negated-multiply-add. Result is -a*b+c. More...

static Simd4Double gmx_simdcall	fnms (Simd4Double a, Simd4Double b, Simd4Double c)
	SIMD4 Fused-negated-multiply-subtract. Result is -a*b-c. More...

static Simd4Double gmx_simdcall	rsqrt (Simd4Double x)
	SIMD4 1.0/sqrt(x) lookup. More...

static Simd4Double gmx_simdcall	abs (Simd4Double a)
	SIMD4 Floating-point abs(). More...

static Simd4Double gmx_simdcall	max (Simd4Double a, Simd4Double b)
	Set each SIMD4 element to the largest from two variables. More...

static Simd4Double gmx_simdcall	min (Simd4Double a, Simd4Double b)
	Set each SIMD4 element to the largest from two variables. More...

static Simd4Double gmx_simdcall	round (Simd4Double a)
	SIMD4 Round to nearest integer value (in floating-point format). More...

static Simd4Double gmx_simdcall	trunc (Simd4Double a)
	Truncate SIMD4, i.e. round towards zero - common hardware instruction. More...

static double gmx_simdcall	dotProduct (Simd4Double a, Simd4Double b)
	Return dot product of two double precision SIMD4 variables. More...

static void gmx_simdcall	transpose (Simd4Double v0, Simd4Double v1, Simd4Double v2, Simd4Double v3)
	SIMD4 double transpose. More...

static Simd4DBool gmx_simdcall	operator== (Simd4Double a, Simd4Double b)
	a==b for SIMD4 double More...

static Simd4DBool gmx_simdcall	operator!= (Simd4Double a, Simd4Double b)
	a!=b for SIMD4 double More...

static Simd4DBool gmx_simdcall	operator< (Simd4Double a, Simd4Double b)
	a<b for SIMD4 double More...

static Simd4DBool gmx_simdcall	operator<= (Simd4Double a, Simd4Double b)
	a<=b for SIMD4 double. More...

static Simd4DBool gmx_simdcall	operator&& (Simd4DBool a, Simd4DBool b)
	Logical and on single precision SIMD4 booleans. More...

static Simd4DBool gmx_simdcall	operator\|\| (Simd4DBool a, Simd4DBool b)
	Logical or on single precision SIMD4 booleans. More...

static bool gmx_simdcall	anyTrue (Simd4DBool a)
	Returns non-zero if any of the boolean in SIMD4 a is True, otherwise 0. More...

static Simd4Double gmx_simdcall	selectByMask (Simd4Double a, Simd4DBool mask)
	Select from single precision SIMD4 variable where boolean is true. More...

static Simd4Double gmx_simdcall	selectByNotMask (Simd4Double a, Simd4DBool mask)
	Select from single precision SIMD4 variable where boolean is false. More...

static Simd4Double gmx_simdcall	blend (Simd4Double a, Simd4Double b, Simd4DBool sel)
	Vector-blend SIMD4 selection. More...

static double gmx_simdcall	reduce (Simd4Double a)
	Return sum of all elements in SIMD4 double variable. More...

Constant width-4 single precision SIMD types and instructions
static Simd4Float gmx_simdcall	load4 (const float *m)
	Load 4 float values from aligned memory into SIMD4 variable. More...

static void gmx_simdcall	store4 (float *m, Simd4Float a)
	Store the contents of SIMD4 float to aligned memory m. More...

static Simd4Float gmx_simdcall	load4U (const float *m)
	Load SIMD4 float from unaligned memory. More...

static void gmx_simdcall	store4U (float *m, Simd4Float a)
	Store SIMD4 float to unaligned memory. More...

static Simd4Float gmx_simdcall	simd4SetZeroF ()
	Set all SIMD4 float elements to 0. More...

static Simd4Float gmx_simdcall	operator& (Simd4Float a, Simd4Float b)
	Bitwise and for two SIMD4 float variables. More...

static Simd4Float gmx_simdcall	andNot (Simd4Float a, Simd4Float b)
	Bitwise andnot for two SIMD4 float variables. c=(~a) & b. More...

static Simd4Float gmx_simdcall	operator\| (Simd4Float a, Simd4Float b)
	Bitwise or for two SIMD4 floats. More...

static Simd4Float gmx_simdcall	operator^ (Simd4Float a, Simd4Float b)
	Bitwise xor for two SIMD4 float variables. More...

static Simd4Float gmx_simdcall	operator+ (Simd4Float a, Simd4Float b)
	Add two float SIMD4 variables. More...

static Simd4Float gmx_simdcall	operator- (Simd4Float a, Simd4Float b)
	Subtract two SIMD4 variables. More...

static Simd4Float gmx_simdcall	operator- (Simd4Float a)
	SIMD4 floating-point negate. More...

static Simd4Float gmx_simdcall	operator* (Simd4Float a, Simd4Float b)
	Multiply two SIMD4 variables. More...

static Simd4Float gmx_simdcall	fma (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-multiply-add. Result is a*b+c. More...

static Simd4Float gmx_simdcall	fms (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-multiply-subtract. Result is a*b-c. More...

static Simd4Float gmx_simdcall	fnma (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-negated-multiply-add. Result is -a*b+c. More...

static Simd4Float gmx_simdcall	fnms (Simd4Float a, Simd4Float b, Simd4Float c)
	SIMD4 Fused-negated-multiply-subtract. Result is -a*b-c. More...

static Simd4Float gmx_simdcall	rsqrt (Simd4Float x)
	SIMD4 1.0/sqrt(x) lookup. More...

static Simd4Float gmx_simdcall	abs (Simd4Float a)
	SIMD4 Floating-point fabs(). More...

static Simd4Float gmx_simdcall	max (Simd4Float a, Simd4Float b)
	Set each SIMD4 element to the largest from two variables. More...

static Simd4Float gmx_simdcall	min (Simd4Float a, Simd4Float b)
	Set each SIMD4 element to the largest from two variables. More...

static Simd4Float gmx_simdcall	round (Simd4Float a)
	SIMD4 Round to nearest integer value (in floating-point format). More...

static Simd4Float gmx_simdcall	trunc (Simd4Float a)
	Truncate SIMD4, i.e. round towards zero - common hardware instruction. More...

static float gmx_simdcall	dotProduct (Simd4Float a, Simd4Float b)
	Return dot product of two single precision SIMD4 variables. More...

static void gmx_simdcall	transpose (Simd4Float v0, Simd4Float v1, Simd4Float v2, Simd4Float v3)
	SIMD4 float transpose. More...

static Simd4FBool gmx_simdcall	operator== (Simd4Float a, Simd4Float b)
	a==b for SIMD4 float More...

static Simd4FBool gmx_simdcall	operator!= (Simd4Float a, Simd4Float b)
	a!=b for SIMD4 float More...

static Simd4FBool gmx_simdcall	operator< (Simd4Float a, Simd4Float b)
	a<b for SIMD4 float More...

static Simd4FBool gmx_simdcall	operator<= (Simd4Float a, Simd4Float b)
	a<=b for SIMD4 float. More...

static Simd4FBool gmx_simdcall	operator&& (Simd4FBool a, Simd4FBool b)
	Logical and on single precision SIMD4 booleans. More...

static Simd4FBool gmx_simdcall	operator\|\| (Simd4FBool a, Simd4FBool b)
	Logical or on single precision SIMD4 booleans. More...

static bool gmx_simdcall	anyTrue (Simd4FBool a)
	Returns non-zero if any of the boolean in SIMD4 a is True, otherwise 0. More...

static Simd4Float gmx_simdcall	selectByMask (Simd4Float a, Simd4FBool mask)
	Select from single precision SIMD4 variable where boolean is true. More...

static Simd4Float gmx_simdcall	selectByNotMask (Simd4Float a, Simd4FBool mask)
	Select from single precision SIMD4 variable where boolean is false. More...

static Simd4Float gmx_simdcall	blend (Simd4Float a, Simd4Float b, Simd4FBool sel)
	Vector-blend SIMD4 selection. More...

static float gmx_simdcall	reduce (Simd4Float a)
	Return sum of all elements in SIMD4 float variable. More...

SIMD implementation load/store operations for double precision floating point
static SimdDouble gmx_simdcall	simdLoad (const double *m, SimdDoubleTag={})
	Load GMX_SIMD_DOUBLE_WIDTH numbers from aligned memory. More...

static void gmx_simdcall	store (double *m, SimdDouble a)
	Store the contents of SIMD double variable to aligned memory m. More...

static SimdDouble gmx_simdcall	simdLoadU (const double *m, SimdDoubleTag={})
	Load SIMD double from unaligned memory. More...

static void gmx_simdcall	storeU (double *m, SimdDouble a)
	Store SIMD double to unaligned memory. More...

static SimdDouble gmx_simdcall	setZeroD ()
	Set all SIMD double variable elements to 0.0. More...

SIMD implementation load/store operations for integers (corresponding to double)
static SimdDInt32 gmx_simdcall	simdLoad (const std::int32_t *m, SimdDInt32Tag)
	Load aligned SIMD integer data, width corresponds to gmx::SimdDouble. More...

static void gmx_simdcall	store (std::int32_t *m, SimdDInt32 a)
	Store aligned SIMD integer data, width corresponds to gmx::SimdDouble. More...

static SimdDInt32 gmx_simdcall	simdLoadU (const std::int32_t *m, SimdDInt32Tag)
	Load unaligned integer SIMD data, width corresponds to gmx::SimdDouble. More...

static void gmx_simdcall	storeU (std::int32_t *m, SimdDInt32 a)
	Store unaligned SIMD integer data, width corresponds to gmx::SimdDouble. More...

static SimdDInt32 gmx_simdcall	setZeroDI ()
	Set all SIMD (double) integer variable elements to 0. More...

template<int index>
static std::int32_t gmx_simdcall	extract (SimdDInt32 a)
	Extract element with index i from gmx::SimdDInt32. More...

SIMD implementation double precision floating-point bitwise logical operations
static SimdDouble gmx_simdcall	operator& (SimdDouble a, SimdDouble b)
	Bitwise and for two SIMD double variables. More...

static SimdDouble gmx_simdcall	andNot (SimdDouble a, SimdDouble b)
	Bitwise andnot for SIMD double. More...

static SimdDouble gmx_simdcall	operator\| (SimdDouble a, SimdDouble b)
	Bitwise or for SIMD double. More...

static SimdDouble gmx_simdcall	operator^ (SimdDouble a, SimdDouble b)
	Bitwise xor for SIMD double. More...

SIMD implementation double precision floating-point arithmetics
static SimdDouble gmx_simdcall	operator+ (SimdDouble a, SimdDouble b)
	Add two double SIMD variables. More...

static SimdDouble gmx_simdcall	operator- (SimdDouble a, SimdDouble b)
	Subtract two double SIMD variables. More...

static SimdDouble gmx_simdcall	operator- (SimdDouble a)
	SIMD double precision negate. More...

static SimdDouble gmx_simdcall	operator* (SimdDouble a, SimdDouble b)
	Multiply two double SIMD variables. More...

static SimdDouble gmx_simdcall	fma (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-multiply-add. Result is a*b+c. More...

static SimdDouble gmx_simdcall	fms (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-multiply-subtract. Result is a*b-c. More...

static SimdDouble gmx_simdcall	fnma (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-negated-multiply-add. Result is -a*b+c. More...

static SimdDouble gmx_simdcall	fnms (SimdDouble a, SimdDouble b, SimdDouble c)
	SIMD double Fused-negated-multiply-subtract. Result is -a*b-c. More...

static SimdDouble gmx_simdcall	rsqrt (SimdDouble x)
	double SIMD 1.0/sqrt(x) lookup. More...

static SimdDouble gmx_simdcall	rcp (SimdDouble x)
	SIMD double 1.0/x lookup. More...

static SimdDouble gmx_simdcall	maskAdd (SimdDouble a, SimdDouble b, SimdDBool m)
	Add two double SIMD variables, masked version. More...

static SimdDouble gmx_simdcall	maskzMul (SimdDouble a, SimdDouble b, SimdDBool m)
	Multiply two double SIMD variables, masked version. More...

static SimdDouble gmx_simdcall	maskzFma (SimdDouble a, SimdDouble b, SimdDouble c, SimdDBool m)
	SIMD double fused multiply-add, masked version. More...

static SimdDouble gmx_simdcall	maskzRsqrt (SimdDouble x, SimdDBool m)
	SIMD double 1.0/sqrt(x) lookup, masked version. More...

static SimdDouble gmx_simdcall	maskzRcp (SimdDouble x, SimdDBool m)
	SIMD double 1.0/x lookup, masked version. More...

static SimdDouble gmx_simdcall	abs (SimdDouble a)
	SIMD double floating-point fabs(). More...

static SimdDouble gmx_simdcall	max (SimdDouble a, SimdDouble b)
	Set each SIMD double element to the largest from two variables. More...

static SimdDouble gmx_simdcall	min (SimdDouble a, SimdDouble b)
	Set each SIMD double element to the smallest from two variables. More...

static SimdDouble gmx_simdcall	round (SimdDouble a)
	SIMD double round to nearest integer value (in floating-point format). More...

static SimdDouble gmx_simdcall	trunc (SimdDouble a)
	Truncate SIMD double, i.e. round towards zero - common hardware instruction. More...

template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall	frexp (SimdDouble value, SimdDInt32 *exponent)
	Extract (integer) exponent and fraction from double precision SIMD. More...

template<MathOptimization opt = MathOptimization::Safe>
static SimdDouble gmx_simdcall	ldexp (SimdDouble value, SimdDInt32 exponent)
	Multiply a SIMD double value by the number 2 raised to an exp power. More...

static double gmx_simdcall	reduce (SimdDouble a)
	Return sum of all elements in SIMD double variable. More...

SIMD implementation double precision floating-point comparison, boolean, selection.
static SimdDBool gmx_simdcall	operator== (SimdDouble a, SimdDouble b)
	SIMD a==b for double SIMD. More...

static SimdDBool gmx_simdcall	operator!= (SimdDouble a, SimdDouble b)
	SIMD a!=b for double SIMD. More...

static SimdDBool gmx_simdcall	operator< (SimdDouble a, SimdDouble b)
	SIMD a<b for double SIMD. More...

static SimdDBool gmx_simdcall	operator<= (SimdDouble a, SimdDouble b)
	SIMD a<=b for double SIMD. More...

static SimdDBool gmx_simdcall	testBits (SimdDouble a)
	Return true if any bits are set in the single precision SIMD. More...

static SimdDBool gmx_simdcall	operator&& (SimdDBool a, SimdDBool b)
	Logical and on double precision SIMD booleans. More...

static SimdDBool gmx_simdcall	operator\|\| (SimdDBool a, SimdDBool b)
	Logical or on double precision SIMD booleans. More...

static bool gmx_simdcall	anyTrue (SimdDBool a)
	Returns non-zero if any of the boolean in SIMD a is True, otherwise 0. More...

static SimdDouble gmx_simdcall	selectByMask (SimdDouble a, SimdDBool mask)
	Select from double precision SIMD variable where boolean is true. More...

static SimdDouble gmx_simdcall	selectByNotMask (SimdDouble a, SimdDBool mask)
	Select from double precision SIMD variable where boolean is false. More...

static SimdDouble gmx_simdcall	blend (SimdDouble a, SimdDouble b, SimdDBool sel)
	Vector-blend SIMD double selection. More...

SIMD implementation integer (corresponding to double) bitwise logical operations
static SimdDInt32 gmx_simdcall	operator& (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise and. More...

static SimdDInt32 gmx_simdcall	andNot (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise not/complement. More...

static SimdDInt32 gmx_simdcall	operator\| (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise or. More...

static SimdDInt32 gmx_simdcall	operator^ (SimdDInt32 a, SimdDInt32 b)
	Integer SIMD bitwise xor. More...

SIMD implementation integer (corresponding to double) arithmetics
static SimdDInt32 gmx_simdcall	operator+ (SimdDInt32 a, SimdDInt32 b)
	Add SIMD integers. More...

static SimdDInt32 gmx_simdcall	operator- (SimdDInt32 a, SimdDInt32 b)
	Subtract SIMD integers. More...

static SimdDInt32 gmx_simdcall	operator* (SimdDInt32 a, SimdDInt32 b)
	Multiply SIMD integers. More...

SIMD implementation integer (corresponding to double) comparisons, boolean selection
static SimdDIBool gmx_simdcall	operator== (SimdDInt32 a, SimdDInt32 b)
	Equality comparison of two integers corresponding to double values. More...

static SimdDIBool gmx_simdcall	operator< (SimdDInt32 a, SimdDInt32 b)
	Less-than comparison of two SIMD integers corresponding to double values. More...

static SimdDIBool gmx_simdcall	testBits (SimdDInt32 a)
	Check if any bit is set in each element. More...

static SimdDIBool gmx_simdcall	operator&& (SimdDIBool a, SimdDIBool b)
	Logical AND on SimdDIBool. More...

static SimdDIBool gmx_simdcall	operator\|\| (SimdDIBool a, SimdDIBool b)
	Logical OR on SimdDIBool. More...

static bool gmx_simdcall	anyTrue (SimdDIBool a)
	Returns true if any of the boolean in x is True, otherwise 0. More...

static SimdDInt32 gmx_simdcall	selectByMask (SimdDInt32 a, SimdDIBool mask)
	Select from gmx::SimdDInt32 variable where boolean is true. More...

static SimdDInt32 gmx_simdcall	selectByNotMask (SimdDInt32 a, SimdDIBool mask)
	Select from gmx::SimdDInt32 variable where boolean is false. More...

static SimdDInt32 gmx_simdcall	blend (SimdDInt32 a, SimdDInt32 b, SimdDIBool sel)
	Vector-blend SIMD integer selection. More...

SIMD implementation conversion operations
static SimdDInt32 gmx_simdcall	cvtR2I (SimdDouble a)
	Round double precision floating point to integer. More...

static SimdDInt32 gmx_simdcall	cvttR2I (SimdDouble a)
	Truncate double precision floating point to integer. More...

static SimdDouble gmx_simdcall	cvtI2R (SimdDInt32 a)
	Convert integer to double precision floating point. More...

static SimdDIBool gmx_simdcall	cvtB2IB (SimdDBool a)
	Convert from double precision boolean to corresponding integer boolean. More...

static SimdDBool gmx_simdcall	cvtIB2B (SimdDIBool a)
	Convert from integer boolean to corresponding double precision boolean. More...

static SimdDouble gmx_simdcall	cvtF2D (SimdFloat f)
	Convert SIMD float to double. More...

static SimdFloat gmx_simdcall	cvtD2F (SimdDouble d)
	Convert SIMD double to float. More...

static void gmx_simdcall	cvtF2DD (SimdFloat f, SimdDouble d0, SimdDouble d1)
	Convert SIMD float to double. More...

static SimdFloat gmx_simdcall	cvtDD2F (SimdDouble d0, SimdDouble d1)
	Convert SIMD double to float. More...

static SimdFInt32 gmx_simdcall	cvtR2I (SimdFloat a)
	Round single precision floating point to integer. More...

static SimdFInt32 gmx_simdcall	cvttR2I (SimdFloat a)
	Truncate single precision floating point to integer. More...

static SimdFloat gmx_simdcall	cvtI2R (SimdFInt32 a)
	Convert integer to single precision floating point. More...

static SimdFIBool gmx_simdcall	cvtB2IB (SimdFBool a)
	Convert from single precision boolean to corresponding integer boolean. More...

static SimdFBool gmx_simdcall	cvtIB2B (SimdFIBool a)
	Convert from integer boolean to corresponding single precision boolean. More...

SIMD implementation load/store operations for single precision floating point
static SimdFloat gmx_simdcall	simdLoad (const float *m, SimdFloatTag={})
	Load GMX_SIMD_FLOAT_WIDTH float numbers from aligned memory. More...

static void gmx_simdcall	store (float *m, SimdFloat a)
	Store the contents of SIMD float variable to aligned memory m. More...

static SimdFloat gmx_simdcall	simdLoadU (const float *m, SimdFloatTag={})
	Load SIMD float from unaligned memory. More...

static void gmx_simdcall	storeU (float *m, SimdFloat a)
	Store SIMD float to unaligned memory. More...

static SimdFloat gmx_simdcall	setZeroF ()
	Set all SIMD float variable elements to 0.0. More...

SIMD implementation load/store operations for integers (corresponding to float)
static SimdFInt32 gmx_simdcall	simdLoad (const std::int32_t *m, SimdFInt32Tag)
	Load aligned SIMD integer data, width corresponds to gmx::SimdFloat. More...

static void gmx_simdcall	store (std::int32_t *m, SimdFInt32 a)
	Store ali

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