gmx Namespace Reference

Description

Generic GROMACS namespace.

Declares the integrator for test particle insertion.

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

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

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	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	ArrayRef
	STL-like container for an interface to a C array of T (or part of a std::vector<T, A> or std::array<T>). More...
class	CommandLineHelpWriter
	Writes help information for Options. More...
class	CommandLineModuleSettings
	Settings to pass information between a module and the general runner. More...
class	ICommandLineModule
	Module that can be run from command line using CommandLineModuleManager. More...
class	ICommandLineOptionsModuleSettings
	Settings to pass information between a CommandLineOptionsModule and generic code that runs it. More...
class	ICommandLineOptionsModule
	Module that can be run from a command line and uses gmx::Options for argument processing. More...
class	CommandLineParser
	Implements command-line parsing for Options objects. More...
struct	StaticLog2
	Evaluate log2(n) for integer n statically at compile time. More...
struct	StaticLog2< 1 >
	Specialization of StaticLog2<n> for n==1. More...
struct	StaticLog2< 0 >
	Specialization of StaticLog2<n> for n==0. More...
class	BasicVector
	C++ class for 3D vectors. 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	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 enumerated string values and writes the selected index into an enum variable. More...
class	BooleanOptionInfo
	Wrapper class for accessing boolean option information. More...
class	IntegerOptionInfo
	Wrapper class for accessing integer option information. More...
class	Int64OptionInfo
	Wrapper class for accessing 64-bit integer option information. More...
class	DoubleOptionInfo
	Wrapper class for accessing floating-point option information. More...
class	FloatOptionInfo
	Wrapper class for accessing floating-point option information. More...
class	StringOptionInfo
	Wrapper class for accessing string option information. More...
class	EnumOptionInfo
	Wrapper class for accessing enum option information. More...
class	FileNameOption
	Specifies an option that provides file names. More...
class	FileNameOptionInfo
	Wrapper class for accessing file name option information. More...
class	FileNameOptionManager
	Handles interaction of file name options with global options. More...
class	IOptionsBehavior
	Interface to provide extension points for options parsing. More...
class	IOptionsContainer
	Interface for adding input options. More...
class	IOptionsContainerWithSections
	Interface for adding input options with sections. More...
class	IOptionManager
	Base class for option managers. More...
class	Options
	Collection of options. More...
class	OptionSection
	Declares a simple option section. More...
class	OptionSectionHandle
	Allows adding options to an OptionSection. More...
class	RepeatingOptionSectionHandle
	Allows adding options to an RepeatingOptionSection. More...
class	RepeatingOptionSection
	Declares an option section that creates a structure for each instance. More...
class	TimeUnitManager
	Provides common functionality for time unit conversions. More...
class	TimeUnitBehavior
	Options behavior to add a time unit option. 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	AnalysisNeighborhoodPositions
	Input positions for neighborhood searching. More...
class	AnalysisNeighborhood
	Neighborhood searching for analysis tools. More...
class	AnalysisNeighborhoodPair
	Value type to represent a pair of positions found in neighborhood searching. More...
class	AnalysisNeighborhoodSearch
	Initialized neighborhood search with a fixed set of reference positions. More...
class	AnalysisNeighborhoodPairSearch
	Initialized neighborhood pair search with a fixed set of positions. More...
class	Selection
	Provides access to a single selection. More...
class	SelectionPosition
	Provides access to information about a single selected position. More...
class	SelectionCollection
	Collection of selections. More...
struct	SelectionTopologyProperties
	Describes topology properties required for selection evaluation. More...
class	SelectionOption
	Specifies an option that provides selection(s). More...
class	SelectionOptionInfo
	Wrapper class for accessing and modifying selection option information. More...
class	ITopologyProvider
	Provides topology information to SelectionOptionBehavior. More...
class	SelectionOptionBehavior
	Options behavior to allow using SelectionOptions. More...
class	SelectionOptionManager
	Handles interaction of selection options with other options and user input. More...
class	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	TopologyInformation
	Topology information passed to a trajectory analysis module. More...
class	TrajectoryAnalysisCommandLineRunner
	Runner for command-line trajectory analysis tools. More...
struct	EmptyArrayRef
	Tag type to initialize empty array references. 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	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	FlagsTemplate
	Template class for typesafe handling of combination of flags. More...
struct	InstallationPrefixInfo
	Provides information about installation prefix (see IProgramContext::installationPrefix()). More...
class	IProgramContext
	Provides context information about the program that is calling the library. More...
class	StringFormatter
	Function object that wraps a call to formatString() that expects a single conversion argument, for use with algorithms. More...
class	IdentityFormatter
	Function object to implement the same interface as StringFormatter to use with strings that should not be formatted further. More...
class	TextLineWrapperSettings
	Stores settings for line wrapping. More...
class	TextLineWrapper
	Wraps lines to a predefined length. 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::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 < ICommandLineModule >	CommandLineModulePointer
	Smart pointer type for managing a ICommandLineModule.
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.
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.
using	PaddedRVecVector = std::vector< RVec, Allocator< RVec, AlignedAllocationPolicy > >
	Temporary definition of a type usable for SIMD-style loads of RVec quantities. More...
template<typename T >
using	PaddedArrayRef = ArrayRef< T >
	Temporary definition of a type usable for SIMD-style loads of RVec quantities from a view. More...
typedef BasicVector< real >	RVec
	Shorthand for C++ rvec-equivalent type.
typedef BasicVector< int >	IVec
	Shorthand for C++ ivec-equivalent type.
typedef double	integrator_t (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, MDAtoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)
	Integrator algorithm implementation. More...
typedef std::array < SimulationSignal, eglsNR >	SimulationSignals
	Convenience typedef for the group of signals used.
typedef std::unique_ptr < IHelpTopic >	HelpTopicPointer
	Smart pointer type to manage a IHelpTopic object.
typedef EnumOption< int >	EnumIntOption
	Shorthand for an enumerated option that stores into an int variable.
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 std::random_device	RandomDevice
	Random device. More...
typedef ThreeFry2x64Fast	DefaultRandomEngine
	Default fast and accurate random engine in Gromacs. More...
typedef std::list < SelectionParserValue >	SelectionParserValueList
	Container for a list of SelectionParserValue objects.
typedef std::unique_ptr < SelectionParserValueList >	SelectionParserValueListPointer
	Smart pointer type for managing a SelectionParserValueList.
typedef std::list < SelectionParserParameter >	SelectionParserParameterList
	Container for a list of SelectionParserParameter objects.
typedef std::unique_ptr < SelectionParserParameterList >	SelectionParserParameterListPointer
	Smart pointer type for managing a SelectionParserParameterList.
typedef std::vector< Selection >	SelectionList
	Container of selections used in public selection interfaces.
typedef std::unique_ptr < internal::SelectionData >	SelectionDataPointer
	Smart pointer for managing an internal selection data object.
typedef std::vector < SelectionDataPointer >	SelectionDataList
	Container for storing a list of selections internally.
typedef std::shared_ptr < SelectionTreeElement >	SelectionTreeElementPointer
	Smart pointer type for selection tree element pointers.
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	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	GpuTaskAssignments = std::vector< GpuTaskAssignment >
	Container of RankGpuTaskAssignments e.g. for all ranks on a node.
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...
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.
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.

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	PinningPolicy : int { CannotBePinned, CanBePinned }
	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	{   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, eawhcoordproviderNR }
	AWH bias reaction coordinate provider.
enum	OptionFileType {   eftUnknown, eftTopology, eftTrajectory, eftEnergy,   eftPDB, eftIndex, eftPlot, eftGenericData,   eftOptionFileType_NR }
	Purpose of file(s) provided through an option.
enum	TimeUnit {   TimeUnit_fs, TimeUnit_ps, TimeUnit_ns, TimeUnit_us,   TimeUnit_ms, TimeUnit_s, TimeUnit_Default = TimeUnit_ps }
	Time values for TimeUnitManager. More...
enum	RandomDomain {   RandomDomain::Other = 0x00000000, RandomDomain::MaxwellVelocities = 0x00001000, RandomDomain::TestParticleInsertion = 0x00002000, RandomDomain::UpdateCoordinates = 0x00003000,   RandomDomain::UpdateConstraints = 0x00004000, RandomDomain::Thermostat = 0x00005000, RandomDomain::Barostat = 0x00006000, RandomDomain::ReplicaExchange = 0x00007000,   RandomDomain::ExpandedEnsemble = 0x00008000, RandomDomain::AwhBiasing = 0x00009000 }
	Enumerated values for fixed part of random seed (domain) More...
enum	TaskTarget : int { Auto, Cpu, Gpu }
	Record where a compute task is targetted.
enum	GpuTask : int { GpuTask::Nonbonded, GpuTask::Pme }
	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, eeCommunication, eeUnknownError }
	Possible error return codes from Gromacs functions. 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...
std::unique_ptr< IMDModule >	createElectricFieldModule ()
	Creates a module for an external electric field. More...
static gmx_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...
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 Grid &grid, const std::string &filename, int numBias, int biasIndex, std::vector< PointState > *pointState)
	Initializes the PMF and target with data read from an input table. More...
static void	normalizeBlock (AwhEnergyBlock *block, const Bias &bias)
	Normalizes block data for output. More...
void	initCorrelationGridHistory (CorrelationGridHistory *correlationGridHistory, int numCorrelationTensors, int tensorSize, int blockDataListSize)
	Initialize correlation grid history, sets all sizes. More...
CorrelationGridHistory	initCorrelationGridHistoryFromState (const CorrelationGrid &corrGrid)
	Allocate a correlation grid history with the same structure as the given correlation grid. More...
void	updateCorrelationGridHistory (CorrelationGridHistory *corrGridHist, const CorrelationGrid &corrGrid)
	Update the correlation grid history for checkpointing. More...
void	restoreCorrelationGridStateFromHistory (const CorrelationGridHistory &corrGridHist, CorrelationGrid *corrGrid)
	Restores the correlation grid state from the correlation grid history. More...
double	getDeviationFromPointAlongGridAxis (const Grid &grid, int dimIndex, int pointIndex, double value)
	Get the deviation along one dimension from the given value to a point in the grid. 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 Grid &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 Grid &grid, const awh_ivec indexMulti)
	Convert a multidimensional grid point index to a linear one. More...
bool	advancePointInSubgrid (const Grid &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 Grid &grid, const std::string &correctFormatMessage)
	Maps each point in the grid to a point in the data grid. More...
static void	readDimParams (int *ninp_p, t_inpfile **inp_p, const char *prefix, AwhDimParams *dimParams, const pull_params_t *pull_params, warninp_t wi, bool bComment)
	Read parameters of an AWH bias dimension. More...
static void	checkInputConsistencyAwhBias (const AwhBiasParams &awhBiasParams, warninp_t wi)
	Check consistency of input at the AWH bias level. More...
static void	read_bias_params (int *ninp_p, t_inpfile **inp_p, AwhBiasParams *awhBiasParams, const char *prefix, const t_inputrec *ir, warninp_t wi, bool bComment)
	Read parameters of an AWH bias. More...
static void	checkInputConsistencyAwh (const AwhParams &awhParams, warninp_t wi)
	Check consistency of input at the AWH level. More...
AwhParams *	readAndCheckAwhParams (int *ninp_p, t_inpfile **inp_p, const t_inputrec *inputrec, warninp_t wi)
	Allocate, initialize and check the AWH parameters with values from the input file. More...
static double	get_pull_coord_period (const pull_params_t *pull_params, int coord_ind, const matrix box)
	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...
void	setStateDependentAwhParams (AwhParams *awhParams, const pull_params_t *pull_params, pull_t *pull_work, const matrix box, int ePBC, const t_grpopts *inputrecGroupOptions, warninp_t wi)
	Sets AWH parameters that need state parameters such as the box vectors. 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	writeKeyValueTreeAsMdp (TextWriter *writer, const KeyValueTreeObject &tree)
	Write a flat key-value tree to writer in mdp style. More...
template<class T >
void	changePinningPolicy (HostVector< T > *v, PinningPolicy pinningPolicy)
	Helper function for changing the pinning policy of a HostVector. 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 gmx_gpu_info_t &gpuInfo, 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 void	gmx_detect_gpus (const gmx::MDLogger &mdlog, const t_commrec *cr)
	Detect GPUs, if that makes sense to attempt.
static void	gmx_collect_hardware_mpi (const gmx::CpuInfo &cpuInfo)
	Reduce the locally collected hwinfo_g over MPI ranks.
static void	spinUpCore () noexcept
	Utility that does dummy computing for max 2 seconds to spin up cores. More...
static void	hardwareTopologyPrepareDetection ()
	Prepare the system before hardware topology detection. More...
static void	hardwareTopologyDoubleCheckDetection (const gmx::MDLogger &mdlog, const gmx::HardwareTopology &hardwareTopology)
	Sanity check hardware topology and print some notes to log. More...
gmx_hw_info_t *	gmx_detect_hardware (const gmx::MDLogger &mdlog, const t_commrec *cr)
	Run detection, consistency checks, and make available on all ranks. More...
bool	compatibleGpusFound (const gmx_gpu_info_t &gpu_info)
	Return whether compatible GPUs were found.
void	gmx_hardware_info_free ()
	Free the hwinfo structure.
int	identifyAvx512FmaUnits ()
	Test whether machine has dual AVX512 FMA units. 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...
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...
static size_t	paddedRVecVectorSize (size_t numAtoms)
	Returns the padded size for PaddedRVecVector given the number of atoms. More...
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.
std::unique_ptr< MDAtoms >	makeMDAtoms (FILE *fp, const gmx_mtop_t &mtop, const t_inputrec &ir, bool useGpuForPme)
	Builder function for MdAtomsWrapper. More...
double	do_cg (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)
	Do conjugate gradients minimization. More...
double	do_lbfgs (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)
	Do L-BFGS conjugate gradients minimization. More...
double	do_steep (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)
	Do steepest descents minimization. More...
double	do_nm (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)
	Do normal modes analysis. More...
double	do_tpi (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)
	Do test particle insertion. 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.
gmx_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...
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...
bool	decideWhetherToUseGpusForNonbondedWithThreadMpi (const TaskTarget nonbondedTarget, const std::vector< int > &gpuIdsToUse, const std::vector< int > &userGpuTaskAssignment, const EmulateGpuNonbonded emulateGpuNonbonded, const bool usingVerletScheme, const bool nonbondedOnGpuIsUseful, const int numRanksPerSimulation)
	Decide whether this thread-MPI simulation will run nonbonded tasks on GPUs. More...
bool	decideWhetherToUseGpusForPmeWithThreadMpi (const bool useGpuForNonbonded, const TaskTarget pmeTarget, const std::vector< int > &gpuIdsToUse, const std::vector< int > &userGpuTaskAssignment, const bool canUseGpuForPme, const int numRanksPerSimulation, const int numPmeRanksPerSimulation)
	Decide whether this thread-MPI simulation will run PME tasks on GPUs. More...
bool	decideWhetherToUseGpusForNonbonded (const TaskTarget nonbondedTarget, const std::vector< int > &userGpuTaskAssignment, const EmulateGpuNonbonded emulateGpuNonbonded, const bool usingVerletScheme, const bool nonbondedOnGpuIsUseful, const bool gpusWereDetected)
	Decide whether the simulation will try to run nonbonded tasks on GPUs. More...
bool	decideWhetherToUseGpusForPme (const bool useGpuForNonbonded, const TaskTarget pmeTarget, const std::vector< int > &userGpuTaskAssignment, const bool canUseGpuForPme, const int numRanksPerSimulation, const int numPmeRanksPerSimulation, const bool gpusWereDetected)
	Decide whether the simulation will try to run tasks of different types on GPUs. More...
GpuTasksOnRanks	findAllGpuTasksOnThisNode (ArrayRef< const GpuTask > gpuTasksOnThisRank, int numRanksOnThisNode, MPI_Comm communicator)
	Returns container of all tasks on all ranks of this node that are eligible for GPU execution. More...
void	reportGpuUsage (const MDLogger &mdlog, bool userSetGpuIds, const GpuTaskAssignments &gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool bPrintHostName)
	Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation. More...
GpuTaskAssignments::value_type	runTaskAssignment (const std::vector< int > &gpuIdsToUse, const std::vector< int > &userGpuTaskAssignment, const gmx_hw_info_t &hardwareInfo, const MDLogger &mdlog, const t_commrec *cr, const std::vector< GpuTask > &gpuTasksOnThisRank)
	Coordinate the final stages of task assignment and reporting, and return the assignment for this rank. More...
template<GpuTask TaskType>
bool	hasTaskType (const GpuTaskMapping &mapping)
	Function for whether the task of mapping has value TaskType.
std::vector< int >	parseUserGpuIds (const std::string &gpuIdString)
	Parse a GPU ID string into a container describing the task types and associated device IDs. 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 gmx_gpu_info_t &gpu_info, const std::vector< int > &compatibleGpus, const std::vector< int > &gpuIds)
	Check that all user-selected GPUs are compatible. More...
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...
template<typename T >
ArrayRef< typename std::conditional < std::is_const< T >::value, const typename T::value_type, typename T::value_type >::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...
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::pair< int, int >	getCudaDriverVersion ()
	Returns a (major, minor) tuple of the CUDA driver version.
std::pair< int, int >	getCudaRuntimeVersion ()
	Returns a (major, minor) tuple of the CUDA runtime version.
const char *	getErrorCodeString (int errorcode)
	Returns a short string description of an error code. More...
void	printFatalErrorMessage (FILE *fp, const std::exception &ex)
	Formats a standard fatal error message for reporting an exception. More...
std::string	formatExceptionMessageToString (const std::exception &ex)
	Formats an error message for reporting an exception. More...
void	formatExceptionMessageToFile (FILE *fp, const std::exception &ex)
	Formats an error message for reporting an exception. More...
void	formatExceptionMessageToWriter (TextWriter *writer, const std::exception &ex)
	Formats an error message for reporting an exception. More...
int	processExceptionAtExit (const std::exception &ex)
	Handles an exception that is causing the program to terminate. More...
void	processExceptionAsFatalError (const std::exception &ex)
	Helper function for terminating the program on an exception. More...
template<class Exception , class Tag , class T >
std::enable_if < std::is_base_of < GromacsException, Exception > ::value, const Exception & > ::type	operator<< (const Exception &ex, const ExceptionInfo< Tag, T > &item)
	Associates extra information with an exception. More...
const DataFileFinder &	getLibraryFileFinder ()
	Gets a finder for locating data files from share/top/. More...
void	setLibraryFileFinder (const DataFileFinder *finder)
	Sets a finder for location data files from share/top/. More...
void	init (int *argc, char ***argv)
	Initializes the GROMACS library. More...
void	finalize ()
	Deinitializes the GROMACS library. More...
void	niceHeader (TextWriter *writer, const char *fn, char commentChar)
	Prints creation time stamp and user information into a string as comments, and returns it. More...
const IProgramContext &	getProgramContext ()
	Returns the global IProgramContext instance. More...
void	setProgramContext (const IProgramContext *context)
	Sets the global IProgramContext instance. More...
std::size_t	countWords (const char *s)
	Returns number of space-separated words in zero-terminated char ptr. More...
std::size_t	countWords (const std::string &str)
	Returns the number of space-separated words in a string object. More...
bool	endsWith (const char *str, const char *suffix)
	Tests whether a string ends with another string. More...
std::string	stripSuffixIfPresent (const std::string &str, const char *suffix)
	Removes a suffix from a string. More...
std::string	stripString (const std::string &str)
	Removes leading and trailing whitespace from a string. More...
std::string	formatString (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...
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 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.
static void	mdrunner_start_fn (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 integrator_t *	my_integrator (unsigned int ei)
	Return the correct integrator function.
static gmx::LoggerOwner	buildLogger (FILE *fplog, const t_commrec *cr)
	Initializes the logger for mdrun.
static TaskTarget	findTaskTarget (const char *optionString)
	Make a TaskTarget from an mdrun argument string.

Variables
static const int	c_linewidth = 80 - 2
	Linewidth used for warning output.
static const int	c_indent = 0
	Indent used for warning output.
static const int	c_biasMaxNumDim = 4
	The maximum dimensionality of the AWH coordinate.
const char *	eawhtarget_names [eawhtargetNR+1]
	String for target distribution. More...
const char *	eawhgrowth_names [eawhgrowthNR+1]
	String for weight histogram growth. More...
const char *	eawhpotential_names [eawhpotentialNR+1]
	String for AWH potential type. More...
const char *	eawhcoordprovider_names [eawhcoordproviderNR+1]
	String for AWH bias reaction coordinate provider. More...
static constexpr Architecture	c_architecture
	Constant that tells what the architecture is. More...
static const bool	bGPUBinary = GMX_GPU != GMX_GPU_NONE
	Convenience macro to help us avoid ifdefs each time we use sysconf. More...
static std::unique_ptr < gmx_hw_info_t >	hwinfo_g
	The hwinfo structure (common to all threads in this process). More...
static int	n_hwinfo = 0
	A reference counter for the hwinfo structure.
static tMPI_Thread_mutex_t	hw_info_lock = TMPI_THREAD_MUTEX_INITIALIZER
	A lock to protect the hwinfo structure.
integrator_t	do_steep
	Steepest descents energy minimization.
integrator_t	do_cg
	Conjugate gradient energy minimization.
integrator_t	do_lbfgs
	Conjugate gradient energy minimization using the L-BFGS algorithm.
integrator_t	do_nm
	Normal mode analysis.
integrator_t	do_tpi
	Test particle insertion.
integrator_t	do_md
	MD simulations.

Typedef Documentation

template<class T >

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

Aligned memory allocator.

Template Parameters

T	Type of objects to allocate

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

typedef ThreeFry2x64Fast gmx::DefaultRandomEngine

Default fast and accurate random engine in Gromacs.

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

template<class T >

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

Memory allocator that uses HostAllocationPolicy.

Template Parameters

T	Type of objects to allocate

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

typedef double gmx::integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, ObservablesHistory *observablesHistory, MDAtoms *mdatoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t *membed, gmx_walltime_accounting_t walltime_accounting)

Integrator algorithm implementation.

Parameters

[in]	fplog	Log file for output
[in]	cr	Communication record
[in]	mdlog	Log writer for important output
[in]	nfile	Number of files
[in]	fnm	Filename structure array
[in]	oenv	Output information
[in]	mdrunOptions	Options for mdrun
[in]	vsite	Virtual site information
[in]	constr	Constraint information
[in]	outputProvider	Additional output provider
[in]	inputrec	Input record with mdp options
[in]	top_global	Molecular topology for the whole system
[in]	fcd	Force and constraint data
[in]	state_global	The state (x, v, f, box etc.) of the whole system
[in]	observablesHistory	The observables statistics history
[in]	mdAtoms	Atom information
[in]	nrnb	Accounting for floating point operations
[in]	wcycle	Wall cycle timing information
[in]	fr	Force record with cut-off information and more
[in]	replExParams	Parameters for the replica exchange algorithm
[in]	membed	Membrane embedding data structure
[in]	walltime_accounting	More timing information

template<typename T >

using gmx::PaddedArrayRef = typedef ArrayRef<T>

Temporary definition of a type usable for SIMD-style loads of RVec quantities from a view.

Todo:

Find a more permanent solution that permits the update code to safely use a padded, aligned array-ref type.

using gmx::PaddedRVecVector = typedef std::vector < RVec, Allocator < RVec, AlignedAllocationPolicy > >

Temporary definition of a type usable for SIMD-style loads of RVec quantities.

Note

When resizing paddedRVecVector, the size should be chosen with paddedRVecVectorSize() to ensure correct padding.

Todo:

Consider replacing the padding applied in resizePaddedRVecVector() by automated padding on resize() of the vector.

Undo the move of allocator.h and alignedallocator.h from the internal to be public API applied in Change-Id: Ifb8dacf, needed to use AlignedAllocationPolicy here, when replacing std::vector here.

template<class T >

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

PageAligned memory allocator.

Template Parameters

T	Type of objects to allocate

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

typedef std::random_device gmx::RandomDevice

Random device.

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

Enumeration Type Documentation

enum gmx::Architecture

strong

Enum for GROMACS CPU hardware detection support.

Enumerator
X86	Not one of the cases below.
Arm	X86.
PowerPC	ARM. IBM PowerPC

enum gmx::AwhOutputEntryType

strong

Enum with the AWH variables to write.

Enumerator
MetaData	Meta data.
CoordValue	Coordinate value.
Pmf	The pmf.
Bias	The bias.
Visits	The number of visits.
Weights	The weights.
Target	The target distribition.
ForceCorrelationVolume	The volume of the force correlation tensor.
FrictionTensor	The full friction tensor.

enum gmx::AwhOutputMetaData

strong

Enum with the types of metadata to write.

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

enum gmx::GpuTask : int

strong

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

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

Enumerator
Nonbonded	Short-ranged interactions.
Pme	Long-ranged interactions.

enum gmx::Normalization

strong

Enum with different ways of normalizing the output.

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

enum gmx::PinningPolicy : int

strong

Helper enum for pinning policy of the allocation of HostAllocationPolicy.

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

enum gmx::RandomDomain

strong

Enumerated values for fixed part of random seed (domain)

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

Note

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

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

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

Function Documentation

static float gmx::abs ( float  a )

inlinestatic

Float Floating-point abs().

Parameters

a	any floating point values

Returns

abs(a) for each element.

Note

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

static double gmx::abs ( double  a )

inlinestatic

double doubleing-point abs().

Parameters

a	any doubleing point values

Returns

abs(a) for each element.

Note

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

static float gmx::acos ( float  x )

inlinestatic

Float acos.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

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

static double gmx::acos ( double  x )

inlinestatic

Double acos.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

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

static double gmx::acosSingleAccuracy ( double  x )

inlinestatic

Double acos, but with single accuracy.

Parameters

x	The argument to evaluate acos for

Returns

Acos(x)

Note

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

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

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

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

Parameters

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

Returns

true if the grid point was updated.

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

inlinestatic

Bitwise andnot for two scalar float variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

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

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

inlinestatic

Bitwise andnot for two scalar double variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

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

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

inlinestatic

Bitwise andnot for two scalar integer variables.

Parameters

a	data1
b	data2

Returns

(~data1) & data2

Note

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

static bool gmx::anyTrue ( bool  a )

inlinestatic

Returns if the boolean is true.

Parameters

a	Logical variable.

Returns

true if a is true, otherwise false.

Note

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

static float gmx::asin ( float  x )

inlinestatic

float asin.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

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

static double gmx::asin ( double  x )

inlinestatic

Double asin.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

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

static double gmx::asinSingleAccuracy ( double  x )

inlinestatic

Double asin, but with single accuracy.

Parameters

x	The argument to evaluate asin for

Returns

Asin(x)

Note

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

static float gmx::atan ( float  x )

inlinestatic

Float atan.

Parameters

x	The argument to evaluate atan for

Returns

Atan(x)

Note

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

static double gmx::atan ( double  x )

inlinestatic

Double atan.

Parameters

x	The argument to evaluate atan for

Returns

Atan(x)

Note

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

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

inlinestatic

Float atan2(y,x).

Parameters

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

Returns

Atan(y,x)

Note

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

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

inlinestatic

Double atan2(y,x).

Parameters

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

Returns

Atan(y,x)

Note

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

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

inlinestatic

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

Parameters

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

Returns

Atan(y,x)

Note

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

static double gmx::atanSingleAccuracy ( double  x )

inlinestatic

Double atan, but with single accuracy.

Parameters

x	The argument to evaluate atan for

Returns

Atan(x)

Note

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

void gmx::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.

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

Parameters

[in]	awhParams	The AWH parameters.
[in]	pointSize	Vector of grid-point sizes for each bias.
[in]	multiSimComm	Struct for multi-simulation communication.

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

inlinestatic

Blend float selection.

Parameters

a	First source
b	Second source
sel	Boolean selector

Returns

Select b if sel is true, a otherwise.

Note

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

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

inlinestatic

Blend double selection.

Parameters

a	First source
b	Second source
sel	Boolean selector

Returns

Select b if sel is true, a otherwise.

Note

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

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

inlinestatic

Blend integer selection.

Parameters

a	First source
b	Second source
sel	Boolean selector

Returns

Select b if sel is true, a otherwise.

Note

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

template<class T >

void gmx::changePinningPolicy	(	HostVector< T > *	v,
		PinningPolicy	pinningPolicy
	)

Helper function for changing the pinning policy of a HostVector.

Declare as a friend function the only supported way to change the pinning policy.

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

static void gmx::checkInputConsistencyAwh ( const AwhParams &  awhParams, warninp_t  wi  )

static

Check consistency of input at the AWH level.

Parameters

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

static void gmx::checkInputConsistencyAwhBias ( const AwhBiasParams &  awhBiasParams, warninp_t  wi  )

static

Check consistency of input at the AWH bias level.

Parameters

[in]	awhBiasParams	AWH bias parameters.
[in,out]	wi	Struct for bookkeeping warnings.

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

static

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

Parameters

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

void gmx::checkUserGpuIds	(	const gmx_gpu_info_t &	gpu_info,
		const std::vector< int > &	compatibleGpus,
		const std::vector< int > &	gpuIds
	)

Check that all user-selected GPUs are compatible.

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

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

Todo:

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

Parameters

[in]	gpu_info	Information detected about GPUs
[in]	compatibleGpus	Vector of GPUs that are compatible
[in]	gpuIds	The GPU IDs selected by the user.

Exceptions

std::bad_alloc

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

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

inlinestatic

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

Parameters

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

Returns

Magnitude of x, sign of y

Note

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

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

inlinestatic

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

Parameters

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

Returns

Magnitude of x, sign of y

Note

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

static float gmx::cos ( float  x )

inlinestatic

Float cos.

Parameters

x	The argument to evaluate cos for

Returns

Cos(x)

Note

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

static double gmx::cos ( double  x )

inlinestatic

Double cos.

Parameters

x	The argument to evaluate cos for

Returns

Cos(x)

Note

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

static double gmx::cosSingleAccuracy ( double  x )

inlinestatic

Double cos, but with single accuracy.

Parameters

x	The argument to evaluate cos for

Returns

Cos(x)

Note

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

static gmx_int64_t gmx::countSamples ( const std::vector< PointState > &  pointState )

static

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

Parameters

[in]

pointState

The state of the points in a bias.

Returns

the total sample count.

static int gmx::countTrailingZeroRows ( const double *const *  data, int  numRows, int  numColumns  )

static

Count trailing data rows containing only zeros.

Parameters

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

Returns

the number of trailing zero rows.

bool gmx::cpuIsX86Nehalem

(

const CpuInfo &

cpuInfo

)

Return true if the CPU is an Intel x86 Nehalem.

Parameters

cpuInfo

Object with cpu information

Returns

True if running on Nehalem CPU

std::unique_ptr< IMDModule > gmx::createElectricFieldModule

(

)

Creates a module for an external electric field.

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

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

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

static bool gmx::cvtB2IB ( bool  a )

inlinestatic

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

Parameters

a

boolean

Returns

same boolean

Note

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

static float gmx::cvtD2F ( double  a )

inlinestatic

Convert double to float (mimicks SIMD conversion)

Parameters

a

double

Returns

a, as float

Note

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

static double gmx::cvtF2D ( float  a )

inlinestatic

Convert float to double (mimicks SIMD conversion)

Parameters

a

float

Returns

a, as double double

Note

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

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

inlinestatic

Return integer.

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

Parameters

a

integer

Returns

same value (a)

Note

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

static bool gmx::cvtIB2B ( bool  a )

inlinestatic

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

Parameters

a

boolean

Returns

same boolean

Note

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

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

inlinestatic

Round single precision floating point to integer.

Parameters

a

float

Returns

Integer format, a rounded to nearest integer.

Note

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

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

inlinestatic

Round single precision doubleing point to integer.

Parameters

a

double

Returns

Integer format, a rounded to nearest integer.

Note

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

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

inlinestatic

Truncate single precision floating point to integer.

Parameters

a

float

Returns

Integer format, a truncated to integer.

Note

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

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

inlinestatic

Truncate single precision doubleing point to integer.

Parameters

a

double

Returns

Integer format, a truncated to integer.

Note

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

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

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

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

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

Parameters

[in]	nonbondedTarget	The user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	emulateGpuNonbonded	Whether we will emulate GPU calculation of nonbonded interactions.
[in]	usingVerletScheme	Whether the nonbondeds are using the Verlet scheme.
[in]	nonbondedOnGpuIsUseful	Whether computing nonbonded interactions on a GPU is useful for this calculation.
[in]	gpusWereDetected	Whether compatible GPUs were detected on any node.

Returns

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

Exceptions

std::bad_alloc

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

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

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

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

Parameters

[in]	nonbondedTarget	The user's choice for mdrun -nb for where to assign short-ranged nonbonded interaction tasks.
[in]	gpuIdsToUse	The compatible GPUs that the user permitted us to use.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	emulateGpuNonbonded	Whether we will emulate GPU calculation of nonbonded interactions.
[in]	usingVerletScheme	Whether the nonbondeds are using the Verlet scheme.
[in]	nonbondedOnGpuIsUseful	Whether computing nonbonded interactions on a GPU is useful for this calculation.
[in]	numRanksPerSimulation	The number of ranks in each simulation.

Returns

Whether the simulation will run nonbonded tasks on GPUs.

Exceptions

std::bad_alloc

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

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

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

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

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

Parameters

[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	pmeTarget	The user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	canUseGpuForPme	Whether the form of PME chosen can run on a GPU
[in]	numRanksPerSimulation	The number of ranks in each simulation.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation.
[in]	gpusWereDetected	Whether compatible GPUs were detected on any node.

Returns

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

Exceptions

std::bad_alloc

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

bool gmx::decideWhetherToUseGpusForPmeWithThreadMpi	(	const bool	useGpuForNonbonded,
		const TaskTarget	pmeTarget,
		const std::vector< int > &	gpuIdsToUse,
		const std::vector< int > &	userGpuTaskAssignment,
		const bool	canUseGpuForPme,
		const int	numRanksPerSimulation,
		const int	numPmeRanksPerSimulation
	)

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

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

Parameters

[in]	useGpuForNonbonded	Whether GPUs will be used for nonbonded interactions.
[in]	pmeTarget	The user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
[in]	gpuIdsToUse	The compatible GPUs that the user permitted us to use.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	canUseGpuForPme	Whether the form of PME chosen can run on a GPU
[in]	numRanksPerSimulation	The number of ranks in each simulation.
[in]	numPmeRanksPerSimulation	The number of PME ranks in each simulation.

Returns

Whether the simulation will run PME tasks on GPUs.

Exceptions

std::bad_alloc

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

double gmx::do_cg	(	FILE *	fplog,
		t_commrec *	cr,
		const gmx::MDLogger &	mdlog,
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions,
		gmx_vsite_t *	vsite,
		gmx_constr_t	constr,
		gmx::IMDOutputProvider *	outputProvider,
		t_inputrec *	inputrec,
		gmx_mtop_t *	top_global,
		t_fcdata *	fcd,
		t_state *	state_global,
		ObservablesHistory *	observablesHistory,
		gmx::MDAtoms *	mdAtoms,
		t_nrnb *	nrnb,
		gmx_wallcycle_t	wcycle,
		t_forcerec *	fr,
		const ReplicaExchangeParameters &	replExParams,
		gmx_membed_t *	membed,
		gmx_walltime_accounting_t	walltime_accounting
	)

Do conjugate gradients minimization.

double gmx::do_lbfgs	(	FILE *	fplog,
		t_commrec *	cr,
		const gmx::MDLogger &	mdlog,
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions,
		gmx_vsite_t *	vsite,
		gmx_constr_t	constr,
		gmx::IMDOutputProvider *	outputProvider,
		t_inputrec *	inputrec,
		gmx_mtop_t *	top_global,
		t_fcdata *	fcd,
		t_state *	state_global,
		ObservablesHistory *	observablesHistory,
		gmx::MDAtoms *	mdAtoms,
		t_nrnb *	nrnb,
		gmx_wallcycle_t	wcycle,
		t_forcerec *	fr,
		const ReplicaExchangeParameters &	replExParams,
		gmx_membed_t *	membed,
		gmx_walltime_accounting_t	walltime_accounting
	)

Do L-BFGS conjugate gradients minimization.

double gmx::do_nm	(	FILE *	fplog,
		t_commrec *	cr,
		const gmx::MDLogger &	mdlog,
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions,
		gmx_vsite_t *	vsite,
		gmx_constr_t	constr,
		gmx::IMDOutputProvider *	outputProvider,
		t_inputrec *	inputrec,
		gmx_mtop_t *	top_global,
		t_fcdata *	fcd,
		t_state *	state_global,
		ObservablesHistory *	observablesHistory,
		gmx::MDAtoms *	mdAtoms,
		t_nrnb *	nrnb,
		gmx_wallcycle_t	wcycle,
		t_forcerec *	fr,
		const ReplicaExchangeParameters &	replExParams,
		gmx_membed_t *	membed,
		gmx_walltime_accounting_t	walltime_accounting
	)

Do normal modes analysis.

double gmx::do_steep	(	FILE *	fplog,
		t_commrec *	cr,
		const gmx::MDLogger &	mdlog,
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions,
		gmx_vsite_t *	vsite,
		gmx_constr_t	constr,
		gmx::IMDOutputProvider *	outputProvider,
		t_inputrec *	inputrec,
		gmx_mtop_t *	top_global,
		t_fcdata *	fcd,
		t_state *	state_global,
		ObservablesHistory *	observablesHistory,
		gmx::MDAtoms *	mdAtoms,
		t_nrnb *	nrnb,
		gmx_wallcycle_t	wcycle,
		t_forcerec *	fr,
		const ReplicaExchangeParameters &	replExParams,
		gmx_membed_t *	membed,
		gmx_walltime_accounting_t	walltime_accounting
	)

Do steepest descents minimization.

double gmx::do_tpi	(	FILE *	fplog,
		t_commrec *	cr,
		const gmx::MDLogger &	mdlog,
		int	nfile,
		const t_filenm	fnm[],
		const gmx_output_env_t *	oenv,
		const MdrunOptions &	mdrunOptions,
		gmx_vsite_t *	vsite,
		gmx_constr_t	constr,
		gmx::IMDOutputProvider *	outputProvider,
		t_inputrec *	inputrec,
		gmx_mtop_t *	top_global,
		t_fcdata *	fcd,
		t_state *	state_global,
		ObservablesHistory *	observablesHistory,
		gmx::MDAtoms *	mdAtoms,
		t_nrnb *	nrnb,
		gmx_wallcycle_t	wcycle,
		t_forcerec *	fr,
		const ReplicaExchangeParameters &	replExParams,
		gmx_membed_t *	membed,
		gmx_walltime_accounting_t	walltime_accounting
	)

Do test particle insertion.

Integrator algorithm implementation. (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,

Parameters

[in]	fplog	Log file for output
[in]	cr	Communication record
[in]	mdlog	Log writer for important output
[in]	nfile	Number of files
[in]	fnm	Filename structure array
[in]	oenv	Output information
[in]	mdrunOptions	Options for mdrun
[in]	vsite	Virtual site information
[in]	constr	Constraint information
[in]	outputProvider	Additional output provider
[in]	inputrec	Input record with mdp options
[in]	top_global	Molecular topology for the whole system
[in]	fcd	Force and constraint data
[in]	state_global	The state (x, v, f, box etc.) of the whole system
[in]	observablesHistory	The observables statistics history
[in]	mdAtoms	Atom information
[in]	nrnb	Accounting for floating point operations
[in]	wcycle	Wall cycle timing information
[in]	fr	Force record with cut-off information and more
[in]	replExParams	Parameters for the replica exchange algorithm
[in]	membed	Membrane embedding data structure
[in]	walltime_accounting	More timing information (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog, int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions, gmx_vsite_t *vsite, gmx_constr_t constr, gmx::IMDOutputProvider *outputProvider, t_inputrec *inputrec, gmx_mtop_t *top_global, t_fcdata *fcd, t_state *state_global, gmx::MDAtoms *mdAtoms, t_nrnb *nrnb, gmx_wallcycle_t wcycle, gmx_edsam_t ed, t_forcerec *fr, const ReplicaExchangeParameters &replExParams, gmx_membed_t gmx_unused *membed, gmx_walltime_accounting_t walltime_accounting)

void gmx::doDeviceTransfers	(	const gmx_gpu_info_t &	gpuInfo,
		ArrayRef< const char >	input,
		ArrayRef< char >	output
	)

Helper function for GPU test code to be platform agnostic.

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

Exceptions

InternalError

Upon any GPU API error condition.

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

static

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

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

Parameters

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

static float gmx::erf ( float  x )

inlinestatic

Float erf(x).

Parameters

x

Argument.

Returns

erf(x)

Note

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

static double gmx::erf ( double  x )

inlinestatic

Double erf(x).

Parameters

x

Argument.

Returns

erf(x)

Note

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

static float gmx::erfc ( float  x )

inlinestatic

Float erfc(x).

Parameters

x

Argument.

Returns

erfc(x)

Note

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

static double gmx::erfc ( double  x )

inlinestatic

Double erfc(x).

Parameters

x

Argument.

Returns

erfc(x)

Note

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

static double gmx::erfcSingleAccuracy ( double  x )

inlinestatic

Double erfc(x), but with single accuracy.

Parameters

x

Argument.

Returns

erfc(x)

Note

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

double gmx::erfinv

(

double

x

)

Inverse error function, double precision.

Parameters

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

Returns

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

float gmx::erfinv

(

float

x

)

Inverse error function, single precision.

Parameters

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

Returns

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

static double gmx::erfSingleAccuracy ( double  x )

inlinestatic

Double erf(x), but with single accuracy.

Parameters

x

Argument.

Returns

erf(x)

Note

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

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::exp ( float  x )

inlinestatic

Float exp(x).

Parameters

x

Argument.

Returns

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

Note

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

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::exp ( double  x )

inlinestatic

Double exp(x).

Parameters

x

Argument.

Returns

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

Note

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

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::exp2 ( float  x )

inlinestatic

Float 2^x.

Parameters

x

Argument.

Returns

2^x. Undefined if input argument caused overflow.

Note

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

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::exp2 ( double  x )

inlinestatic

Double 2^x.

Parameters

x

Argument.

Returns

2^x. Undefined if input argument caused overflow.

Note

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

static double gmx::exp2SingleAccuracy ( double  x )

inlinestatic

Double 2^x, but with single accuracy.

Parameters

x

Argument.

Returns

2^x. Undefined if input argument caused overflow.

Note

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

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

inlinestatic

Copy single float to three variables.

Parameters

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

Note

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

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

inlinestatic

Copy single double to three variables.

Parameters

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

Note

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

static double gmx::expSingleAccuracy ( double  x )

inlinestatic

Double exp(x), but with single accuracy.

Parameters

x

Argument.

Returns

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

Note

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

GpuTasksOnRanks gmx::findAllGpuTasksOnThisNode	(	ArrayRef< const GpuTask >	gpuTasksOnThisRank,
		int	numRanksOnThisNode,
		MPI_Comm	communicator
	)

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

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

a*b + c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

a*b + c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

a*b - c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

a*b - c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b + c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b + c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b - c

Note

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

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

inlinestatic

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

Parameters

a	factor1
b	factor2
c	term

Returns

-a*b - c

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

Alignment of the memory from which we read.

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

Alignment of the memory from which we read.

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

Alignment of the memory from which we read.

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

Alignment of the memory from which we read.

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

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

Template Parameters

align

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

Parameters

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

Note

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

template<class RealType = real, unsigned int Bits, class Rng >

RealType gmx::generateCanonical

(

Rng &

g

)

Generate a floating-point value with specified number of random bits.

Template Parameters

RealType	Floating-point type to generate
Bits	Number of random bits to generate
Rng	Random number generator class

Parameters

g	Random number generator to use

This implementation avoids the bug in libc++ and stdlibc++ (which is due to the C++ standard being unclear) where 1.0 can be returned occasionally.

static double gmx::get_pull_coord_period ( const pull_params_t *  pull_params, int  coord_ind, const matrix  box  )

static

Gets the period of a pull coordinate.

Parameters

[in]	pull_params	Pull parameters.
[in]	coord_ind	Pull coordinate index.
[in]	box	Box vectors.

Returns

the period (or 0 if not periodic).

double gmx::getDeviationFromPointAlongGridAxis	(	const Grid &	grid,
		int	dimIndex,
		int	pointIndex,
		double	value
	)

Get the deviation along one dimension from the given value to a point in the grid.

Parameters

[in]	grid	The grid.
[in]	dimIndex	Dimensional index in [0, ndim -1].
[in]	pointIndex	Grid point index.
[in]	value	Value along the given dimension.

Returns

the deviation of the given value to the given point.

static int gmx::getNearestIndexInGrid ( const awh_dvec  value, const std::vector< GridAxis > &  axis  )

static

Map a value to the nearest point in the grid.

Parameters

[in]	value	Value.
[in]	axis	The grid axes.

Returns

the point index nearest to the value.

static std::size_t gmx::getPageSize ( )

static

Return a page size, from a sysconf/WinAPI query if available, or a default guess (4096 bytes).

Todo:

Move this function into sysinfo.cpp where other OS-specific code/includes live

gmx_hw_info_t * gmx::gmx_detect_hardware	(	const gmx::MDLogger &	mdlog,
		const t_commrec *	cr
	)

Run detection, consistency checks, and make available on all ranks.

This routine constructs the global hwinfo structure and returns a pointer to it. It will run a preamble before executing cpu and hardware checks, and then run consistency checks afterwards. The results will also be made available on all nodes. Caller is responsible for calling gmx_hardware_info_free() when finished.

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

static

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

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

std::int64_t gmx::greatestCommonDivisor	(	std::int64_t	p,
		std::int64_t	q
	)

Find greatest common divisor of two numbers.

Parameters

p	First number, positive
q	Second number, positive

Returns

Greatest common divisor of p and q

static void gmx::hardwareTopologyDoubleCheckDetection ( const gmx::MDLogger &  mdlog, const gmx::HardwareTopology &  hardwareTopology  )

static

Sanity check hardware topology and print some notes to log.

Parameters

mdlog	Logger.
hardwareTopology	Reference to hardwareTopology object.

static void gmx::hardwareTopologyPrepareDetection ( )

static

Prepare the system before hardware topology detection.

This routine should perform any actions we want to put the system in a state where we want it to be before detecting the hardware topology. For most processors there is nothing to do, but some architectures (in particular ARM) have support for taking configured cores offline, which will make them disappear from the online processor count.

This routine checks if there is a mismatch between the number of cores configured and online, and in that case we issue a small workload that attempts to wake sleeping cores before doing the actual detection.

This type of mismatch can also occur for x86 or PowerPC on Linux, if SMT has only been disabled in the kernel (rather than bios). Since those cores will never come online automatically, we currently skip this test for x86 & PowerPC to avoid wasting 2 seconds. We also skip the test if there is no thread support.

Note

Cores will sleep relatively quickly again, so it's important to issue the real detection code directly after this routine.

bool gmx::haveBiasSharingWithinSimulation

(

const AwhParams &

awhParams

)

Returns if any bias is sharing within a simulation.

Parameters

[in]

awhParams

The AWH parameters.

int gmx::identifyAvx512FmaUnits

(

)

Test whether machine has dual AVX512 FMA units.

Returns

1 or 2 for the number of AVX512 FMA units if AVX512 support is present, 0 if we know the hardware does not have AVX512 support, or -1 if the test cannot run because the compiler lacked AVX512 support.

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

Initialize correlation grid history, sets all sizes.

Parameters

[in,out]	correlationGridHistory	Correlation grid history for master rank.
[in]	numCorrelationTensors	Number of correlation tensors in the grid.
[in]	tensorSize	Number of correlation elements in each tensor.
[in]	blockDataListSize	The number of blocks in the list of each tensor element.

CorrelationGridHistory gmx::initCorrelationGridHistoryFromState

(

const CorrelationGrid &

corrGrid

)

Allocate a correlation grid history with the same structure as the given correlation grid.

This function would be called at the start of a new simulation. Note that only sizes and memory are initialized here. History data is set by updateCorrelationGridHistory.

Parameters

[in,out]

corrGrid

Correlation grid state to initialize with.

Returns

the correlation grid history struct.

static bool gmx::intervalIsInPeriodicInterval ( double  origin, double  end, double  period  )

static

Checks if the given interval is defined in the correct periodic interval.

Parameters

[in]	origin	Start value of interval.
[in]	end	End value of interval.
[in]	period	Period (or 0 if not periodic).

Returns

true if the end point values are in the correct periodic interval.

static float gmx::inv ( float  x )

inlinestatic

Calculate 1/x for float.

Parameters

x	Argument that must be nonzero. This routine does not check arguments.

Returns

1/x. Result is undefined if your argument was invalid.

Note

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

static double gmx::inv ( double  x )

inlinestatic

Calculate 1/x for double.

Parameters

x	Argument that must be nonzero. This routine does not check arguments.

Returns

1/x. Result is undefined if your argument was invalid.

Note

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

static float gmx::invcbrt ( float  x )

inlinestatic

Calculate inverse cube root of x in single precision.

Parameters

x

Argument

Returns

x^(-1/3)

This routine is typically faster than using std::pow().

static double gmx::invcbrt ( double  x )

inlinestatic

Calculate inverse sixth root of x in double precision.

Parameters

x

Argument

Returns

x^(-1/3)

This routine is typically faster than using std::pow().

static double gmx::invcbrt ( int  x )

inlinestatic

Calculate inverse sixth root of integer x in double precision.

Parameters

x

Argument

Returns

x^(-1/3)

This routine is typically faster than using std::pow().

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

Invert a simulation-box matrix in src, return in dest.

This routine assumes that src is a simulation-box matrix, i.e. has zeroes in the upper-right triangle. A fatal error occurs if the product of the leading diagonal is too small. The inversion can be done "in place", i.e src and dest can be the same matrix.

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

Invert a general 3x3 matrix in src, return in dest.

A fatal error occurs if the determinant is too small. src and dest cannot be the same matrix.

static double gmx::invSingleAccuracy ( double  x )

inlinestatic

Calculate 1/x for double, but with single accuracy.

Parameters

x	Argument that must be nonzero. This routine does not check arguments.

Returns

1/x. Result is undefined if your argument was invalid.

Note

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

static float gmx::invsixthroot ( float  x )

inlinestatic

Calculate inverse sixth root of x in single precision.

Parameters

x	Argument, must be greater than zero.

Returns

x^(-1/6)

This routine is typically faster than using std::pow().

static double gmx::invsixthroot ( double  x )

inlinestatic

Calculate inverse sixth root of x in double precision.

Parameters

x	Argument, must be greater than zero.

Returns

x^(-1/6)

This routine is typically faster than using std::pow().

static double gmx::invsixthroot ( int  x )

inlinestatic

Calculate inverse sixth root of integer x in double precision.

Parameters

x	Argument, must be greater than zero.

Returns

x^(-1/6)

This routine is typically faster than using std::pow().

static float gmx::invsqrt ( float  x )

inlinestatic

Calculate 1.0/sqrt(x) in single precision.

Parameters

x	Positive value to calculate inverse square root for

For now this is implemented with std::sqrt(x) since gcc seems to do a decent job optimizing it. However, we might decide to use instrinsics or compiler-specific functions in the future.

Returns

1.0/sqrt(x)

static double gmx::invsqrt ( double  x )

inlinestatic

Calculate 1.0/sqrt(x) in double precision, but single range.

Parameters

x	Positive value to calculate inverse square root for, must be in the input domain valid for single precision.

For now this is implemented with std::sqrt(x). However, we might decide to use instrinsics or compiler-specific functions in the future, and then we want to have the freedom to do the first step in single precision.

Returns

1.0/sqrt(x)

static double gmx::invsqrt ( int  x )

inlinestatic

Calculate 1.0/sqrt(x) for integer x in double precision.

Parameters

x	Positive value to calculate inverse square root for.

Returns

1.0/sqrt(x)

static void gmx::invsqrtPair ( float  x0, float  x1, float *  out0, float *  out1  )

inlinestatic

Calculate 1/sqrt(x) for two floats.

Parameters

	x0	First argument, x0 must be positive - no argument checking.
	x1	Second argument, x1 must be positive - no argument checking.
[out]	out0	Result 1/sqrt(x0)
[out]	out1	Result 1/sqrt(x1)

Note

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

static void gmx::invsqrtPair ( double  x0, double  x1, double *  out0, double *  out1  )

inlinestatic

Calculate 1/sqrt(x) for two doubles.

Parameters

	x0	First argument, x0 must be positive - no argument checking.
	x1	Second argument, x1 must be positive - no argument checking.
[out]	out0	Result 1/sqrt(x0)
[out]	out1	Result 1/sqrt(x1)

Note

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

static void gmx::invsqrtPairSingleAccuracy ( double  x0, double  x1, double *  out0, double *  out1  )

inlinestatic

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

Parameters

	x0	First argument, x0 must be positive - no argument checking.
	x1	Second argument, x1 must be positive - no argument checking.
[out]	out0	Result 1/sqrt(x0)
[out]	out1	Result 1/sqrt(x1)

Note

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

static double gmx::invsqrtSingleAccuracy ( double  x )

inlinestatic

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

Parameters

x	Argument that must be >0. This routine does not check arguments.

Returns

1/sqrt(x). Result is undefined if your argument was invalid.

Note

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

void gmx::linearArrayIndexToMultiDim	(	int	indexLinear,
		int	ndim,
		const awh_ivec	numPointsDim,
		awh_ivec	indexMulti
	)

Convert a linear array index to a multidimensional one.

Parameters

[in]	indexLinear	Linear array index
[in]	ndim	Number of dimensions of the array.
[in]	numPointsDim	Number of points for each dimension.
[out]	indexMulti	The multidimensional index.

void gmx::linearGridindexToMultiDim	(	const Grid &	grid,
		int	indexLinear,
		awh_ivec	indexMulti
	)

Convert a linear grid point index to a multidimensional one.

Parameters

[in]	grid	The grid.
[in]	indexLinear	Linear grid point index to convert to a multidimensional one.
[out]	indexMulti	The multidimensional index.

static float gmx::log ( float  x )

inlinestatic

Float log(x). This is the natural logarithm.

Parameters

x	Argument, should be >0.

Returns

The natural logarithm of x. Undefined if argument is invalid.

Note

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

static double gmx::log ( double  x )

inlinestatic

Double log(x). This is the natural logarithm.

Parameters

x	Argument, should be >0.

Returns

The natural logarithm of x. Undefined if argument is invalid.

Note

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

unsigned int gmx::log2I

(

std::uint32_t

x

)

Compute floor of logarithm to base 2, 32 bit unsigned argument.

Parameters

x	32-bit unsigned argument

Returns

log2(x)

Note

This version of the overloaded function uses unsigned arguments to be able to handle arguments using all 32 bits.

unsigned int gmx::log2I

(

std::uint64_t

x

)

Compute floor of logarithm to base 2, 64 bit unsigned argument.

Parameters

x	64-bit unsigned argument

Returns

log2(x)

Note

This version of the overloaded function uses unsigned arguments to be able to handle arguments using all 64 bits.

unsigned int gmx::log2I

(

std::int32_t

x

)

Compute floor of logarithm to base 2, 32 bit signed argument.

Parameters

x	32-bit signed argument

Returns

log2(x)

Note

This version of the overloaded function will assert that x is not negative.

unsigned int gmx::log2I

(

std::int64_t

x

)

Compute floor of logarithm to base 2, 64 bit signed argument.

Parameters

x	64-bit signed argument

Returns

log2(x)

Note

This version of the overloaded function will assert that x is not negative.

static double gmx::logSingleAccuracy ( double  x )

inlinestatic

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

Parameters

x	Argument, should be >0.

Returns

The natural logarithm of x. Undefined if argument is invalid.

Note

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

template<typename T >

ArrayRef<typename std::conditional<std::is_const<T>::value, const typename T::value_type, typename T::value_type>::type> gmx::makeArrayRef

(

T &

c

)

Create ArrayRef from container with type deduction.

See Also

ArrayRef

template<typename T >

ArrayRef<const typename T::value_type> gmx::makeConstArrayRef

(

const T &

c

)

Create ArrayRef to const T from container with type deduction.

See Also

ArrayRef

std::vector< int > gmx::makeGpuIds	(	ArrayRef< const int >	compatibleGpus,
		size_t	numGpuTasks
	)

Make a vector containing numGpuTasks IDs of the IDs found in compatibleGpus.

Exceptions

std::bad_alloc

If out of memory

Returns

A sorted vector of IDs of compatible vectors, whose length matches that of the number of GPU tasks required.

std::string gmx::makeGpuIdString	(	const std::vector< int > &	gpuIds,
		int	totalNumberOfTasks
	)

Convert a container of GPU deviced IDs to a string that can be used by gmx tune_pme as input to mdrun -gputasks.

Produce a valid input for mdrun -gputasks that refers to the device IDs in gpuIds but produces a mapping for totalNumberOfTasks tasks. Note that gmx tune_pme does not currently support filling mdrun -gputasks.

Parameters

[in]	gpuIds	Container of device IDs
[in]	totalNumberOfTasks	Total number of tasks for the output mapping produced by the returned string.

Returns

A string that is suitable to pass to mdrun -gputasks.

Exceptions

std::bad_alloc

If out of memory.

std::unique_ptr< MDAtoms > gmx::makeMDAtoms	(	FILE *	fp,
		const gmx_mtop_t &	mtop,
		const t_inputrec &	ir,
		bool	useGpuForPme
	)

Builder function for MdAtomsWrapper.

Builder function.

gmx_uint64_t gmx::makeRandomSeed

(

)

Return 64 random bits from the random device, suitable as seed.

If the internal random device output is smaller than 64 bits, this routine will use multiple calls internally until we have 64 bits of random data.

Returns

64-bit unsigned integer with random bits.

void gmx::mapGridToDataGrid	(	std::vector< int > *	gridpointToDatapoint,
		const double *const *	data,
		int	numDataPoints,
		const std::string &	dataFilename,
		const Grid &	grid,
		const std::string &	correctFormatMessage
	)

Maps each point in the grid to a point in the data grid.

This functions maps an AWH bias grid to a user provided input data grid. The value of data grid point i along dimension d is given by data[d][i]. The number of dimensions of the data should equal that of the grid. A fatal error is thrown if extracting the data fails or the data does not cover the whole grid.

Parameters

[out]	gridpointToDatapoint	Array mapping each grid point to a data point index.
[in]	data	2D array in format ndim x ndatapoints with data grid point values.
[in]	numDataPoints	Number of data points.
[in]	dataFilename	The data filename.
[in]	grid	The grid.
[in]	correctFormatMessage	String to include in error message if extracting the data fails.

static float gmx::maskAdd ( float  a, float  b, float  m  )

inlinestatic

Add two float variables, masked version.

Parameters

a	term1
b	term2
m	mask

Returns

a+b where mask is true, a otherwise.

Note

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

static double gmx::maskAdd ( double  a, double  b, double  m  )

inlinestatic

Add two double variables, masked version.

Parameters

a	term1
b	term2
m	mask

Returns

a+b where mask is true, a otherwise.

Note

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

static float gmx::maskzFma ( float  a, float  b, float  c, float  m  )

inlinestatic

Float fused multiply-add, masked version.

Parameters

a	factor1
b	factor2
c	term
m	mask

Returns

a*b+c where mask is true, 0.0 otherwise.

Note

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

static double gmx::maskzFma ( double  a, double  b, double  c, double  m  )

inlinestatic

double fused multiply-add, masked version.

Parameters

a	factor1
b	factor2
c	term
m	mask

Returns

a*b+c where mask is true, 0.0 otherwise.

Note

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

static float gmx::maskzInv ( float  x, bool  m  )

inlinestatic

Calculate 1/x for masked entry of float.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out float will not lead to floating-point exceptions.

Parameters

x	Argument that must be nonzero if masked-in.
m	Mask

Returns

1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

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

static double gmx::maskzInv ( double  x, bool  m  )

inlinestatic

Calculate 1/x for masked entry of double.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be nonzero if masked-in.
m	Mask

Returns

1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

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

static double gmx::maskzInvSingleAccuracy ( double  x, bool  m  )

inlinestatic

Calculate 1/x for masked entry of double, but with single accuracy.

This routine only evaluates 1/x if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be nonzero if masked-in.
m	Mask

Returns

1/x. Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

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

static float gmx::maskzInvsqrt ( float  x, bool  m  )

inlinestatic

Calculate 1/sqrt(x) for masked entry of float.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out float will not lead to floating-point exceptions.

Parameters

x	Argument that must be >0 if masked-in.
m	Mask

Returns

1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

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

static double gmx::maskzInvsqrt ( double  x, bool  m  )

inlinestatic

Calculate 1/sqrt(x) for masked entry of double.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be >0 if masked-in.
m	Mask

Returns

1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

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

static double gmx::maskzInvsqrtSingleAccuracy ( double  x, bool  m  )

inlinestatic

Calculate 1/sqrt(x) for masked entry of double, but with single accuracy.

This routine only evaluates 1/sqrt(x) if mask is true. Illegal values for a masked-out double will not lead to floating-point exceptions.

Parameters

x	Argument that must be >0 if masked-in.
m	Mask

Returns

1/sqrt(x). Result is undefined if your argument was invalid or entry was not masked, and 0.0 for masked-out entries.

Note

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

static float gmx::maskzMul ( float  a, float  b, float  m  )

inlinestatic

Multiply two float variables, masked version.

Parameters

a	factor1
b	factor2
m	mask

Returns

a*b where mask is true, 0.0 otherwise.

Note

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

static double gmx::maskzMul ( double  a, double  b, double  m  )

inlinestatic

Multiply two double variables, masked version.

Parameters

a	factor1
b	factor2
m	mask

Returns

a*b where mask is true, 0.0 otherwise.

Note

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

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

inlinestatic

Set each float element to the largest from two variables.

Parameters

a	Any floating-point value
b	Any floating-point value

Returns

max(a,b) for each element.

Note

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

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

inlinestatic

Set each double element to the largest from two variables.

Parameters

a	Any doubleing-point value
b	Any doubleing-point value

Returns

max(a,b) for each element.

Note

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

static void gmx::mdrunner_start_fn ( void *  arg )

static

The callback used for running on spawned threads.

Obtains the pointer to the master mdrunner object from the one argument permitted to the thread-launch API call, copies it to make a new runner for this thread, reinitializes necessary data, and proceeds to the simulation.

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

inlinestatic

Set each float element to the smallest from two variables.

Parameters

a	Any floating-point value
b	Any floating-point value

Returns

min(a,b) for each element.

Note

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

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

inlinestatic

Set each double element to the smallest from two variables.

Parameters

a	Any doubleing-point value
b	Any doubleing-point value

Returns

min(a,b) for each element.

Note

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

int gmx::multiDimArrayIndexToLinear	(	const awh_ivec	indexMulti,
		int	numDim,
		const awh_ivec	numPointsDim
	)

Convert multidimensional array index to a linear one.

Parameters

[in]	indexMulti	Multidimensional index to convert to a linear one.
[in]	numDim	Number of dimensions of the array.
[in]	numPointsDim	Number of points of the array.

Returns

the linear index.

Note

This function can be used without having an initialized grid.

int gmx::multiDimGridIndexToLinear	(	const Grid &	grid,
		const awh_ivec	indexMulti
	)

Convert a multidimensional grid point index to a linear one.

Parameters

[in]	grid	The grid.
[in]	indexMulti	Multidimensional grid point index to convert to a linear one.

Returns

the linear index.

void gmx::niceHeader	(	TextWriter *	writer,
		const char *	fn,
		char	commentChar
	)

Prints creation time stamp and user information into a string as comments, and returns it.

Parameters

[out]	writer	Where to print the information.
[in]	fn	Name of the file being written; if nullptr, described as "unknown".
[in]	commentChar	Character to use as the starting delimiter for comments.

Exceptions

std::bad_alloc

if out of memory.

static void gmx::normalizeBlock ( AwhEnergyBlock *  block, const Bias &  bias  )

static

Normalizes block data for output.

Parameters

[in,out]	block	The block to normalize.
[in]	bias	The AWH bias.

static void gmx::normalizeFreeEnergyAndPmfSum ( std::vector< PointState > *  pointState )

static

Normalizes the free energy and PMF sum.

Parameters

[in]

pointState

The state of the points.

static size_t gmx::paddedRVecVectorSize ( size_t  numAtoms )

inlinestatic

Returns the padded size for PaddedRVecVector given the number of atoms.

Parameters

[in]

numAtoms

The number of atoms for which data will be stored in a PaddedRVecVector

std::size_t gmx::pageSize

(

)

Return the memory page size on this system.

Implements the "construct on first use" idiom to avoid the static initialization order fiasco where a possible static page-aligned container would be initialized before the alignment variable was.

Note that thread-safety is guaranteed by the C++11 language standard.

std::vector< int > gmx::parseUserGpuIds

(

const std::string &

gpuIdString

)

Parse a GPU ID string into a container describing the task types and associated device IDs.

Parameters

[in]

gpuIdString

String like "013" or "0,1,3" typically supplied by the user to mdrun -gpu_id or -gputasks. Must contain only decimal digits, or only decimal digits separated by comma delimiters. A terminal comma is accceptable (and required to specify a single ID that is larger than 9).

Returns

A vector of GPU ID task mappings, like { 0, 1, 3 }

Exceptions

std::bad_alloc

If out of memory. InvalidInputError If an invalid character is found (ie not a digit or ',').

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

noexcept

Pin the allocation to physical memory.

Requires that pointer is not nullptr.

Does not throw.

static float gmx::pmeForceCorrection ( float  z2 )

inlinestatic

Calculate the force correction due to PME analytically in float.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on force

Note

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

static double gmx::pmeForceCorrection ( double  z2 )

inlinestatic

Calculate the force correction due to PME analytically in double.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on force

Note

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

static double gmx::pmeForceCorrectionSingleAccuracy ( double  z2 )

inlinestatic

Force correction due to PME in double, but with single accuracy.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on force

Note

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

static float gmx::pmePotentialCorrection ( float  z2 )

inlinestatic

Calculate the potential correction due to PME analytically in float.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on potential.

Note

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

static double gmx::pmePotentialCorrection ( double  z2 )

inlinestatic

Calculate the potential correction due to PME analytically in double.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on potential.

Note

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

static double gmx::pmePotentialCorrectionSingleAccuracy ( double  z2 )

inlinestatic

Potential correction due to PME in double, but with single accuracy.

See the SIMD version of this function for details.

Parameters

z2	input parameter

Returns

Correction to use on potential.

Note

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

static int gmx::pointDistanceAlongAxis ( const GridAxis &  axis, double  x, double  x0  )

static

Returns the point distance between from value x to value x0 along the given axis.

Note that the returned distance may be negative or larger than the number of points in the axis. For a periodic axis, the distance is chosen to be in [0, period), i.e. always positive but not the shortest one.

Parameters

[in]	axis	Grid axis.
[in]	x	From value.
[in]	x0	To value.

Returns

(x - x0) in number of points.

template<typename T >

T gmx::power12

(

T

x

)

calculate x^12

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^12

template<typename T >

T gmx::power3

(

T

x

)

calculate x^3

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^3

template<typename T >

T gmx::power4

(

T

x

)

calculate x^4

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^4

template<typename T >

T gmx::power5

(

T

x

)

calculate x^5

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^5

template<typename T >

T gmx::power6

(

T

x

)

calculate x^6

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^6

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

Print basic information about the executable.

Parameters

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

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

Print basic information about the executable with custom settings.

Parameters

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

See Also

BinaryInformationSettings

void gmx::printBinaryInformation	(	TextWriter *	writer,
		const IProgramContext &	programContext,
		const BinaryInformationSettings &	settings
	)

Print basic information about the executable with custom settings.

Needed to read the members without otherwise unnecessary accessors.

Parameters

[out]	writer	Where to print the information.
[in]	programContext	Program information object to use.
[in]	settings	Specifies what to print.

Exceptions

std::bad_alloc

if out of memory.

See Also

BinaryInformationSettings

int gmx::processExceptionAtExitForCommandLine

(

const std::exception &

ex

)

Handles an exception and deinitializes after initForCommandLine.

Parameters

[in]

ex

Exception that is the cause for terminating the program.

Returns

Return code to return from main().

This method should be called as the last thing before terminating the program because of an exception. See processExceptionAtExit() for details. Additionally this method undoes the work done by initForCommandLine.

Does not throw.

static void gmx::read_bias_params ( int *  ninp_p, t_inpfile **  inp_p, AwhBiasParams *  awhBiasParams, const char *  prefix, const t_inputrec *  ir, warninp_t  wi, bool  bComment  )

static

Read parameters of an AWH bias.

Parameters

[in,out]	ninp_p	Number of read input file entries.
[in,out]	inp_p	Input file entries.
[in,out]	awhBiasParams	AWH dimensional parameters.
[in]	prefix	Prefix for bias parameters.
[in]	ir	Input parameter struct.
[in,out]	wi	Struct for bookeeping warnings.
[in]	bComment	True if comments should be printed.

AwhParams * gmx::readAndCheckAwhParams	(	int *	ninp_p,
		t_inpfile **	inp_p,
		const t_inputrec *	inputrec,
		warninp_t	wi
	)

Allocate, initialize and check the AWH parameters with values from the input file.

Parameters

[in,out]	ninp_p	Number of read input file entries.
[in,out]	inp_p	Input file entries.
[in]	inputrec	Input parameter struct.
[in,out]	wi	Struct for bookeeping warnings.

Returns

AWH parameters.

static void gmx::readDimParams ( int *  ninp_p, t_inpfile **  inp_p, const char *  prefix, AwhDimParams *  dimParams, const pull_params_t *  pull_params, warninp_t  wi, bool  bComment  )

static

Read parameters of an AWH bias dimension.

Parameters

[in,out]	ninp_p	Number of read input file entries.
[in,out]	inp_p	Input file entries.
[in]	prefix	Prefix for dimension parameters.
[in,out]	dimParams	AWH dimensional parameters.
[in]	pull_params	Pull parameters.
[in,out]	wi	Struct for bookeeping warnings.
[in]	bComment	True if comments should be printed.

static void gmx::readUserPmfAndTargetDistribution ( const std::vector< DimParams > &  dimParams, const Grid &  grid, const std::string &  filename, int  numBias, int  biasIndex, std::vector< PointState > *  pointState  )

static

Initializes the PMF and target with data read from an input table.

Parameters

[in]	dimParams	The dimension parameters.
[in]	grid	The grid.
[in]	filename	The filename to read PMF and target from.
[in]	numBias	Number of biases.
[in]	biasIndex	The index of the bias.
[in,out]	pointState	The state of the points in this bias.

static float gmx::reduce ( float  a )

inlinestatic

Return sum of all elements in float variable (i.e., the variable itself).

Parameters

a	variable to reduce/sum.

Returns

The argument variable itself.

Note

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

static double gmx::reduce ( double  a )

inlinestatic

Return sum of all elements in double variable (i.e., the variable itself).

Parameters

a	variable to reduce/sum.

Returns

The argument variable itself.

Note

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

static float gmx::reduceIncr4ReturnSum ( float *  m, float  v0, float  v1, float  v2, float  v3  )

inlinestatic

Add each float to four consecutive memory locations, return sum.

Parameters

m	Pointer to memory where four floats should be incremented
v0	float to be added to m[0]
v1	float to be added to m[1]
v2	float to be added to m[2]
v3	float to be added to m[3]

Returns

v0+v1+v2+v3.

Note

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

static double gmx::reduceIncr4ReturnSum ( double *  m, double  v0, double  v1, double  v2, double  v3  )

inlinestatic

Add each double to four consecutive memory locations, return sum.

Parameters

m	Pointer to memory where four floats should be incremented
v0	double to be added to m[0]
v1	double to be added to m[1]
v2	double to be added to m[2]
v3	double to be added to m[3]

Returns

v0+v1+v2+v3.

Note

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

void gmx::reportGpuUsage	(	const MDLogger &	mdlog,
		bool	userSetGpuIds,
		const GpuTaskAssignments &	gpuTaskAssignmentOnRanksOfThisNode,
		size_t	numGpuTasksOnThisNode,
		size_t	numPpRanks,
		bool	bPrintHostName
	)

Log a report on how GPUs are being used on the ranks of the physical node of rank 0 of the simulation.

Todo:

It could be useful to report also whether any nodes differed, and in what way.

Parameters

[in]	mdlog	Logging object.
[in]	userSetGpuIds	Whether the user selected the GPU ids
[in]	gpuTaskAssignmentOnRanksOfThisNode	The selected GPU IDs.
[in]	numGpuTasksOnThisNode	The number of GPU tasks on this node.
[in]	numPpRanks	Number of PP ranks on this node
[in]	bPrintHostName	Print the hostname in the usage information

Exceptions

std::bad_alloc

if out of memory

void gmx::restoreCorrelationGridStateFromHistory	(	const CorrelationGridHistory &	corrGridHist,
		CorrelationGrid *	corrGrid
	)

Restores the correlation grid state from the correlation grid history.

Parameters

[in]	corrGridHist	Correlation grid history to read.
[in,out]	corrGrid	Correlation grid state to set.

static float gmx::round ( float  a )

inlinestatic

Float round to nearest integer value (in floating-point format).

Parameters

a	Any floating-point value

Returns

The nearest integer, represented in floating-point format.

Note

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

static double gmx::round ( double  a )

inlinestatic

double round to nearest integer value (in doubleing-point format).

Parameters

a	Any doubleing-point value

Returns

The nearest integer, represented in doubleing-point format.

Note

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

int gmx::runCommandLineModule	(	int	argc,
		char *	argv[],
		ICommandLineModule *	module
	)

Implements a main() method that runs a single module.

Parameters

argc	argc passed to main().
argv	argv passed to main().
module	Module to run.

This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).

The signature assumes that module construction does not throw (because otherwise the caller would need to duplicate all the exception handling code). It is possible to move the construction inside the try/catch in this method using an indirection similar to TrajectoryAnalysisCommandLineRunner::runAsMain(), but until that is necessary, the current approach leads to simpler code.

Usage:

int main(int argc, char *argv[])
{
    CustomCommandLineModule module;
    return gmx::runCommandLineModule(argc, argv, &module);
}

Does not throw. All exceptions are caught and handled internally.

int gmx::runCommandLineModule	(	int	argc,
		char *	argv[],
		const char *	name,
		const char *	description,
		std::function< std::unique_ptr< ICommandLineOptionsModule >()>	factory
	)

Implements a main() method that runs a single module.

Parameters

	argc	argc passed to main().
	argv	argv passed to main().
[in]	name	Name for the module.
[in]	description	Short description for the module.
	factory	Factory method that creates the module to run.

This method allows for uniform behavior for binaries that only contain a single module without duplicating any of the implementation from CommandLineModuleManager (startup headers, common options etc.).

Usage:

class CustomCommandLineOptionsModule : public ICommandLineOptionsModule
{
    // <...>
};

static ICommandLineOptionsModule *create()
{
    return new CustomCommandLineOptionsModule();
}

int main(int argc, char *argv[])
{
    return gmx::runCommandLineModule(
            argc, argv, "mymodule", "short description", &create);
}

Does not throw. All exceptions are caught and handled internally.

GpuTaskAssignments::value_type gmx::runTaskAssignment	(	const std::vector< int > &	gpuIdsToUse,
		const std::vector< int > &	userGpuTaskAssignment,
		const gmx_hw_info_t &	hardwareInfo,
		const MDLogger &	mdlog,
		const t_commrec *	cr,
		const std::vector< GpuTask > &	gpuTasksOnThisRank
	)

Coordinate the final stages of task assignment and reporting, and return the assignment for this rank.

Communicates between ranks on a node to coordinate task assignment between them onto available hardware, e.g. accelerators.

Releases the taskAssigner once its work is complete.

Parameters

[in]	gpuIdsToUse	The compatible GPUs that the user permitted us to use.
[in]	userGpuTaskAssignment	The user-specified assignment of GPU tasks to device IDs.
[in]	hardwareInfo	The detected hardware
[in]	mdlog	Logging object to write to.
[in]	cr	Communication object.
[in]	gpuTasksOnThisRank	Information about what GPU tasks exist on this rank.

Returns

A GPU task assignment for this rank.

Exceptions

std::bad_alloc

If out of memory. InconsistentInputError If user and/or detected inputs are inconsistent.

static float gmx::selectByMask ( float  a, bool  mask  )

inlinestatic

Select from single precision variable where boolean is true.

Parameters

a	Floating-point variable to select from
mask	Boolean selector

Returns

a is selected for true, 0 for false.

Note

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

static double gmx::selectByMask ( double  a, bool  mask  )

inlinestatic

Select from double precision variable where boolean is true.

Parameters

a	double variable to select from
mask	Boolean selector

Returns

a is selected for true, 0 for false.

Note

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

static std::int32_t gmx::selectByMask ( std::int32_t  a, bool  mask  )

inlinestatic

Select from integer variable where boolean is true.

Parameters

a	Integer variable to select from
mask	Boolean selector

Returns

a is selected for true, 0 for false.

Note

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

static float gmx::selectByNotMask ( float  a, bool  mask  )

inlinestatic

Select from single precision variable where boolean is false.

Parameters

a	Floating-point variable to select from
mask	Boolean selector

Returns

a is selected for false, 0 for true.

Note

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

static double gmx::selectByNotMask ( double  a, bool  mask  )

inlinestatic

Select from double precision variable where boolean is false.

Parameters

a	double variable to select from
mask	Boolean selector

Returns

a is selected for false, 0 for true.

Note

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

static std::int32_t gmx::selectByNotMask ( std::int32_t  a, bool  mask  )

inlinestatic

Select from integer variable where boolean is false.

Parameters

a	Integer variable to select from
mask	Boolean selector

Returns

a is selected for false, 0 for true.

Note

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

static real gmx::series_sinhx ( real  x )

inlinestatic

Maclaurin series for sinh(x)/x.

Used for NH chains and MTTK pressure control. Here, we compute it to 10th order, which might be an overkill. 8th is probably enough, but it's not very much more expensive.

void gmx::setLibraryFileFinder

(

const DataFileFinder *

finder

)

Sets a finder for location data files from share/top/.

Parameters

[in]

finder

finder to set (can be NULL to restore the default finder).

The library does not take ownership of finder. The provided object must remain valid until the global instance is changed by another call to setLibraryFileFinder().

The global instance is used by gmxlibfn() and libopen().

This method is not thread-safe. See setProgramContext(); the same constraints apply here as well.

Does not throw.

void gmx::setStateDependentAwhParams	(	AwhParams *	awhParams,
		const pull_params_t *	pull_params,
		pull_t *	pull_work,
		const matrix	box,
		int	ePBC,
		const t_grpopts *	inputrecGroupOptions,
		warninp_t	wi
	)

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

Parameters

[in,out]	awhParams	AWH parameters.
[in]	pull_params	Pull parameters.
[in,out]	pull_work	Pull working struct to register AWH bias in.
[in]	box	Box vectors.
[in]	ePBC	Periodic boundary conditions enum.
[in]	inputrecGroupOptions	Parameters for atom groups.
[in,out]	wi	Struct for bookeeping warnings.

Note

This function currently relies on the function set_pull_init to have been called.

static void gmx::simdPrefetch ( void *  m )

inlinestatic

Prefetch memory at address m.

This typically prefetches one cache line of memory from address m, usually 64bytes or more, but the exact amount will depend on the implementation. On many platforms this is simply a no-op. Technically it might not be part of the SIMD instruction set, but since it is a hardware-specific function that is normally only used in tight loops where we also apply SIMD, it fits well here.

There are no guarantees about the level of cache or temporality, but usually we expect stuff to end up in level 2, and be used in a few hundred clock cycles, after which it stays in cache until evicted (normal caching).

Parameters

m	Pointer to location prefetch. There are no alignment requirements, but if the pointer is not aligned the prefetch might start at the lower cache line boundary (meaning fewer bytes are prefetched).

static float gmx::sin ( float  x )

inlinestatic

Float sin.

Parameters

x	The argument to evaluate sin for

Returns

Sin(x)

Note

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

static double gmx::sin ( double  x )

inlinestatic

Double sin.

Parameters

x	The argument to evaluate sin for

Returns

Sin(x)

Note

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

static void gmx::sincos ( float  x, float *  sinval, float *  cosval  )

inlinestatic

Float sin & cos.

Parameters

	x	The argument to evaluate sin/cos for
[out]	sinval	Sin(x)
[out]	cosval	Cos(x)

Note

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

static void gmx::sincos ( double  x, double *  sinval, double *  cosval  )

inlinestatic

Double sin & cos.

Parameters

	x	The argument to evaluate sin/cos for
[out]	sinval	Sin(x)
[out]	cosval	Cos(x)

Note

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

static void gmx::sincosSingleAccuracy ( double  x, double *  sinval, double *  cosval  )

inlinestatic

Double sin & cos, but with single accuracy.

Parameters

	x	The argument to evaluate sin/cos for
[out]	sinval	Sin(x)
[out]	cosval	Cos(x)

Note

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

static double gmx::sinSingleAccuracy ( double  x )

inlinestatic

Double sin, but with single accuracy.

Parameters

x	The argument to evaluate sin for

Returns

Sin(x)

Note

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

static float gmx::sixthroot ( float  x )

inlinestatic

Calculate sixth root of x in single precision.

Parameters

x	Argument, must be greater than or equal to zero.

Returns

x^(1/6)

This routine is typically faster than using std::pow().

static double gmx::sixthroot ( double  x )

inlinestatic

Calculate sixth root of x in double precision.

Parameters

x	Argument, must be greater than or equal to zero.

Returns

x^(1/6)

This routine is typically faster than using std::pow().

static double gmx::sixthroot ( int  x )

inlinestatic

Calculate sixth root of integer x, return double.

Parameters

x	Argument, must be greater than or equal to zero.

Returns

x^(1/6)

This routine is typically faster than using std::pow().

static void gmx::spinUpCore ( )

staticnoexcept

Utility that does dummy computing for max 2 seconds to spin up cores.

This routine will check the number of cores configured and online (using sysconf), and the spins doing dummy compute operations for up to 2 seconds, or until all cores have come online. This can be used prior to hardware detection for platforms that take unused processors offline.

This routine will not throw exceptions.

template<MathOptimization opt = MathOptimization::Safe>

static float gmx::sqrt ( float  x )

inlinestatic

Float sqrt(x). This is the square root.

Parameters

x	Argument, should be >= 0.

Returns

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

Note

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

template<MathOptimization opt = MathOptimization::Safe>

static double gmx::sqrt ( double  x )

inlinestatic

Double sqrt(x). This is the square root.

Parameters

x	Argument, should be >= 0.

Returns

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

Note

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

static double gmx::sqrtSingleAccuracy ( double  x )

inlinestatic

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

Parameters

x	Argument that must be >=0.

Returns

sqrt(x).

Note

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

template<typename T >

T gmx::square

(

T

x

)

calculate x^2

Template Parameters

T	Type of argument and return value

Parameters

x

argument

Returns

x^2

static void gmx::store ( float *  m, float  a  )

inlinestatic

Store contents of float variable to aligned memory m.

Parameters

[out]	m	Pointer to memory.
	a	float variable to store

Note

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

static void gmx::store ( double *  m, double  a  )

inlinestatic

Store contents of double variable to aligned memory m.

Parameters

[out]	m	Pointer to memory.
	a	double variable to store

Note

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

static void gmx::store ( std::int32_t *  m, std::int32_t  a  )

inlinestatic

Store contents of integer variable to aligned memory m.

Parameters

[out]	m	Pointer to memory.
	a	integer variable to store

Note

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

static void gmx::storeU ( float *  m, float  a  )

inlinestatic

Store contents of float variable to unaligned memory m.

Parameters

[out]	m	Pointer to memory, no alignment requirement.
	a	float variable to store.

Note

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

static void gmx::storeU ( double *  m, double  a  )

inlinestatic

Store contents of double variable to unaligned memory m.

Parameters

[out]	m	Pointer to memory, no alignment requirement.
	a	double variable to store.

Note

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

static void gmx::storeU ( std::int32_t *  m, std::int32_t  a  )

inlinestatic

Store contents of integer variable to unaligned memory m.

Parameters

[out]	m	Pointer to memory, no alignment requirement.
	a	integer variable to store.

Note

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

static float gmx::tan ( float  x )

inlinestatic

Float tan.

Parameters

x	The argument to evaluate tan for

Returns

Tan(x)

Note

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

static double gmx::tan ( double  x )

inlinestatic

Double tan.

Parameters

x	The argument to evaluate tan for

Returns

Tan(x)

Note

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

static double gmx::tanSingleAccuracy ( double  x )

inlinestatic

Double tan, but with single accuracy.

Parameters

x	The argument to evaluate tan for

Returns

Tan(x)

Note

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

static bool gmx::testBits ( float  a )

inlinestatic

Return true if any bits are set in the float variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels. Note that it will return true even for -0.0f (sign bit set), so it is not identical to not-equal.

Parameters

a

value

Returns

True if any bit in a is nonzero.

Note

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

static bool gmx::testBits ( double  a )

inlinestatic

Return true if any bits are set in the double variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels. Note that it will return true even for -0.0 (sign bit set), so it is not identical to not-equal.

Parameters

a

value

Returns

True if any bit in a is nonzero.

Note

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

static bool gmx::testBits ( std::int32_t  a )

inlinestatic

Return true if any bits are set in the integer variable.

This function is used to handle bitmasks, mainly for exclusions in the inner kernels.

Parameters

a

value

Returns

True if any bit in a is nonzero.

Note

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

template<int align>

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

inlinestatic

Subtract 3 floats from base/offset.

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

Subtract 3 doubles from base/offset.

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

Add 3 floats to base/offset.

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

Add 3 doubles to base/offset.

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

Store 3 floats to 3 to base/offset.

Template Parameters

align

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

Parameters

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

Note

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

template<int align>

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

inlinestatic

Store 3 doubles to 3 to base/offset.

Template Parameters

align

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

Parameters

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

Note

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

static float gmx::trunc ( float  a )

inlinestatic

Truncate float, i.e. round towards zero - common hardware instruction.

Parameters

a	Any floating-point value

Returns

Integer rounded towards zero, represented in floating-point format.

Note

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

static double gmx::trunc ( double  a )

inlinestatic

Truncate double, i.e. round towards zero - common hardware instruction.

Parameters

a	Any doubleing-point value

Returns

Integer rounded towards zero, represented in doubleing-point format.

Note

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

void gmx::unpinBuffer ( void *  pointer )

noexcept

Unpin the allocation.

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

Does not throw.

void gmx::updateCorrelationGridHistory	(	CorrelationGridHistory *	corrGridHist,
		const CorrelationGrid &	corrGrid
	)

Update the correlation grid history for checkpointing.

Parameters

[in,out]	corrGridHist	Correlation grid history to set.
[in]	corrGrid	Correlation grid state to read.

static bool gmx::valueIsInGrid ( const awh_dvec  value, const std::vector< GridAxis > &  axis  )

static

Query if a value is in range of the grid.

Parameters

[in]	value	Value to check.
[in]	axis	The grid axes.

Returns

true if the value is in the grid.

static bool gmx::valueIsInInterval ( double  origin, double  end, double  period, double  value  )

static

Checks if a value is within an interval.

Parameters

[in]	origin	Start value of interval.
[in]	end	End value of interval.
[in]	period	Period (or 0 if not periodic).
[in]	value	Value to check.

Returns

true if the value is within the interval.

void gmx::writeKeyValueTreeAsMdp	(	TextWriter *	writer,
		const KeyValueTreeObject &	tree
	)

Write a flat key-value tree to writer in mdp style.

Sub-objects will output nothing, so they can be used to contain a special key-value pair to create a comment, as well as the normal key and value. The comment pair will have a key of "comment", and the value will be used as a comment (if non-empty).

Variable Documentation

const bool gmx::bGPUBinary = GMX_GPU != GMX_GPU_NONE

static

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

Convenience macro to help us avoid ifdefs each time we use sysconf Constant used to help minimize preprocessed code

constexpr Architecture gmx::c_architecture

static

Initial value:

=







    Architecture::Unknown

Constant that tells what the architecture is.

const char * gmx::eawhcoordprovider_names

Initial value:

= {
    "pull", nullptr
}

String for AWH bias reaction coordinate provider.

const char * gmx::eawhgrowth_names

Initial value:

= {
    "exp-linear", "linear", nullptr
}

String for weight histogram growth.

const char * gmx::eawhpotential_names

Initial value:

= {
    "convolved", "umbrella", nullptr
}

String for AWH potential type.

const char * gmx::eawhtarget_names

Initial value:

= {
    "constant", "cutoff", "boltzmann", "local-boltzmann", nullptr
}

String for target distribution.

std::unique_ptr<gmx_hw_info_t> gmx::hwinfo_g

static

The hwinfo structure (common to all threads in this process).

Todo:

This should become a shared_ptr owned by e.g. Mdrunner::runner() that is shared across any threads as needed (e.g. for thread-MPI). That offers about the same run time performance as we get here, and avoids a lot of custom code.