Description

Testing utilities namespace.

This namespace contains utilities for writing unit tests, mostly from the Testing Utilities (testutils) module.

Classes
class	AnalysisDataTestInputPointSet
	Represents a single set of points in AnalysisDataTestInputFrame structure. More...

class	AnalysisDataTestInputFrame
	Represents a single frame in AnalysisDataTestInput structure. More...

class	AnalysisDataTestInput
	Represents static input data for AbstractAnalysisData tests. More...

class	AnalysisDataTestFixture
	Test fixture for AbstractAnalysisData testing. More...

class	ModuleSelection
	Helper class for tests that need an initialized selection. More...

class	ModuleTest
	Test fixture to test matching file types for modules. More...

class	SetAtomsSupportedFiles
	Helper to test supported file names. More...

class	SetAtomsUnSupportedFiles
	Helper to test supported file names. More...

class	AnyOutputSupportedFiles
	Helper to test supported file names. More...

class	NoOptionalOutput
	Helper to test support for disabling all output options. More...

class	OutputSelectorDeathTest
	Helper to test that invalid selection is rejected. More...

class	SetVelocitySupportedFiles
	Helper to test supported file names. More...

class	SetVelocityUnSupportedFiles
	Helper to test supported file names. More...

class	SetForceSupportedFiles
	Helper to test supported file names. More...

class	SetForceUnSupportedFiles
	Helper to test supported file names. More...

class	SetPrecisionSupportedFiles
	Helper to test supported file names. More...

class	SetPrecisionUnSupportedFiles
	Helper to test supported file names. More...

class	FlagTest
	Test fixture to test user inputs. More...

class	AllocatorTest
	Templated test fixture. More...

class	CommandLine
	Helper class for tests that need to construct command lines. More...

class	CommandLineTestHelper
	Helper class for tests that construct command lines that need to reference existing files. More...

class	CommandLineTestBase
	Test fixture for tests that call a single command-line program with input/output files. More...

class	ConfMatch
	Match the contents as an gro file. More...

class	IFileMatcher
	Represents a file matcher, matching file contents against reference (or other) data. More...

class	IFileMatcherSettings
	Represents a factory for creating a file matcher. More...

class	TextFileMatch
	Use a ITextBlockMatcher for matching the contents. More...

class	NoContentsMatch
	Do not check the contents of the file. More...

class	InteractiveTestHelper
	Helper class for testing interactive sessions. More...

class	LoggerTestHelper
	Helper class for tests to check output written to a logger. More...

class	TestReferenceData
	Handles creation of and comparison to test reference data. More...

class	TestReferenceChecker
	Handles comparison to test reference data. More...

class	StdioTestHelper
	Helper class for tests where code reads directly from `stdin`. More...

class	StringTestBase
	Test fixture for tests that check string formatting. More...

class	FloatingPointDifference
	Computes and represents a floating-point difference value. More...

class	FloatingPointTolerance
	Specifies a floating-point comparison tolerance and checks whether a difference is within the tolerance. More...

class	TestException
	Exception class for reporting errors in tests. More...

class	TestFileManager
	Helper for tests that need input and output files. More...

class	TestFileInputRedirector
	In-memory implementation for IFileInputRedirector for tests. More...

class	TestFileOutputRedirector
	In-memory implementation of IFileOutputRedirector for tests. More...

class	TestOptionsProvider
	Provides additional options for the test executable. More...

class	ITextBlockMatcher
	Represents a text matcher, matching text stream contents against reference data. More...

class	ITextBlockMatcherSettings
	Represents a factory for creating a text matcher. More...

class	ExactTextMatch
	Use an exact text match (the contents should be exactly equal). More...

class	NoTextMatch
	Do not match the text (the contents are ignored). More...

class	FilteringExactTextMatch
	Use an exact text match after scrubbing lines of the text that match the supplied regular expressions. More...

class	TprAndFileManager
	Helper to bundle generated TPR and the file manager to clean it up. More...

class	XvgMatch
	Match the contents as an xvg file. More...

Typedefs
typedef std::shared_ptr < MockAnalysisDataModule >	MockAnalysisDataModulePointer
	Smart pointer to manage an MockAnalysisDataModule object.

typedef std::tuple < AwhHistogramGrowthType, AwhPotentialType, BiasParams::DisableUpdateSkips >	BiasTestParameters
	Convenience typedef: growth type enum, potential type enum, disable update skips.

typedef gmx::unique_cptr < gmx_pme_t, gmx_pme_destroy >	PmeSafePointer
	A safe pointer type for PME.

typedef std::vector< real >	ChargesVector
	Charges.

typedef std::vector< RVec >	CoordinatesVector
	Coordinates.

typedef ArrayRef< RVec >	ForcesVector
	Forces.

typedef std::vector< IVec >	GridLineIndicesVector
	Gridline indices.

typedef ArrayRef< const real >	SplineParamsDimVector
	Spline parameters (theta or dtheta). A reference to a single dimension's spline data; this means (atomCount * pmeOrder) values or derivatives.

typedef std::array < SplineParamsDimVector, DIM >	SplineParamsVector
	Spline parameters (theta or dtheta) in all 3 dimensions.

template<typename ValueType >
using	SparseGridValuesInput = std::map< IVec, ValueType >
	Non-zero grid values for test input; keys are 3d indices (IVec)

typedef SparseGridValuesInput < real >	SparseRealGridValuesInput
	Non-zero real grid values.

typedef SparseGridValuesInput < t_complex >	SparseComplexGridValuesInput
	Non-zero complex grid values.

template<typename ValueType >
using	SparseGridValuesOutput = std::map< std::string, ValueType >
	Non-zero grid values for test output; keys are string representations of the cells' 3d indices (IVec); this allows for better sorting.

typedef SparseGridValuesOutput < real >	SparseRealGridValuesOutput
	Non-zero real grid values.

typedef SparseGridValuesOutput < t_complex >	SparseComplexGridValuesOutput
	Non-zero complex grid values.

typedef std::array< real, DIM *DIM >	Matrix3x3
	TODO: make proper C++ matrix for the whole Gromacs, get rid of this.

using	GpuFftTestParams = std::tuple< IVec, int, int, FftBackend >

typedef ::testing::Types < int32_t, real, RVec, test::MoveOnly >	TestTypes
	The types used in testing of all operations.

using	TestTypesCopyable = ::testing::Types< int32_t, real, RVec >
	The types used in testing minus move only types.

template<typename T >
using	HostAllocatorTestCopyable = HostAllocatorTest< T >
	Typed test fixture for tests requiring a copyable type.

using	AllocatorTypesToTest = ::testing::Types< HostAllocator< real >, HostAllocator< int32_t >, HostAllocator< RVec >, HostAllocator< MoveOnly >>
	Declare allocator types to test.

using	Implementations = ::testing::Types< std::allocator< int32_t >, std::allocator< float >, std::allocator< double >, std::allocator< BasicVector< float >>, std::allocator< BasicVector< double >>, AlignedAllocator< int32_t >, AlignedAllocator< float >, AlignedAllocator< double >, AlignedAllocator< BasicVector< float >>, AlignedAllocator< BasicVector< double >>>
	The types used in testing.

using	MtsIntervalTestParams = std::tuple< std::string, int >
	Test fixture base for parametrizing interval tests.

typedef gmx::test::DispersionCorrectionTestFixture	DispersionCorrectionTest
	Test fixture for mdrun with dispersion correction.

using	EnergyTermsToCompare = std::unordered_map< std::string, FloatingPointTolerance >
	Convenience type.

typedef std::unique_ptr < EnergyFrameReader >	EnergyFrameReaderPtr
	Convenience smart pointer typedef.

typedef unique_cptr< ener_file, done_ener_file >	ener_file_ptr
	Convenience smart pointer typedef.

typedef unique_cptr < t_enxframe, done_enxframe >	enxframe_ptr
	Convenience smart pointer typedef.

typedef gmx::test::ImdTestFixture	ImdTest
	Test fixture for mdrun with IMD settings.

typedef MultiSimTest	MultiSimTerminationTest
	Convenience typedef.

typedef std::unique_ptr < CommandLine >	CommandLinePointer
	Convenience typedef.

typedef std::tuple < NumRanksPerSimulation, IntegrationAlgorithm, TemperatureCoupling, PressureCoupling >	MultiSimTestParams
	The parameters of the MultiSimTest class.

typedef gmx::test::OriresTestFixture	OriresTest
	Test fixture for mdrun with orires.

using	PropagationParameters = MdpFieldValues
	Mdp parameters that determine the manner of simulation propagation.

using	PeriodicOutputParameters = MdpFieldValues
	Mdp parameters that should only affect the observations, not the simulation propagation.

using	OutputParameterGeneratorFunction ) = std::vector< PeriodicOutputParameters >(*)(
	Function type to produce sets of .mdp parameters for testing periodic output.

typedef MultiSimTest	ReplicaExchangeEnsembleTest
	Convenience typedef.

typedef MultiSimTest	ReplicaExchangeTerminationTest
	Convenience typedef.

typedef MultiSimTest	ReplicaExchangeTest
	Convenience typedef.

typedef std::tuple < std::string, std::string >	SimulationOptionTuple

typedef gmx::test::SwapTestFixture	CompelTest
	Test fixture for mdrun with "Computational Electrophysiology" settings,.

typedef MdrunTestFixture	MdrunTerminationTest
	Convenience typedef.

typedef std::unique_ptr < IFileMatcher >	FileMatcherPointer
	Smart pointer for managing a IFileMatcher.

using	MdpFieldValues = std::map< std::string, std::string >
	Helper typedef.

typedef std::unique_ptr < ITextBlockMatcher >	TextBlockMatcherPointer
	Smart pointer for managing a ITextBlockMatcher.

typedef unique_cptr < gmx_output_env_t, output_env_done >	oenv_ptr
	Convenience smart pointer typedef.

typedef unique_cptr < t_trxstatus, close_trx >	trxstatus_file_ptr
	Convenience smart pointer typedef.

typedef unique_cptr < t_trxframe, done_trxframe >	trxframe_ptr
	Convenience smart pointer typedef.

Enumerations
enum	TestEnums { efTestString, efTestInt, efTestFloat }
	Test enums to decide on how to use options framework.

enum	PmeLayoutTransform { GpuToHost, HostToGpu }
	A binary enum for spline data layout transformation.

enum	CodePath : int { CodePath::CPU, CodePath::GPU, CodePath::Count }
	Hardware code path being tested. More...

enum	PmeSolveAlgorithm : int { PmeSolveAlgorithm::Coulomb, PmeSolveAlgorithm::LennardJones, PmeSolveAlgorithm::Count }
	PME solver type. More...

enum	SimulationRunnerMdpSource { SimulationRunnerMdpSource::Undefined, SimulationRunnerMdpSource::String, SimulationRunnerMdpSource::File, SimulationRunnerMdpSource::Count }

enum	ComparisonConditions : int { CompareIfBothFound, NoComparison, MustCompare, CompareIfReferenceFound, CompareIfTestFound, Count }
	Enumeration controlling how data within trajectory frames are compared.

enum	ReferenceDataMode : int { ReferenceDataMode::Compare, ReferenceDataMode::CreateMissing, ReferenceDataMode::UpdateChanged, ReferenceDataMode::UpdateAll, ReferenceDataMode::Count }
	Mode of operation for reference data handling. More...

enum	MdpParameterDatabase { Default, Pull, Awh, Count }
	Strong type denoting mdp parameters needed to test specific algorithms.

Functions
std::vector< char >	awhDimParamSerialized (AwhCoordinateProviderType inputCoordinateProvider, int inputCoordIndex, double inputOrigin, double inputEnd, double inputPeriod, double inputDiffusion)

static std::vector< char >	awhBiasParamSerialized (AwhHistogramGrowthType eawhgrowth, double beta, double inputErrorScaling, ArrayRef< const std::vector< char >> dimensionParameterBuffers, int shareGroup, bool inputUserData)

static std::vector< char >	awhParamSerialized (AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, double beta, double inputErrorScaling, int64_t inputSeed, ArrayRef< const std::vector< char >> dimensionParameterBuffers, int biasShareGroup, bool inputUserData)

AwhTestParameters	getAwhTestParameters (AwhHistogramGrowthType eawhgrowth, AwhPotentialType eawhpotential, ArrayRef< const std::vector< char >> dimensionParameterBuffers, bool inputUserData, double beta, bool useAwhFep, double inputErrorScaling, int numFepLambdaStates, int biasShareGroup)
	Helper function to set up the C-style AWH parameters for the test. More...

TrajectoryFrameWriterPointer	createMinimalTrajectoryFrameWriter (const std::string &filename, const TopologyInformation &topology, const Selection &selection, OutputRequirements requirements)
	Create minimal TrajectoryFrameWriter using the provided builder. More...

static void	splitAndAddValues (OptionsAssigner *assigner, const std::string &optionValues, TestEnums type)
	Helper function to split string with multiple values into option settings. More...

MessageStringCollector	getSkipMessagesIfNecessary (const gmx_hw_info_t &hwinfo, const t_inputrec &inputRec, CodePath mode)
	Returns message describing why PME in this `mode` is not supported for this `inputRec` on this `hwinfo`, or empty of messages when PME is supported.

uint64_t	getSplineModuliDoublePrecisionUlps (int splineOrder)
	For double precision checks, the recursive interpolation and use of trig functions in make_dft_mod require a lot more flops, and thus opportunity for deviation between implementations.

PmeSafePointer	pmeInitWrapper (const t_inputrec inputRec, const CodePath mode, const DeviceContext deviceContext, const DeviceStream deviceStream, const PmeGpuProgram pmeGpuProgram, const Matrix3x3 &box, const real ewaldCoeff_q, const real ewaldCoeff_lj)
	PME initialization.

PmeSafePointer	pmeInitEmpty (const t_inputrec *inputRec)
	Simple PME initialization based on inputrec only.

std::unique_ptr < StatePropagatorDataGpu >	makeStatePropagatorDataGpu (const gmx_pme_t &pme, const DeviceContext deviceContext, const DeviceStream deviceStream)
	Make a GPU state-propagator manager.

void	pmeInitAtoms (gmx_pme_t pme, StatePropagatorDataGpu stateGpu, const CodePath mode, const CoordinatesVector &coordinates, const ChargesVector &charges)
	PME initialization with atom data. More...

static real *	pmeGetRealGridInternal (const gmx_pme_t *pme)
	Getting local PME real grid pointer for test I/O.

static void	pmeGetRealGridSizesInternal (const gmx_pme_t *pme, CodePath mode, IVec &gridSize, IVec &paddedGridSize)
	Getting local PME real grid dimensions.

static t_complex *	pmeGetComplexGridInternal (const gmx_pme_t *pme)
	Getting local PME complex grid pointer for test I/O.

static void	pmeGetComplexGridSizesInternal (const gmx_pme_t *pme, IVec &gridSize, IVec &paddedGridSize)
	Getting local PME complex grid dimensions.

template<typename ValueType >
static void	pmeGetGridAndSizesInternal (const gmx_pme_t , CodePath, ValueType &, IVec &, IVec &)
	Getting the PME grid memory buffer and its sizes - template definition.

template<>
void	pmeGetGridAndSizesInternal< real > (const gmx_pme_t pme, CodePath mode, real &grid, IVec &gridSize, IVec &paddedGridSize)
	Getting the PME real grid memory buffer and its sizes.

template<>
void	pmeGetGridAndSizesInternal< t_complex > (const gmx_pme_t pme, CodePath, t_complex &grid, IVec &gridSize, IVec &paddedGridSize)
	Getting the PME complex grid memory buffer and its sizes.

void	pmePerformSplineAndSpread (gmx_pme_t *pme, CodePath mode, bool computeSplines, bool spreadCharges)
	PME spline calculation and charge spreading. More...

static real *	pmeGetSplineDataInternal (const gmx_pme_t *pme, PmeSplineDataType type, int dimIndex)
	Getting the internal spline data buffer pointer.

void	pmePerformSolve (const gmx_pme_t *pme, CodePath mode, PmeSolveAlgorithm method, real cellVolume, GridOrdering gridOrdering, bool computeEnergyAndVirial)
	PME solving.

void	pmePerformGather (gmx_pme_t *pme, CodePath mode, ForcesVector &forces)
	PME force gathering.

void	pmeFinalizeTest (const gmx_pme_t *pme, CodePath mode)
	PME test finalization before fetching the outputs.

static int	getSplineParamFullIndex (int order, int splineIndex, int dimIndex, int atomIndex, int atomsPerWarp)
	Gets a unique index to an element in a spline parameter buffer. More...

static int	pme_gpu_get_atoms_per_warp (const PmeGpu *pmeGpu)
	Return the number of atoms per warp.

static void	pme_gpu_transform_spline_atom_data (const PmeGpu pmeGpu, const PmeAtomComm atc, PmeSplineDataType type, int dimIndex, PmeLayoutTransform transform)
	Rearranges the atom spline data between the GPU and host layouts. Only used for test purposes so far, likely to be horribly slow. More...

void	pmeSetSplineData (const gmx_pme_t *pme, CodePath mode, const SplineParamsDimVector &splineValues, PmeSplineDataType type, int dimIndex)
	Setting atom spline values/derivatives to be used in spread/gather. More...

void	pmeSetGridLineIndices (gmx_pme_t *pme, CodePath mode, const GridLineIndicesVector &gridLineIndices)
	Setting gridline indices to be used in spread/gather. More...

size_t	pmeGetGridPlainIndexInternal (const IVec &index, const IVec &paddedGridSize, GridOrdering gridOrdering)
	Getting plain index into the complex 3d grid.

template<typename ValueType >
static void	pmeSetGridInternal (const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering, const SparseGridValuesInput< ValueType > &gridValues)
	Setting real or complex grid.

void	pmeSetRealGrid (const gmx_pme_t *pme, CodePath mode, const SparseRealGridValuesInput &gridValues)
	Setting real grid to be used in gather.

void	pmeSetComplexGrid (const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering, const SparseComplexGridValuesInput &gridValues)
	Setting complex grid to be used in solve.

SplineParamsDimVector	pmeGetSplineData (const gmx_pme_t *pme, CodePath mode, PmeSplineDataType type, int dimIndex)
	Getting the single dimension's spline values or derivatives.

GridLineIndicesVector	pmeGetGridlineIndices (const gmx_pme_t *pme, CodePath mode)
	Getting the gridline indices.

template<typename ValueType >
static SparseGridValuesOutput < ValueType >	pmeGetGridInternal (const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering)
	Getting real or complex grid - only non zero values.

SparseRealGridValuesOutput	pmeGetRealGrid (const gmx_pme_t *pme, CodePath mode)
	Getting the real grid (spreading output of pmePerformSplineAndSpread())

SparseComplexGridValuesOutput	pmeGetComplexGrid (const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering)
	Getting the complex grid output of pmePerformSolve()

PmeOutput	pmeGetReciprocalEnergyAndVirial (const gmx_pme_t *pme, CodePath mode, PmeSolveAlgorithm method)
	Getting the reciprocal energy and virial.

std::string	makeRefDataFileName ()
	Construct a refdata filename for a test. More...

std::string	makeHardwareContextName (int hardwareContextIndex)
	Make a terse description of the hardware context suitable for use in naming the test case. More...

ArrayRef< const PmeTestHardwareContext >	getPmeTestHardwareContexts ()
	Return a view of the current PME test hardware contexts.

void	registerTestsDynamically ()
	Declaration of function used to dynamically register GoogleTest tests. More...

static void	checkRealGrid (const IVec realGridSizeFull, const ivec realGridSize, const ivec realGridSizePadded, ArrayRef< const real > inputRealGrid, ArrayRef< real > outputRealGridValues)
	Check that the real grid after forward and backward 3D transforms matches the input real grid.

static unsigned long int	getRequiredNumberOfDevices ()

template<typename T >
ArrayRef< char >	charArrayRefFromArray (T *data, size_t size)
	Convenience function to transform a view into one with base type of (non-const) char. More...

template<typename T >
void	runTest (const DeviceInformation &deviceInfo, ArrayRef< T > input, ArrayRef< T > output)
	Does a device transfer of `input` to the device in `gpuInfo`, and back to `output`.

void	convertRVecToFloat3OnHost (ArrayRef< gmx::RVec > rVecOutput, ArrayRef< const gmx::RVec > rVecInput)
	Tests the compatibility of RVec and float3 using the conversion on host. More...

void	convertRVecToFloat3OnDevice (ArrayRef< gmx::RVec > rVecOutput, ArrayRef< const gmx::RVec > rVecInput, const TestDevice *testDevice)
	Tests the compatibility of RVec and float3 using the conversion on device. More...

template<typename T >
void	fillInputContents (ArrayRef< T > inputRef, int scaleFactorForElements)
	Initialization overload for non-BasicVector.

template<typename T >
void	fillInputContents (ArrayRef< BasicVector< T >> inputRef, int scaleFactorForElements)
	Initialization overload for BasicVector.

template<typename PaddedVectorOfT >
void	resizeAndFillInput (PaddedVectorOfT *input, int newSize, int scaleFactorForElements)
	Dispatcher function for filling.

template<typename T >
void	compareViews (ArrayRef< T > input, ArrayRef< T > output)
	Comparison overload for non-BasicVector.

template<typename T , typename U >
std::enable_if_t < std::is_same_v < std::remove_const_t< T > , std::remove_const_t< U > >, void >	compareViewsIgnoreConst (ArrayRef< T > input, ArrayRef< U > output)
	Comparison for non-BasicVector ignoring const qualifiers.

template<typename T >
void	compareViews (ArrayRef< BasicVector< T >> input, ArrayRef< BasicVector< T >> output)
	Comparison overload for BasicVector<T>

static const std::array < gmx::RVec, 51 >	c_waterPositions ({{{.130,-.041,-.291},{.120,-.056,-.192},{.044,-.005,-.327},{-.854,-.406,.477},{-.900,-.334,.425},{-.858,-.386,.575},{.351,-.061,.853},{.401,-.147,.859},{.416,.016,.850},{-.067,-.796,.873},{-.129,-.811,.797},{-.119,-.785,.958},{-.635,-.312,-.356},{-.629,-.389,-.292},{-.687,-.338,-.436},{.321,-.919,.242},{.403,-.880,.200},{.294,-1.001,.193},{-.404,.735,.728},{-.409,.670,.803},{-.324,.794,.741},{.461,-.596,-.135},{.411,-.595,-.221},{.398,-.614,-.059},{-.751,-.086,.237},{-.811,-.148,.287},{-.720,-.130,.152},{.202,.285,-.364},{.122,.345,-.377},{.192,.236,-.278},{-.230,-.485,.081},{-.262,-.391,.071},{-.306,-.548,.069},{.464,-.119,.323},{.497,-.080,.409},{.540,-.126,.258},{-.462,.107,.426},{-.486,.070,.336},{-.363,.123,.430},{.249,-.077,-.621},{.306,-.142,-.571},{.233,-.110,-.714},{-.922,-.164,.904},{-.842,-.221,.925},{-.971,-.204,.827},{.382,.700,.480},{.427,.610,.477},{.288,.689,.513},{.781,.264,-.113},{.848,.203,-.070},{.708,.283,-.048}}})
	Database of 51 water atom input positions (taken from spc216.gro) for use as test inputs.

static void	readTprInput (const TprAndFileManager tprHandle, gmx_mtop_t mtop, t_inputrec *ir)
	Reads a tpr for the test. More...

static void	compareDifferentIndices (const StringTableBuilder &builder, const StringTableEntry &firstSymbol, const StringTableEntry &otherSymbol, bool expectedOutcome)
	Check that symbols obtained from symtab compare correctly. More...

static int	readIndexFromSerializer (const StringTableEntry &symbol)
	Helper to obtain the integer index from an entry. More...

static void	stringMatches (const StringTable &symtab, const StringTableEntry &symbol, const char *string)
	Helper function to check that a string in matches when looked up in non finalized table. More...

void	checkEnergiesAgainstReferenceData (const std::string &energyFilename, const EnergyTermsToCompare &energyTermsToCompare, TestReferenceChecker *checker, MaxNumFrames maxNumEnergyFrames)
	Check a subset of the energies found in an energy file against reference data. More...

void	checkEnergiesAgainstReferenceData (const std::string &energyFilename, const EnergyTermsToCompare &energyTermsToCompare, TestReferenceChecker *checker)
	Check a subset of the energies found in an energy file against reference data. More...

EnergyFrameReaderPtr	openEnergyFileToReadTerms (const std::string &filename, const std::vector< std::string > &requiredEnergyTermNames)
	Open the file and return an object that can read the required terms from frames of an .edr file. More...

static t_enxframe *	make_enxframe ()
	Helper function to obtain resources.

void	done_enxframe (t_enxframe *fr)
	Helper function to clean up resources. More...

template<typename Reader , typename Comparator >
bool	compareFrames (Reader referenceFrameReader, Reader testFrameReader, const Comparator &comparator)
	Compare the next frame returned by `testFrameReader` with the matching frame from `referenceTestReader` using `comparator`. More...

std::vector < PeriodicOutputParameters >	outputParameters ()
	Return vector of mdp parameter sets to test. More...

std::vector < PropagationParameters >	simplePropagationParameters ()
	Returns sets of simple simulation propagators.

std::vector < PropagationParameters >	propagationParametersWithCoupling ()
	Returns sets of simulation propagators including coupling. More...

std::vector < PropagationParameters >	propagationParametersWithConstraints ()
	Returns sets of simulation propagators including coupling. More...

static std::string	getReplicaExchangeOutputFromLogFile (const std::string &logFileName)
	Return replica exchange related output from logfile. More...

void	runGrompp (SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options)

void	runMdrun (SimulationRunner *runner, const std::vector< SimulationOptionTuple > &options)

void	compareEnergies (const std::string &edr1Name, const std::string &edr2Name, const EnergyTermsToCompare &energyTermsToCompare, const MaxNumFrames maxNumFrames)

void	compareTrajectories (const std::string &trajectory1Name, const std::string &trajectory2Name, const TrajectoryComparison &trajectoryComparison)

static void	organizeMdpFile (SimulationRunner *runner, int nsteps=2)
	Build a simple .mdp file.

static void	compareBox (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const FloatingPointTolerance tolerance)
	Compares the box from `reference` and `test` according to the `matchSettings` and `tolerance`. More...

static std::vector< RVec >	putAtomsInBox (const TrajectoryFrame &frame)
	Help put all atom coordinates in `frame` into its box. More...

static bool	shouldDoComparison (const ComparisonConditions comparisonConditions, const bool referenceIsEmpty, const bool testIsEmpty)
	Return whether the `comparisonConditions` and emptiness of reference and test frames means that a comparison should be attempted. More...

static void	compareCoordinates (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const FloatingPointTolerance tolerance)
	Compares the position coordinates from `reference` and `test` according to the `matchSettings` and `tolerance`.

static void	compareVelocities (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const FloatingPointTolerance tolerance)
	Compares the velocities from `reference` and `test` according to the `matchSettings` and `tolerance`.

static void	compareForces (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const FloatingPointTolerance tolerance)
	Compares the forces from `reference` and `test` according to the `matchSettings` and `tolerance`.

static bool	shouldDoComparison (ArrayRef< const RVec > values, ComparisonConditions comparisonConditions)
	Return whether the `comparisonConditions` and emptiness of the test frame means that a comparison should be attempted. More...

static void	checkPositionsAgainstReference (const TrajectoryFrame &frame, const TrajectoryFrameMatchSettings &matchSettings, const TrajectoryTolerances &tolerance, TestReferenceChecker *checker)
	Compares the positions from `frame` to reference data according to the `matchSettings` and `tolerance`.

static void	checkVelocitiesAgainstReference (const TrajectoryFrame &frame, const TrajectoryFrameMatchSettings &matchSettings, const TrajectoryTolerances &tolerance, TestReferenceChecker *checker)
	Compares the velocities from `frame` to reference data according to the `matchSettings` and `tolerance`.

static void	checkForcesAgainstReference (const TrajectoryFrame &frame, const TrajectoryFrameMatchSettings &matchSettings, const TrajectoryTolerances &tolerance, TestReferenceChecker *checker)
	Compares the forces from `frame` to reference data according to the `matchSettings` and `tolerance`.

static void	checkBoxAgainstReference (const TrajectoryFrame &frame, const TrajectoryFrameMatchSettings &matchSettings, const TrajectoryTolerances &tolerance, TestReferenceChecker *checker)
	Compares the box from `frame` to reference data according to the `matchSettings` and `tolerance`.

void	checkConfFile (TextInputStream input, TestReferenceChecker checker, const ConfMatchSettings &settings)
	Adds content of a gro file to TestReferenceChecker object. More...

int	getNumberOfTestMpiRanks ()
	Returns the number of MPI ranks to use for an MPI test. More...

void	initReferenceData (IOptionsContainer *options)
	Initializes reference data handling. More...

int	gmxSetenv (const char name, const char value, int overwrite)
	Workaround to make setenv work on Windows.

int	gmxUnsetenv (const char *name)
	Workaround to make unsetenv work on Windows.

bool	isNumberOfPpRanksSupported (const std::string &simulationName, int possibleNumberOfPpRanks)
	Return whether the number of ranks is supported by the simulation `simulationName` in the database. More...

std::string	reportNumbersOfPpRanksSupported (const std::string &simulationName)
	Return a string describing the numbers of ranks supported for the simulation `simulationName` in the database.

MdpFieldValues	prepareMdpFieldValues (const std::string &simulationName, const std::string &integrator, const std::string &tcoupl, const std::string &pcoupl, MdpParameterDatabase additionalMdpParameters=MdpParameterDatabase::Default)
	Set up values for an .mdp file that permits a highly reproducible simulation. More...

MdpFieldValues	prepareMdpFieldValues (const char simulationName, const char integrator, const char tcoupl, const char pcoupl, MdpParameterDatabase additionalMdpParameters=MdpParameterDatabase::Default)
	Set up values for an .mdp file that permits a highly reproducible simulation. More...

std::string	prepareMdpFileContents (const MdpFieldValues &mdpFieldValues)
	Make a string containing an .mdp file from the `mdpFieldValues`. More...

const TestHardwareEnvironment *	getTestHardwareEnvironment ()
	Get the global test environment.

void	checkTestNameLength (std::optional< std::string > testName=std::nullopt)
	Gives a GoogleTest assertion if the test's name is too long. More...

template<typename TestFixture , typename TestCase , typename Combinations >
void	registerTests (const std::string &testSuiteName, std::string(makeBriefNameOfTestCase)(const typename::testing::TestParamInfo< typename TestFixture::ParamType > &), std::string(makeFullNameOfTestCase)(const typename::testing::TestParamInfo< typename TestFixture::ParamType > &, const std::string &), const Combinations &combinations)
	Register tests dynamically based on the execution context. More...

testing::Matcher< std::tuple < float, float > >	FloatEq (const FloatingPointTolerance &tolerance)
	Make matcher for floats for use with GoogleMock that compare equal when `tolerance` is satisifed. More...

testing::Matcher< std::tuple < double, double > >	DoubleEq (const FloatingPointTolerance &tolerance)
	Make matcher for doubles for use with GoogleMock that compare equal when `tolerance` is satisifed. More...

testing::Matcher< std::tuple < real, real > >	RealEq (const FloatingPointTolerance &tolerance)
	Make matcher for reals for use with GoogleMock that compare equal when `tolerance` is satisifed. More...

testing::Matcher< std::tuple < BasicVector< real > , BasicVector< real > > >	RVecEq (const FloatingPointTolerance &tolerance)
	Make matcher for RVecs for use with GoogleMock that compare equal when `tolerance` is satisifed. More...

void	registerTestOptions (const char name, TestOptionsProvider provider)
	Registers a test option provider with the test framework. More...

void	initTestOptions (IOptionsContainer *options)
	Initializes the options from all registered test providers. More...

void	done_trxframe (t_trxframe *fr)
	Helper function to free all resources. More...

void	checkXvgFile (TextInputStream input, TestReferenceChecker checker, const XvgMatchSettings &settings)
	Adds content of xvg file to TestReferenceChecker object. More...

static void	throwIfNonEmptyAndOnlyWhitespace (const std::string &s, const char *id)
	Throw a TestException if the caller tries to write particular refdata that can't work. More...

static double	convertDoubleReferenceValue (const std::string &value)
	Helper function to parse a floating-point reference data value.

static t_trxframe *	make_trxframe ()
	Helper function to obtain resources.


void	registerDynamicalPmeGatherTests (const Range< int > hardwareContextIndexRange)

void	registerDynamicalPmeSolveTests (const Range< int > hardwareContextIndexRange)

void	registerDynamicalPmeSplineSpreadTests (Range< int > contextIndexRange)
	Functions that dynamically register test cases. More...


void	checkTrajectoryAgainstReferenceData (const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker)

void	checkTrajectoryAgainstReferenceData (const std::string &trajectoryFilename, const TrajectoryComparison &trajectoryComparison, TestReferenceChecker *checker, MaxNumFrames maxNumFrames)

Variables
constexpr double	g_coords []
	Database of 21 test coordinates that represent a trajectory */. More...

static constexpr int	c_numLambdaStates = 16
	The number of lambda states to use in the tests.

const char *const	trajectoryFileNames []
	Character array of different file names to test. More...

const char *const	setAtomsSupported []
	Names here work for setAtoms module. More...

const char *const	setAtomsUnSupported [] = { "spc2-traj.trr", "spc2-traj.xtc", "spc2-traj.g96" }
	Names here don't work for setAtoms module.

const char *const	anySupported []
	Names here work for stuff that has no specific requirements. More...

const char *const	setVelocitySupported []
	Names here work for setVelocity module. More...

const char *const	setVelocityUnSupported [] = { "spc2-traj.xtc", "spc2-traj.pdb", "spc2-traj.g96" }
	Names here don't work for setVelocity module.

const char *const	setForceSupported []
	Names here work for setForce module. More...

const char *const	setForceUnSupported []
	Names here don't work for setForce module. More...

const char *const	setPrecisionSupported []
	Names here work for setPrecision module. More...

const char *const	setPrecisionUnSupported []
	Names here don't work for setPrecision module. More...

const std::map< std::string, Matrix3x3 >	c_inputBoxes
	A couple of valid inputs for boxes. More...

std::vector< int >	c_inputPmeOrders { 3, 4, 5 }
	Valid PME orders for testing.

constexpr int64_t	c_splineModuliSinglePrecisionUlps = 1
	Spline moduli are computed in double precision, so they're very good in single precision.

std::vector< GpuFftTestParams > const	inputs

static PeriodicOutputParameters	g_basicPeriodicOutputParameters
	Some common choices of periodic output mdp parameters to simplify defining values for the combinations under test. More...

static const char *	g_butaneTopFileFormatString
	Format string for building a configurable .top file.

static std::mutex	s_testHardwareEnvironmentMutex
	Mutex for making the test hardware environment.

static std::unique_ptr < TestHardwareEnvironment >	s_testHardwareEnvironment
	The test hardware environment.

static bool	g_bDeleteFilesAfterTest = true
	Controls whether TestFileManager should delete temporary files after the test finishes. More...

Enumeration Type Documentation

enum gmx::test::CodePath : int

strong

Hardware code path being tested.

Enumerator
CPU	CPU code path.
GPU	GPU code path.
Count	Total number of code paths.

enum gmx::test::PmeSolveAlgorithm : int

strong

PME solver type.

Enumerator
Coulomb	Coulomb electrostatics.
LennardJones	Lennard-Jones.
Count	Total number of solvers.

enum gmx::test::SimulationRunnerMdpSource

strong

Enumerator
Undefined	The default behavior. Will result in an empty mdp file.
String	Mdp options are set via string using SimulationRunner::useStringAsMdpFile.
File	Mdp options are read from a file set in SimulationRunner::useTopGroAndMdpFromFepTestDatabase.
Count	Signals the last enum entry.

Function Documentation

template<typename T >

ArrayRef<char> gmx::test::charArrayRefFromArray	(	T *	data,
		size_t	size
	)

Convenience function to transform a view into one with base type of (non-const) char.

This transformation is useful for using containers with C APIs where the function signature is not declared const even where the semantics of the usage actually are const.

Parameters

[in]	data	The data pointer.
[in]	size	The size of the data pointer (in T).

Template Parameters

T	The base type of the container

void gmx::test::checkConfFile	(	TextInputStream *	input,
		TestReferenceChecker *	checker,
		const ConfMatchSettings &	settings
	)

Adds content of a gro file to TestReferenceChecker object.

Parameters

[in]	input	Stream that provides the gro content.
[in,out]	checker	Checker to use.
[in]	settings	Settings to use for matching.

Parses a gro file from the input stream, and checks the contents against reference data (only first two lines for now).

See Also: ConfMatch

void gmx::test::checkEnergiesAgainstReferenceData	(	const std::string &	energyFilename,
		const EnergyTermsToCompare &	energyTermsToCompare,
		TestReferenceChecker *	checker,
		MaxNumFrames	maxNumEnergyFrames
	)

Check a subset of the energies found in an energy file against reference data.

Opens the energy file, loops over all frames, matching the indicated energies against refdata at the given tolerance.

Parameters

[in]	energyFilename	The name of an energy file.
[in]	energyTermsToCompare	Set of energies to match at given tolerances.
[in]	checker	Root checker for reference data.
[in]	maxNumEnergyFrames	The maximum number of frames to check

Todo:: This is quite similar to the functionality used in PmeTest, and we should consider reducing the duplication.

void gmx::test::checkEnergiesAgainstReferenceData	(	const std::string &	energyFilename,
		const EnergyTermsToCompare &	energyTermsToCompare,
		TestReferenceChecker *	checker
	)

Check a subset of the energies found in an energy file against reference data.

Convenience overload using all frames

See Also: checkEnergiesAgainstReferenceData(const std::string&, const EnergyTermsToCompare&, TestReferenceChecker*, MaxNumFrames)

void gmx::test::checkXvgFile	(	TextInputStream *	input,
		TestReferenceChecker *	checker,
		const XvgMatchSettings &	settings
	)

Adds content of xvg file to TestReferenceChecker object.

Parameters

[in]	input	Stream that provides the xvg content.
[in,out]	checker	Checker to use.
[in]	settings	Settings to use for matching.

Parses an xvg file from the input stream, and checks the contents against reference data. settings can be used to customize the matching. Only a single data set is supported (but multiple columns work). A subset of xmgrace formatting is also checked; static content that is nearly always the same is skipped.

See Also: XvgMatch

static void gmx::test::compareBox	(	const TrajectoryFrame &	reference,
		const TrajectoryFrame &	test,
		const TrajectoryFrameMatchSettings &	matchSettings,
		const FloatingPointTolerance	tolerance
	)

static

Compares the box from reference and test according to the matchSettings and tolerance.

Todo:: This could be streamlined when we have a proper 3D matrix class and view.

static void gmx::test::compareDifferentIndices	(	const StringTableBuilder &	builder,
		const StringTableEntry &	firstSymbol,
		const StringTableEntry &	otherSymbol,
		bool	expectedOutcome
	)

static

Check that symbols obtained from symtab compare correctly.

Helper function to find out if two entries obtained by a symtab lookup are equivalent or not, according to testing criteria. Checks that the indices match before finalizing storage.

Parameters

[in]	builder	StringTableBuilder table that contains the entries to validate.
[in]	firstSymbol	Handle into `builder` obtained from placing string in `builder`.
[in]	otherSymbol	Other handle from obtained from separate string deposit.
[in]	expectedOutcome	If the handles should result in equal entries or not.

template<typename Reader , typename Comparator >

bool gmx::test::compareFrames	(	Reader	referenceFrameReader,
		Reader	testFrameReader,
		const Comparator &	comparator
	)

Compare the next frame returned by testFrameReader with the matching frame from referenceTestReader using comparator.

Returns: True when a successful comparison was made

void gmx::test::convertRVecToFloat3OnDevice	(	ArrayRef< gmx::RVec >	rVecOutput,
		ArrayRef< const gmx::RVec >	rVecInput,
		const TestDevice *	testDevice
	)

Tests the compatibility of RVec and float3 using the conversion on device.

Parameters

[out]	rVecOutput	Data in RVec format for the output.
[in]	rVecInput	Data in RVec format with the input.
[in]	testDevice	Test herdware environment to get DeviceContext and DeviceStream from.

void gmx::test::convertRVecToFloat3OnHost	(	ArrayRef< gmx::RVec >	rVecOutput,
		ArrayRef< const gmx::RVec >	rVecInput
	)

Tests the compatibility of RVec and float3 using the conversion on host.

Parameters

[out]	rVecOutput	Data in RVec format for the output.
[in]	rVecInput	Data in RVec format with the input.

TrajectoryFrameWriterPointer gmx::test::createMinimalTrajectoryFrameWriter	(	const std::string &	filename,
		const TopologyInformation &	topology,
		const Selection &	selection,
		OutputRequirements	requirements
	)

inline

Create minimal TrajectoryFrameWriter using the provided builder.

Parameters

[in]	filename	Name of file to create object for.
[in]	topology	Reference to input top.
[in]	selection	Reference to input selection.
[in]	requirements	Requirements for constructing OutputManagar.

Exceptions

InconsistentInputError When builder can not create the CoordinateFile.

Returns: unique_ptr to new CoordinateFile object.

void gmx::test::done_enxframe ( t_enxframe * fr )

Helper function to clean up resources.

Helper function to free resources (NB free_enxframe only frees the contents, not the pointer itself)

void gmx::test::done_trxframe ( t_trxframe * fr )

Helper function to free all resources.

Helper function to clean up resources.

testing::Matcher< std::tuple< double, double > > gmx::test::DoubleEq ( const FloatingPointTolerance & tolerance )

Make matcher for doubles for use with GoogleMock that compare equal when tolerance is satisifed.

Used like

EXPECT_THAT(testDoubles, Pointwise(DoubleEq(tolerance), referenceDoubles));

testing::Matcher< std::tuple< float, float > > gmx::test::FloatEq ( const FloatingPointTolerance & tolerance )

Make matcher for floats for use with GoogleMock that compare equal when tolerance is satisifed.

Used like

EXPECT_THAT(testFloats, Pointwise(FloatEq(tolerance), referenceFloats));

AwhTestParameters gmx::test::getAwhTestParameters	(	AwhHistogramGrowthType	eawhgrowth,
		AwhPotentialType	eawhpotential,
		ArrayRef< const std::vector< char >>	dimensionParameterBuffers,
		bool	inputUserData,
		double	beta,
		bool	useAwhFep,
		double	inputErrorScaling,
		int	numFepLambdaStates,
		int	biasShareGroup
	)

Helper function to set up the C-style AWH parameters for the test.

Builds the test input data from serialized data.

static std::string gmx::test::getReplicaExchangeOutputFromLogFile ( const std::string & logFileName )

static

Return replica exchange related output from logfile.

All replica exchange related output in log files start with 'Repl', making extraction easy. This function also removes the printing of energy differences, as the log files are compared exactly, and energy differences will slightly vary between runs.

Parameters

logFileName Name of log file

Returns: Replica exchange related output in log file

static int gmx::test::getSplineParamFullIndex	(	int	order,
		int	splineIndex,
		int	dimIndex,
		int	atomIndex,
		int	atomsPerWarp
	)

static

Gets a unique index to an element in a spline parameter buffer.

These theta/dtheta buffers are laid out for GPU spread/gather kernels. The index is wrt the execution block, in range(0, atomsPerBlock * order * DIM).

This is a wrapper, only used in unit tests.

Parameters

[in]	order	PME order
[in]	splineIndex	Spline contribution index (from 0 to `order` - 1)
[in]	dimIndex	Dimension index (from 0 to 2)
[in]	atomIndex	Atom index wrt the block.
[in]	atomsPerWarp	Number of atoms processed by a warp.

Returns: Index into theta or dtheta array using GPU layout.

bool gmx::test::isNumberOfPpRanksSupported	(	const std::string &	simulationName,
		int	possibleNumberOfPpRanks
	)

Return whether the number of ranks is supported by the simulation simulationName in the database.

This method lets test runners understand when end-to-end tests should be expected to work.

std::string gmx::test::makeHardwareContextName ( int hardwareContextIndex )

Make a terse description of the hardware context suitable for use in naming the test case.

The full hardware device description is used in a SCOPED_TRACE message, but that is too long for the test name and has too many possible characters that might break GoogleTest.

std::string gmx::test::makeRefDataFileName ( )

Construct a refdata filename for a test.

We want the same reference data to apply to every hardware context for which we test PME. That means we need to store it in a file whose name relates to the name of the test, but excluding the part related to the context.

EnergyFrameReaderPtr gmx::test::openEnergyFileToReadTerms	(	const std::string &	filename,
		const std::vector< std::string > &	requiredEnergyTermNames
	)

Open the file and return an object that can read the required terms from frames of an .edr file.

Parameters

[in]	filename	Name of the energy file to use
[in]	requiredEnergyTermNames	Names of the energy terms that the caller requires to be present for an .edr file frame to be considered valid

Exceptions

FileIOError	If the .edr file cannot be opened
APIError	If any required energy term is not present in the file
std::bad_alloc	When out of memory

This function is intended to have the main responsibility for making EnergyFrameReader objects.

std::vector< PeriodicOutputParameters > gmx::test::outputParameters ( )

Return vector of mdp parameter sets to test.

These are constructed to observe the mdp parameter choices that only affect when output is written agree with those that were written from a reference run where output was done every step. The numbers are chosen in the context of the defaults in prepareDefaultMdpFieldValues().

Todo:: Test nstlog, nstdhdl, nstxout-compressed

static void gmx::test::pme_gpu_transform_spline_atom_data	(	const PmeGpu *	pmeGpu,
		const PmeAtomComm *	atc,
		PmeSplineDataType	type,
		int	dimIndex,
		PmeLayoutTransform	transform
	)

static

Rearranges the atom spline data between the GPU and host layouts. Only used for test purposes so far, likely to be horribly slow.

Parameters

[in]	pmeGpu	The PME GPU structure.
[out]	atc	The PME CPU atom data structure (with a single-threaded layout).
[in]	type	The spline data type (values or derivatives).
[in]	dimIndex	Dimension index.
[in]	transform	Layout transform type

void gmx::test::pmeInitAtoms	(	gmx_pme_t *	pme,
		StatePropagatorDataGpu *	stateGpu,
		const CodePath	mode,
		const CoordinatesVector &	coordinates,
		const ChargesVector &	charges
	)

PME initialization with atom data.

PME initialization with atom data and system box.

void gmx::test::pmePerformSplineAndSpread	(	gmx_pme_t *	pme,
		CodePath	mode,
		bool	computeSplines,
		bool	spreadCharges
	)

PME spline calculation and charge spreading.

PME spline computation and charge spreading.

void gmx::test::pmeSetGridLineIndices	(	gmx_pme_t *	pme,
		CodePath	mode,
		const GridLineIndicesVector &	gridLineIndices
	)

Setting gridline indices to be used in spread/gather.

Setting gridline indices be used in spread/gather.

void gmx::test::pmeSetSplineData	(	const gmx_pme_t *	pme,
		CodePath	mode,
		const SplineParamsDimVector &	splineValues,
		PmeSplineDataType	type,
		int	dimIndex
	)

Setting atom spline values/derivatives to be used in spread/gather.

Setting atom spline values or derivatives to be used in spread/gather.

MdpFieldValues gmx::test::prepareMdpFieldValues	(	const std::string &	simulationName,
		const std::string &	integrator,
		const std::string &	tcoupl,
		const std::string &	pcoupl,
		MdpParameterDatabase	additionalMdpParameters = `MdpParameterDatabase::Default`
	)

Set up values for an .mdp file that permits a highly reproducible simulation.

An internal database of several kinds of simulation useful for such comparisons is available, whose simulationName keys are

argon12
argon5832
tip3p5
spc2
spc216
alanine_vsite_vacuo
alanine_vsite_solvated
glycine_vacuo
glycine_no_constraints_vacuo
nonanol_vacuo

Some of these systems are pretty minimal, because having few atoms means few interactions, highly reproducible forces, and allows tests to focus on the correctness of the implementation of high-level mdrun features. The boxes are of a reasonable size so that domain decomposition is possible. The pressure-coupling parameters are isotropic, and set up so that there will not be dramatic collapse of volume over the handful of MD steps that will be run. A single temperature-coupling group is used.

Parameters

[in]	simulationName	The name of the simulation, which indexes the database
[in]	integrator	The integrator to use
[in]	tcoupl	The temperature-coupling algorithm to use
[in]	pcoupl	The pressure-coupling algorithm to use
[in]	additionalMdpParameters	Additional mdp parameters to be added

Returns: Mdp file values

Exceptions

std::bad_alloc if out of memory std::out_of_range if simulationName is not in the database

MdpFieldValues gmx::test::prepareMdpFieldValues	(	const char *	simulationName,
		const char *	integrator,
		const char *	tcoupl,
		const char *	pcoupl,
		MdpParameterDatabase	additionalMdpParameters = `MdpParameterDatabase::Default`
	)

Set up values for an .mdp file that permits a highly reproducible simulation.

An internal database of several kinds of simulation useful for such comparisons is available, whose simulationName keys are

argon12
argon5832
tip3p5
spc2
spc216
alanine_vsite_vacuo
alanine_vsite_solvated
glycine_vacuo
glycine_no_constraints_vacuo
nonanol_vacuo

Some of these systems are pretty minimal, because having few atoms means few interactions, highly reproducible forces, and allows tests to focus on the correctness of the implementation of high-level mdrun features. The boxes are of a reasonable size so that domain decomposition is possible. The pressure-coupling parameters are isotropic, and set up so that there will not be dramatic collapse of volume over the handful of MD steps that will be run. A single temperature-coupling group is used.

Parameters

[in]	simulationName	The name of the simulation, which indexes the database
[in]	integrator	The integrator to use
[in]	tcoupl	The temperature-coupling algorithm to use
[in]	pcoupl	The pressure-coupling algorithm to use
[in]	additionalMdpParameters	Additional mdp parameters to be added

Returns: Mdp file values

Exceptions

std::bad_alloc if out of memory std::out_of_range if simulationName is not in the database

std::string gmx::test::prepareMdpFileContents ( const MdpFieldValues & mdpFieldValues )

Make a string containing an .mdp file from the mdpFieldValues.

Exceptions

std::bad_alloc if out of memory

std::vector< PropagationParameters > gmx::test::propagationParametersWithConstraints ( )

Returns sets of simulation propagators including coupling.

These are chosen to cover the commonly used space of propagation algorithms on systems with constraints.

std::vector< PropagationParameters > gmx::test::propagationParametersWithCoupling ( )

Returns sets of simulation propagators including coupling.

These are chosen to cover the commonly used space of propagation algorithms togther with the perdiods between their actions. The periods tested are chosen to be mutually co-prime and distinct from the pair search and user output period (4), so that over the duration of a short simulation many kinds of simulation step behavior are tested.

static std::vector<RVec> gmx::test::putAtomsInBox ( const TrajectoryFrame & frame )

static

Help put all atom coordinates in frame into its box.

This can perhaps go away when frame->x is a container.

static int gmx::test::readIndexFromSerializer ( const StringTableEntry & symbol )

static

Helper to obtain the integer index from an entry.

As the index is only used during (de-) serialization, use this machinery to obtain it.

Parameters

[in] symbol Single StringTableEntry to obtain the index of.

Returns: Integer index to be used to obtain value from StringTable.

static void gmx::test::readTprInput	(	const TprAndFileManager *	tprHandle,
		gmx_mtop_t *	mtop,
		t_inputrec *	ir
	)

static

Reads a tpr for the test.

Reads a tpr to have access to the system information for print out.

Parameters

[in]	tprHandle	Handle to the tpr to red in.
[in]	mtop	Pointer to topology datastructure to populate.
[in]	ir	Pointer to inputrec to populate.

testing::Matcher< std::tuple< real, real > > gmx::test::RealEq ( const FloatingPointTolerance & tolerance )

Make matcher for reals for use with GoogleMock that compare equal when tolerance is satisifed.

Used like

EXPECT_THAT(testReals, Pointwise(RealEq(tolerance), referenceReals));

void gmx::test::registerDynamicalPmeSplineSpreadTests ( Range< int > contextIndexRange )

Functions that dynamically register test cases.

This are called by registerTestsDynamically and customize the range of test cases to suit the available hardware.

template<typename TestFixture , typename TestCase , typename Combinations >

void gmx::test::registerTests	(	const std::string &	testSuiteName,
		std::string(*)(const typename::testing::TestParamInfo< typename TestFixture::ParamType > &)	makeBriefNameOfTestCase,
		std::string(*)(const typename::testing::TestParamInfo< typename TestFixture::ParamType > &, const std::string &)	makeFullNameOfTestCase,
		const Combinations &	combinations
	)

Register tests dynamically based on the execution context.

This template reduces code duplication across the dynamically registered tests, letting them register their tests more tersely.

Template Parameters

TestFixture	The type of the test fixture
TestCase	The type of the test case (derived from `TestFixture`)
Combinations	The interal GoogleTest type describing the return from `testing::Combine()` intended to generate test parameters of type `TestFixture::ParamType` (which is typically a tuple).

Parameters

[in]	testSuiteName	The name of the test suite that shares the `TestFixture`
[in]	makeBriefNameOfTestCase	Function that will make the brief name of the test case, used for naming the refdata file
[in]	makeFullNameOfTestCase	Function that will make the full name of the test case
[in]	combinations	A generator of test values produced with `testing::Combine()`

Note that Combinations is actually well defined relative to TestFixture::ParamType, but its concrete type is an internal GoogleTest type, so we do not want to express it in code. In C++20, it would be better to declare the function parameter like const auto& combinations to achieve the same effect of hiding the concrete type.

void gmx::test::registerTestsDynamically ( )

Declaration of function used to dynamically register GoogleTest tests.

When a test binary uses gmx_add_gtest_executable(exename DYNAMIC_REGISTRATION ...) it must provide an implementation of this method. The method is called before RUN_ALL_TESTS() and is expected to call testing::RegisterTest to register tests dynamically. This approach might be necessary to run the tests in a stable way over whichever hardware is detected at run time.

Normal test binaries do not need to implement this function.

::gmx::test::TestHardwareEnvironment::gmxSetUp() should be called before this method, in case the test hardware environment is needed to help decide which tests to register.

testing::Matcher< std::tuple< RVec, RVec > > gmx::test::RVecEq ( const FloatingPointTolerance & tolerance )

Make matcher for RVecs for use with GoogleMock that compare equal when tolerance is satisifed.

Used like

EXPECT_THAT(testRVecs, Pointwise(RVecEq(tolerance), referenceRVecs));

static bool gmx::test::shouldDoComparison	(	const ComparisonConditions	comparisonConditions,
		const bool	referenceIsEmpty,
		const bool	testIsEmpty
	)

static

Return whether the comparisonConditions and emptiness of reference and test frames means that a comparison should be attempted.

This allows the framework to determine whether it is an error if a comparison cannot be made.

static bool gmx::test::shouldDoComparison	(	ArrayRef< const RVec >	values,
		ComparisonConditions	comparisonConditions
	)

static

Return whether the comparisonConditions and emptiness of the test frame means that a comparison should be attempted.

This allows the framework to determine whether it is an error if a comparison cannot be made.

static void gmx::test::splitAndAddValues	(	OptionsAssigner *	assigner,
		const std::string &	optionValues,
		TestEnums	type
	)

static

Helper function to split string with multiple values into option settings.

Parameters

[in]	assigner	Options assigner to use.
[in]	optionValues	String to split that contains option values.
[in]	type	Determine which input time we are using.

static void gmx::test::stringMatches	(	const StringTable &	symtab,
		const StringTableEntry &	symbol,
		const char *	string
	)

static

Helper function to check that a string in matches when looked up in non finalized table.

Checks that a string looked up by using the index in the symbol table matches the string stored in the wrapper object obtained by entering a string.

Parameters

[in]	symtab	Symbol table that contains the entries.
[in]	symbol	The entry obtained from placing a string in the symbol table.
[in]	string	The string the entry should match.

static void gmx::test::throwIfNonEmptyAndOnlyWhitespace	(	const std::string &	s,
		const char *	id
	)

static

Throw a TestException if the caller tries to write particular refdata that can't work.

If the string to write is non-empty and has only whitespace, TinyXML2 can't read it correctly, so throw an exception for this case, so that we can't accidentally use it and run into mysterious problems.

Todo:: Eliminate this limitation of TinyXML2. See e.g. https://github.com/leethomason/tinyxml2/issues/432

Variable Documentation

const char* const gmx::test::anySupported[]

Initial value:

= { "spc2-traj.trr",
                                     "spc2-traj.xtc",
                                     "spc2-traj.g96" }

Names here work for stuff that has no specific requirements.

PDB and GRO format are not tested here because they also require atoms information that is incompatible with the other output formats.

const std::map< std::string, Matrix3x3 > gmx::test::c_inputBoxes

Initial value:

= {
    { "rect", { { 8.0F, 0.0F, 0.0F, 0.0F, 3.4F, 0.0F, 0.0F, 0.0F, 2.0F } } },
    { "tric", { { 7.0F, 0.0F, 0.0F, 0.0F, 4.1F, 0.0F, 3.5F, 2.0F, 12.2F } } },
}

A couple of valid inputs for boxes.

PeriodicOutputParameters gmx::test::g_basicPeriodicOutputParameters

static

Initial value:

= {
    { "nstenergy", "0" }, { "nstlog", "0" },           { "nstxout", "0" },
    { "nstvout", "0" },   { "nstfout", "0" },          { "nstxout-compressed", "0" },
    { "nstdhdl", "0" },   { "description", "unknown" }
}

Some common choices of periodic output mdp parameters to simplify defining values for the combinations under test.

bool gmx::test::g_bDeleteFilesAfterTest = true

static

Controls whether TestFileManager should delete temporary files after the test finishes.

constexpr double gmx::test::g_coords[]

Initial value:

= { 0.62, 0.70, 0.68, 0.80, 0.93, 0.87, 1.16, 1.14, 0.95, 0.89, 0.91,

0.86, 0.88, 0.79, 0.75, 0.82, 0.74, 0.70, 0.68, 0.71, 0.73 }

Database of 21 test coordinates that represent a trajectory */.

std::vector<GpuFftTestParams> const gmx::test::inputs

Initial value:

{
    { IVec{ 5, 6, 9 }, 4, 1, FftBackend::HeFFTe_CUDA }, 
    { IVec{ 5, 6, 9 }, 2, 2, FftBackend::HeFFTe_CUDA }  
}

const char* const gmx::test::setAtomsSupported[]

Initial value:

= {
    "spc2-traj.gro",
    "spc2-traj.pdb",
}

Names here work for setAtoms module.

const char* const gmx::test::setForceSupported[]

Initial value:

= {
    "spc2-traj.trr",
}

Names here work for setForce module.

const char* const gmx::test::setForceUnSupported[]

Initial value:

= { "spc2-traj.xtc",
                                            "spc2-traj.pdb",
                                            "spc2-traj.gro",
                                            "spc2-traj.g96" }

Names here don't work for setForce module.

const char* const gmx::test::setPrecisionSupported[]

Initial value:

= {
    "spc2-traj.xtc",
}

Names here work for setPrecision module.

const char* const gmx::test::setPrecisionUnSupported[]

Initial value:

= { "spc2-traj.trr",
                                                "spc2-traj.pdb",
                                                "spc2-traj.gro",
                                                "spc2-traj.g96" }

Names here don't work for setPrecision module.

const char* const gmx::test::setVelocitySupported[]

Initial value:

= {
    "spc2-traj.gro",
    "spc2-traj.trr",
}

Names here work for setVelocity module.

const char* const gmx::test::trajectoryFileNames[]

Initial value:

= { "spc2-traj.trr",
                                            "spc2-traj.xtc", "spc2-traj.pdb",
                                            "spc2-traj.gro", "spc2-traj.g96" }

Character array of different file names to test.

Description

Classes

Typedefs

Enumerations

Functions

Variables

Enumeration Type Documentation

Function Documentation

Variable Documentation