gmx::test Namespace Reference

Description

Testing utilities namespace.

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

Namespaces
	anonymous_namespace{base.cpp}
	anonymous_namespace{bootstrap_loadstore.cpp}
	anonymous_namespace{clustsize.cpp}
	anonymous_namespace{cmdlinemodulemanagertest.cpp}
	anonymous_namespace{conftest.cpp}
	anonymous_namespace{filematchers.cpp}
	anonymous_namespace{initialconstraints.cpp}
	anonymous_namespace{legacyenergy.cpp}
	anonymous_namespace{loggertest.cpp}
	anonymous_namespace{mdebin.cpp}
	anonymous_namespace{mock_datamodule.cpp}
	anonymous_namespace{moduletest.cpp}
	anonymous_namespace{mutex.cpp}
	anonymous_namespace{pinnedmemorychecker.cpp}
	anonymous_namespace{pmebsplinetest.cpp}
	anonymous_namespace{pmegathertest.cpp}
	anonymous_namespace{pmesolvetest.cpp}
	anonymous_namespace{pmesplinespreadtest.cpp}
	anonymous_namespace{pmetest.cpp}
	anonymous_namespace{refdata-xml.cpp}
	anonymous_namespace{refdata.cpp}
	anonymous_namespace{scalar.cpp}
	anonymous_namespace{scalar_math.cpp}
	anonymous_namespace{scalar_util.cpp}
	anonymous_namespace{simd4_floatingpoint.cpp}
	anonymous_namespace{simd4_math.cpp}
	anonymous_namespace{simd4_vector_operations.cpp}
	anonymous_namespace{simd_floatingpoint.cpp}
	anonymous_namespace{simd_floatingpoint_util.cpp}
	anonymous_namespace{simd_integer.cpp}
	anonymous_namespace{simd_math.cpp}
	anonymous_namespace{simd_vector_operations.cpp}
	anonymous_namespace{splinetable.cpp}
	anonymous_namespace{stringtest.cpp}
	anonymous_namespace{stringutil.cpp}
	anonymous_namespace{testasserts.cpp}
	anonymous_namespace{testasserts.h}
	anonymous_namespace{testinit.cpp}
	anonymous_namespace{testoptions.cpp}
	anonymous_namespace{textblockmatchers.cpp}
	anonymous_namespace{textreader.cpp}
	anonymous_namespace{usergpuids.cpp}
	anonymous_namespace{xvgtest.cpp}

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...
struct	AwhTestParameters
	Struct that gathers all input for setting up and using a Bias. More...
class	BiasTest
	Test fixture for testing Bias updates. More...
class	BiasStateTest
	Test fixture for testing Bias updates. More...
class	MockModule
	Mock implementation of gmx::ICommandLineModule. More...
class	MockOptionsModule
	Mock implementation of gmx::ICommandLineOptionsModule. More...
class	CommandLineModuleManagerTestBase
	Test fixture for tests using gmx::CommandLineModuleManager. More...
struct	TestHardwareContext
	A structure to describe a hardware context - an abstraction over gmx_device_info_t with a human-readable string. TODO: currently this does not know which CodePath it belongs too. It probably should! That would save us one loop in all the PME tests. More...
class	PmeTestEnvironment
	This class performs one-time test initialization (enumerating the hardware) More...
class	SettleTest
	Test fixture for testing SETTLE position updates. More...
class	SignalTest
	Test fixture for mdrun signalling. More...
class	SimdBaseTest
	Base class for SIMD test fixtures. More...
class	SimdTest
	Test fixture for SIMD tests. More...
class	Simd4Test
	Test fixture for SIMD4 tests - contains test settings. More...
class	AbstractTrajectoryAnalysisModuleTestFixture
	Test fixture for trajectory analysis modules. More...
class	TrajectoryAnalysisModuleTestFixture
	Test fixture for a trajectory analysis module. More...
class	AllocatorTest
	Templated test fixture. More...
class	EnergyFrameReader
	Manages returning an EnergyFrame containing required energy field values read from successive frames of an .edr file. More...
class	EnergyFrame
	Contains the content of an .edr frame read by an EnergyFrameReader. More...
class	SimulationRunner
	Helper object for running grompp and mdrun in integration tests of mdrun functionality. More...
class	MdrunTestFixtureBase
	Declares test fixture base class for integration tests of mdrun functionality. More...
class	MdrunTestFixture
	Declares test fixture class for integration tests of mdrun functionality that use a single call of mdrun. More...
class	ParameterizedMdrunTestFixture
	Parameterized test fixture for mdrun integration tests. More...
class	MultiSimTest
	Test fixture for multi-sim functionality. More...
class	BondedInteractionsTest
	Test fixture for bonded interactions. More...
class	TerminationHelper
	Help test mdrun termination behaviour. More...
class	TrajectoryFrameReader
	Manages returning a t_trxframe whose contents were read from successive frames of an trajectory file. More...
class	TrajectoryFrame
	Contains the content of a trajectory frame read by an TrajectoryFrameReader. 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 ITextStreamMatcher 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	TestReferenceChecker
	Handles comparison to test reference data. More...
class	TestReferenceData
	Handles creation of and 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	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< int, int, 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 ArrayRef< const real >	ChargesVector
	Charges.
typedef std::vector< RVec >	CoordinatesVector
	Coordinates.
typedef ArrayRef< RVec >	ForcesVector
	Forces.
typedef ArrayRef< const 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, 3 >	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, 3 *3 >	Matrix3x3
	TODO: make proper C++ matrix for the whole Gromacs, get rid of this.
typedef std::tuple< real, Matrix3x3 >	PmeSolveOutput
	PME solver results - reciprocal energy and virial.
typedef std::list < TestHardwareContext >	TestHardwareContexts
	A list of hardware contexts.
typedef std::tuple< int, bool, bool, bool >	SettleTestParameters
	Convenience typedef.
using	AllocatorTypesToTest = ::testing::Types< AlignedAllocator< real >, PageAlignedAllocator< real >, AlignedAllocator< int >, PageAlignedAllocator< int >, AlignedAllocator< RVec >, PageAlignedAllocator< RVec > >
	Declare allocator types to test.
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 MultiSimTest	ReplicaExchangeEnsembleTest
	Convenience typedef.
typedef MultiSimTest	ReplicaExchangeTerminationTest
	Convenience typedef.
typedef gmx::test::SwapTestFixture	CompelTest
	Test fixture for mdrun with "Computational Electrophysiology" settings,.
typedef MdrunTestFixture	MdrunTerminationTest
	Convenience typedef.
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.
typedef std::unique_ptr < TrajectoryFrameReader >	TrajectoryFrameReaderPtr
	Convenience smart pointer typedef.
typedef std::unique_ptr < IFileMatcher >	FileMatcherPointer
	Smart pointer for managing a IFileMatcher.
typedef std::unique_ptr < ITextBlockMatcher >	TextBlockMatcherPointer
	Smart pointer for managing a ITextBlockMatcher.

Enumerations
enum	PmeSolveAlgorithm { Coulomb, LennardJones }
	PME solver type.
enum	CodePath { CPU, CUDA }
	Hardware code path being tested.
enum	ReferenceDataMode { erefdataCompare, erefdataCreateMissing, erefdataUpdateChanged, erefdataUpdateAll }
	Mode of operation for reference data handling. More...

Functions
static AwhTestParameters	getAwhTestParameters (int eawhgrowth, int eawhpotential)
	Helper function to set up the C-style AWH parameters for the test.
static AwhTestParameters	getAwhTestParameters ()
	Helper function to set up the C-style AWH parameters for the test.
bool	pmeSupportsInputForMode (const t_inputrec *inputRec, CodePath mode)
	Tells if this generally valid PME input is supported for this mode.
gmx_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.
static PmeSafePointer	pmeInitInternal (const t_inputrec *inputRec, CodePath mode, gmx_device_info_t *gpuInfo, size_t atomCount, const Matrix3x3 &box, real ewaldCoeff_q=1.0f, real ewaldCoeff_lj=1.0f)
	PME initialization - internal.
PmeSafePointer	pmeInitEmpty (const t_inputrec *inputRec, CodePath mode, gmx_device_info_t *gpuInfo, const Matrix3x3 &box, real ewaldCoeff_q, real ewaldCoeff_lj)
	Simple PME initialization based on input, no atom data. More...
PmeSafePointer	pmeInitAtoms (const t_inputrec *inputRec, CodePath mode, gmx_device_info_t *gpuInfo, const CoordinatesVector &coordinates, const ChargesVector &charges, const Matrix3x3 &box)
	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, PmeForceOutputHandling inputTreatment, ForcesVector &forces)
	PME force gathering.
void	pmeFinalizeTest (const gmx_pme_t *pme, CodePath mode)
	PME test finalization before fetching the outputs.
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 (const 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()
PmeSolveOutput	pmeGetReciprocalEnergyAndVirial (const gmx_pme_t *pme, CodePath mode, PmeSolveAlgorithm method)
	Getting the reciprocal energy and virial.
const PmeTestEnvironment *	getPmeTestEnv ()
	Get the test environment.
void	callAddGlobalTestEnvironment ()
	This constructs the test environment during setup of the unit test so that they can use the hardware context. More...
static gmx_hw_info_t *	hardwareInit ()
	Simple hardware initialization.
::std::vector< real >	simdReal2Vector (const SimdReal simd)
	Convert SIMD real to std::vector<real>. More...
SimdReal	vector2SimdReal (const std::vector< real > &v)
	Return floating-point SIMD value from std::vector<real>. More...
SimdReal	setSimdRealFrom3R (real r0, real r1, real r2)
	Set SIMD register contents from three real values. More...
SimdReal	setSimdRealFrom1R (real value)
	Set SIMD register contents from single real value. More...
std::vector< std::int32_t >	simdInt2Vector (const SimdInt32 simd)
	Convert SIMD integer to std::vector<int>. More...
SimdInt32	vector2SimdInt (const std::vector< std::int32_t > &v)
	Return 32-bit integer SIMD value from std::vector<int>. More...
SimdInt32	setSimdIntFrom3I (int i0, int i1, int i2)
	Set SIMD register contents from three int values. More...
SimdInt32	setSimdIntFrom1I (int value)
	Set SIMD register contents from single integer value. More...
::std::vector< real >	simd4Real2Vector (const Simd4Real simd4)
	Convert SIMD4 real to std::vector<real>. More...
Simd4Real	vector2Simd4Real (const std::vector< real > &v)
	Return floating-point SIMD4 value from std::vector<real>. More...
Simd4Real	setSimd4RealFrom3R (real r0, real r1, real r2)
	Set SIMD4 register contents from three real values. More...
Simd4Real	setSimd4RealFrom1R (real value)
	Set SIMD4 register contents from single real value. More...
EnergyFrameReaderPtr	openEnergyFileToReadFields (const std::string &filename, const std::vector< std::string > &requiredEnergyFieldNames)
	Open the file and return an object that can read the required fields 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...
void	compareFrames (const std::pair< EnergyFrame, EnergyFrame > &frames, FloatingPointTolerance tolerance)
	Compare all fields of reference with all matching fields from test. More...
static void	organizeMdpFile (SimulationRunner *runner)
	Build a simple .mdp file.
static t_trxframe *	make_trxframe ()
	Helper function to obtain resources.
void	done_trxframe (t_trxframe *fr)
	Helper function to clean up resources. More...
void	compareFrames (const std::pair< TrajectoryFrame, TrajectoryFrame > &frames, FloatingPointTolerance tolerance)
	Compare the fields of the two frames for equality within the tolerance. More...
void	checkConfFile (TextInputStream *input, TestReferenceChecker *checker, const ConfMatchSettings &settings)
	Adds content of a gro file to TestReferenceChecker object. More...
void	initMPIOutput ()
	Customizes test output and test failure handling for MPI runs. More...
int	getNumberOfTestMpiRanks ()
	Returns the number of MPI ranks to use for an MPI test. More...
bool	threadMpiTestRunner (std::function< void()> testBody)
	Helper function for GMX_MPI_TEST().
static double	convertDoubleReferenceValue (const std::string &value)
	Helper function to parse a floating-point reference data value.
ReferenceDataEntry::EntryPointer	readReferenceDataFile (const std::string &path)
	Loads reference data from an XML file. More...
void	writeReferenceDataFile (const std::string &path, const ReferenceDataEntry &root)
	Saves reference data to an XML file. More...
void	initReferenceData (IOptionsContainer *options)
	Initializes reference data handling. 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 inline::testing::AssertionResult	plainAssertHelper (const char *, const ::testing::AssertionResult &expr)
	Helper method for (EXPECT|ASSERT)_PLAIN. More...
void	initTestUtils (const char *dataPath, const char *tempPath, bool usesMpi, bool usesHardwareDetection, int *argc, char ***argv)
	Initializes the test utilities library. More...
void	finalizeTestUtils ()
	Finalizes the test utilities library. 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	checkXvgFile (TextInputStream *input, TestReferenceChecker *checker, const XvgMatchSettings &settings)
	Adds content of xvg file to TestReferenceChecker object. More...
Assertions for floating-point comparison
These routines extend (EXPECT|ASSERT)_(FLOAT|DOUBLE)_EQ and (EXPECT|ASSERT)_NEAR from Google Test to provide more flexible assertions for floating-point values. See gmx::test::FloatingPointTolerance for the possible ways to specify the tolerance, and gmx::test::FloatingPointDifference for some additional details of the difference calculation.
template<typename FloatType >
static inline::testing::AssertionResult	assertEqualWithinTolerance (const char *expr1, const char *expr2, const char *, FloatType value1, FloatType value2, const FloatingPointTolerance &tolerance)
	Assertion predicate formatter for comparing two floating-point values. More...

Variables
const double	g_coords []
	Database of 21 test coordinates that represent a trajectory */. More...
constexpr gmx_int64_t	c_splineModuliSinglePrecisionUlps = 1
	Spline moduli are computed in double precision, so they're very good in single precision.
const double	g_positions []
	Database of 51 water atom input positions (DIM reals per atom, taken from spc216.gro) for use as test inputs.
matrix	g_box = {{real(1.86206), 0, 0}, {0, real(1.86206), 0}, {0, 0, real(1.86206)}}
	Simple cubic simulation box to use in tests.
const real	czero = 0.0
	Value 0.0 in real precision.
const real	c0 = 0.0 + 1.0/3.0
	Random fp value using entire mantissa.
const real	c1 = 1.0 + 5.0/7.0
	Random fp value using entire mantissa.
const real	c2 = 2.0 + 9.0/13.0
	Random fp value using entire mantissa.
const real	c3 = 3.0 + 17.0/19.0
	Random fp value using entire mantissa.
const real	c4 = 4.0 + 23.0/29.0
	Random fp value using entire mantissa.
const real	c5 = 5.0 + 31.0/37.0
	Random fp value using entire mantissa.
const real	c6 = 6.0 + 41.0/43.0
	Random fp value using entire mantissa.
const real	c7 = 7.0 + 47.0/53.0
	Random fp value using entire mantissa.
const real	c8 = 8.0 + 59.0/61.0
	Random fp value using entire mantissa.
const real	c9
	Random fp value using entire mantissa.
const SimdReal	rSimd_c0c1c2 = setSimdRealFrom3R( c0, c1, c2)
	c0,c1,c2 repeated
const SimdReal	rSimd_c3c4c5 = setSimdRealFrom3R( c3, c4, c5)
	c3,c4,c5 repeated
const SimdReal	rSimd_c6c7c8 = setSimdRealFrom3R( c6, c7, c8)
	c6,c7,c8 repeated
const SimdReal	rSimd_c3c0c4 = setSimdRealFrom3R( c3, c0, c4)
	c3,c0,c4 repeated
const SimdReal	rSimd_c4c6c8 = setSimdRealFrom3R( c4, c6, c8)
	c4,c6,c8 repeated
const SimdReal	rSimd_c7c2c3 = setSimdRealFrom3R( c7, c2, c3)
	c7,c2,c3 repeated
const SimdReal	rSimd_m0m1m2 = setSimdRealFrom3R(-c0, -c1, -c2)
	-c0,-c1,-c2 repeated
const SimdReal	rSimd_m3m0m4 = setSimdRealFrom3R(-c3, -c0, -c4)
	-c3,-c0,-c4 repeated
const SimdReal	rSimd_2p25 = setSimdRealFrom1R( 2.25)
	Value that rounds down.
const SimdReal	rSimd_3p25 = setSimdRealFrom1R( 3.25)
	Value that rounds down.
const SimdReal	rSimd_3p75 = setSimdRealFrom1R( 3.75)
	Value that rounds up.
const SimdReal	rSimd_m2p25 = setSimdRealFrom1R(-2.25)
	Negative value that rounds up.
const SimdReal	rSimd_m3p25 = setSimdRealFrom1R(-3.25)
	Negative value that rounds up.
const SimdReal	rSimd_m3p75 = setSimdRealFrom1R(-3.75)
	Negative value that rounds down. More...
const SimdReal	rSimd_Exp
	Three large floating-point values whose exponents are >32. More...
const SimdReal	rSimd_logicalA = setSimdRealFrom1R(1.3333282470703125)
	Bit pattern to test logical ops.
const SimdReal	rSimd_logicalB = setSimdRealFrom1R(1.79998779296875)
	Bit pattern to test logical ops.
const SimdReal	rSimd_logicalResultAnd = setSimdRealFrom1R(1.26666259765625)
	Result or bitwise 'and' of A and B.
const SimdReal	rSimd_logicalResultOr = setSimdRealFrom1R(1.8666534423828125)
	Result or bitwise 'or' of A and B.
const SimdInt32	iSimd_1_2_3 = setSimdIntFrom3I(1, 2, 3)
	Three generic ints.
const SimdInt32	iSimd_4_5_6 = setSimdIntFrom3I(4, 5, 6)
	Three generic ints.
const SimdInt32	iSimd_7_8_9 = setSimdIntFrom3I(7, 8, 9)
	Three generic ints.
const SimdInt32	iSimd_5_7_9 = setSimdIntFrom3I(5, 7, 9)
	iSimd_1_2_3 + iSimd_4_5_6.
const SimdInt32	iSimd_1M_2M_3M = setSimdIntFrom3I(1000000, 2000000, 3000000)
	Term1 for 32bit add/sub.
const SimdInt32	iSimd_4M_5M_6M = setSimdIntFrom3I(4000000, 5000000, 6000000)
	Term2 for 32bit add/sub.
const SimdInt32	iSimd_5M_7M_9M = setSimdIntFrom3I(5000000, 7000000, 9000000)
	iSimd_1M_2M_3M + iSimd_4M_5M_6M.
const SimdInt32	iSimd_0xF0F0F0F0 = setSimdIntFrom1I(0xF0F0F0F0)
	Bitpattern to test integer logical operations.
const SimdInt32	iSimd_0xCCCCCCCC = setSimdIntFrom1I(0xCCCCCCCC)
	Bitpattern to test integer logical operations.
const SimdReal	rSimd_Bits1
	Pattern F0 repeated to fill single/double.
const SimdReal	rSimd_Bits2
	Pattern CC repeated to fill single/double.
const SimdReal	rSimd_Bits3
	Pattern C0 repeated to fill single/double.
const SimdReal	rSimd_Bits4
	Pattern 0C repeated to fill single/double.
const SimdReal	rSimd_Bits5
	Pattern FC repeated to fill single/double.
const SimdReal	rSimd_Bits6
	Pattern 3C repeated to fill single/double.
const Simd4Real	rSimd4_c0c1c2 = setSimd4RealFrom3R( c0, c1, c2)
	c0,c1,c2 repeated
const Simd4Real	rSimd4_c3c4c5 = setSimd4RealFrom3R( c3, c4, c5)
	c3,c4,c5 repeated
const Simd4Real	rSimd4_c6c7c8 = setSimd4RealFrom3R( c6, c7, c8)
	c6,c7,c8 repeated
const Simd4Real	rSimd4_c3c0c4 = setSimd4RealFrom3R( c3, c0, c4)
	c3,c0,c4 repeated
const Simd4Real	rSimd4_c4c6c8 = setSimd4RealFrom3R( c4, c6, c8)
	c4,c6,c8 repeated
const Simd4Real	rSimd4_c7c2c3 = setSimd4RealFrom3R( c7, c2, c3)
	c7,c2,c3 repeated
const Simd4Real	rSimd4_m0m1m2 = setSimd4RealFrom3R(-c0, -c1, -c2)
	-c0,-c1,-c2 repeated
const Simd4Real	rSimd4_m3m0m4 = setSimd4RealFrom3R(-c3, -c0, -c4)
	-c3,-c0,-c4 repeated
const Simd4Real	rSimd4_2p25 = setSimd4RealFrom1R(2.25)
	Value that rounds down.
const Simd4Real	rSimd4_3p75 = setSimd4RealFrom1R(3.75)
	Value that rounds up.
const Simd4Real	rSimd4_m2p25 = setSimd4RealFrom1R(-2.25)
	Negative value that rounds up.
const Simd4Real	rSimd4_m3p75 = setSimd4RealFrom1R(-3.75)
	Negative value that rounds down. More...
const Simd4Real	rSimd4_logicalA = setSimd4RealFrom1R(1.3333282470703125)
	Bit pattern to test logical ops.
const Simd4Real	rSimd4_logicalB = setSimd4RealFrom1R(1.79998779296875)
	Bit pattern to test logical ops.
const Simd4Real	rSimd4_logicalResultAnd = setSimd4RealFrom1R(1.26666259765625)
	Result or bitwise 'and' of A and B.
const Simd4Real	rSimd4_logicalResultOr = setSimd4RealFrom1R(1.8666534423828125)
	Result or bitwise 'or' of A and B.
const Simd4Real	rSimd4_Exp
	Three large floating-point values whose exponents are >32.
const Simd4Real	rSimd4_Bits1
	Pattern F0 repeated to fill single/double.
const Simd4Real	rSimd4_Bits2
	Pattern CC repeated to fill single/double.
const Simd4Real	rSimd4_Bits3
	Pattern C0 repeated to fill single/double.
const Simd4Real	rSimd4_Bits4
	Pattern 0C repeated to fill single/double.
const Simd4Real	rSimd4_Bits5
	Pattern FC repeated to fill single/double.
const Simd4Real	rSimd4_Bits6
	Pattern 3C repeated to fill single/double.
const char *	g_butaneTopFileFormatString
	Format string for building a configurable .top file.
static bool	g_bDeleteFilesAfterTest = true
	Controls whether TestFileManager should delete temporary files after the test finishes. More...

Function Documentation

void gmx::test::callAddGlobalTestEnvironment

(

)

This constructs the test environment during setup of the unit test so that they can use the hardware context.

Implement a stub definition for tests that don't ask for a real one.

Declare a function that all unit test implementations can use to set up any environment that they need.

When registering the unit test in CMake, the HARDWARE_DETECTION flag requires that the code for that unit test implements this function. Otherwise, a default stub implementation is provided.

This approach conforms to the recommendation by GoogleTest to arrange for the code that sets up the global test environment to be called from main, rather than potentially rely on brittle static initialization order.

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::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

void gmx::test::compareFrames	(	const std::pair< TrajectoryFrame, TrajectoryFrame > &	frames,
		FloatingPointTolerance	tolerance
	)

Compare the fields of the two frames for equality within the tolerance.

The two frames are required to have valid and matching values for time and step. Positions, velocities and/or forces will be compared when present in both frames, and expected to be equal within tolerance.

void gmx::test::compareFrames	(	const std::pair< EnergyFrame, EnergyFrame > &	frames,
		FloatingPointTolerance	tolerance
	)

Compare all fields of reference with all matching fields from test.

Ignore any key found in either reference or test that is not found in the other. For all keys found in both frames, compare the values with EXPECT_REAL_EQ_TOL and the given tolerance.

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 clean up resources.

Helper function to free all resources.

EnergyFrameReaderPtr gmx::test::openEnergyFileToReadFields	(	const std::string &	filename,
		const std::vector< std::string > &	requiredEnergyFieldNames
	)

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

Parameters

[in]	filename	Name of the energy file to use
[in]	requiredEnergyFieldNames	Names of the energy fields 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 field 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.

PmeSafePointer gmx::test::pmeInitAtoms	(	const t_inputrec *	inputRec,
		CodePath	mode,
		gmx_device_info_t *	gpuInfo,
		const CoordinatesVector &	coordinates,
		const ChargesVector &	charges,
		const Matrix3x3 &	box
	)

PME initialization with atom data.

PME initialization with atom data and system box.

PmeSafePointer gmx::test::pmeInitEmpty	(	const t_inputrec *	inputRec,
		CodePath	mode,
		gmx_device_info_t *	gpuInfo,
		const Matrix3x3 &	box,
		real	ewaldCoeff_q,
		real	ewaldCoeff_lj
	)

Simple PME initialization based on input, no atom data.

Simple PME initialization (no atom data)

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	(	const 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.

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

bool gmx::test::g_bDeleteFilesAfterTest = true

static

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

const 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 */.