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{cmdlinemodulemanagertest.cpp}

	anonymous_namespace{cmdlinetest.cpp}

	anonymous_namespace{conftest.cpp}

	anonymous_namespace{mdruncomparisonfixture.cpp}

	anonymous_namespace{mock_datamodule.cpp}

	anonymous_namespace{moduletest.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{stringtest.cpp}

	anonymous_namespace{testasserts.cpp}

	anonymous_namespace{testinit.cpp}

	anonymous_namespace{testoptions.cpp}

	anonymous_namespace{textblockmatchers.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...

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...

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	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	MdrunComparisonFixture
	Declares abstract base text fixture class for integration tests of mdrun functionality that will compare multiple calls to mdrun. 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	IntegrationTestFixture
	Test fixture for integration tests. More...

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

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

class	TestReferenceData
	Handles creation of and comparison to test reference data. 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, bool, bool, bool >	SettleTestParameters
	Convenience typedef.

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

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

typedef scoped_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 scoped_cptr < gmx_output_env_t, output_env_done >	oenv_ptr
	Convenience smart pointer typedef.

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

typedef scoped_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 < ITextBlockMatcher >	TextBlockMatcherPointer
	Smart pointer for managing a ITextBlockMatcher.

Enumerations
enum	ReferenceDataMode { erefdataCompare, erefdataCreateMissing, erefdataUpdateChanged, erefdataUpdateAll }
	Mode of operation for reference data handling. More...

Functions
::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< int >	simdInt2Vector (const SimdInt32 simd)
	Convert SIMD integer to std::vector<int>. More...

SimdInt32	vector2SimdInt (const std::vector< int > &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...

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...

void	organizeMdpFile (SimulationRunner *runner)
	Build a simple .mdp file.

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...

double	convertDouble (const std::string &value)
	Helper function to parse a floating-point value.

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, 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_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 SimdReal	rSimd_1_2_3 = setSimdRealFrom3R(1, 2, 3)
	Generic (different) fp values.

const SimdReal	rSimd_4_5_6 = setSimdRealFrom3R(4, 5, 6)
	Generic (different) fp values.

const SimdReal	rSimd_7_8_9 = setSimdRealFrom3R(7, 8, 9)
	Generic (different) fp values.

const SimdReal	rSimd_5_7_9 = setSimdRealFrom3R(5, 7, 9)
	rSimd_1_2_3 + rSimd_4_5_6.

const SimdReal	rSimd_m1_m2_m3 = setSimdRealFrom3R(-1, -2, -3)
	Generic negative floating-point values.

const SimdReal	rSimd_3_1_4 = setSimdRealFrom3R(3, 1, 4)
	Used to test min/max.

const SimdReal	rSimd_m3_m1_m4 = setSimdRealFrom3R(-3, -1, -4)
	negative rSimd_3_1_4.

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 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_1_2_3 = setSimd4RealFrom3R(1, 2, 3)
	Generic (different) fp values.

const Simd4Real	rSimd4_4_5_6 = setSimd4RealFrom3R(4, 5, 6)
	Generic (different) fp values.

const Simd4Real	rSimd4_7_8_9 = setSimd4RealFrom3R(7, 8, 9)
	Generic (different) fp values.

const Simd4Real	rSimd4_5_7_9 = setSimd4RealFrom3R(5, 7, 9)
	rSimd_1_2_3 + rSimd_4_5_6.

const Simd4Real	rSimd4_m1_m2_m3 = setSimd4RealFrom3R(-1, -2, -3)
	Generic negative fp values.

const Simd4Real	rSimd4_3_1_4 = setSimd4RealFrom3R(3, 1, 4)
	Used to test min/max.

const Simd4Real	rSimd4_m3_m1_m4 = setSimd4RealFrom3R(-3, -1, -4)
	negative rSimd_3_1_4.

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_Exp
	Three large floating-point values whose exponents are >32. More...

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::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.

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.

Description

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Function Documentation

Variable Documentation