Gromacs
2019
|
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 | 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 | 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 | FilteringExactTextMatch |
Use an exact text match after scrubbing lines of the text that match the supplied regular expressions. 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::vector < std::unique_ptr < TestHardwareContext > > | TestHardwareContexts |
A container of handles to hardware contexts. | |
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. | |
typedef std::tuple< int, bool, bool, bool > | SettleTestParameters |
Convenience typedef. | |
using | EnergyTolerances = 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 MultiSimTest | ReplicaExchangeEnsembleTest |
Convenience typedef. | |
typedef MultiSimTest | ReplicaExchangeTerminationTest |
Convenience typedef. | |
using | MdpFieldValues = std::map< std::string, std::string > |
Helper 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 < 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, GPU } |
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 gmx_hw_info_t &hwinfo, const t_inputrec *inputRec, CodePath mode) |
Tells if this generally valid PME input is supported for this mode. | |
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, const gmx_device_info_t *gpuInfo, PmeGpuProgramHandle pmeGpuProgram, 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, const gmx_device_info_t *gpuInfo, PmeGpuProgramHandle pmeGpuProgram, 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, const gmx_device_info_t *gpuInfo, PmeGpuProgramHandle pmeGpuProgram, 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() | |
PmeOutput | pmeGetReciprocalEnergyAndVirial (const gmx_pme_t *pme, CodePath mode, PmeSolveAlgorithm method) |
Getting the reciprocal energy and virial. | |
const char * | codePathToString (CodePath codePath) |
Return a string useful for human-readable messages describing a codePath . | |
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. | |
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 gmx_gpu_info_t &gpuInfo, ArrayRef< T > input, ArrayRef< T > output) |
Does a device transfer of input to the device in gpuInfo , and back to output . | |
template<typename VectorType > | |
bool | isPinned (const VectorType &v) |
Helper function for wrapping a call to isHostMemoryPinned. | |
template<typename T > | |
void | fillInputContents (ArrayRef< T > inputRef, int scaleFactor) |
Initialization overload for non-BasicVector. | |
template<typename T > | |
void | fillInputContents (ArrayRef< BasicVector< T >> inputRef, int scaleFactor) |
Initialization overload for BasicVector. | |
template<typename PaddedVectorOfT > | |
void | fillInput (PaddedVectorOfT *input, int scaleFactor) |
Dispatcher function for filling. | |
template<typename T > | |
void | compareViews (ArrayRef< T > input, ArrayRef< T > output) |
Comparison overload for non-BasicVector. | |
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. | |
void | compareEnergyFrames (const EnergyFrame &reference, const EnergyFrame &test, const EnergyTolerances &tolerances) |
Compare all fields of reference with all matching fields from test. More... | |
void | checkEnergiesAgainstReferenceData (const std::string &energyFilename, const EnergyTolerances &energiesToMatch, TestReferenceChecker *checker) |
Check a subset of the energies found in an energy file against reference data. 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... | |
template<typename Map > | |
std::vector< std::string > | getKeys (const Map &m) |
Convenience function to get std::string keys from a map. More... | |
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 char *simulationName, const char *integrator, const char *tcoupl, const char *pcoupl) |
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... | |
static void | organizeMdpFile (SimulationRunner *runner) |
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 positions in frame into its box. More... | |
static void | comparePositions (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const FloatingPointTolerance tolerance) |
Compares the positions 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 . | |
void | compareTrajectoryFrames (const TrajectoryFrame &reference, const TrajectoryFrame &test, const TrajectoryFrameMatchSettings &matchSettings, const TrajectoryTolerances &tolerances) |
Compare the fields of the two frames for equality given the matchSettings and tolerances . More... | |
static t_trxframe * | make_trxframe () |
Helper function to obtain resources. | |
void | done_trxframe (t_trxframe *fr) |
Helper function to clean up resources. More... | |
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... | |
static double | convertDoubleReferenceValue (const std::string &value) |
Helper function to parse a floating-point reference data value. | |
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... | |
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 < RVec, RVec > > | 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 | checkXvgFile (TextInputStream *input, TestReferenceChecker *checker, const XvgMatchSettings &settings) |
Adds content of xvg file to TestReferenceChecker object. More... | |
Variables | |
const double | g_coords [] |
Database of 21 test coordinates that represent a trajectory */. More... | |
constexpr int64_t | c_splineModuliSinglePrecisionUlps = 1 |
Spline moduli are computed in double precision, so they're very good in single precision. | |
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. | |
static 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... | |
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.
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.
[in] | data | The data pointer. |
[in] | size | The size of the data pointer (in T). |
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.
[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).
void gmx::test::checkEnergiesAgainstReferenceData | ( | const std::string & | energyFilename, |
const EnergyTolerances & | energiesToMatch, | ||
TestReferenceChecker * | checker | ||
) |
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.
[in] | energyFilename | The name of an energy file. |
[in] | energiesToMatch | Set of energies to match at given tolerances. |
[in] | checker | Root checker for reference data. |
void gmx::test::checkXvgFile | ( | TextInputStream * | input, |
TestReferenceChecker * | checker, | ||
const XvgMatchSettings & | settings | ||
) |
Adds content of xvg file to TestReferenceChecker object.
[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.
|
static |
Compares the box from reference
and test
according to the matchSettings
and tolerance
.
void gmx::test::compareEnergyFrames | ( | const EnergyFrame & | reference, |
const EnergyFrame & | test, | ||
const EnergyTolerances & | tolerances | ||
) |
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 for that key.
void gmx::test::compareTrajectoryFrames | ( | const TrajectoryFrame & | reference, |
const TrajectoryFrame & | test, | ||
const TrajectoryFrameMatchSettings & | matchSettings, | ||
const TrajectoryTolerances & | tolerances | ||
) |
Compare the fields of the two frames for equality given the matchSettings
and tolerances
.
The two frames are required to have valid and matching values for time and step. According to matchSettings
, box, positions, velocities and/or forces will be compared between frames, using the tolerances
. Comparisons will only occur when both frames have the requisite data, and will be expected to be equal within the matching component of tolerances
. If a comparison fails, a GoogleTest expectation failure will be given. If a comparison is required by matchSettings
but cannot be done because either (or both) frames lack the requisite data, descriptive expectation failures will be given.
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.
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));
std::vector<std::string> gmx::test::getKeys | ( | const Map & | m | ) |
Convenience function to get std::string keys from a map.
This function can be used to provide an input for openEnergyFileToReadFields().
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.
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.
[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 |
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, | ||
const gmx_device_info_t * | gpuInfo, | ||
PmeGpuProgramHandle | pmeGpuProgram, | ||
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, | ||
const gmx_device_info_t * | gpuInfo, | ||
PmeGpuProgramHandle | pmeGpuProgram, | ||
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.
MdpFieldValues gmx::test::prepareMdpFieldValues | ( | const char * | simulationName, |
const char * | integrator, | ||
const char * | tcoupl, | ||
const char * | pcoupl | ||
) |
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
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.
[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 |
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
.
std::bad_alloc | if out of memory |
|
static |
Help put all atom positions in frame
into its box.
This can perhaps go away when frame->x is a container.
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));
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 |
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.
|
static |
Controls whether TestFileManager should delete temporary files after the test finishes.
const double gmx::test::g_coords[] |
Database of 21 test coordinates that represent a trajectory */.