gmx::test::DensityFittingTest Class Reference

Inheritance diagram for gmx::test::DensityFittingTest:

Collaboration diagram for gmx::test::DensityFittingTest:

Description

End to end test for the density fitting functionality in mdrun.

This test checks whether the density fitting related .mdp input options are understood by grompp and that the density fitting module in mdrun computes the correct density fitting energies and stores them in the .edr output file.

Public Member Functions
void	checkMdrun (real energyTermMagnitude)
	Check the output of mdrun.

Public Attributes
const std::string	mdpEminDensfitYesUnsetValues
	Mdp values for steepest-decent energy minimization with default density fitting parameters. More...
const std::string	mdpMdDensfitYesUnsetValues
	Mdp values for md integrator with default density fitting parameters. More...
const std::string	mdpDensiftAllDefaultsChanged_
	Mdp values for steepest-decent energy minimization with density fitting values set to non-defaults. More...
const std::string	mdpEnergyAndDensityfittingIntervalMismatch_
	Set mdp values so that energy calculation interval and density guided simulation interval mismatch. More...
const std::string	mdpSkipDensityfittingEveryOtherStep_
	Set mdp values so that we skip every other step. More...
const std::string	mdpTranslationSet_
	A properly set shift vector. More...
const std::string	mdpTranslationSetWrongValues_
	A shift vector that is lacking an entry. More...
const std::string	mdpTransformationMatrix1degAroundY_
	A 45 degree rotation around the y axis expressed as matrix transformation. More...
const std::string	mdpTransformationMatrixIdentity_
	The identity matrix as transformation matrix. More...
const std::string	mdpTransformationMatrixWrongValues_
	A transformation matrix string where only eight values are given. More...
CommandLine	commandLineForMdrun_
	The command line to call mdrun.
Public Attributes inherited from gmx::test::MdrunTestFixture
TestFileManager	fileManager_
	Manages temporary files during the test.
SimulationRunner	runner_
	Helper object to manage the preparation for and call of mdrun.

Additional Inherited Members
Static Public Member Functions inherited from gmx::test::MdrunTestFixtureBase
static void	SetUpTestSuite ()
	Per-test-case setup for lengthy processes that need run only once.
static void	TearDownTestSuite ()
	Per-test-case tear down.
Static Public Attributes inherited from gmx::test::MdrunTestFixtureBase
static MPI_Comm	s_communicator = MPI_COMM_NULL
	Communicator over which the test fixture works.
static std::unique_ptr < gmx_hw_info_t >	s_hwinfo
	Hardware information object. More...

Member Data Documentation

const std::string gmx::test::DensityFittingTest::mdpDensiftAllDefaultsChanged_

Initial value:

= formatString(
            "density-guided-simulation-similarity-measure = relative-entropy\n"
            "density-guided-simulation-atom-spreading-weight = mass\n"
            "density-guided-simulation-force-constant = -1\n"
            "density-guided-simulation-gaussian-transform-spreading-width = 0.8\n"
            "density-guided-simulation-gaussian-transform-spreading-range-in-multiples-of-width = "
            "6\n"
            "density-guided-simulation-normalize-densities = false\n")

Mdp values for steepest-decent energy minimization with density fitting values set to non-defaults.

const std::string gmx::test::DensityFittingTest::mdpEminDensfitYesUnsetValues

Initial value:

= formatString(
            "integrator                       = steep\n"
            "nsteps                           = 2\n"
            "cutoff-scheme                    = verlet\n"
            "density-guided-simulation-active = yes\n"
            "density-guided-simulation-group  = FirstThreeOfTwelve\n"
            "density-guided-simulation-reference-density-filename = %s\n",
            TestFileManager::getInputFilePath("ellipsoid-density.mrc").string().c_str())

Mdp values for steepest-decent energy minimization with default density fitting parameters.

const std::string gmx::test::DensityFittingTest::mdpEnergyAndDensityfittingIntervalMismatch_

Initial value:

= formatString(
            "nstcalcenergy = 7\n"
            "density-guided-simulation-nst = 3\n")

Set mdp values so that energy calculation interval and density guided simulation interval mismatch.

const std::string gmx::test::DensityFittingTest::mdpMdDensfitYesUnsetValues

Initial value:

= formatString(
            "integrator                       = md\n"
            "nsteps                           = 2\n"
            "cutoff-scheme                    = verlet\n"
            "density-guided-simulation-active = yes\n"
            "density-guided-simulation-group  = FirstThreeOfTwelve\n"
            "density-guided-simulation-reference-density-filename = %s\n",
            TestFileManager::getInputFilePath("ellipsoid-density.mrc").string().c_str())

Mdp values for md integrator with default density fitting parameters.

const std::string gmx::test::DensityFittingTest::mdpSkipDensityfittingEveryOtherStep_

Initial value:

= formatString(
            "nstenergy = 2\n"
            "density-guided-simulation-nst = 2\n")

Set mdp values so that we skip every other step.

const std::string gmx::test::DensityFittingTest::mdpTransformationMatrix1degAroundY_

Initial value:

= formatString(
            "density-guided-simulation-transformation-matrix = 0.9998477 0.0000000 0.0174524 "
            "0.0000000 1.0000000 0.0000000 -0.0174524 0.0000000 0.9998477 \n")

A 45 degree rotation around the y axis expressed as matrix transformation.

const std::string gmx::test::DensityFittingTest::mdpTransformationMatrixIdentity_

Initial value:

= formatString(
            "density-guided-simulation-transformation-matrix = 1 0 0 "
            "0 1 0 0 0 1 \n")

The identity matrix as transformation matrix.

const std::string gmx::test::DensityFittingTest::mdpTransformationMatrixWrongValues_

Initial value:

= formatString(
            "density-guided-simulation-transformation-matrix = 0.7071068 0.0000000 0.7071068 "
            "0.0000000 0.0000000 -0.7071068 0.0000000 0.7071068 \n")

A transformation matrix string where only eight values are given.

const std::string gmx::test::DensityFittingTest::mdpTranslationSet_

Initial value:

=
            formatString("density-guided-simulation-shift-vector = 0.1 -0.2 0.3\n")

A properly set shift vector.

const std::string gmx::test::DensityFittingTest::mdpTranslationSetWrongValues_

Initial value:

=
            formatString("density-guided-simulation-shift-vector = 0.1 -0.2\n")

A shift vector that is lacking an entry.

---

The documentation for this class was generated from the following file:

• src/programs/mdrun/tests/densityfittingmodule.cpp