Description

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

An internal database of several kinds of simulation useful for such comparisons is available.

Any method in this class may throw std::bad_alloc if out of memory.

Public Types
typedef std::map< std::string, std::string >	MdpFieldValues
	Helper typedef.

Public Member Functions
virtual	~MdrunComparisonFixture ()
	Destructor.

MdpFieldValues	prepareMdpFieldValues (const char *simulationName)
	Prepare .mdp values to do a simulation. More...

void	prepareMdpFile (const MdpFieldValues &mdpFieldValues, const char integrator, const char tcoupl, const char *pcoupl)
	Set up an .mdp file that permits a highly reproducible simulation. More...

virtual void	runTest (const CommandLine &gromppCallerRef, const char simulationName, const char integrator, const char tcoupl, const char pcoupl, FloatingPointTolerance tolerance)=0
	Run mdrun two ways in a test. Subclasses must override this method. More...

virtual void	runTest (const char simulationName, const char integrator, const char tcoupl, const char pcoupl, FloatingPointTolerance tolerance)
	Convenience overload of runTest() for cases that don't need to customize the command line for grompp.

Additional Inherited Members
Public Attributes inherited from gmx::test::MdrunTestFixture
SimulationRunner	runner_
	Helper object to manage the preparation for and call of mdrun.

Public Attributes inherited from gmx::test::IntegrationTestFixture
::gmx::test::TestFileManager	fileManager_
	Object that manages finding input files, writing temporary output files and cleaning up files.

Protected Member Functions inherited from gmx::test::IntegrationTestFixture
void	redirectStringToStdin (const char *theString)
	Accepts a string as input, writes it to a temporary file and then reopens stdin to read the contents of that string. More...

void	redirectStdoutToDevNull ()
	Discards stdout while running a test. More...

void	redirectStderrToDevNull ()
	Discards stderr while running a test. More...

Member Function Documentation

MdrunComparisonFixture::MdpFieldValues gmx::test::MdrunComparisonFixture::prepareMdpFieldValues ( const char * simulationName )

Prepare .mdp values to do a simulation.

A database of several kinds of simulation useful for different kinds of tests is available.

argon12
argon5832
spc5
spc216
alanine_vsite_vacuo
alanine_vsite_solvated
nonanol

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.

This is separate from prepareMdpFile, so that derived classes can react to the .mdp settings, e.g. by stopping a run after half the steps.

Exceptions

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

void gmx::test::MdrunComparisonFixture::prepareMdpFile	(	const MdpFieldValues &	mdpFieldValues,
		const char *	integrator,
		const char *	tcoupl,
		const char *	pcoupl
	)

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

Exceptions

std::bad_alloc if out of memory

virtual void gmx::test::MdrunComparisonFixture::runTest	(	const CommandLine &	gromppCallerRef,
		const char *	simulationName,
		const char *	integrator,
		const char *	tcoupl,
		const char *	pcoupl,
		FloatingPointTolerance	tolerance
	)

pure virtual

Run mdrun two ways in a test. Subclasses must override this method.

It is expected that this method calls prepareMdpFieldValues() and prepareMdpFile() to help set up a call to grompp with gromppCallerRef. Then mdrun will be called and perhaps energies and forces compared.

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

src/programs/mdrun/tests/mdruncomparisonfixture.h
src/programs/mdrun/tests/mdruncomparisonfixture.cpp

Description

Public Types

Public Member Functions

Additional Inherited Members

Member Function Documentation