Description

Input data storage for colvars.

Public Member Functions
void	initMdpTransform (IKeyValueTreeTransformRules *rules) override
	From IMdpOptionProvider.

void	buildMdpOutput (KeyValueTreeObjectBuilder *builder) const override
	Build mdp parameters for colvars to be output after pre-processing. More...

void	initMdpOptions (IOptionsContainerWithSections *options) override
	Connect option name and data.

void	writeInternalParametersToKvt (KeyValueTreeObjectBuilder treeBuilder)
	Store the paramers that are not mdp options in the tpr file.

void	readInternalParametersFromKvt (const KeyValueTreeObject &tree)
	Set the internal parameters that are stored in the tpr file.

void	processTopology (gmx_mtop_t *mtop)
	Store the topology of the system. More...

void	processCoordinates (const CoordinatesAndBoxPreprocessed &coord)
	Process coordinates, PbcType and Box in order to validate the colvars input. More...

void	setLogger (const MDLogger &logger)
	Set the MDLogger instance.

void	processEdrFilename (const EdrOutputFilename &filename)
	Process EdrOutputFilename notification during mdrun. Used to set the prefix of Colvars output files based on the .edr filename. More...

void	processTemperature (const EnsembleTemperature &temp)
	Store the ensemble temperature of the system if available. More...

bool	isActive () const
	Report if this colvars module is active.

const std::string &	colvarsFileName () const
	Return the file name of the colvars config.

const std::string &	colvarsConfigContent () const
	Return the content of the colvars config file.

const std::vector< RVec > &	colvarsAtomCoords () const
	Return the colvars atoms coordinates.

const std::string &	colvarsOutputPrefix () const
	Return the prefix for output colvars files.

const real &	colvarsEnsTemp () const
	Return the ensemble temperature.

const std::map< std::string, std::string > &	colvarsInputFiles () const
	Return the map of all others colvars input files.

int	colvarsSeed () const
	Return the colvars seed.

void	setParameters (const std::string &colvarsfile, const t_atoms &topology, ArrayRef< const RVec > coords, PbcType pbcType, const matrix boxValues, real temperature)
	Function to set internal paramaters outside the way done through the MDModule notifiers and callbacks. Use exclusively in the test framework. More...

Member Function Documentation

void gmx::ColvarsOptions::buildMdpOutput ( KeyValueTreeObjectBuilder * builder ) const

overridevirtual

Build mdp parameters for colvars to be output after pre-processing.

Parameters

[in,out] builder the builder for the mdp options output KV-tree.

Implements gmx::IMdpOptionProvider.

void gmx::ColvarsOptions::processCoordinates ( const CoordinatesAndBoxPreprocessed & coord )

Process coordinates, PbcType and Box in order to validate the colvars input.

Parameters

[in] coord structure with coordinates and box dimensions

void gmx::ColvarsOptions::processEdrFilename ( const EdrOutputFilename & filename )

Process EdrOutputFilename notification during mdrun. Used to set the prefix of Colvars output files based on the .edr filename.

Parameters

[in] filename name of the *.edr file that mdrun will produce

void gmx::ColvarsOptions::processTemperature ( const EnsembleTemperature & temp )

Store the ensemble temperature of the system if available.

Parameters

[in] temp temperature object

void gmx::ColvarsOptions::processTopology ( gmx_mtop_t * mtop )

Store the topology of the system.

Parameters

[in,out] mtop topology object

void gmx::ColvarsOptions::setParameters	(	const std::string &	colvarsfile,
		const t_atoms &	topology,
		ArrayRef< const RVec >	coords,
		PbcType	pbcType,
		const matrix	boxValues,
		real	temperature
	)

Function to set internal paramaters outside the way done through the MDModule notifiers and callbacks. Use exclusively in the test framework.

Parameters

[in]	colvarsfile	Name of the colvars input file.
[in]	topology	Atoms topology
[in]	coords	Coordinates of each atom in the system
[in]	pbcType	Periodic boundary conditions
[in]	boxValues	Matrix with full box of the system
[in]	temperature	the constant ensemble temperature

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

src/gromacs/applied_forces/colvars/colvarsoptions.h
src/gromacs/applied_forces/colvars/colvarsoptions.cpp

Description

Public Member Functions

Member Function Documentation