Description

Implements IForceProvider for colvars. Override the ColvarProxyGromacs generic class for the communication.

Public Member Functions
	ColvarsForceProvider (const std::string &colvarsConfigString, t_atoms atoms, PbcType pbcType, const MDLogger logger, const std::map< std::string, std::string > &inputStrings, real ensembleTemperature, int seed, LocalAtomSetManager localAtomSetManager, const t_commrec *cr, double simulationTimeStep, const std::vector< RVec > &colvarsCoords, const std::string &outputPrefix, const ColvarsForceProviderState &state)
	Construct ColvarsForceProvider from its parameters. More...

void	calculateForces (const ForceProviderInput &forceProviderInput, ForceProviderOutput *forceProviderOutput) override
	Calculate colvars forces. More...

void	writeCheckpointData (MDModulesWriteCheckpointData checkpointWriting, const std::string &moduleName)
	Write internal colvars data to checkpoint file. More...

void	processAtomsRedistributedSignal (const MDModulesAtomsRedistributedSignal &atomsRedistributedSignal)
	Process atomsRedistributedSignal notification during mdrun. More...

void	add_energy (cvm::real energy) override
	From colvarproxy. More...

Public Member Functions inherited from gmx::ColvarProxyGromacs
	ColvarProxyGromacs (const std::string &colvarsConfigString, t_atoms atoms, PbcType pbcType, const MDLogger *logger, bool doParsing, const std::map< std::string, std::string > &inputStrings, real ensembleTemperature, int seed)
	Construct ColvarProxyGromacs from its parameters. More...

void	updateAtomProperties (int index)
	Update colvars topology of one atom mass and charge from the GROMACS topology.

cvm::real	rand_gaussian () override
	From colvarproxy. More...

void	log (std::string const &message) override
	Print a message to the main log.

void	error (std::string const &message) override
	Print a message to the main log and let GROMACS handle the error.

int	backup_file (char const *filename) override
	Rename the given file, before overwriting it.

int	set_unit_system (std::string const &unitsIn, bool colvarsDefined) override
	Request to set the units used internally by Colvars.

int	init_atom (int atomNumber) override
	Initialize colvars atom from GROMACS topology.

int	check_atom_id (int atomNumber) override
	Check if atom belongs to the global index of atoms. More...

cvm::rvector	position_distance (cvm::atom_pos const &pos1, cvm::atom_pos const &pos2) const override
	Compute the minimum distance with respect to the PBC between 2 atoms.

Static Public Member Functions
static void	addVirialTerm (matrix vir, const rvec &f, const gmx::RVec &x)
	Compute virial tensor for position r and force f, and add to matrix vir.

Friends
class	cvm::atom

Additional Inherited Members
Protected Attributes inherited from gmx::ColvarProxyGromacs
t_atoms	gmxAtoms_
	Atoms topology.

PbcType	pbcType_
	Box infos.

t_pbc	gmxPbc_

const MDLogger *	logger_ = nullptr

bool	doParsing_
	Activate or not the parsing of the Colvars config file.

DefaultRandomEngine	rng_

TabulatedNormalDistribution	normalDistribution_

Constructor & Destructor Documentation

gmx::ColvarsForceProvider::ColvarsForceProvider	(	const std::string &	colvarsConfigString,
		t_atoms	atoms,
		PbcType	pbcType,
		const MDLogger *	logger,
		const std::map< std::string, std::string > &	inputStrings,
		real	ensembleTemperature,
		int	seed,
		LocalAtomSetManager *	localAtomSetManager,
		const t_commrec *	cr,
		double	simulationTimeStep,
		const std::vector< RVec > &	colvarsCoords,
		const std::string &	outputPrefix,
		const ColvarsForceProviderState &	state
	)

Construct ColvarsForceProvider from its parameters.

Parameters

[in]	colvarsConfigString	Content of the colvars input file.
[in]	atoms	Atoms topology
[in]	pbcType	Periodic boundary conditions
[in]	logger	GROMACS logger instance
[in]	inputStrings	Input files stored as string in the TPR's KVT
[in]	ensembleTemperature	the constant ensemble temperature
[in]	seed	The colvars seed for random number generator
[in]	localAtomSetManager	Atom Manager to retrieve Colvars index atoms
[in]	cr	Communication Record
[in]	simulationTimeStep	The simulation time step
[in]	colvarsCoords	The colvars atoms coordinates retrived from the TPR's KVT
[in]	outputPrefix	The prefix for output colvars files
[in]	state	The state of colvars force provider to be written in the checkpoint

Member Function Documentation

void gmx::ColvarsForceProvider::add_energy ( cvm::real energy )

override

From colvarproxy.

add energy to the total count of bias energy biasEnergy

Parameters

[in] energy the value of energy to add

void gmx::ColvarsForceProvider::calculateForces	(	const ForceProviderInput &	forceProviderInput,
		ForceProviderOutput *	forceProviderOutput
	)

overridevirtual

Calculate colvars forces.

Parameters

[in]	forceProviderInput	input for force provider
[out]	forceProviderOutput	output for force provider

Implements gmx::IForceProvider.

void gmx::ColvarsForceProvider::processAtomsRedistributedSignal ( const MDModulesAtomsRedistributedSignal & atomsRedistributedSignal )

Process atomsRedistributedSignal notification during mdrun.

Parameters

[in] atomsRedistributedSignal signal recieved

void gmx::ColvarsForceProvider::writeCheckpointData	(	MDModulesWriteCheckpointData	checkpointWriting,
		const std::string &	moduleName
	)

Write internal colvars data to checkpoint file.

Parameters

[in]	checkpointWriting	enables writing to the Key-Value-Tree that is used for storing the checkpoint information
[in]	moduleName	names the module that is checkpointing this force-provider

Note: The provided state to checkpoint has to change if checkpointing is moved before the force provider call in the MD-loop.

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

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

Description

Public Member Functions

Static Public Member Functions

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation