gmx::ColvarProxyGromacs Class Reference

#include <gromacs/applied_forces/colvars/colvarproxygromacs.h>

Inheritance diagram for gmx::ColvarProxyGromacs:

Collaboration diagram for gmx::ColvarProxyGromacs:

Description

Implements a GROMACS version of colvarproxy. This class hold for the communication between colvars and GROMACS. 2 child class will inherit from this one: one during pre processing (ColvarsPreProcessor) and one during the simulation (ColvarsForceProvider). Most of the work needed for the communication will be implemented in this class.

Public Member Functions
	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.

Protected Attributes
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_

Friends
class	cvm::atom

Constructor & Destructor Documentation

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.

Parameters

[in]	colvarsConfigString	Content of the colvars input file.
[in]	atoms	Atoms topology
[in]	pbcType	Periodic boundary conditions
[in]	logger	GROMACS logger instance
[in]	doParsing	Wether the input file should be parsed.
[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

From colvarproxy The 5 variables below are defined in the colvarproxy base class

Member Function Documentation

int gmx::ColvarProxyGromacs::check_atom_id ( int  atomNumber )

override

Check if atom belongs to the global index of atoms.

Parameters

[in]

atomNumber

Colvars index of the atom to check

cvm::real gmx::ColvarProxyGromacs::rand_gaussian ( )

override

From colvarproxy.

Return a random number from a Gaussian distribution

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

• src/gromacs/applied_forces/colvars/colvarproxygromacs.h
• src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp