gmx::ColvarsPreProcessor Class Reference

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

Inheritance diagram for gmx::ColvarsPreProcessor:

Collaboration diagram for gmx::ColvarsPreProcessor:

Description

Class that read a colvars configuration file during pre-processing and retrieve the colvars atoms coordinates to be stored in tpr KVT.

Public Member Functions
	ColvarsPreProcessor (const std::string &colvarsConfigString, t_atoms atoms, PbcType pbcType, const MDLogger &logger, real ensembleTemperature, int seed, const matrix box, ArrayRef< const RVec > x)
	Construct ColvarsPreProcessor from its parameters. More...
std::vector< RVec >	getColvarsCoords ()
	Return a vector of the colvars atoms coordinates.
bool	inputStreamsToKVT (KeyValueTreeObjectBuilder treeBuilder, const std::string &tag)
	Save all input files of colvars (outside the config file) in the tpr file through the key-value-tree.
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.

Additional Inherited Members
Protected Attributes inherited from gmx::ColvarProxyGromacs
t_atoms	gmxAtoms_
	Atoms topology.
PbcType	pbcType_
	Box infos.
t_pbc	gmxPbc_
const MDLogger &	logger_
bool	doParsing_
	Activate or not the parsing of the Colvars config file.
DefaultRandomEngine	rng_
TabulatedNormalDistribution	normalDistribution_

Constructor & Destructor Documentation

gmx::ColvarsPreProcessor::ColvarsPreProcessor	(	const std::string &	colvarsConfigString,
		t_atoms	atoms,
		PbcType	pbcType,
		const MDLogger &	logger,
		real	ensembleTemperature,
		int	seed,
		const matrix	box,
		ArrayRef< const RVec >	x
	)

Construct ColvarsPreProcessor 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]	ensembleTemperature	the constant ensemble temperature
[in]	seed	the colvars seed for random number generator
[in]	box	Matrix with full box of the system
[in]	x	Coordinates of each atom in the system

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

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