Gromacs  2025-dev-20240613-b88f907
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Groups Pages
List of all members | Public Member Functions
gmx::ColvarsPreProcessor Class Reference

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

+ Inheritance diagram for gmx::ColvarsPreProcessor:
+ Collaboration diagram for gmx::ColvarsPreProcessor:


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< RVecgetColvarsCoords ()
 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 MDLoggerlogger_ = nullptr
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.

[in]colvarsConfigStringContent of the colvars input file.
[in]atomsAtoms topology
[in]pbcTypePeriodic boundary conditions
[in]loggerGROMACS logger instance
[in]ensembleTemperaturethe constant ensemble temperature
[in]seedthe colvars seed for random number generator
[in]boxMatrix with full box of the system
[in]xCoordinates of each atom in the system

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