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gmx::ColvarsOptions Class Referencefinal

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

+ Inheritance diagram for gmx::ColvarsOptions:
+ Collaboration diagram for gmx::ColvarsOptions:

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. More...
 
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 realcolvarsEnsTemp () 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]builderthe 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]coordstructure 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]filenamename 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]temptemperature object
void gmx::ColvarsOptions::processTopology ( gmx_mtop_t *  mtop)

Store the topology of the system.

Parameters
[in,out]mtoptopology 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]colvarsfileName of the colvars input file.
[in]topologyAtoms topology
[in]coordsCoordinates of each atom in the system
[in]pbcTypePeriodic boundary conditions
[in]boxValuesMatrix with full box of the system
[in]temperaturethe constant ensemble temperature
void gmx::ColvarsOptions::writeInternalParametersToKvt ( KeyValueTreeObjectBuilder  treeBuilder)

Store the paramers that are not mdp options in the tpr file.

Vector with colvars atoms coordinates


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