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gmx::QMMMOptions Class Referencefinal

#include <gromacs/applied_forces/qmmm/qmmmoptions.h>

+ Inheritance diagram for gmx::QMMMOptions:
+ Collaboration diagram for gmx::QMMMOptions:

Description

Input data storage for QM/MM.

Public Member Functions

void initMdpTransform (IKeyValueTreeTransformRules *rules) override
 Implementation of IMdpOptionProvider method.
 
void buildMdpOutput (KeyValueTreeObjectBuilder *builder) const override
 Build mdp parameters for QMMM to be output after pre-processing. More...
 
void initMdpOptions (IOptionsContainerWithSections *options) override
 Connects options names and data.
 
bool active () const
 Report if this set of MDP options is active (i.e. QMMM MdModule is active)
 
const QMMMParametersparameters ()
 Get parameters_ instance.
 
void setQMMMGroupIndices (const IndexGroupsAndNames &indexGroupsAndNames)
 Evaluate and store atom indices. During pre-processing, use the group string from the options to evaluate the indices of both QM atoms and MM atoms, also stores them as vectors into the parameters_. More...
 
void setQMExternalInputFile (const QMInputFileName &qmExternalInputFileName)
 Process external QM input file in case it is provided with -qmi option of grompp. Produces parameters_.qmInput in case parameters_.qmMethod_ = INPUT. More...
 
void processCoordinates (const CoordinatesAndBoxPreprocessed &coord)
 Process coordinates, PbcType and Box in order to produce CP2K sample input. Produces qmPdb_ in all cases. Produces parameters_.qmInput_, parameters_.qmTrans_ and parameters_.qmBox_ in case parameters_.qmMethod_ != INPUT. More...
 
void modifyQMMMTopology (gmx_mtop_t *mtop)
 Modifies topology in case of active QMMM module using QMMMTopologyPreprocessor. More...
 
void writeInternalParametersToKvt (KeyValueTreeObjectBuilder treeBuilder)
 Store the paramers that are not mdp options in the tpr file.
 
void readInternalParametersFromKvt (const KeyValueTreeObject &tree)
 Set the internal parameters that are stored in the tpr file.
 
void processTprFilename (const MdRunInputFilename &tprFilename)
 Process MdRunInputFilename notification during mdrun. In case parameters_.qmFileNameBase_ is empty sets it to tpr name with _cp2k suffix. More...
 
void setLogger (const MDLogger &logger)
 Set the MDLogger instance.
 
void setWarninp (WarningHandler *wi)
 Set the warninp instance.
 

Member Function Documentation

void gmx::QMMMOptions::buildMdpOutput ( KeyValueTreeObjectBuilder builder) const
overridevirtual

Build mdp parameters for QMMM to be output after pre-processing.

Parameters
[in,out]builderthe builder for the mdp options output KVT.

Implements gmx::IMdpOptionProvider.

void gmx::QMMMOptions::modifyQMMMTopology ( gmx_mtop_t *  mtop)

Modifies topology in case of active QMMM module using QMMMTopologyPreprocessor.

Parameters
[in,out]mtoptopology to modify for QMMM
void gmx::QMMMOptions::processCoordinates ( const CoordinatesAndBoxPreprocessed coord)

Process coordinates, PbcType and Box in order to produce CP2K sample input. Produces qmPdb_ in all cases. Produces parameters_.qmInput_, parameters_.qmTrans_ and parameters_.qmBox_ in case parameters_.qmMethod_ != INPUT.

Parameters
[in]coordstructure with coordinates and box dimensions
void gmx::QMMMOptions::processTprFilename ( const MdRunInputFilename tprFilename)

Process MdRunInputFilename notification during mdrun. In case parameters_.qmFileNameBase_ is empty sets it to tpr name with _cp2k suffix.

Parameters
[in]tprFilenamename of the *.tpr file that mdrun simulates
void gmx::QMMMOptions::setQMExternalInputFile ( const QMInputFileName qmExternalInputFileName)

Process external QM input file in case it is provided with -qmi option of grompp. Produces parameters_.qmInput in case parameters_.qmMethod_ = INPUT.

Parameters
[in]qmExternalInputFileNamestructure with information about external QM input
void gmx::QMMMOptions::setQMMMGroupIndices ( const IndexGroupsAndNames indexGroupsAndNames)

Evaluate and store atom indices. During pre-processing, use the group string from the options to evaluate the indices of both QM atoms and MM atoms, also stores them as vectors into the parameters_.

Parameters
[in]indexGroupsAndNamesobject containing data about index groups and names

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