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 QMMMParameters &	parameters ()
	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] builder the 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] mtop topology 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] coord structure 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] tprFilename name 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] qmExternalInputFileName structure 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] indexGroupsAndNames object containing data about index groups and names

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

src/gromacs/applied_forces/qmmm/qmmmoptions.h
src/gromacs/applied_forces/qmmm/qmmmoptions.cpp

Description

Public Member Functions

Member Function Documentation