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. 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.

const MDLogger &	logger () const
	Get the logger instance.

void	setWarninp (WarningHandler *wi)
	Set the warninp instance.

Additional Inherited Members
Protected Member Functions inherited from gmx::IMdpOptionProvider
	IMdpOptionProvider ()=default
	Default constructors and assignment operators. More...

	IMdpOptionProvider (const IMdpOptionProvider &)=default

IMdpOptionProvider &	operator= (const IMdpOptionProvider &)=default

	IMdpOptionProvider (IMdpOptionProvider &&) noexcept=default

IMdpOptionProvider &	operator= (IMdpOptionProvider &&) noexcept=default

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.

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

Additional Inherited Members

Member Function Documentation