qmmmtopologypreprocessor.h File Reference

#include <set>
#include <string>
#include <vector>
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
#include "qmmmtypes.h"

Include dependency graph for qmmmtopologypreprocessor.h:

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Description

QMMMTopologyPrepocessor class responsible for all modificatios of the topology during input pre-processing.

Author

Dmitry Morozov dmitr.nosp@m.y.mo.nosp@m.rozov.nosp@m.@jyu.nosp@m..fi

Classes
class	gmx::QMMMTopologyPreprocessor
	Class implementing gmx_mtop_t QMMM modifications during preprocessing. More...

Functions
std::vector< bool >	gmx::splitQMBlocks (gmx_mtop_t *mtop, const std::set< int > &qmIndices)
	Splits QM containing molecules out of MM blocks in topology. More...
std::vector< real >	gmx::removeQMClassicalCharges (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const std::vector< bool > &bQMBlock, real refQ, const MDLogger &logger, WarningHandler *wi)
	Removes classical charges from QM atoms and virtual sites. More...
void	gmx::addQMLJExclusions (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const MDLogger &logger)
	Build exclusion list for non-bonded interactions between QM atoms. More...
std::vector< int >	gmx::buildQMMMAtomNumbers (const gmx_mtop_t &mtop)
	Builds and returns a vector of atom numbers for all atoms in mtop. More...
void	gmx::modifyQMMMTwoCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const std::vector< bool > &bQMBlock, const MDLogger &logger)
	Modifies pairwise bonded interactions. More...
void	gmx::modifyQMMMThreeCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const std::vector< bool > &bQMBlock, const MDLogger &logger)
	Modifies three-centers interactions (i.e. Angles, Settles) More...
void	gmx::modifyQMMMFourCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const std::vector< bool > &bQMBlock, const MDLogger &logger)
	Modifies four-centers interactions. More...
void	gmx::checkConstrainedBonds (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const std::vector< bool > &bQMBlock, WarningHandler *wi)
	Checks for constrained bonds within QM subsystem. More...
std::vector< LinkFrontier >	gmx::buildQMMMLink (gmx_mtop_t *mtop, const std::set< int > &qmIndices, const std::vector< bool > &bQMBlock, const MDLogger &logger)
	Builds link frontier vector with pairs of atoms indicting broken QM - MM chemical bonds. More...