embedded_system_preprocessing.cpp File Reference

#include "gromacs/topology/embedded_system_preprocessing.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_atomloops.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/logger.h"

Include dependency graph for embedded_system_preprocessing.cpp:

Description

Implements embedded system topology preprocessing functions.

Author

Lukas Müllender lukas.nosp@m..mue.nosp@m.llend.nosp@m.er@g.nosp@m.mail..nosp@m.com

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

Functions
static bool	gmx::isEmbeddedAtom (Index globalAtomIndex, const std::set< int > &embeddedIndices)
std::vector< bool >	gmx::splitEmbeddedBlocks (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices)
	Splits embedded atom containing molecules out of MM blocks in topology. More...
std::vector< real >	gmx::removeEmbeddedClassicalCharges (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, real refQ, const MDLogger &logger, WarningHandler *wi)
	Removes classical charges from embedded atoms and virtual sites. More...
void	gmx::addEmbeddedNBExclusions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const MDLogger &logger)
	Build exclusion list for non-bonded interactions between embedded atoms. More...
std::vector< int >	gmx::buildEmbeddedAtomNumbers (const gmx_mtop_t &mtop)
	Builds and returns a vector of atom numbers for all atoms in mtop. More...
void	gmx::modifyEmbeddedTwoCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies pairwise bonded interactions. More...
std::vector< LinkFrontierAtom >	gmx::buildLinkFrontier (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Builds link frontier vector with pairs of atoms indicting broken embedded - MM chemical bonds. More...
void	gmx::modifyEmbeddedThreeCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies three-centers interactions (i.e. Angles, Settles) More...
void	gmx::modifyEmbeddedFourCenterInteractions (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, const MDLogger &logger)
	Modifies four-centers interactions. More...
void	gmx::checkConstrainedBonds (gmx_mtop_t *mtop, const std::set< int > &embeddedIndices, const std::vector< bool > &isEmbeddedBlock, WarningHandler *wi)
	Checks for constrained bonds within embedded subsystem. More...