makebondedlinks.cpp File Reference

#include "gmxpre.h"
#include "gromacs/domdec/makebondedlinks.h"
#include <cstdio>
#include <algorithm>
#include <memory>
#include <vector>
#include "gromacs/domdec/domdec_internal.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/options.h"
#include "gromacs/domdec/reversetopology.h"
#include "gromacs/mdtypes/atominfo.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/listoflists.h"

Include dependency graph for makebondedlinks.cpp:

Description

Defines a function that makes the list of links between atoms connected by bonded interactions.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions
static void	check_link (std::vector< int > *links, const int atom)
	Check if a link is stored in links to atom and if this is not the case, store a link.
static gmx::ListOfLists< int >	genBondedLinks (const gmx_mtop_t &mtop, gmx::ArrayRef< gmx::AtomInfoWithinMoleculeBlock > atomInfoForEachMoleculeBlock)
	Creates and return a list of bonded links for all atoms in the system.
void	makeBondedLinks (gmx_domdec_t *dd, const gmx_mtop_t &mtop, gmx::ArrayRef< gmx::AtomInfoWithinMoleculeBlock > atomInfoForEachMoleculeBlock)
	Generate a list of links between atoms that are linked by bonded interactions. More...

Function Documentation

void makeBondedLinks	(	gmx_domdec_t *	dd,
		const gmx_mtop_t &	mtop,
		gmx::ArrayRef< gmx::AtomInfoWithinMoleculeBlock >	atomInfoForEachMoleculeBlock
	)

Generate a list of links between atoms that are linked by bonded interactions.

Also stores whether atoms are linked in atomInfoForEachMoleculeBlock.