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#include "gmxpre.h"
#include "gromacs/domdec/makebondedlinks.h"
#include <algorithm>
#include "gromacs/domdec/domdec_internal.h"
#include "gromacs/domdec/options.h"
#include "gromacs/domdec/reversetopology.h"
#include "gromacs/mdtypes/atominfo.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.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.