reversetopology.cpp File Reference

#include "gmxpre.h"
#include "gromacs/domdec/reversetopology.h"
#include <cstdio>
#include <algorithm>
#include <memory>
#include <vector>
#include "gromacs/domdec/domdec_constraints.h"
#include "gromacs/domdec/domdec_internal.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/domdec_vsite.h"
#include "gromacs/domdec/options.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/topology/topology_enums.h"
#include "gromacs/topology/topsort.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"

Include dependency graph for reversetopology.cpp:

Description

This file defines functions used in making the reverse topology.

Author

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

Classes
struct	gmx_reverse_top_t::Impl
	Struct for the reverse topology: links bonded interactions to atoms. More...

Functions
int	nral_rt (int ftype)
	Returns the number of atom entries for il in gmx_reverse_top_t.
bool	dd_check_ftype (const int ftype, const ReverseTopOptions &rtOptions)
	Return whether interactions of type ftype need to be assigned exactly once.
MolecularTopologyAtomIndices	globalAtomIndexToMoltypeIndices (const gmx::ArrayRef< const MolblockIndices > molblockIndices, const int globalAtomIndex)
	Return global topology molecule information for global atom index globalAtomIndex.
static int	getMaxNumExclusionsPerAtom (const ListOfLists< int > &excls)
	Returns the maximum number of exclusions per atom.
static void	low_make_reverse_ilist (const InteractionLists &il_mt, const t_atom *atom, int *count, const ReverseTopOptions &rtOptions, gmx::ArrayRef< const int > r_index, gmx::ArrayRef< int > r_il, const AtomLinkRule atomLinkRule, const bool assignReverseIlist)
	Run the reverse ilist generation and store it in r_il when bAssign = TRUE.
void	make_reverse_ilist (const InteractionLists &ilist, const t_atoms *atoms, const ReverseTopOptions &rtOptions, const AtomLinkRule atomLinkRule, reverse_ilist_t *ril_mt)
	Make the reverse ilist: a list of bonded interactions linked to atoms.
void	dd_make_reverse_top (FILE *fplog, gmx_domdec_t *dd, const gmx_mtop_t &mtop, const gmx::VirtualSitesHandler *vsite, const t_inputrec &inputrec, const DDBondedChecking ddBondedChecking)