reversetopology.h File Reference

#include <cstdio>
#include <memory>
#include <vector>
#include "gromacs/mdlib/vsite.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/listoflists.h"

Include dependency graph for reversetopology.h:

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Description

This file makes declarations used for building the reverse topology.

Classes
struct	thread_work_t
	Struct for thread local work data for local topology generation. More...
struct	ReverseTopOptions
	Options for setting up gmx_reverse_top_t. More...
class	gmx_reverse_top_t
	Reverse topology class. More...
struct	MolecularTopologyAtomIndices
	Molecular topology indices of a global molecule a global atom belongs to. More...

Enumerations
enum	AtomLinkRule { AtomLinkRule::FirstAtom, AtomLinkRule::AllAtomsInBondeds }
	Options for linking atoms in make_reverse_ilist. More...

Functions
int	nral_rt (InteractionFunction ftype)
	Returns the number of atom entries for il in gmx_reverse_top_t.
bool	dd_check_ftype (InteractionFunction ftype, const ReverseTopOptions &rtOptions)
	Return whether interactions of type ftype need to be assigned exactly once.
MolecularTopologyAtomIndices	globalAtomIndexToMoltypeIndices (gmx::ArrayRef< const MolblockIndices > molblockIndices, int globalAtomIndex)
	Return global topology molecule information for global atom index globalAtomIndex.
void	make_reverse_ilist (const InteractionLists &ilist, const t_atoms *atoms, const ReverseTopOptions &rtOptions, 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, gmx::DDBondedChecking ddBondedChecking)
	Generate and store the reverse topology.

Enumeration Type Documentation

enum AtomLinkRule

strong

Options for linking atoms in make_reverse_ilist.

Enumerator
FirstAtom	Link all interactions to the first atom in the atom list.
AllAtomsInBondeds	Link bonded interactions to all atoms involved, don't link vsites.