computemultibodycutoffs.cpp File Reference

#include "gmxpre.h"
#include "gromacs/domdec/computemultibodycutoffs.h"
#include <cmath>
#include <memory>
#include <optional>
#include <vector>
#include "gromacs/domdec/options.h"
#include "gromacs/domdec/reversetopology.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/forcefieldparameters.h"
#include "gromacs/topology/idef.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/enumerationhelpers.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/vec.h"

Include dependency graph for computemultibodycutoffs.cpp:

Description

This file defines functions used by the domdec module while managing the construction, use and error checking for topologies local to a DD rank.

Author

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

Functions
static void	update_max_bonded_distance (const real r2, const std::optional< InteractionFunction > ftype, const int a1, const int a2, std::optional< bonded_distance_t > *bd)
	Compare distance^2 r2 against the distance in bd and if larger store it along with ftype and atom indices a1 and a2.
template<bool usePbc>
static real	distanceSquared (const t_pbc *pbc, const RVec &x1, const RVec &x2)
	Returns the squared distance between two atoms, with or without PBC correction.
template<bool usePbc>
static void	bonded_cg_distance_mol (const gmx_moltype_t *molt, const DDBondedChecking ddBondedChecking, gmx_bool bExcl, const t_pbc *pbc, ArrayRef< const RVec > x, std::optional< bonded_distance_t > *bd_2b, std::optional< bonded_distance_t > *bd_mb)
	Set the distance, function type and atom indices for the longest distance between atoms of molecule type molt for two-body and multi-body bonded interactions.
static void	bonded_distance_intermol (const InteractionLists &ilists_intermol, const DDBondedChecking ddBondedChecking, ArrayRef< const RVec > x, PbcType pbcType, const matrix box, std::optional< bonded_distance_t > *bd_2b, std::optional< bonded_distance_t > *bd_mb)
	Set the distance, function type and atom indices for the longest atom distance involved in intermolecular interactions for two-body and multi-body bonded interactions.
static bool	moltypeHasVsite (const gmx_moltype_t &molt)
	Returns whether molt has at least one virtual site.
static void	getWholeMoleculeCoordinates (const gmx_moltype_t *molt, const gmx_ffparams_t *ffparams, PbcType pbcType, t_graph *graph, const matrix box, ArrayRef< const RVec > x, ArrayRef< RVec > xs)
	Returns coordinates not broken over PBC for a molecule.
void	dd_bonded_cg_distance (const gmx::MDLogger &mdlog, const gmx_mtop_t &mtop, const t_inputrec &inputrec, ArrayRef< const RVec > x, const matrix box, const DDBondedChecking ddBondedChecking, real *r_2b, real *r_mb)