domdec_vsite.cpp File Reference

#include "gmxpre.h"
#include "domdec_vsite.h"
#include <cassert>
#include <cstdio>
#include <algorithm>
#include <memory>
#include <vector>
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/domdec/hashedmap.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/vec.h"
#include "gromacs/utility/vectypes.h"
#include "domdec_specatomcomm.h"

Include dependency graph for domdec_vsite.cpp:

Description

This file implements functions for domdec to use while managing inter-atomic constraints.

Author

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

Functions
void	dd_move_f_vsites (const gmx_domdec_t &dd, gmx::ArrayRef< gmx::RVec > f, gmx::ArrayRef< gmx::RVec > fshift)
	Communicates the virtual site forces, reduces the shift forces when fshift != NULL.
void	dd_clear_f_vsites (const gmx_domdec_t &dd, gmx::ArrayRef< gmx::RVec > f)
	Clears the forces for virtual sites.
void	dd_move_x_vsites (const gmx_domdec_t &dd, const matrix box, gmx::ArrayRef< gmx::RVec > x)
	Communicates the coordinates involved in virtual sites.
void	dd_move_x_and_v_vsites (const gmx_domdec_t &dd, const matrix box, gmx::ArrayRef< gmx::RVec > x, gmx::ArrayRef< gmx::RVec > v)
	Communicates the positions and velocities involved in virtual sites.
void	dd_clear_local_vsite_indices (gmx_domdec_t *dd)
	Clears the local indices for the virtual site communication setup.
int	dd_make_local_vsites (gmx_domdec_t *dd, int at_start, gmx::EnumerationArray< InteractionFunction, InteractionList > &lil)
	Sets up communication and atom indices for all local vsites.
void	init_domdec_vsites (gmx_domdec_t *dd, int n_intercg_vsite)
	Initializes the data structures for virtual site communication.