/*
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*
- * This source code is part of
- *
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- *
- * VERSION 3.2.0
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* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
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-
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+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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+ * consider code for inclusion in the official distribution, but
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*/
#ifndef _vsite_h
#define _vsite_h
#include <stdio.h>
-#include "typedefs.h"
-#include "types/commrec.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/pbcutil/ishift.h"
#ifdef __cplusplus
extern "C" {
#endif
-typedef struct {
- int * left_import_construct;
- int left_import_nconstruct;
- int * left_export_construct;
- int left_export_nconstruct;
- int * right_import_construct;
- int right_import_nconstruct;
- int * right_export_construct;
- int right_export_nconstruct;
- rvec * send_buf;
- rvec * recv_buf;
-} t_comm_vsites;
-
typedef struct {
t_ilist ilist[F_NRE]; /* vsite ilists for this thread */
rvec fshift[SHIFTS]; /* fshift accumulation buffer */
int ***vsite_pbc_molt; /* The pbc atoms for intercg vsites */
int **vsite_pbc_loc; /* The local pbc atoms */
int *vsite_pbc_loc_nalloc; /* Sizes of vsite_pbc_loc */
- gmx_bool bPDvsitecomm; /* Do we need vsite communication with PD? */
- t_comm_vsites *vsitecomm; /* The PD vsite communication struct */
int nthreads; /* Number of threads used for vsites */
gmx_vsite_thread_t *tdata; /* Thread local vsites and work structs */
int *th_ind; /* Work array */
int th_ind_nalloc; /* Size of th_ind */
} gmx_vsite_t;
-void construct_vsites(FILE *log, gmx_vsite_t *vsite,
- rvec x[], t_nrnb *nrnb,
+struct t_graph;
+
+void construct_vsites(gmx_vsite_t *vsite,
+ rvec x[],
real dt, rvec v[],
t_iparams ip[], t_ilist ilist[],
- int ePBC, gmx_bool bMolPBC, t_graph *graph,
+ int ePBC, gmx_bool bMolPBC,
t_commrec *cr, matrix box);
/* Create positions of vsite atoms based on surrounding atoms
* for the local system.
* for the integration, they are only useful for analysis.
*/
-void construct_vsites_mtop(FILE *log, gmx_vsite_t *vsite,
+void construct_vsites_mtop(gmx_vsite_t *vsite,
gmx_mtop_t *mtop, rvec x[]);
/* Create positions of vsite atoms based on surrounding atoms
* for the whole system.
* This function assumes that all molecules are whole.
*/
-void spread_vsite_f(FILE *log, gmx_vsite_t *vsite,
+void spread_vsite_f(gmx_vsite_t *vsite,
rvec x[], rvec f[], rvec *fshift,
gmx_bool VirCorr, matrix vir,
t_nrnb *nrnb, t_idef *idef,
- int ePBC, gmx_bool bMolPBC, t_graph *g, matrix box,
+ int ePBC, gmx_bool bMolPBC, struct t_graph *g, matrix box,
t_commrec *cr);
/* Spread the force operating on the vsite atoms on the surrounding atoms.
* If fshift!=NULL also update the shift forces.
*/
void split_vsites_over_threads(const t_ilist *ilist,
+ const t_iparams *ip,
const t_mdatoms *mdatoms,
gmx_bool bLimitRange,
gmx_vsite_t *vsite);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff