/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
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- * as published by the Free Software Foundation; either version 2
+ * 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,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
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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 */
- matrix dxdf; /* virial dx*df accumulation buffer */
+ rvec fshift[SHIFTS]; /* fshift accumulation buffer */
+ matrix dxdf; /* virial dx*df accumulation buffer */
} gmx_vsite_thread_t;
typedef struct {
- gmx_bool bHaveChargeGroups; /* Do we have charge groups? */
- int n_intercg_vsite; /* The number of inter charge group vsites */
- int nvsite_pbc_molt; /* The array size of vsite_pbc_molt */
- 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_bool bHaveChargeGroups; /* Do we have charge groups? */
+ int n_intercg_vsite; /* The number of inter charge group vsites */
+ int nvsite_pbc_molt; /* The array size of vsite_pbc_molt */
+ 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 */
+ 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,
- real dt,rvec v[],
- t_iparams ip[],t_ilist ilist[],
- int ePBC,gmx_bool bMolPBC,t_graph *graph,
- t_commrec *cr,matrix box);
+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_commrec *cr, matrix box);
/* Create positions of vsite atoms based on surrounding atoms
* for the local system.
* If v is passed, the velocities of the vsites will be calculated
* for the integration, they are only useful for analysis.
*/
-void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
- gmx_mtop_t *mtop,rvec x[]);
+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,
- 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,
- t_commrec *cr);
+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, 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.
* If VirCorr=TRUE add the virial correction for non-linear vsite constructs
* as for instance for the PME mesh contribution.
*/
-gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr,
- gmx_bool bSerial_NoPBC);
+gmx_vsite_t *init_vsite(gmx_mtop_t *mtop, t_commrec *cr,
+ gmx_bool bSerial_NoPBC);
/* Initialize the virtual site struct,
* returns NULL when there are no virtual sites.
* bSerial_NoPBC is to generate a simple vsite setup to be
* this is useful for correction vsites of the initial configuration.
*/
-void split_vsites_over_threads(const t_ilist *ilist,
+void split_vsites_over_threads(const t_ilist *ilist,
+ const t_iparams *ip,
const t_mdatoms *mdatoms,
- gmx_bool bLimitRange,
- gmx_vsite_t *vsite);
+ gmx_bool bLimitRange,
+ gmx_vsite_t *vsite);
/* Divide the vsite work-load over the threads.
* Should be called at the end of the domain decomposition.
*/
-void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
- t_commrec *cr);
+void set_vsite_top(gmx_vsite_t *vsite, gmx_localtop_t *top, t_mdatoms *md,
+ t_commrec *cr);
/* Set some vsite data for runs without domain decomposition.
* Should be called once after init_vsite, before calling other routines.
*/
#endif
#endif
-
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