include/vsite.h

   1 /*
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   9  *                        VERSION 3.2.0
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  35
  36 #ifndef _vsite_h
  37 #define _vsite_h
  38
  39 #ifdef HAVE_CONFIG_H
  40 #include <config.h>
  41 #endif
  42
  43 #include <stdio.h>
  44 #include "typedefs.h"
  45
  46 #ifdef __cplusplus
  47 extern "C" {
  48 #endif
  49
  50 typedef struct {
  51         int *      left_import_construct;
  52         int        left_import_nconstruct;
  53         int *      left_export_construct;
  54         int        left_export_nconstruct;
  55         int *      right_import_construct;
  56         int        right_import_nconstruct;
  57         int *      right_export_construct;
  58         int        right_export_nconstruct;
  59         rvec *     send_buf;
  60         rvec *     recv_buf;
  61 } t_comm_vsites;
  62
  63 typedef struct {
  64   int  n_intercg_vsite;       /* The number of inter charge group vsites */
  65   int  nvsite_pbc_molt;       /* The array size of vsite_pbc_molt        */
  66   int  ***vsite_pbc_molt;     /* The pbc atoms for intercg vsites        */
  67   int  **vsite_pbc_loc;       /* The local pbc atoms                     */
  68   int  *vsite_pbc_loc_nalloc;
  69   bool bPDvsitecomm;          /* Do we need vsite communication with PD? */
  70   t_comm_vsites *vsitecomm;   /* The PD vsite communication struct       */
  71 } gmx_vsite_t;
  72
  73 extern void construct_vsites(FILE *log,gmx_vsite_t *vsite,
  74                              rvec x[],t_nrnb *nrnb,
  75                              real dt,rvec v[],
  76                              t_iparams ip[],t_ilist ilist[],
  77                              int ePBC,bool bMolPBC,t_graph *graph,
  78                              t_commrec *cr,matrix box);
  79 /* Create positions of vsite atoms based on surrounding atoms
  80  * for the local system.
  81  * If v is passed, the velocities of the vsites will be calculated
  82  * as the new positions minus the old positions divided by dt,
  83  * thus v should only be passed when the coordinates have been
  84  * updated with a full time step.
  85  * Note that velocitis of vsites are completely irrelevant
  86  * for the integration, they are only useful for analysis.
  87  */
  88
  89 void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
  90                            gmx_mtop_t *mtop,rvec x[]);
  91 /* Create positions of vsite atoms based on surrounding atoms
  92  * for the whole system.
  93  * This function assumes that all molecules are whole.
  94  */
  95
  96 extern void spread_vsite_f(FILE *log,gmx_vsite_t *vsite,
  97                            rvec x[],rvec f[],rvec *fshift,
  98                            t_nrnb *nrnb,t_idef *idef,
  99                            int ePBC,bool bMolPBC,t_graph *g,matrix box,
 100                            t_commrec *cr);
 101 /* Spread the force operating on the vsite atoms on the surrounding atoms.
 102  * If fshift!=NULL also update the shift forces.
 103  */
 104
 105 extern gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr);
 106 /* Initialize the virtual site struct,
 107  * returns NULL when there are no virtual sites.
 108  */
 109
 110 extern void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
 111                           t_commrec *cr);
 112 /* Set some vsite data for runs without domain decomposition.
 113  * Should be called once after init_vsite, before calling other routines.
 114  */
 115
 116 #ifdef __cplusplus
 117 }
 118 #endif
 119
 120 #endif
 121