include/vsite.h

   1 /*
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   6  *
   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
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  35
  36 #ifndef _vsite_h
  37 #define _vsite_h
  38
  39 #include <stdio.h>
  40 #include "typedefs.h"
  41
  42 #ifdef __cplusplus
  43 extern "C" {
  44 #endif
  45
  46 typedef struct {
  47         int *      left_import_construct;
  48         int        left_import_nconstruct;
  49         int *      left_export_construct;
  50         int        left_export_nconstruct;
  51         int *      right_import_construct;
  52         int        right_import_nconstruct;
  53         int *      right_export_construct;
  54         int        right_export_nconstruct;
  55         rvec *     send_buf;
  56         rvec *     recv_buf;
  57 } t_comm_vsites;
  58
  59 typedef struct {
  60   int  n_intercg_vsite;       /* The number of inter charge group vsites */
  61   int  nvsite_pbc_molt;       /* The array size of vsite_pbc_molt        */
  62   int  ***vsite_pbc_molt;     /* The pbc atoms for intercg vsites        */
  63   int  **vsite_pbc_loc;       /* The local pbc atoms                     */
  64   int  *vsite_pbc_loc_nalloc;
  65   gmx_bool bPDvsitecomm;          /* Do we need vsite communication with PD? */
  66   t_comm_vsites *vsitecomm;   /* The PD vsite communication struct       */
  67 } gmx_vsite_t;
  68
  69 void construct_vsites(FILE *log,gmx_vsite_t *vsite,
  70                              rvec x[],t_nrnb *nrnb,
  71                              real dt,rvec v[],
  72                              t_iparams ip[],t_ilist ilist[],
  73                              int ePBC,gmx_bool bMolPBC,t_graph *graph,
  74                              t_commrec *cr,matrix box);
  75 /* Create positions of vsite atoms based on surrounding atoms
  76  * for the local system.
  77  * If v is passed, the velocities of the vsites will be calculated
  78  * as the new positions minus the old positions divided by dt,
  79  * thus v should only be passed when the coordinates have been
  80  * updated with a full time step.
  81  * Note that velocitis of vsites are completely irrelevant
  82  * for the integration, they are only useful for analysis.
  83  */
  84
  85 void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
  86                            gmx_mtop_t *mtop,rvec x[]);
  87 /* Create positions of vsite atoms based on surrounding atoms
  88  * for the whole system.
  89  * This function assumes that all molecules are whole.
  90  */
  91
  92 void spread_vsite_f(FILE *log,gmx_vsite_t *vsite,
  93                            rvec x[],rvec f[],rvec *fshift,
  94                            t_nrnb *nrnb,t_idef *idef,
  95                            int ePBC,gmx_bool bMolPBC,t_graph *g,matrix box,
  96                            t_commrec *cr);
  97 /* Spread the force operating on the vsite atoms on the surrounding atoms.
  98  * If fshift!=NULL also update the shift forces.
  99  */
 100
 101 gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr);
 102 /* Initialize the virtual site struct,
 103  * returns NULL when there are no virtual sites.
 104  */
 105
 106 void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
 107                           t_commrec *cr);
 108 /* Set some vsite data for runs without domain decomposition.
 109  * Should be called once after init_vsite, before calling other routines.
 110  */
 111
 112 #ifdef __cplusplus
 113 }
 114 #endif
 115
 116 #endif
 117