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 #include <stdio.h>
  40 #include "typedefs.h"
  41 #include "types/commrec.h"
  42
  43 #ifdef __cplusplus
  44 extern "C" {
  45 #endif
  46
  47 typedef struct {
  48         int *      left_import_construct;
  49         int        left_import_nconstruct;
  50         int *      left_export_construct;
  51         int        left_export_nconstruct;
  52         int *      right_import_construct;
  53         int        right_import_nconstruct;
  54         int *      right_export_construct;
  55         int        right_export_nconstruct;
  56         rvec *     send_buf;
  57         rvec *     recv_buf;
  58 } t_comm_vsites;
  59
  60 typedef struct {
  61   int  n_intercg_vsite;       /* The number of inter charge group vsites */
  62   int  nvsite_pbc_molt;       /* The array size of vsite_pbc_molt        */
  63   int  ***vsite_pbc_molt;     /* The pbc atoms for intercg vsites        */
  64   int  **vsite_pbc_loc;       /* The local pbc atoms                     */
  65   int  *vsite_pbc_loc_nalloc;
  66   gmx_bool bPDvsitecomm;          /* Do we need vsite communication with PD? */
  67   t_comm_vsites *vsitecomm;   /* The PD vsite communication struct       */
  68 } gmx_vsite_t;
  69
  70 void construct_vsites(FILE *log,gmx_vsite_t *vsite,
  71                              rvec x[],t_nrnb *nrnb,
  72                              real dt,rvec v[],
  73                              t_iparams ip[],t_ilist ilist[],
  74                              int ePBC,gmx_bool bMolPBC,t_graph *graph,
  75                              t_commrec *cr,matrix box);
  76 /* Create positions of vsite atoms based on surrounding atoms
  77  * for the local system.
  78  * If v is passed, the velocities of the vsites will be calculated
  79  * as the new positions minus the old positions divided by dt,
  80  * thus v should only be passed when the coordinates have been
  81  * updated with a full time step.
  82  * Note that velocitis of vsites are completely irrelevant
  83  * for the integration, they are only useful for analysis.
  84  */
  85
  86 void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
  87                            gmx_mtop_t *mtop,rvec x[]);
  88 /* Create positions of vsite atoms based on surrounding atoms
  89  * for the whole system.
  90  * This function assumes that all molecules are whole.
  91  */
  92
  93 void spread_vsite_f(FILE *log,gmx_vsite_t *vsite,
  94                     rvec x[],rvec f[],rvec *fshift,
  95                     gmx_bool VirCorr,matrix vir,
  96                     t_nrnb *nrnb,t_idef *idef,
  97                     int ePBC,gmx_bool bMolPBC,t_graph *g,matrix box,
  98                     t_commrec *cr);
  99 /* Spread the force operating on the vsite atoms on the surrounding atoms.
 100  * If fshift!=NULL also update the shift forces.
 101  * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
 102  * to vir. This correction is required when the virial is not calculated
 103  * afterwards from the particle position and forces, but in a different way,
 104  * as for instance for the PME mesh contribution.
 105  */
 106
 107 gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr);
 108 /* Initialize the virtual site struct,
 109  * returns NULL when there are no virtual sites.
 110  */
 111
 112 void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
 113                           t_commrec *cr);
 114 /* Set some vsite data for runs without domain decomposition.
 115  * Should be called once after init_vsite, before calling other routines.
 116  */
 117
 118 #ifdef __cplusplus
 119 }
 120 #endif
 121
 122 #endif
 123