include/vsite.h

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  38
  39 #ifndef _vsite_h
  40 #define _vsite_h
  41 #include <stdio.h>
  42 #include "visibility.h"
  43 #include "typedefs.h"
  44 #include "types/commrec.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     t_ilist ilist[F_NRE];     /* vsite ilists for this thread            */
  65     rvec fshift[SHIFTS];      /* fshift accumulation buffer              */
  66     matrix dxdf;              /* virial dx*df accumulation buffer        */
  67 } gmx_vsite_thread_t;
  68
  69 typedef struct {
  70   gmx_bool bHaveChargeGroups; /* Do we have charge groups?               */
  71   int  n_intercg_vsite;       /* The number of inter charge group vsites */
  72   int  nvsite_pbc_molt;       /* The array size of vsite_pbc_molt        */
  73   int  ***vsite_pbc_molt;     /* The pbc atoms for intercg vsites        */
  74   int  **vsite_pbc_loc;       /* The local pbc atoms                     */
  75   int  *vsite_pbc_loc_nalloc; /* Sizes of vsite_pbc_loc                  */
  76   gmx_bool bPDvsitecomm;      /* Do we need vsite communication with PD? */
  77   t_comm_vsites *vsitecomm;   /* The PD vsite communication struct       */
  78   int  nthreads;              /* Number of threads used for vsites       */
  79   gmx_vsite_thread_t *tdata;  /* Thread local vsites and work structs    */
  80   int  *th_ind;               /* Work array                              */
  81   int  th_ind_nalloc;         /* Size of th_ind                          */
  82 } gmx_vsite_t;
  83
  84 GMX_LIBMD_EXPORT
  85 void construct_vsites(FILE *log,gmx_vsite_t *vsite,
  86                              rvec x[],t_nrnb *nrnb,
  87                              real dt,rvec v[],
  88                              t_iparams ip[],t_ilist ilist[],
  89                              int ePBC,gmx_bool bMolPBC,t_graph *graph,
  90                              t_commrec *cr,matrix box);
  91 /* Create positions of vsite atoms based on surrounding atoms
  92  * for the local system.
  93  * If v is passed, the velocities of the vsites will be calculated
  94  * as the new positions minus the old positions divided by dt,
  95  * thus v should only be passed when the coordinates have been
  96  * updated with a full time step.
  97  * Note that velocitis of vsites are completely irrelevant
  98  * for the integration, they are only useful for analysis.
  99  */
 100
 101 GMX_LIBMD_EXPORT
 102 void construct_vsites_mtop(FILE *log,gmx_vsite_t *vsite,
 103                            gmx_mtop_t *mtop,rvec x[]);
 104 /* Create positions of vsite atoms based on surrounding atoms
 105  * for the whole system.
 106  * This function assumes that all molecules are whole.
 107  */
 108
 109 void spread_vsite_f(FILE *log,gmx_vsite_t *vsite,
 110                     rvec x[],rvec f[],rvec *fshift,
 111                     gmx_bool VirCorr,matrix vir,
 112                     t_nrnb *nrnb,t_idef *idef,
 113                     int ePBC,gmx_bool bMolPBC,t_graph *g,matrix box,
 114                     t_commrec *cr);
 115 /* Spread the force operating on the vsite atoms on the surrounding atoms.
 116  * If fshift!=NULL also update the shift forces.
 117  * If VirCorr=TRUE add the virial correction for non-linear vsite constructs
 118  * to vir. This correction is required when the virial is not calculated
 119  * afterwards from the particle position and forces, but in a different way,
 120  * as for instance for the PME mesh contribution.
 121  */
 122
 123 GMX_LIBMD_EXPORT
 124 gmx_vsite_t *init_vsite(gmx_mtop_t *mtop,t_commrec *cr,
 125                         gmx_bool bSerial_NoPBC);
 126 /* Initialize the virtual site struct,
 127  * returns NULL when there are no virtual sites.
 128  * bSerial_NoPBC is to generate a simple vsite setup to be
 129  * used only serial (no MPI or thread parallelization) and without pbc;
 130  * this is useful for correction vsites of the initial configuration.
 131  */
 132
 133 void split_vsites_over_threads(const t_ilist *ilist,
 134                                const t_mdatoms *mdatoms,
 135                                gmx_bool bLimitRange,
 136                                gmx_vsite_t *vsite);
 137 /* Divide the vsite work-load over the threads.
 138  * Should be called at the end of the domain decomposition.
 139  */
 140
 141 GMX_LIBMD_EXPORT
 142 void set_vsite_top(gmx_vsite_t *vsite,gmx_localtop_t *top,t_mdatoms *md,
 143                           t_commrec *cr);
 144 /* Set some vsite data for runs without domain decomposition.
 145  * Should be called once after init_vsite, before calling other routines.
 146  */
 147
 148 #ifdef __cplusplus
 149 }
 150 #endif
 151
 152 #endif
 153