src/gromacs/domdec/domdec_vsite.cpp

   1 /*
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   3  *
   4  * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35
  36 /*! \internal \file
  37  *
  38  * \brief This file implements functions for domdec to use
  39  * while managing inter-atomic constraints.
  40  *
  41  * \author Berk Hess <hess@kth.se>
  42  * \ingroup module_domdec
  43  */
  44
  45 #include "gmxpre.h"
  46
  47 #include "domdec_vsite.h"
  48
  49 #include <assert.h>
  50
  51 #include <algorithm>
  52
  53 #include "gromacs/domdec/domdec.h"
  54 #include "gromacs/domdec/ga2la.h"
  55 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
  56 #include "gromacs/legacyheaders/types/commrec.h"
  57 #include "gromacs/math/vec.h"
  58 #include "gromacs/pbcutil/ishift.h"
  59 #include "gromacs/topology/mtop_util.h"
  60 #include "gromacs/utility/fatalerror.h"
  61 #include "gromacs/utility/gmxassert.h"
  62 #include "gromacs/utility/smalloc.h"
  63
  64 #include "domdec_specatomcomm.h"
  65 #include "hash.h"
  66
  67 void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift)
  68 {
  69     if (dd->vsite_comm)
  70     {
  71         dd_move_f_specat(dd, dd->vsite_comm, f, fshift);
  72     }
  73 }
  74
  75 void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f)
  76 {
  77     int i;
  78
  79     if (dd->vsite_comm)
  80     {
  81         for (i = dd->vsite_comm->at_start; i < dd->vsite_comm->at_end; i++)
  82         {
  83             clear_rvec(f[i]);
  84         }
  85     }
  86 }
  87
  88 void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x)
  89 {
  90     if (dd->vsite_comm)
  91     {
  92         dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
  93     }
  94 }
  95
  96 int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
  97 {
  98     gmx_domdec_specat_comm_t   *spac;
  99     ind_req_t                  *ireq;
 100     gmx_hash_t                 *ga2la_specat;
 101     int  ftype, nral, i, j, a;
 102     t_ilist                    *lilf;
 103     t_iatom                    *iatoms;
 104     int  at_end;
 105
 106     spac         = dd->vsite_comm;
 107     ireq         = &spac->ireq[0];
 108     ga2la_specat = dd->ga2la_vsite;
 109
 110     ireq->n = 0;
 111     /* Loop over all the home vsites */
 112     for (ftype = 0; ftype < F_NRE; ftype++)
 113     {
 114         if (interaction_function[ftype].flags & IF_VSITE)
 115         {
 116             nral = NRAL(ftype);
 117             lilf = &lil[ftype];
 118             for (i = 0; i < lilf->nr; i += 1+nral)
 119             {
 120                 iatoms = lilf->iatoms + i;
 121                 /* Check if we have the other atoms */
 122                 for (j = 1; j < 1+nral; j++)
 123                 {
 124                     if (iatoms[j] < 0)
 125                     {
 126                         /* This is not a home atom,
 127                          * we need to ask our neighbors.
 128                          */
 129                         a = -iatoms[j] - 1;
 130                         /* Check to not ask for the same atom more than once */
 131                         if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
 132                         {
 133                             /* Add this non-home atom to the list */
 134                             if (ireq->n+1 > ireq->nalloc)
 135                             {
 136                                 ireq->nalloc = over_alloc_large(ireq->n+1);
 137                                 srenew(ireq->ind, ireq->nalloc);
 138                             }
 139                             ireq->ind[ireq->n++] = a;
 140                             /* Temporarily mark with -2,
 141                              * we get the index later.
 142                              */
 143                             gmx_hash_set(ga2la_specat, a, -2);
 144                         }
 145                     }
 146                 }
 147             }
 148         }
 149     }
 150
 151     at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
 152                                         at_start, 1, "vsite", "");
 153
 154     /* Fill in the missing indices */
 155     for (ftype = 0; ftype < F_NRE; ftype++)
 156     {
 157         if (interaction_function[ftype].flags & IF_VSITE)
 158         {
 159             nral = NRAL(ftype);
 160             lilf = &lil[ftype];
 161             for (i = 0; i < lilf->nr; i += 1+nral)
 162             {
 163                 iatoms = lilf->iatoms + i;
 164                 for (j = 1; j < 1+nral; j++)
 165                 {
 166                     if (iatoms[j] < 0)
 167                     {
 168                         iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
 169                     }
 170                 }
 171             }
 172         }
 173     }
 174
 175     return at_end;
 176 }
 177
 178 void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
 179 {
 180     if (debug)
 181     {
 182         fprintf(debug, "Begin init_domdec_vsites\n");
 183     }
 184
 185     /* Use a hash table for the global to local index.
 186      * The number of keys is a rough estimate, it will be optimized later.
 187      */
 188     dd->ga2la_vsite = gmx_hash_init(std::min(n_intercg_vsite/20,
 189                                              n_intercg_vsite/(2*dd->nnodes)));
 190
 191     dd->vsite_comm = specat_comm_init(1);
 192 }