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/domdec_struct.h"
  55 #include "gromacs/domdec/ga2la.h"
  56 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
  57 #include "gromacs/legacyheaders/types/commrec.h"
  58 #include "gromacs/math/vec.h"
  59 #include "gromacs/pbcutil/ishift.h"
  60 #include "gromacs/topology/mtop_util.h"
  61 #include "gromacs/utility/fatalerror.h"
  62 #include "gromacs/utility/gmxassert.h"
  63 #include "gromacs/utility/smalloc.h"
  64
  65 #include "domdec_specatomcomm.h"
  66 #include "hash.h"
  67
  68 void dd_move_f_vsites(gmx_domdec_t *dd, rvec *f, rvec *fshift)
  69 {
  70     if (dd->vsite_comm)
  71     {
  72         dd_move_f_specat(dd, dd->vsite_comm, f, fshift);
  73     }
  74 }
  75
  76 void dd_clear_f_vsites(gmx_domdec_t *dd, rvec *f)
  77 {
  78     int i;
  79
  80     if (dd->vsite_comm)
  81     {
  82         for (i = dd->vsite_comm->at_start; i < dd->vsite_comm->at_end; i++)
  83         {
  84             clear_rvec(f[i]);
  85         }
  86     }
  87 }
  88
  89 void dd_move_x_vsites(gmx_domdec_t *dd, matrix box, rvec *x)
  90 {
  91     if (dd->vsite_comm)
  92     {
  93         dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
  94     }
  95 }
  96
  97 int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
  98 {
  99     gmx_domdec_specat_comm_t   *spac;
 100     ind_req_t                  *ireq;
 101     gmx_hash_t                 *ga2la_specat;
 102     int  ftype, nral, i, j, a;
 103     t_ilist                    *lilf;
 104     t_iatom                    *iatoms;
 105     int  at_end;
 106
 107     spac         = dd->vsite_comm;
 108     ireq         = &spac->ireq[0];
 109     ga2la_specat = dd->ga2la_vsite;
 110
 111     ireq->n = 0;
 112     /* Loop over all the home vsites */
 113     for (ftype = 0; ftype < F_NRE; ftype++)
 114     {
 115         if (interaction_function[ftype].flags & IF_VSITE)
 116         {
 117             nral = NRAL(ftype);
 118             lilf = &lil[ftype];
 119             for (i = 0; i < lilf->nr; i += 1+nral)
 120             {
 121                 iatoms = lilf->iatoms + i;
 122                 /* Check if we have the other atoms */
 123                 for (j = 1; j < 1+nral; j++)
 124                 {
 125                     if (iatoms[j] < 0)
 126                     {
 127                         /* This is not a home atom,
 128                          * we need to ask our neighbors.
 129                          */
 130                         a = -iatoms[j] - 1;
 131                         /* Check to not ask for the same atom more than once */
 132                         if (gmx_hash_get_minone(dd->ga2la_vsite, a) == -1)
 133                         {
 134                             /* Add this non-home atom to the list */
 135                             if (ireq->n+1 > ireq->nalloc)
 136                             {
 137                                 ireq->nalloc = over_alloc_large(ireq->n+1);
 138                                 srenew(ireq->ind, ireq->nalloc);
 139                             }
 140                             ireq->ind[ireq->n++] = a;
 141                             /* Temporarily mark with -2,
 142                              * we get the index later.
 143                              */
 144                             gmx_hash_set(ga2la_specat, a, -2);
 145                         }
 146                     }
 147                 }
 148             }
 149         }
 150     }
 151
 152     at_end = setup_specat_communication(dd, ireq, dd->vsite_comm, ga2la_specat,
 153                                         at_start, 1, "vsite", "");
 154
 155     /* Fill in the missing indices */
 156     for (ftype = 0; ftype < F_NRE; ftype++)
 157     {
 158         if (interaction_function[ftype].flags & IF_VSITE)
 159         {
 160             nral = NRAL(ftype);
 161             lilf = &lil[ftype];
 162             for (i = 0; i < lilf->nr; i += 1+nral)
 163             {
 164                 iatoms = lilf->iatoms + i;
 165                 for (j = 1; j < 1+nral; j++)
 166                 {
 167                     if (iatoms[j] < 0)
 168                     {
 169                         iatoms[j] = gmx_hash_get_minone(ga2la_specat, -iatoms[j]-1);
 170                     }
 171                 }
 172             }
 173         }
 174     }
 175
 176     return at_end;
 177 }
 178
 179 void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
 180 {
 181     if (debug)
 182     {
 183         fprintf(debug, "Begin init_domdec_vsites\n");
 184     }
 185
 186     /* Use a hash table for the global to local index.
 187      * The number of keys is a rough estimate, it will be optimized later.
 188      */
 189     dd->ga2la_vsite = gmx_hash_init(std::min(n_intercg_vsite/20,
 190                                              n_intercg_vsite/(2*dd->nnodes)));
 191
 192     dd->vsite_comm = specat_comm_init(1);
 193 }