src/gromacs/domdec/domdec_vsite.cpp

   1 /*
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   4  * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
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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 <cassert>
  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/domdec/hashedmap.h"
  57 #include "gromacs/math/vec.h"
  58 #include "gromacs/mdtypes/commrec.h"
  59 #include "gromacs/pbcutil/ishift.h"
  60 #include "gromacs/topology/ifunc.h"
  61 #include "gromacs/topology/mtop_util.h"
  62 #include "gromacs/utility/fatalerror.h"
  63 #include "gromacs/utility/gmxassert.h"
  64
  65 #include "domdec_specatomcomm.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, const matrix box, rvec *x)
  89 {
  90     if (dd->vsite_comm)
  91     {
  92         dd_move_x_specat(dd, dd->vsite_comm, box, x, nullptr, FALSE);
  93     }
  94 }
  95
  96 void dd_clear_local_vsite_indices(gmx_domdec_t *dd)
  97 {
  98     if (dd->vsite_comm)
  99     {
 100         dd->ga2la_vsite->clear();
 101     }
 102 }
 103
 104 int dd_make_local_vsites(gmx_domdec_t *dd, int at_start, t_ilist *lil)
 105 {
 106     std::vector<int>    &ireq         = dd->vsite_requestedGlobalAtomIndices;
 107     gmx::HashedMap<int> *ga2la_specat = dd->ga2la_vsite;
 108
 109     ireq.clear();
 110     /* Loop over all the home vsites */
 111     for (int ftype = 0; ftype < F_NRE; ftype++)
 112     {
 113         if (interaction_function[ftype].flags & IF_VSITE)
 114         {
 115             const int      nral = NRAL(ftype);
 116             const t_ilist &lilf = lil[ftype];
 117             for (int i = 0; i < lilf.nr; i += 1 + nral)
 118             {
 119                 const t_iatom *iatoms = lilf.iatoms + i;
 120                 /* Check if we have the other atoms */
 121                 for (int j = 1; j < 1 + nral; j++)
 122                 {
 123                     if (iatoms[j] < 0)
 124                     {
 125                         /* This is not a home atom,
 126                          * we need to ask our neighbors.
 127                          */
 128                         int a = -iatoms[j] - 1;
 129                         /* Check to not ask for the same atom more than once */
 130                         if (!dd->ga2la_vsite->find(a))
 131                         {
 132                             /* Add this non-home atom to the list */
 133                             ireq.push_back(a);
 134                             /* Temporarily mark with -2,
 135                              * we get the index later.
 136                              */
 137                             ga2la_specat->insert(a, -2);
 138                         }
 139                     }
 140                 }
 141             }
 142         }
 143     }
 144
 145     int at_end =
 146         setup_specat_communication(dd, &ireq, dd->vsite_comm, ga2la_specat,
 147                                    at_start, 1, "vsite", "");
 148
 149     /* Fill in the missing indices */
 150     for (int ftype = 0; ftype < F_NRE; ftype++)
 151     {
 152         if (interaction_function[ftype].flags & IF_VSITE)
 153         {
 154             const int  nral = NRAL(ftype);
 155             t_ilist   &lilf = lil[ftype];
 156             for (int i = 0; i < lilf.nr; i += 1 + nral)
 157             {
 158                 t_iatom *iatoms = lilf.iatoms + i;
 159                 for (int j = 1; j < 1 + nral; j++)
 160                 {
 161                     if (iatoms[j] < 0)
 162                     {
 163                         const int *a = ga2la_specat->find(-iatoms[j] - 1);
 164                         GMX_ASSERT(a, "We have checked before that this atom index has been set");
 165                         iatoms[j] = *a;
 166                     }
 167                 }
 168             }
 169         }
 170     }
 171
 172     return at_end;
 173 }
 174
 175 void init_domdec_vsites(gmx_domdec_t *dd, int n_intercg_vsite)
 176 {
 177     if (debug)
 178     {
 179         fprintf(debug, "Begin init_domdec_vsites\n");
 180     }
 181
 182     /* Use a hash table for the global to local index.
 183      * The number of keys is a rough estimate, it will be optimized later.
 184      */
 185     int numKeysEstimate = std::min(n_intercg_vsite/20,
 186                                    n_intercg_vsite/(2*dd->nnodes));
 187     dd->ga2la_vsite = new gmx::HashedMap<int>(numKeysEstimate);
 188
 189     dd->vsite_comm = new gmx_domdec_specat_comm_t;
 190 }