src/gromacs/mdlib/domdec_con.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  * This file is part of Gromacs        Copyright (c) 1991-2008
   5  * David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
   6  *
   7  * This program is free software; you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation; either version 2
  10  * of the License, or (at your option) any later version.
  11  *
  12  * To help us fund GROMACS development, we humbly ask that you cite
  13  * the research papers on the package. Check out http://www.gromacs.org
  14  *
  15  * And Hey:
  16  * Gnomes, ROck Monsters And Chili Sauce
  17  */
  18
  19 #ifdef HAVE_CONFIG_H
  20 #include <config.h>
  21 #endif
  22 #include <assert.h>
  23
  24 #include "smalloc.h"
  25 #include "vec.h"
  26 #include "constr.h"
  27 #include "domdec.h"
  28 #include "domdec_network.h"
  29 #include "mtop_util.h"
  30 #include "gmx_ga2la.h"
  31 #include "gmx_hash.h"
  32 #include "gmx_omp_nthreads.h"
  33 #include "macros.h"
  34
  35 typedef struct {
  36     int nsend;
  37     int *a;
  38     int a_nalloc;
  39     int nrecv;
  40 } gmx_specatsend_t;
  41
  42 typedef struct {
  43     int *ind;
  44     int nalloc;
  45     int n;
  46 } ind_req_t;
  47
  48 typedef struct gmx_domdec_specat_comm {
  49     /* The number of indices to receive during the setup */
  50     int  nreq[DIM][2][2];
  51     /* The atoms to send */
  52     gmx_specatsend_t spas[DIM][2];
  53     gmx_bool *bSendAtom;
  54     int   bSendAtom_nalloc;
  55     /* Send buffers */
  56     int  *ibuf;
  57     int  ibuf_nalloc;
  58     rvec *vbuf;
  59     int  vbuf_nalloc;
  60     rvec *vbuf2;
  61     int  vbuf2_nalloc;
  62     /* The range in the local buffer(s) for received atoms */
  63     int  at_start;
  64     int  at_end;
  65
  66     /* The atom indices we need from the surrounding cells.
  67      * We can gather the indices over nthread threads.
  68      */
  69     int nthread;
  70     ind_req_t *ireq;
  71 } gmx_domdec_specat_comm_t;
  72
  73 typedef struct gmx_domdec_constraints {
  74     int  *molb_con_offset;
  75     int  *molb_ncon_mol;
  76     /* The fully local and connected constraints */
  77     int  ncon;
  78     /* The global constraint number, only required for clearing gc_req */
  79     int  *con_gl;
  80     int  *con_nlocat;
  81     int  con_nalloc;
  82     /* Boolean that tells if a global constraint index has been requested */
  83     char *gc_req;
  84     /* Global to local communicated constraint atom only index */
  85     gmx_hash_t ga2la;
  86
  87     /* Multi-threading stuff */
  88     int nthread;
  89     t_ilist *ils;
  90 } gmx_domdec_constraints_t;
  91
  92
  93 static void dd_move_f_specat(gmx_domdec_t *dd,gmx_domdec_specat_comm_t *spac,
  94                              rvec *f,rvec *fshift)
  95 {
  96     gmx_specatsend_t *spas;
  97     rvec *vbuf;
  98     int  n,n0,n1,d,dim,dir,i;
  99     ivec vis;
 100     int  is;
 101     gmx_bool bPBC,bScrew;
 102
 103     n = spac->at_end;
 104     for(d=dd->ndim-1; d>=0; d--)
 105     {
 106         dim = dd->dim[d];
 107         if (dd->nc[dim] > 2)
 108         {
 109             /* Pulse the grid forward and backward */
 110             spas = spac->spas[d];
 111             n0 = spas[0].nrecv;
 112             n1 = spas[1].nrecv;
 113             n -= n1 + n0;
 114             vbuf = spac->vbuf;
 115             /* Send and receive the coordinates */
 116             dd_sendrecv2_rvec(dd,d,
 117                               f+n+n1,n0,vbuf              ,spas[0].nsend,
 118                               f+n   ,n1,vbuf+spas[0].nsend,spas[1].nsend);
 119             for(dir=0; dir<2; dir++)
 120             {
 121                 bPBC   = ((dir == 0 && dd->ci[dim] == 0) ||
 122                           (dir == 1 && dd->ci[dim] == dd->nc[dim]-1));
 123                 bScrew = (bPBC && dd->bScrewPBC && dim == XX);
 124
 125                 spas = &spac->spas[d][dir];
 126                 /* Sum the buffer into the required forces */
 127                 if (!bPBC || (!bScrew && fshift == NULL))
 128                 {
 129                     for(i=0; i<spas->nsend; i++)
 130                     {
 131                         rvec_inc(f[spas->a[i]],*vbuf);
 132                         vbuf++;
 133                     }
 134                 }
 135                 else
 136                 {
 137                     clear_ivec(vis);
 138                     vis[dim] = (dir==0 ? 1 : -1);
 139                     is = IVEC2IS(vis);
 140                     if (!bScrew)
 141                     {
 142                         /* Sum and add to shift forces */
 143                         for(i=0; i<spas->nsend; i++)
 144                         {
 145                             rvec_inc(f[spas->a[i]],*vbuf);
 146                             rvec_inc(fshift[is],*vbuf);
 147                             vbuf++;
 148                         }
 149                     }
 150                     else
 151                     {
 152                         /* Rotate the forces */
 153                         for(i=0; i<spas->nsend; i++)
 154                         {
 155                             f[spas->a[i]][XX] += (*vbuf)[XX];
 156                             f[spas->a[i]][YY] -= (*vbuf)[YY];
 157                             f[spas->a[i]][ZZ] -= (*vbuf)[ZZ];
 158                             if (fshift)
 159                             {
 160                                 rvec_inc(fshift[is],*vbuf);
 161                             }
 162                             vbuf++;
 163                         }
 164                     }
 165                 }
 166             }
 167         }
 168         else
 169         {
 170             /* Two cells, so we only need to communicate one way */
 171             spas = &spac->spas[d][0];
 172             n -= spas->nrecv;
 173             /* Send and receive the coordinates */
 174             dd_sendrecv_rvec(dd,d,dddirForward,
 175                              f+n,spas->nrecv,spac->vbuf,spas->nsend);
 176             /* Sum the buffer into the required forces */
 177             if (dd->bScrewPBC && dim == XX &&
 178                 (dd->ci[dim] == 0 ||
 179                  dd->ci[dim] == dd->nc[dim]-1))
 180             {
 181                 for(i=0; i<spas->nsend; i++)
 182                 {
 183                     /* Rotate the force */
 184                     f[spas->a[i]][XX] += spac->vbuf[i][XX];
 185                     f[spas->a[i]][YY] -= spac->vbuf[i][YY];
 186                     f[spas->a[i]][ZZ] -= spac->vbuf[i][ZZ];
 187                 }
 188             }
 189             else
 190             {
 191                 for(i=0; i<spas->nsend; i++)
 192                 {
 193                     rvec_inc(f[spas->a[i]],spac->vbuf[i]);
 194                 }
 195             }
 196         }
 197     }
 198 }
 199
 200 void dd_move_f_vsites(gmx_domdec_t *dd,rvec *f,rvec *fshift)
 201 {
 202     if (dd->vsite_comm)
 203     {
 204         dd_move_f_specat(dd,dd->vsite_comm,f,fshift);
 205     }
 206 }
 207
 208 void dd_clear_f_vsites(gmx_domdec_t *dd,rvec *f)
 209 {
 210     int i;
 211
 212     if (dd->vsite_comm)
 213     {
 214         for(i=dd->vsite_comm->at_start; i<dd->vsite_comm->at_end; i++)
 215         {
 216             clear_rvec(f[i]);
 217         }
 218     }
 219 }
 220
 221 static void dd_move_x_specat(gmx_domdec_t *dd,gmx_domdec_specat_comm_t *spac,
 222                              matrix box,rvec *x0,rvec *x1)
 223 {
 224     gmx_specatsend_t *spas;
 225     rvec *x,*vbuf,*rbuf;
 226     int  nvec,v,n,nn,ns0,ns1,nr0,nr1,nr,d,dim,dir,i;
 227     gmx_bool bPBC,bScrew=FALSE;
 228     rvec shift={0,0,0};
 229
 230     nvec = 1;
 231     if (x1)
 232     {
 233         nvec++;
 234     }
 235
 236     n = spac->at_start;
 237     for(d=0; d<dd->ndim; d++)
 238     {
 239         dim = dd->dim[d];
 240         if (dd->nc[dim] > 2)
 241         {
 242             /* Pulse the grid forward and backward */
 243             vbuf = spac->vbuf;
 244             for(dir=0; dir<2; dir++)
 245             {
 246                 if (dir == 0 && dd->ci[dim] == 0)
 247                 {
 248                     bPBC   = TRUE;
 249                     bScrew = (dd->bScrewPBC && dim == XX);
 250                     copy_rvec(box[dim],shift);
 251                 }
 252                 else if (dir == 1 && dd->ci[dim] == dd->nc[dim]-1)
 253                 {
 254                     bPBC = TRUE;
 255                     bScrew = (dd->bScrewPBC && dim == XX);
 256                     for(i=0; i<DIM; i++)
 257                     {
 258                         shift[i] = -box[dim][i];
 259                     }
 260                 }
 261                 else
 262                 {
 263                     bPBC = FALSE;
 264                     bScrew = FALSE;
 265                 }
 266                 spas = &spac->spas[d][dir];
 267                 for(v=0; v<nvec; v++)
 268                 {
 269                     x = (v == 0 ? x0 : x1);
 270                     /* Copy the required coordinates to the send buffer */
 271                     if (!bPBC)
 272                     {
 273                         /* Only copy */
 274                         for(i=0; i<spas->nsend; i++)
 275                         {
 276                             copy_rvec(x[spas->a[i]],*vbuf);
 277                             vbuf++;
 278                         }
 279                     }
 280                     else if (!bScrew)
 281                     {
 282                         /* Shift coordinates */
 283                         for(i=0; i<spas->nsend; i++)
 284                         {
 285                             rvec_add(x[spas->a[i]],shift,*vbuf);
 286                             vbuf++;
 287                         }
 288                     }
 289                     else
 290                     {
 291                         /* Shift and rotate coordinates */
 292                         for(i=0; i<spas->nsend; i++)
 293                         {
 294                             (*vbuf)[XX] =               x[spas->a[i]][XX] + shift[XX];
 295                             (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY] + shift[YY];
 296                             (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ] + shift[ZZ];
 297                             vbuf++;
 298                         }
 299                     }
 300                 }
 301             }
 302             /* Send and receive the coordinates */
 303             spas = spac->spas[d];
 304             ns0 = spas[0].nsend;
 305             nr0 = spas[0].nrecv;
 306             ns1 = spas[1].nsend;
 307             nr1 = spas[1].nrecv;
 308             if (nvec == 1)
 309             {
 310                 dd_sendrecv2_rvec(dd,d,
 311                                   spac->vbuf+ns0,ns1,x0+n    ,nr1,
 312                                   spac->vbuf    ,ns0,x0+n+nr1,nr0);
 313             }
 314             else
 315             {
 316                 /* Communicate both vectors in one buffer */
 317                 rbuf = spac->vbuf2;
 318                 dd_sendrecv2_rvec(dd,d,
 319                                   spac->vbuf+2*ns0,2*ns1,rbuf      ,2*nr1,
 320                                   spac->vbuf      ,2*ns0,rbuf+2*nr1,2*nr0);
 321                 /* Split the buffer into the two vectors */
 322                 nn = n;
 323                 for(dir=1; dir>=0; dir--)
 324                 {
 325                     nr = spas[dir].nrecv;
 326                     for(v=0; v<2; v++)
 327                     {
 328                         x = (v == 0 ? x0 : x1);
 329                         for(i=0; i<nr; i++)
 330                         {
 331                             copy_rvec(*rbuf,x[nn+i]);
 332                             rbuf++;
 333                         }
 334                     }
 335                     nn += nr;
 336                 }
 337             }
 338             n += nr0 + nr1;
 339         }
 340         else
 341         {
 342             spas = &spac->spas[d][0];
 343             /* Copy the required coordinates to the send buffer */
 344             vbuf = spac->vbuf;
 345             for(v=0; v<nvec; v++)
 346             {
 347                 x = (v == 0 ? x0 : x1);
 348                 if (dd->bScrewPBC && dim == XX &&
 349                     (dd->ci[XX] == 0 || dd->ci[XX] == dd->nc[XX]-1))
 350                 {
 351                     /* Here we only perform the rotation, the rest of the pbc
 352                      * is handled in the constraint or viste routines.
 353                      */
 354                     for(i=0; i<spas->nsend; i++)
 355                     {
 356                         (*vbuf)[XX] =               x[spas->a[i]][XX];
 357                         (*vbuf)[YY] = box[YY][YY] - x[spas->a[i]][YY];
 358                         (*vbuf)[ZZ] = box[ZZ][ZZ] - x[spas->a[i]][ZZ];
 359                         vbuf++;
 360                     }
 361                 }
 362                 else
 363                 {
 364                     for(i=0; i<spas->nsend; i++)
 365                     {
 366                         copy_rvec(x[spas->a[i]],*vbuf);
 367                         vbuf++;
 368                     }
 369                 }
 370             }
 371             /* Send and receive the coordinates */
 372             if (nvec == 1)
 373             {
 374                 dd_sendrecv_rvec(dd,d,dddirBackward,
 375                                  spac->vbuf,spas->nsend,x0+n,spas->nrecv);
 376             }
 377             else
 378             {
 379                 /* Communicate both vectors in one buffer */
 380                 rbuf = spac->vbuf2;
 381                 dd_sendrecv_rvec(dd,d,dddirBackward,
 382                                  spac->vbuf,2*spas->nsend,rbuf,2*spas->nrecv);
 383                 /* Split the buffer into the two vectors */
 384                 nr = spas[0].nrecv;
 385                 for(v=0; v<2; v++)
 386                 {
 387                     x = (v == 0 ? x0 : x1);
 388                     for(i=0; i<nr; i++)
 389                     {
 390                         copy_rvec(*rbuf,x[n+i]);
 391                         rbuf++;
 392                     }
 393                 }
 394             }
 395             n += spas->nrecv;
 396         }
 397     }
 398 }
 399
 400 void dd_move_x_constraints(gmx_domdec_t *dd,matrix box,rvec *x0,rvec *x1)
 401 {
 402     if (dd->constraint_comm)
 403     {
 404         dd_move_x_specat(dd,dd->constraint_comm,box,x0,x1);
 405     }
 406 }
 407
 408 void dd_move_x_vsites(gmx_domdec_t *dd,matrix box,rvec *x)
 409 {
 410     if (dd->vsite_comm)
 411     {
 412         dd_move_x_specat(dd,dd->vsite_comm,box,x,NULL);
 413     }
 414 }
 415
 416 int *dd_constraints_nlocalatoms(gmx_domdec_t *dd)
 417 {
 418     if (dd->constraints)
 419     {
 420         return dd->constraints->con_nlocat;
 421     }
 422     else
 423     {
 424         return NULL;
 425     }
 426 }
 427
 428 void dd_clear_local_constraint_indices(gmx_domdec_t *dd)
 429 {
 430     gmx_domdec_constraints_t *dc;
 431     int i;
 432
 433     dc = dd->constraints;
 434
 435     for(i=0; i<dc->ncon; i++)
 436     {
 437         dc->gc_req[dc->con_gl[i]] = 0;
 438     }
 439
 440     if (dd->constraint_comm)
 441     {
 442         gmx_hash_clear_and_optimize(dc->ga2la);
 443     }
 444 }
 445
 446 void dd_clear_local_vsite_indices(gmx_domdec_t *dd)
 447 {
 448     int i;
 449
 450     if (dd->vsite_comm)
 451     {
 452         gmx_hash_clear_and_optimize(dd->ga2la_vsite);
 453     }
 454 }
 455
 456 static int setup_specat_communication(gmx_domdec_t *dd,
 457                                       ind_req_t *ireq,
 458                                       gmx_domdec_specat_comm_t *spac,
 459                                       gmx_hash_t ga2la_specat,
 460                                       int at_start,
 461                                       int vbuf_fac,
 462                                       const char *specat_type,
 463                                       const char *add_err)
 464 {
 465     int  nsend[2],nlast,nsend_zero[2]={0,0},*nsend_ptr;
 466     int  d,dim,ndir,dir,nr,ns,i,nrecv_local,n0,start,indr,ind,buf[2];
 467     int  nat_tot_specat,nat_tot_prev,nalloc_old;
 468     gmx_bool bPBC,bFirst;
 469     gmx_specatsend_t *spas;
 470
 471     if (debug)
 472     {
 473         fprintf(debug,"Begin setup_specat_communication for %s\n",specat_type);
 474     }
 475
 476     /* nsend[0]: the number of atoms requested by this node only,
 477      *           we communicate this for more efficients checks
 478      * nsend[1]: the total number of requested atoms
 479      */
 480     nsend[0] = ireq->n;
 481     nsend[1] = nsend[0];
 482     nlast    = nsend[1];
 483     for(d=dd->ndim-1; d>=0; d--)
 484     {
 485         /* Pulse the grid forward and backward */
 486         dim = dd->dim[d];
 487         bPBC = (dim < dd->npbcdim);
 488         if (dd->nc[dim] == 2)
 489         {
 490             /* Only 2 cells, so we only need to communicate once */
 491             ndir = 1;
 492         }
 493         else
 494         {
 495             ndir = 2;
 496         }
 497         for(dir=0; dir<ndir; dir++)
 498         {
 499             if (!bPBC &&
 500                 dd->nc[dim] > 2 &&
 501                 ((dir == 0 && dd->ci[dim] == dd->nc[dim] - 1) ||
 502                  (dir == 1 && dd->ci[dim] == 0)))
 503             {
 504                 /* No pbc: the fist/last cell should not request atoms */
 505                 nsend_ptr = nsend_zero;
 506             }
 507             else
 508             {
 509                 nsend_ptr = nsend;
 510             }
 511             /* Communicate the number of indices */
 512             dd_sendrecv_int(dd,d,dir==0 ? dddirForward : dddirBackward,
 513                             nsend_ptr,2,spac->nreq[d][dir],2);
 514             nr = spac->nreq[d][dir][1];
 515             if (nlast+nr > ireq->nalloc)
 516             {
 517                 ireq->nalloc = over_alloc_dd(nlast+nr);
 518                 srenew(ireq->ind,ireq->nalloc);
 519             }
 520             /* Communicate the indices */
 521             dd_sendrecv_int(dd,d,dir==0 ? dddirForward : dddirBackward,
 522                             ireq->ind,nsend_ptr[1],ireq->ind+nlast,nr);
 523             nlast += nr;
 524         }
 525         nsend[1] = nlast;
 526     }
 527     if (debug)
 528     {
 529         fprintf(debug,"Communicated the counts\n");
 530     }
 531
 532     /* Search for the requested atoms and communicate the indices we have */
 533     nat_tot_specat = at_start;
 534     nrecv_local = 0;
 535     for(d=0; d<dd->ndim; d++)
 536     {
 537         bFirst = (d == 0);
 538         /* Pulse the grid forward and backward */
 539         if (dd->dim[d] >= dd->npbcdim || dd->nc[dd->dim[d]] > 2)
 540         {
 541             ndir = 2;
 542         }
 543         else
 544         {
 545             ndir = 1;
 546         }
 547         nat_tot_prev = nat_tot_specat;
 548         for(dir=ndir-1; dir>=0; dir--)
 549         {
 550             if (nat_tot_specat > spac->bSendAtom_nalloc)
 551             {
 552                 nalloc_old = spac->bSendAtom_nalloc;
 553                 spac->bSendAtom_nalloc = over_alloc_dd(nat_tot_specat);
 554                 srenew(spac->bSendAtom,spac->bSendAtom_nalloc);
 555                 for(i=nalloc_old; i<spac->bSendAtom_nalloc; i++)
 556                 {
 557                     spac->bSendAtom[i] = FALSE;
 558                 }
 559             }
 560             spas = &spac->spas[d][dir];
 561             n0 = spac->nreq[d][dir][0];
 562             nr = spac->nreq[d][dir][1];
 563             if (debug)
 564             {
 565                 fprintf(debug,"dim=%d, dir=%d, searching for %d atoms\n",
 566                         d,dir,nr);
 567             }
 568             start = nlast - nr;
 569             spas->nsend = 0;
 570             nsend[0] = 0;
 571             for(i=0; i<nr; i++)
 572             {
 573                 indr = ireq->ind[start+i];
 574                 ind = -1;
 575                 /* Check if this is a home atom and if so ind will be set */
 576                 if (!ga2la_get_home(dd->ga2la,indr,&ind))
 577                 {
 578                     /* Search in the communicated atoms */
 579                     ind = gmx_hash_get_minone(ga2la_specat,indr);
 580                 }
 581                 if (ind >= 0)
 582                 {
 583                     if (i < n0 || !spac->bSendAtom[ind])
 584                     {
 585                         if (spas->nsend+1 > spas->a_nalloc)
 586                         {
 587                             spas->a_nalloc = over_alloc_large(spas->nsend+1);
 588                             srenew(spas->a,spas->a_nalloc);
 589                         }
 590                         /* Store the local index so we know which coordinates
 591                          * to send out later.
 592                          */
 593                         spas->a[spas->nsend] = ind;
 594                         spac->bSendAtom[ind] = TRUE;
 595                         if (spas->nsend+1 > spac->ibuf_nalloc)
 596                         {
 597                             spac->ibuf_nalloc = over_alloc_large(spas->nsend+1);
 598                             srenew(spac->ibuf,spac->ibuf_nalloc);
 599                         }
 600                         /* Store the global index so we can send it now */
 601                         spac->ibuf[spas->nsend] = indr;
 602                         if (i < n0)
 603                         {
 604                             nsend[0]++;
 605                         }
 606                         spas->nsend++;
 607                     }
 608                 }
 609             }
 610             nlast = start;
 611             /* Clear the local flags */
 612             for(i=0; i<spas->nsend; i++)
 613             {
 614                 spac->bSendAtom[spas->a[i]] = FALSE;
 615             }
 616             /* Send and receive the number of indices to communicate */
 617             nsend[1] = spas->nsend;
 618             dd_sendrecv_int(dd,d,dir==0 ? dddirBackward : dddirForward,
 619                             nsend,2,buf,2);
 620             if (debug)
 621             {
 622                 fprintf(debug,"Send to node %d, %d (%d) indices, "
 623                         "receive from node %d, %d (%d) indices\n",
 624                         dd->neighbor[d][1-dir],nsend[1],nsend[0],
 625                         dd->neighbor[d][dir],buf[1],buf[0]);
 626                 if (gmx_debug_at)
 627                 {
 628                     for(i=0; i<spas->nsend; i++)
 629                     {
 630                         fprintf(debug," %d",spac->ibuf[i]+1);
 631                     }
 632                     fprintf(debug,"\n");
 633                 }
 634             }
 635             nrecv_local += buf[0];
 636             spas->nrecv  = buf[1];
 637             if (nat_tot_specat + spas->nrecv > dd->gatindex_nalloc)
 638             {
 639                 dd->gatindex_nalloc =
 640                     over_alloc_dd(nat_tot_specat + spas->nrecv);
 641                 srenew(dd->gatindex,dd->gatindex_nalloc);
 642             }
 643             /* Send and receive the indices */
 644             dd_sendrecv_int(dd,d,dir==0 ? dddirBackward : dddirForward,
 645                             spac->ibuf,spas->nsend,
 646                             dd->gatindex+nat_tot_specat,spas->nrecv);
 647             nat_tot_specat += spas->nrecv;
 648         }
 649
 650         /* Allocate the x/f communication buffers */
 651         ns = spac->spas[d][0].nsend;
 652         nr = spac->spas[d][0].nrecv;
 653         if (ndir == 2)
 654         {
 655             ns += spac->spas[d][1].nsend;
 656             nr += spac->spas[d][1].nrecv;
 657         }
 658         if (vbuf_fac*ns > spac->vbuf_nalloc)
 659         {
 660             spac->vbuf_nalloc = over_alloc_dd(vbuf_fac*ns);
 661             srenew(spac->vbuf,spac->vbuf_nalloc);
 662         }
 663         if (vbuf_fac == 2 && vbuf_fac*nr > spac->vbuf2_nalloc)
 664         {
 665             spac->vbuf2_nalloc = over_alloc_dd(vbuf_fac*nr);
 666             srenew(spac->vbuf2,spac->vbuf2_nalloc);
 667         }
 668
 669         /* Make a global to local index for the communication atoms */
 670         for(i=nat_tot_prev; i<nat_tot_specat; i++)
 671         {
 672             gmx_hash_change_or_set(ga2la_specat,dd->gatindex[i],i);
 673         }
 674     }
 675
 676     /* Check that in the end we got the number of atoms we asked for */
 677     if (nrecv_local != ireq->n)
 678     {
 679         if (debug)
 680         {
 681             fprintf(debug,"Requested %d, received %d (tot recv %d)\n",
 682                     ireq->n,nrecv_local,nat_tot_specat-at_start);
 683             if (gmx_debug_at)
 684             {
 685                 for(i=0; i<ireq->n; i++)
 686                 {
 687                     ind = gmx_hash_get_minone(ga2la_specat,ireq->ind[i]);
 688                     fprintf(debug," %s%d",
 689                             (ind >= 0) ? "" : "!",
 690                             ireq->ind[i]+1);
 691                 }
 692                 fprintf(debug,"\n");
 693             }
 694         }
 695         fprintf(stderr,"\nDD cell %d %d %d: Neighboring cells do not have atoms:",
 696                 dd->ci[XX],dd->ci[YY],dd->ci[ZZ]);
 697         for(i=0; i<ireq->n; i++)
 698         {
 699             if (gmx_hash_get_minone(ga2la_specat,ireq->ind[i]) < 0)
 700             {
 701                 fprintf(stderr," %d",ireq->ind[i]+1);
 702             }
 703         }
 704         fprintf(stderr,"\n");
 705         gmx_fatal(FARGS,"DD cell %d %d %d could only obtain %d of the %d atoms that are connected via %ss from the neighboring cells. This probably means your %s lengths are too long compared to the domain decomposition cell size. Decrease the number of domain decomposition grid cells%s%s.",
 706                   dd->ci[XX],dd->ci[YY],dd->ci[ZZ],
 707                   nrecv_local,ireq->n,specat_type,
 708                   specat_type,add_err,
 709                   dd->bGridJump ? " or use the -rcon option of mdrun" : "");
 710     }
 711
 712     spac->at_start = at_start;
 713     spac->at_end   = nat_tot_specat;
 714
 715     if (debug)
 716     {
 717         fprintf(debug,"Done setup_specat_communication\n");
 718     }
 719
 720     return nat_tot_specat;
 721 }
 722
 723 static void walk_out(int con,int con_offset,int a,int offset,int nrec,
 724                      int ncon1,const t_iatom *ia1,const t_iatom *ia2,
 725                      const t_blocka *at2con,
 726                      const gmx_ga2la_t ga2la,gmx_bool bHomeConnect,
 727                      gmx_domdec_constraints_t *dc,
 728                      gmx_domdec_specat_comm_t *dcc,
 729                      t_ilist *il_local,
 730                      ind_req_t *ireq)
 731 {
 732     int a1_gl,a2_gl,a_loc,i,coni,b;
 733     const t_iatom *iap;
 734
 735     if (dc->gc_req[con_offset+con] == 0)
 736     {
 737         /* Add this non-home constraint to the list */
 738         if (dc->ncon+1 > dc->con_nalloc)
 739         {
 740             dc->con_nalloc = over_alloc_large(dc->ncon+1);
 741             srenew(dc->con_gl,dc->con_nalloc);
 742             srenew(dc->con_nlocat,dc->con_nalloc);
 743         }
 744         dc->con_gl[dc->ncon] = con_offset + con;
 745         dc->con_nlocat[dc->ncon] = (bHomeConnect ? 1 : 0);
 746         dc->gc_req[con_offset+con] = 1;
 747         if (il_local->nr + 3 > il_local->nalloc)
 748         {
 749             il_local->nalloc = over_alloc_dd(il_local->nr+3);
 750             srenew(il_local->iatoms,il_local->nalloc);
 751         }
 752         iap = constr_iatomptr(ncon1,ia1,ia2,con);
 753         il_local->iatoms[il_local->nr++] = iap[0];
 754         a1_gl = offset + iap[1];
 755         a2_gl = offset + iap[2];
 756         /* The following indexing code can probably be optizimed */
 757         if (ga2la_get_home(ga2la,a1_gl,&a_loc))
 758         {
 759             il_local->iatoms[il_local->nr++] = a_loc;
 760         }
 761         else
 762         {
 763             /* We set this index later */
 764             il_local->iatoms[il_local->nr++] = -a1_gl - 1;
 765         }
 766         if (ga2la_get_home(ga2la,a2_gl,&a_loc))
 767         {
 768             il_local->iatoms[il_local->nr++] = a_loc;
 769         }
 770         else
 771         {
 772             /* We set this index later */
 773             il_local->iatoms[il_local->nr++] = -a2_gl - 1;
 774         }
 775         dc->ncon++;
 776     }
 777     /* Check to not ask for the same atom more than once */
 778     if (gmx_hash_get_minone(dc->ga2la,offset+a) == -1)
 779     {
 780         assert(dcc);
 781         /* Add this non-home atom to the list */
 782         if (ireq->n+1 > ireq->nalloc)
 783         {
 784             ireq->nalloc = over_alloc_large(ireq->n+1);
 785             srenew(ireq->ind,ireq->nalloc);
 786         }
 787         ireq->ind[ireq->n++] = offset + a;
 788         /* Temporarily mark with -2, we get the index later */
 789         gmx_hash_set(dc->ga2la,offset+a,-2);
 790     }
 791
 792     if (nrec > 0)
 793     {
 794         for(i=at2con->index[a]; i<at2con->index[a+1]; i++)
 795         {
 796             coni = at2con->a[i];
 797             if (coni != con)
 798             {
 799                 /* Walk further */
 800                 iap = constr_iatomptr(ncon1,ia1,ia2,coni);
 801                 if (a == iap[1])
 802                 {
 803                     b = iap[2];
 804                 }
 805                 else
 806                 {
 807                     b = iap[1];
 808                 }
 809                 if (!ga2la_get_home(ga2la,offset+b,&a_loc))
 810                 {
 811                     walk_out(coni,con_offset,b,offset,nrec-1,
 812                              ncon1,ia1,ia2,at2con,
 813                              ga2la,FALSE,dc,dcc,il_local,ireq);
 814                 }
 815             }
 816         }
 817     }
 818 }
 819
 820 static void atoms_to_settles(gmx_domdec_t *dd,
 821                              const gmx_mtop_t *mtop,
 822                              const int *cginfo,
 823                              const int **at2settle_mt,
 824                              int cg_start,int cg_end,
 825                              t_ilist *ils_local,
 826                              ind_req_t *ireq)
 827 {
 828     gmx_ga2la_t ga2la;
 829     gmx_mtop_atomlookup_t alook;
 830     int settle;
 831     int nral,sa;
 832     int cg,a,a_gl,a_glsa,a_gls[3],a_locs[3];
 833     int mb,molnr,a_mol,offset;
 834     const gmx_molblock_t *molb;
 835     const t_iatom *ia1;
 836     gmx_bool a_home[3];
 837     int nlocal;
 838     gmx_bool bAssign;
 839
 840     ga2la  = dd->ga2la;
 841
 842     alook = gmx_mtop_atomlookup_settle_init(mtop);
 843
 844     nral = NRAL(F_SETTLE);
 845
 846     for(cg=cg_start; cg<cg_end; cg++)
 847     {
 848         if (GET_CGINFO_SETTLE(cginfo[cg]))
 849         {
 850             for(a=dd->cgindex[cg]; a<dd->cgindex[cg+1]; a++)
 851             {
 852                 a_gl = dd->gatindex[a];
 853
 854                 gmx_mtop_atomnr_to_molblock_ind(alook,a_gl,&mb,&molnr,&a_mol);
 855                 molb = &mtop->molblock[mb];
 856
 857                 settle = at2settle_mt[molb->type][a_mol];
 858
 859                 if (settle >= 0)
 860                 {
 861                     offset = a_gl - a_mol;
 862
 863                     ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
 864
 865                     bAssign = FALSE;
 866                     nlocal = 0;
 867                     for(sa=0; sa<nral; sa++)
 868                     {
 869                         a_glsa = offset + ia1[settle*(1+nral)+1+sa];
 870                         a_gls[sa] = a_glsa;
 871                         a_home[sa] = ga2la_get_home(ga2la,a_glsa,&a_locs[sa]);
 872                         if (a_home[sa])
 873                         {
 874                             if (nlocal == 0 && a_gl == a_glsa)
 875                             {
 876                                 bAssign = TRUE;
 877                             }
 878                             nlocal++;
 879                         }
 880                     }
 881
 882                     if (bAssign)
 883                     {
 884                         if (ils_local->nr+1+nral > ils_local->nalloc)
 885                         {
 886                             ils_local->nalloc = over_alloc_dd(ils_local->nr+1+nral);
 887                             srenew(ils_local->iatoms,ils_local->nalloc);
 888                         }
 889
 890                         ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
 891
 892                         for(sa=0; sa<nral; sa++)
 893                         {
 894                             if (ga2la_get_home(ga2la,a_gls[sa],&a_locs[sa]))
 895                             {
 896                                 ils_local->iatoms[ils_local->nr++] = a_locs[sa];
 897                             }
 898                             else
 899                             {
 900                                 ils_local->iatoms[ils_local->nr++] = -a_gls[sa] - 1;
 901                                 /* Add this non-home atom to the list */
 902                                 if (ireq->n+1 > ireq->nalloc)
 903                                 {
 904                                     ireq->nalloc = over_alloc_large(ireq->n+1);
 905                                     srenew(ireq->ind,ireq->nalloc);
 906                                 }
 907                                 ireq->ind[ireq->n++] = a_gls[sa];
 908                                 /* A check on double atom requests is
 909                                  * not required for settle.
 910                                  */
 911                             }
 912                         }
 913                     }
 914                 }
 915             }
 916         }
 917     }
 918
 919     gmx_mtop_atomlookup_destroy(alook);
 920 }
 921
 922 static void atoms_to_constraints(gmx_domdec_t *dd,
 923                                  const gmx_mtop_t *mtop,
 924                                  const int *cginfo,
 925                                  const t_blocka *at2con_mt,int nrec,
 926                                  t_ilist *ilc_local,
 927                                  ind_req_t *ireq)
 928 {
 929     const t_blocka *at2con;
 930     gmx_ga2la_t ga2la;
 931     gmx_mtop_atomlookup_t alook;
 932     int ncon1;
 933     gmx_molblock_t *molb;
 934     t_iatom *ia1,*ia2,*iap;
 935     int nhome,cg,a,a_gl,a_mol,a_loc,b_lo,offset,mb,molnr,b_mol,i,con,con_offset;
 936     gmx_domdec_constraints_t *dc;
 937     gmx_domdec_specat_comm_t *dcc;
 938
 939     dc  = dd->constraints;
 940     dcc = dd->constraint_comm;
 941
 942     ga2la  = dd->ga2la;
 943
 944     alook = gmx_mtop_atomlookup_init(mtop);
 945
 946     nhome = 0;
 947     for(cg=0; cg<dd->ncg_home; cg++)
 948     {
 949         if (GET_CGINFO_CONSTR(cginfo[cg]))
 950         {
 951             for(a=dd->cgindex[cg]; a<dd->cgindex[cg+1]; a++)
 952             {
 953                 a_gl = dd->gatindex[a];
 954
 955                 gmx_mtop_atomnr_to_molblock_ind(alook,a_gl,&mb,&molnr,&a_mol);
 956                 molb = &mtop->molblock[mb];
 957
 958                 ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
 959
 960                 ia1 = mtop->moltype[molb->type].ilist[F_CONSTR].iatoms;
 961                 ia2 = mtop->moltype[molb->type].ilist[F_CONSTRNC].iatoms;
 962
 963                 /* Calculate the global constraint number offset for the molecule.
 964                  * This is only required for the global index to make sure
 965                  * that we use each constraint only once.
 966                  */
 967                 con_offset =
 968                     dc->molb_con_offset[mb] + molnr*dc->molb_ncon_mol[mb];
 969
 970                 /* The global atom number offset for this molecule */
 971                 offset = a_gl - a_mol;
 972                 at2con = &at2con_mt[molb->type];
 973                 for(i=at2con->index[a_mol]; i<at2con->index[a_mol+1]; i++)
 974                 {
 975                     con = at2con->a[i];
 976                     iap = constr_iatomptr(ncon1,ia1,ia2,con);
 977                     if (a_mol == iap[1])
 978                     {
 979                         b_mol = iap[2];
 980                     }
 981                     else
 982                     {
 983                         b_mol = iap[1];
 984                     }
 985                     if (ga2la_get_home(ga2la,offset+b_mol,&a_loc))
 986                     {
 987                         /* Add this fully home constraint at the first atom */
 988                         if (a_mol < b_mol)
 989                         {
 990                             if (dc->ncon+1 > dc->con_nalloc)
 991                             {
 992                                 dc->con_nalloc = over_alloc_large(dc->ncon+1);
 993                                 srenew(dc->con_gl,dc->con_nalloc);
 994                                 srenew(dc->con_nlocat,dc->con_nalloc);
 995                             }
 996                             dc->con_gl[dc->ncon] = con_offset + con;
 997                             dc->con_nlocat[dc->ncon] = 2;
 998                             if (ilc_local->nr + 3 > ilc_local->nalloc)
 999                             {
1000                                 ilc_local->nalloc = over_alloc_dd(ilc_local->nr + 3);
1001                                 srenew(ilc_local->iatoms,ilc_local->nalloc);
1002                             }
1003                             b_lo = a_loc;
1004                             ilc_local->iatoms[ilc_local->nr++] = iap[0];
1005                             ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? a    : b_lo);
1006                             ilc_local->iatoms[ilc_local->nr++] = (a_gl == iap[1] ? b_lo : a   );
1007                             dc->ncon++;
1008                             nhome++;
1009                         }
1010                     }
1011                     else
1012                     {
1013                         /* We need the nrec constraints coupled to this constraint,
1014                          * so we need to walk out of the home cell by nrec+1 atoms,
1015                          * since already atom bg is not locally present.
1016                          * Therefore we call walk_out with nrec recursions to go
1017                          * after this first call.
1018                          */
1019                         walk_out(con,con_offset,b_mol,offset,nrec,
1020                                  ncon1,ia1,ia2,at2con,
1021                                  dd->ga2la,TRUE,dc,dcc,ilc_local,ireq);
1022                     }
1023                 }
1024             }
1025         }
1026     }
1027
1028     gmx_mtop_atomlookup_destroy(alook);
1029
1030     if (debug)
1031     {
1032         fprintf(debug,
1033                 "Constraints: home %3d border %3d atoms: %3d\n",
1034                 nhome,dc->ncon-nhome,
1035                 dd->constraint_comm ? ireq->n : 0);
1036     }
1037 }
1038
1039 int dd_make_local_constraints(gmx_domdec_t *dd,int at_start,
1040                               const gmx_mtop_t *mtop,
1041                               const int *cginfo,
1042                               gmx_constr_t constr,int nrec,
1043                               t_ilist *il_local)
1044 {
1045     gmx_domdec_constraints_t *dc;
1046     t_ilist *ilc_local,*ils_local;
1047     ind_req_t *ireq;
1048     const t_blocka *at2con_mt;
1049     const int **at2settle_mt;
1050     gmx_hash_t ga2la_specat;
1051     int at_end,i,j;
1052     t_iatom *iap;
1053
1054     dc = dd->constraints;
1055
1056     ilc_local = &il_local[F_CONSTR];
1057     ils_local = &il_local[F_SETTLE];
1058
1059     dc->ncon      = 0;
1060     ilc_local->nr = 0;
1061     if (dd->constraint_comm)
1062     {
1063         at2con_mt = atom2constraints_moltype(constr);
1064         ireq = &dd->constraint_comm->ireq[0];
1065         ireq->n = 0;
1066     }
1067     else
1068     {
1069         at2con_mt = NULL;
1070         ireq = NULL;
1071     }
1072
1073     if (dd->bInterCGsettles)
1074     {
1075         at2settle_mt = atom2settle_moltype(constr);
1076         ils_local->nr = 0;
1077     }
1078     else
1079     {
1080         /* Settle works inside charge groups, we assigned them already */
1081         at2settle_mt = NULL;
1082     }
1083
1084     if (at2settle_mt == NULL)
1085     {
1086         atoms_to_constraints(dd,mtop,cginfo,at2con_mt,nrec,
1087                              ilc_local,ireq);
1088     }
1089     else
1090     {
1091         int t0_set;
1092         int thread;
1093
1094         /* Do the constraints, if present, on the first thread.
1095          * Do the settles on all other threads.
1096          */
1097         t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
1098
1099 #pragma omp parallel for num_threads(dc->nthread) schedule(static)
1100         for(thread=0; thread<dc->nthread; thread++)
1101         {
1102             if (at2con_mt && thread == 0)
1103             {
1104                 atoms_to_constraints(dd,mtop,cginfo,at2con_mt,nrec,
1105                                      ilc_local,ireq);
1106             }
1107
1108             if (thread >= t0_set)
1109             {
1110                 int cg0,cg1;
1111                 t_ilist *ilst;
1112                 ind_req_t *ireqt;
1113
1114                 /* Distribute the settle check+assignments over
1115                  * dc->nthread or dc->nthread-1 threads.
1116                  */
1117                 cg0 = (dd->ncg_home*(thread-t0_set  ))/(dc->nthread-t0_set);
1118                 cg1 = (dd->ncg_home*(thread-t0_set+1))/(dc->nthread-t0_set);
1119
1120                 if (thread == t0_set)
1121                 {
1122                     ilst = ils_local;
1123                 }
1124                 else
1125                 {
1126                     ilst = &dc->ils[thread];
1127                 }
1128                 ilst->nr = 0;
1129
1130                 ireqt = &dd->constraint_comm->ireq[thread];
1131                 if (thread > 0)
1132                 {
1133                     ireqt->n = 0;
1134                 }
1135
1136                 atoms_to_settles(dd,mtop,cginfo,at2settle_mt,
1137                                  cg0,cg1,
1138                                  ilst,ireqt);
1139             }
1140         }
1141
1142         /* Combine the generate settles and requested indices */
1143         for(thread=1; thread<dc->nthread; thread++)
1144         {
1145             t_ilist *ilst;
1146             ind_req_t *ireqt;
1147             int ia;
1148
1149             if (thread > t0_set)
1150             {
1151                 ilst = &dc->ils[thread];
1152                 if (ils_local->nr + ilst->nr > ils_local->nalloc)
1153                 {
1154                     ils_local->nalloc = over_alloc_large(ils_local->nr + ilst->nr);
1155                     srenew(ils_local->iatoms,ils_local->nalloc);
1156                 }
1157                 for(ia=0; ia<ilst->nr; ia++)
1158                 {
1159                     ils_local->iatoms[ils_local->nr+ia] = ilst->iatoms[ia];
1160                 }
1161                 ils_local->nr += ilst->nr;
1162             }
1163
1164             ireqt = &dd->constraint_comm->ireq[thread];
1165             if (ireq->n+ireqt->n > ireq->nalloc)
1166             {
1167                 ireq->nalloc = over_alloc_large(ireq->n+ireqt->n);
1168                 srenew(ireq->ind,ireq->nalloc);
1169             }
1170             for(ia=0; ia<ireqt->n; ia++)
1171             {
1172                 ireq->ind[ireq->n+ia] = ireqt->ind[ia];
1173             }
1174             ireq->n += ireqt->n;
1175         }
1176
1177         if (debug)
1178         {
1179             fprintf(debug,"Settles: total %3d\n",ils_local->nr/4);
1180         }
1181     }
1182
1183     if (dd->constraint_comm) {
1184         int nral1;
1185
1186         at_end =
1187             setup_specat_communication(dd,ireq,dd->constraint_comm,
1188                                        dd->constraints->ga2la,
1189                                        at_start,2,
1190                                        "constraint"," or lincs-order");
1191
1192         /* Fill in the missing indices */
1193         ga2la_specat = dd->constraints->ga2la;
1194
1195         nral1 = 1 + NRAL(F_CONSTR);
1196         for(i=0; i<ilc_local->nr; i+=nral1)
1197         {
1198             iap = ilc_local->iatoms + i;
1199             for(j=1; j<nral1; j++)
1200             {
1201                 if (iap[j] < 0)
1202                 {
1203                     iap[j] = gmx_hash_get_minone(ga2la_specat,-iap[j]-1);
1204                 }
1205             }
1206         }
1207
1208         nral1 = 1 + NRAL(F_SETTLE);
1209         for(i=0; i<ils_local->nr; i+=nral1)
1210         {
1211             iap = ils_local->iatoms + i;
1212             for(j=1; j<nral1; j++)
1213             {
1214                 if (iap[j] < 0)
1215                 {
1216                     iap[j] = gmx_hash_get_minone(ga2la_specat,-iap[j]-1);
1217                 }
1218             }
1219         }
1220     }
1221     else
1222     {
1223         at_end = at_start;
1224     }
1225
1226     return at_end;
1227 }
1228
1229 int dd_make_local_vsites(gmx_domdec_t *dd,int at_start,t_ilist *lil)
1230 {
1231     gmx_domdec_specat_comm_t *spac;
1232     ind_req_t *ireq;
1233     gmx_hash_t ga2la_specat;
1234     int  ftype,nral,i,j,gat,a;
1235     t_ilist *lilf;
1236     t_iatom *iatoms;
1237     int  at_end;
1238
1239     spac         = dd->vsite_comm;
1240     ireq         = &spac->ireq[0];
1241     ga2la_specat = dd->ga2la_vsite;
1242
1243     ireq->n = 0;
1244     /* Loop over all the home vsites */
1245     for(ftype=0; ftype<F_NRE; ftype++)
1246     {
1247         if (interaction_function[ftype].flags & IF_VSITE)
1248         {
1249             nral = NRAL(ftype);
1250             lilf = &lil[ftype];
1251             for(i=0; i<lilf->nr; i+=1+nral)
1252             {
1253                 iatoms = lilf->iatoms + i;
1254                 /* Check if we have the other atoms */
1255                 for(j=1; j<1+nral; j++)
1256                 {
1257                     if (iatoms[j] < 0) {
1258                         /* This is not a home atom,
1259                          * we need to ask our neighbors.
1260                          */
1261                         a = -iatoms[j] - 1;
1262                         /* Check to not ask for the same atom more than once */
1263                         if (gmx_hash_get_minone(dd->ga2la_vsite,a) == -1)
1264                         {
1265                             /* Add this non-home atom to the list */
1266                             if (ireq->n+1 > ireq->nalloc)
1267                             {
1268                                 ireq->nalloc = over_alloc_large(ireq->n+1);
1269                                 srenew(ireq->ind,ireq->nalloc);
1270                             }
1271                             ireq->ind[ireq->n++] = a;
1272                             /* Temporarily mark with -2,
1273                              * we get the index later.
1274                              */
1275                             gmx_hash_set(ga2la_specat,a,-2);
1276                         }
1277                     }
1278                 }
1279             }
1280         }
1281     }
1282
1283     at_end = setup_specat_communication(dd,ireq,dd->vsite_comm,ga2la_specat,
1284                                         at_start,1,"vsite","");
1285
1286     /* Fill in the missing indices */
1287     for(ftype=0; ftype<F_NRE; ftype++)
1288     {
1289         if (interaction_function[ftype].flags & IF_VSITE)
1290         {
1291             nral = NRAL(ftype);
1292             lilf = &lil[ftype];
1293             for(i=0; i<lilf->nr; i+=1+nral)
1294             {
1295                 iatoms = lilf->iatoms + i;
1296                 for(j=1; j<1+nral; j++)
1297                 {
1298                     if (iatoms[j] < 0)
1299                     {
1300                         iatoms[j] = gmx_hash_get_minone(ga2la_specat,-iatoms[j]-1);
1301                     }
1302                 }
1303             }
1304         }
1305     }
1306
1307     return at_end;
1308 }
1309
1310 static gmx_domdec_specat_comm_t *specat_comm_init(int nthread)
1311 {
1312     gmx_domdec_specat_comm_t *spac;
1313
1314     snew(spac,1);
1315     spac->nthread = nthread;
1316     snew(spac->ireq,spac->nthread);
1317
1318     return spac;
1319 }
1320
1321 void init_domdec_constraints(gmx_domdec_t *dd,
1322                              gmx_mtop_t *mtop,
1323                              gmx_constr_t constr)
1324 {
1325     gmx_domdec_constraints_t *dc;
1326     gmx_molblock_t *molb;
1327     int mb,ncon,c,a;
1328
1329     if (debug)
1330     {
1331         fprintf(debug,"Begin init_domdec_constraints\n");
1332     }
1333
1334     snew(dd->constraints,1);
1335     dc = dd->constraints;
1336
1337     snew(dc->molb_con_offset,mtop->nmolblock);
1338     snew(dc->molb_ncon_mol,mtop->nmolblock);
1339
1340     ncon = 0;
1341     for(mb=0; mb<mtop->nmolblock; mb++)
1342     {
1343         molb = &mtop->molblock[mb];
1344         dc->molb_con_offset[mb] = ncon;
1345         dc->molb_ncon_mol[mb] =
1346             mtop->moltype[molb->type].ilist[F_CONSTR].nr/3 +
1347             mtop->moltype[molb->type].ilist[F_CONSTRNC].nr/3;
1348         ncon += molb->nmol*dc->molb_ncon_mol[mb];
1349     }
1350
1351     if (ncon > 0)
1352     {
1353         snew(dc->gc_req,ncon);
1354         for(c=0; c<ncon; c++)
1355         {
1356             dc->gc_req[c] = 0;
1357         }
1358     }
1359
1360     /* Use a hash table for the global to local index.
1361      * The number of keys is a rough estimate, it will be optimized later.
1362      */
1363     dc->ga2la = gmx_hash_init(min(mtop->natoms/20,
1364                                   mtop->natoms/(2*dd->nnodes)));
1365
1366     dc->nthread = gmx_omp_nthreads_get(emntDomdec);
1367     snew(dc->ils,dc->nthread);
1368
1369     dd->constraint_comm = specat_comm_init(dc->nthread);
1370 }
1371
1372 void init_domdec_vsites(gmx_domdec_t *dd,int n_intercg_vsite)
1373 {
1374     int i;
1375     gmx_domdec_constraints_t *dc;
1376
1377     if (debug)
1378     {
1379         fprintf(debug,"Begin init_domdec_vsites\n");
1380     }
1381
1382     /* Use a hash table for the global to local index.
1383      * The number of keys is a rough estimate, it will be optimized later.
1384      */
1385     dd->ga2la_vsite = gmx_hash_init(min(n_intercg_vsite/20,
1386                                         n_intercg_vsite/(2*dd->nnodes)));
1387
1388     dd->vsite_comm = specat_comm_init(1);
1389 }