src/gromacs/mdlib/ns.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 #include "gmxpre.h"
  38
  39 #include "ns.h"
  40
  41 #include <math.h>
  42 #include <stdlib.h>
  43 #include <string.h>
  44
  45 #include <cmath>
  46
  47 #include <algorithm>
  48
  49 #include "gromacs/domdec/domdec.h"
  50 #include "gromacs/domdec/domdec_struct.h"
  51 #include "gromacs/gmxlib/network.h"
  52 #include "gromacs/gmxlib/nrnb.h"
  53 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
  54 #include "gromacs/math/functions.h"
  55 #include "gromacs/math/utilities.h"
  56 #include "gromacs/math/vec.h"
  57 #include "gromacs/math/vecdump.h"
  58 #include "gromacs/mdlib/force.h"
  59 #include "gromacs/mdlib/nsgrid.h"
  60 #include "gromacs/mdlib/qmmm.h"
  61 #include "gromacs/mdtypes/commrec.h"
  62 #include "gromacs/mdtypes/group.h"
  63 #include "gromacs/mdtypes/inputrec.h"
  64 #include "gromacs/mdtypes/md_enums.h"
  65 #include "gromacs/pbcutil/ishift.h"
  66 #include "gromacs/pbcutil/pbc.h"
  67 #include "gromacs/topology/mtop_util.h"
  68 #include "gromacs/utility/fatalerror.h"
  69 #include "gromacs/utility/smalloc.h"
  70
  71 /*
  72  *    E X C L U S I O N   H A N D L I N G
  73  */
  74
  75 #ifdef DEBUG
  76 static void SETEXCL_(t_excl e[], int i, int j)
  77 {
  78     e[j] = e[j] | (1<<i);
  79 }
  80 static void RMEXCL_(t_excl e[], int i, int j)
  81 {
  82     e[j] = e[j] & ~(1<<i);
  83 }
  84 static gmx_bool ISEXCL_(t_excl e[], int i, int j)
  85 {
  86     return (gmx_bool)(e[j] & (1<<i));
  87 }
  88 static gmx_bool NOTEXCL_(t_excl e[], int i, int j)
  89 {
  90     return !(ISEXCL(e, i, j));
  91 }
  92 #else
  93 #define SETEXCL(e, i, j) (e)[((int) (j))] |= (1<<((int) (i)))
  94 #define RMEXCL(e, i, j)  (e)[((int) (j))] &= (~(1<<((int) (i))))
  95 #define ISEXCL(e, i, j)  (gmx_bool) ((e)[((int) (j))] & (1<<((int) (i))))
  96 #define NOTEXCL(e, i, j) !(ISEXCL(e, i, j))
  97 #endif
  98
  99 static int
 100 round_up_to_simd_width(int length, int simd_width)
 101 {
 102     int offset;
 103
 104     offset = (simd_width > 0) ? length % simd_width : 0;
 105
 106     return (offset == 0) ? length : length-offset+simd_width;
 107 }
 108 /************************************************
 109  *
 110  *  U T I L I T I E S    F O R    N S
 111  *
 112  ************************************************/
 113
 114 void reallocate_nblist(t_nblist *nl)
 115 {
 116     if (gmx_debug_at)
 117     {
 118         fprintf(debug, "reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, type=%d), maxnri=%d\n",
 119                 nl->ielec, nl->ivdw, nl->igeometry, nl->type, nl->maxnri);
 120     }
 121     srenew(nl->iinr,   nl->maxnri);
 122     if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
 123     {
 124         srenew(nl->iinr_end, nl->maxnri);
 125     }
 126     srenew(nl->gid,    nl->maxnri);
 127     srenew(nl->shift,  nl->maxnri);
 128     srenew(nl->jindex, nl->maxnri+1);
 129 }
 130
 131
 132 static void init_nblist(FILE *log, t_nblist *nl_sr,
 133                         int maxsr,
 134                         int ivdw, int ivdwmod,
 135                         int ielec, int ielecmod,
 136                         int igeometry, int type,
 137                         gmx_bool bElecAndVdwSwitchDiffers)
 138 {
 139     t_nblist *nl;
 140     int       homenr;
 141
 142     {
 143         nl     = nl_sr;
 144         homenr = maxsr;
 145
 146         if (nl == NULL)
 147         {
 148             return;
 149         }
 150
 151
 152         /* Set coul/vdw in neighborlist, and for the normal loops we determine
 153          * an index of which one to call.
 154          */
 155         nl->ivdw        = ivdw;
 156         nl->ivdwmod     = ivdwmod;
 157         nl->ielec       = ielec;
 158         nl->ielecmod    = ielecmod;
 159         nl->type        = type;
 160         nl->igeometry   = igeometry;
 161
 162         if (nl->type == GMX_NBLIST_INTERACTION_FREE_ENERGY)
 163         {
 164             nl->igeometry  = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
 165         }
 166
 167         /* This will also set the simd_padding_width field */
 168         gmx_nonbonded_set_kernel_pointers(log, nl, bElecAndVdwSwitchDiffers);
 169
 170         /* maxnri is influenced by the number of shifts (maximum is 8)
 171          * and the number of energy groups.
 172          * If it is not enough, nl memory will be reallocated during the run.
 173          * 4 seems to be a reasonable factor, which only causes reallocation
 174          * during runs with tiny and many energygroups.
 175          */
 176         nl->maxnri      = homenr*4;
 177         nl->maxnrj      = 0;
 178         nl->nri         = -1;
 179         nl->nrj         = 0;
 180         nl->iinr        = NULL;
 181         nl->gid         = NULL;
 182         nl->shift       = NULL;
 183         nl->jindex      = NULL;
 184         nl->jjnr        = NULL;
 185         nl->excl_fep    = NULL;
 186         reallocate_nblist(nl);
 187         nl->jindex[0] = 0;
 188
 189         if (debug)
 190         {
 191             fprintf(debug, "Initiating neighbourlist (ielec=%d, ivdw=%d, type=%d) for %s interactions,\nwith %d SR atoms.\n",
 192                     nl->ielec, nl->ivdw, nl->type, gmx_nblist_geometry_names[nl->igeometry], maxsr);
 193         }
 194     }
 195 }
 196
 197 void init_neighbor_list(FILE *log, t_forcerec *fr, int homenr)
 198 {
 199     int        maxsr, maxsr_wat;
 200     int        ielec, ivdw, ielecmod, ivdwmod, type;
 201     int        igeometry_def, igeometry_w, igeometry_ww;
 202     int        i;
 203     gmx_bool   bElecAndVdwSwitchDiffers;
 204     t_nblists *nbl;
 205
 206     /* maxsr     = homenr-fr->nWatMol*3; */
 207     maxsr     = homenr;
 208
 209     if (maxsr < 0)
 210     {
 211         gmx_fatal(FARGS, "%s, %d: Negative number of short range atoms.\n"
 212                   "Call your GROMACS dealer for assistance.", __FILE__, __LINE__);
 213     }
 214     /* This is just for initial allocation, so we do not reallocate
 215      * all the nlist arrays many times in a row.
 216      * The numbers seem very accurate, but they are uncritical.
 217      */
 218     maxsr_wat = std::min(fr->nWatMol, (homenr+2)/3);
 219
 220     /* Determine the values for ielec/ivdw. */
 221     ielec                    = fr->nbkernel_elec_interaction;
 222     ivdw                     = fr->nbkernel_vdw_interaction;
 223     ielecmod                 = fr->nbkernel_elec_modifier;
 224     ivdwmod                  = fr->nbkernel_vdw_modifier;
 225     type                     = GMX_NBLIST_INTERACTION_STANDARD;
 226     bElecAndVdwSwitchDiffers = ( (fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw));
 227
 228     fr->ns->bCGlist = (getenv("GMX_NBLISTCG") != 0);
 229     if (!fr->ns->bCGlist)
 230     {
 231         igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
 232     }
 233     else
 234     {
 235         igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
 236         if (log != NULL)
 237         {
 238             fprintf(log, "\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
 239         }
 240     }
 241
 242     if (fr->solvent_opt == esolTIP4P)
 243     {
 244         igeometry_w  = GMX_NBLIST_GEOMETRY_WATER4_PARTICLE;
 245         igeometry_ww = GMX_NBLIST_GEOMETRY_WATER4_WATER4;
 246     }
 247     else
 248     {
 249         igeometry_w  = GMX_NBLIST_GEOMETRY_WATER3_PARTICLE;
 250         igeometry_ww = GMX_NBLIST_GEOMETRY_WATER3_WATER3;
 251     }
 252
 253     for (i = 0; i < fr->nnblists; i++)
 254     {
 255         nbl = &(fr->nblists[i]);
 256
 257         init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ],
 258                     maxsr, ivdw, ivdwmod, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
 259         init_nblist(log, &nbl->nlist_sr[eNL_VDW],
 260                     maxsr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, igeometry_def, type, bElecAndVdwSwitchDiffers);
 261         init_nblist(log, &nbl->nlist_sr[eNL_QQ],
 262                     maxsr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_def, type, bElecAndVdwSwitchDiffers);
 263         init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATER],
 264                     maxsr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
 265         init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATER],
 266                     maxsr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_w, type, bElecAndVdwSwitchDiffers);
 267         init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_WATERWATER],
 268                     maxsr_wat, ivdw, ivdwmod, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
 269         init_nblist(log, &nbl->nlist_sr[eNL_QQ_WATERWATER],
 270                     maxsr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
 271
 272         /* Did we get the solvent loops so we can use optimized water kernels? */
 273         if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL
 274             || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL
 275             || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL
 276             || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL)
 277         {
 278             fr->solvent_opt = esolNO;
 279             if (log != NULL)
 280             {
 281                 fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
 282             }
 283         }
 284
 285         if (fr->efep != efepNO)
 286         {
 287             init_nblist(log, &nbl->nlist_sr[eNL_VDWQQ_FREE],
 288                         maxsr, ivdw, ivdwmod, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
 289             init_nblist(log, &nbl->nlist_sr[eNL_VDW_FREE],
 290                         maxsr, ivdw, ivdwmod, GMX_NBKERNEL_ELEC_NONE, eintmodNONE, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
 291             init_nblist(log, &nbl->nlist_sr[eNL_QQ_FREE],
 292                         maxsr, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_FREE_ENERGY, bElecAndVdwSwitchDiffers);
 293         }
 294     }
 295     /* QMMM MM list */
 296     if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
 297     {
 298         if (NULL == fr->QMMMlist)
 299         {
 300             snew(fr->QMMMlist, 1);
 301         }
 302         init_nblist(log, fr->QMMMlist,
 303                     maxsr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD, bElecAndVdwSwitchDiffers);
 304     }
 305
 306     if (log != NULL)
 307     {
 308         fprintf(log, "\n");
 309     }
 310
 311     fr->ns->nblist_initialized = TRUE;
 312 }
 313
 314 static void reset_nblist(t_nblist *nl)
 315 {
 316     nl->nri       = -1;
 317     nl->nrj       = 0;
 318     if (nl->jindex)
 319     {
 320         nl->jindex[0] = 0;
 321     }
 322 }
 323
 324 static void reset_neighbor_lists(t_forcerec *fr)
 325 {
 326     int n, i;
 327
 328     if (fr->bQMMM)
 329     {
 330         /* only reset the short-range nblist */
 331         reset_nblist(fr->QMMMlist);
 332     }
 333
 334     for (n = 0; n < fr->nnblists; n++)
 335     {
 336         for (i = 0; i < eNL_NR; i++)
 337         {
 338             reset_nblist( &(fr->nblists[n].nlist_sr[i]) );
 339         }
 340     }
 341 }
 342
 343
 344
 345
 346 static gmx_inline void new_i_nblist(t_nblist *nlist, int i_atom, int shift, int gid)
 347 {
 348     int    nri = nlist->nri;
 349
 350     /* Check whether we have to increase the i counter */
 351     if ((nri == -1) ||
 352         (nlist->iinr[nri]  != i_atom) ||
 353         (nlist->shift[nri] != shift) ||
 354         (nlist->gid[nri]   != gid))
 355     {
 356         /* This is something else. Now see if any entries have
 357          * been added in the list of the previous atom.
 358          */
 359         if ((nri == -1) ||
 360             ((nlist->jindex[nri+1] > nlist->jindex[nri]) &&
 361              (nlist->gid[nri] != -1)))
 362         {
 363             /* If so increase the counter */
 364             nlist->nri++;
 365             nri++;
 366             if (nlist->nri >= nlist->maxnri)
 367             {
 368                 nlist->maxnri += over_alloc_large(nlist->nri);
 369                 reallocate_nblist(nlist);
 370             }
 371         }
 372         /* Set the number of neighbours and the atom number */
 373         nlist->jindex[nri+1] = nlist->jindex[nri];
 374         nlist->iinr[nri]     = i_atom;
 375         nlist->gid[nri]      = gid;
 376         nlist->shift[nri]    = shift;
 377     }
 378     else
 379     {
 380         /* Adding to previous list. First remove possible previous padding */
 381         if (nlist->simd_padding_width > 1)
 382         {
 383             while (nlist->nrj > 0 && nlist->jjnr[nlist->nrj-1] < 0)
 384             {
 385                 nlist->nrj--;
 386             }
 387         }
 388     }
 389 }
 390
 391 static gmx_inline void close_i_nblist(t_nblist *nlist)
 392 {
 393     int nri = nlist->nri;
 394     int len;
 395
 396     if (nri >= 0)
 397     {
 398         /* Add elements up to padding. Since we allocate memory in units
 399          * of the simd_padding width, we do not have to check for possible
 400          * list reallocation here.
 401          */
 402         while ((nlist->nrj % nlist->simd_padding_width) != 0)
 403         {
 404             /* Use -4 here, so we can write forces for 4 atoms before real data */
 405             nlist->jjnr[nlist->nrj++] = -4;
 406         }
 407         nlist->jindex[nri+1] = nlist->nrj;
 408
 409         len = nlist->nrj -  nlist->jindex[nri];
 410         /* If there are no j-particles we have to reduce the
 411          * number of i-particles again, to prevent errors in the
 412          * kernel functions.
 413          */
 414         if ((len == 0) && (nlist->nri > 0))
 415         {
 416             nlist->nri--;
 417         }
 418     }
 419 }
 420
 421 static gmx_inline void close_nblist(t_nblist *nlist)
 422 {
 423     /* Only close this nblist when it has been initialized.
 424      * Avoid the creation of i-lists with no j-particles.
 425      */
 426     if (nlist->nrj == 0)
 427     {
 428         /* Some assembly kernels do not support empty lists,
 429          * make sure here that we don't generate any empty lists.
 430          * With the current ns code this branch is taken in two cases:
 431          * No i-particles at all: nri=-1 here
 432          * There are i-particles, but no j-particles; nri=0 here
 433          */
 434         nlist->nri = 0;
 435     }
 436     else
 437     {
 438         /* Close list number nri by incrementing the count */
 439         nlist->nri++;
 440     }
 441 }
 442
 443 static gmx_inline void close_neighbor_lists(t_forcerec *fr, gmx_bool bMakeQMMMnblist)
 444 {
 445     int n, i;
 446
 447     if (bMakeQMMMnblist)
 448     {
 449         close_nblist(fr->QMMMlist);
 450     }
 451
 452     for (n = 0; n < fr->nnblists; n++)
 453     {
 454         for (i = 0; (i < eNL_NR); i++)
 455         {
 456             close_nblist(&(fr->nblists[n].nlist_sr[i]));
 457         }
 458     }
 459 }
 460
 461
 462 static gmx_inline void add_j_to_nblist(t_nblist *nlist, int j_atom)
 463 {
 464     int nrj = nlist->nrj;
 465
 466     if (nlist->nrj >= nlist->maxnrj)
 467     {
 468         nlist->maxnrj = round_up_to_simd_width(over_alloc_small(nlist->nrj + 1), nlist->simd_padding_width);
 469
 470         if (gmx_debug_at)
 471         {
 472             fprintf(debug, "Increasing SR nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
 473                     nlist->ielec, nlist->ivdw, nlist->type, nlist->igeometry, nlist->maxnrj);
 474         }
 475
 476         srenew(nlist->jjnr, nlist->maxnrj);
 477     }
 478
 479     nlist->jjnr[nrj] = j_atom;
 480     nlist->nrj++;
 481 }
 482
 483 static gmx_inline void add_j_to_nblist_cg(t_nblist *nlist,
 484                                           int j_start, int j_end,
 485                                           t_excl *bexcl, gmx_bool i_is_j)
 486 {
 487     int nrj = nlist->nrj;
 488     int j;
 489
 490     if (nlist->nrj >= nlist->maxnrj)
 491     {
 492         nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
 493         if (gmx_debug_at)
 494         {
 495             fprintf(debug, "Increasing SR nblist (ielec=%d,ivdw=%d,type=%d,igeometry=%d) j size to %d\n",
 496                     nlist->ielec, nlist->ivdw, nlist->type, nlist->igeometry, nlist->maxnrj);
 497         }
 498
 499         srenew(nlist->jjnr, nlist->maxnrj);
 500         srenew(nlist->jjnr_end, nlist->maxnrj);
 501         srenew(nlist->excl, nlist->maxnrj*MAX_CGCGSIZE);
 502     }
 503
 504     nlist->jjnr[nrj]     = j_start;
 505     nlist->jjnr_end[nrj] = j_end;
 506
 507     if (j_end - j_start > MAX_CGCGSIZE)
 508     {
 509         gmx_fatal(FARGS, "The charge-group - charge-group neighborlist do not support charge groups larger than %d, found a charge group of size %d", MAX_CGCGSIZE, j_end-j_start);
 510     }
 511
 512     /* Set the exclusions */
 513     for (j = j_start; j < j_end; j++)
 514     {
 515         nlist->excl[nrj*MAX_CGCGSIZE + j - j_start] = bexcl[j];
 516     }
 517     if (i_is_j)
 518     {
 519         /* Avoid double counting of intra-cg interactions */
 520         for (j = 1; j < j_end-j_start; j++)
 521         {
 522             nlist->excl[nrj*MAX_CGCGSIZE + j] |= (1<<j) - 1;
 523         }
 524     }
 525
 526     nlist->nrj++;
 527 }
 528
 529 typedef void
 530     put_in_list_t (gmx_bool              bHaveVdW[],
 531                    int                   ngid,
 532                    t_mdatoms     *       md,
 533                    int                   icg,
 534                    int                   jgid,
 535                    int                   nj,
 536                    int                   jjcg[],
 537                    int                   index[],
 538                    t_excl                bExcl[],
 539                    int                   shift,
 540                    t_forcerec     *      fr,
 541                    gmx_bool              bDoVdW,
 542                    gmx_bool              bDoCoul,
 543                    int                   solvent_opt);
 544
 545 static void
 546 put_in_list_at(gmx_bool              bHaveVdW[],
 547                int                   ngid,
 548                t_mdatoms     *       md,
 549                int                   icg,
 550                int                   jgid,
 551                int                   nj,
 552                int                   jjcg[],
 553                int                   index[],
 554                t_excl                bExcl[],
 555                int                   shift,
 556                t_forcerec     *      fr,
 557                gmx_bool              bDoVdW,
 558                gmx_bool              bDoCoul,
 559                int                   solvent_opt)
 560 {
 561     /* The a[] index has been removed,
 562      * to put it back in i_atom should be a[i0] and jj should be a[jj].
 563      */
 564     t_nblist  *   vdwc;
 565     t_nblist  *   vdw;
 566     t_nblist  *   coul;
 567     t_nblist  *   vdwc_free  = NULL;
 568     t_nblist  *   vdw_free   = NULL;
 569     t_nblist  *   coul_free  = NULL;
 570     t_nblist  *   vdwc_ww    = NULL;
 571     t_nblist  *   coul_ww    = NULL;
 572
 573     int           i, j, jcg, igid, gid, nbl_ind;
 574     int           jj, jj0, jj1, i_atom;
 575     int           i0, nicg;
 576
 577     int          *cginfo;
 578     int          *type, *typeB;
 579     real         *charge, *chargeB;
 580     real          qi, qiB;
 581     gmx_bool      bFreeEnergy, bFree, bFreeJ, bNotEx, *bPert;
 582     gmx_bool      bDoVdW_i, bDoCoul_i, bDoCoul_i_sol;
 583     int           iwater, jwater;
 584     t_nblist     *nlist;
 585
 586     /* Copy some pointers */
 587     cginfo  = fr->cginfo;
 588     charge  = md->chargeA;
 589     chargeB = md->chargeB;
 590     type    = md->typeA;
 591     typeB   = md->typeB;
 592     bPert   = md->bPerturbed;
 593
 594     /* Get atom range */
 595     i0     = index[icg];
 596     nicg   = index[icg+1]-i0;
 597
 598     /* Get the i charge group info */
 599     igid   = GET_CGINFO_GID(cginfo[icg]);
 600
 601     iwater = (solvent_opt != esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
 602
 603     bFreeEnergy = FALSE;
 604     if (md->nPerturbed)
 605     {
 606         /* Check if any of the particles involved are perturbed.
 607          * If not we can do the cheaper normal put_in_list
 608          * and use more solvent optimization.
 609          */
 610         for (i = 0; i < nicg; i++)
 611         {
 612             bFreeEnergy |= bPert[i0+i];
 613         }
 614         /* Loop over the j charge groups */
 615         for (j = 0; (j < nj && !bFreeEnergy); j++)
 616         {
 617             jcg = jjcg[j];
 618             jj0 = index[jcg];
 619             jj1 = index[jcg+1];
 620             /* Finally loop over the atoms in the j-charge group */
 621             for (jj = jj0; jj < jj1; jj++)
 622             {
 623                 bFreeEnergy |= bPert[jj];
 624             }
 625         }
 626     }
 627
 628     /* Unpack pointers to neighbourlist structs */
 629     if (fr->nnblists == 1)
 630     {
 631         nbl_ind = 0;
 632     }
 633     else
 634     {
 635         nbl_ind = fr->gid2nblists[GID(igid, jgid, ngid)];
 636     }
 637     nlist = fr->nblists[nbl_ind].nlist_sr;
 638
 639     if (iwater != esolNO)
 640     {
 641         vdwc    = &nlist[eNL_VDWQQ_WATER];
 642         vdw     = &nlist[eNL_VDW];
 643         coul    = &nlist[eNL_QQ_WATER];
 644         vdwc_ww = &nlist[eNL_VDWQQ_WATERWATER];
 645         coul_ww = &nlist[eNL_QQ_WATERWATER];
 646     }
 647     else
 648     {
 649         vdwc = &nlist[eNL_VDWQQ];
 650         vdw  = &nlist[eNL_VDW];
 651         coul = &nlist[eNL_QQ];
 652     }
 653
 654     if (!bFreeEnergy)
 655     {
 656         if (iwater != esolNO)
 657         {
 658             /* Loop over the atoms in the i charge group */
 659             i_atom  = i0;
 660             gid     = GID(igid, jgid, ngid);
 661             /* Create new i_atom for each energy group */
 662             if (bDoCoul && bDoVdW)
 663             {
 664                 new_i_nblist(vdwc, i_atom, shift, gid);
 665                 new_i_nblist(vdwc_ww, i_atom, shift, gid);
 666             }
 667             if (bDoVdW)
 668             {
 669                 new_i_nblist(vdw, i_atom, shift, gid);
 670             }
 671             if (bDoCoul)
 672             {
 673                 new_i_nblist(coul, i_atom, shift, gid);
 674                 new_i_nblist(coul_ww, i_atom, shift, gid);
 675             }
 676             /* Loop over the j charge groups */
 677             for (j = 0; (j < nj); j++)
 678             {
 679                 jcg = jjcg[j];
 680
 681                 if (jcg == icg)
 682                 {
 683                     continue;
 684                 }
 685
 686                 jj0    = index[jcg];
 687                 jwater = GET_CGINFO_SOLOPT(cginfo[jcg]);
 688
 689                 if (iwater == esolSPC && jwater == esolSPC)
 690                 {
 691                     /* Interaction between two SPC molecules */
 692                     if (!bDoCoul)
 693                     {
 694                         /* VdW only - only first atoms in each water interact */
 695                         add_j_to_nblist(vdw, jj0);
 696                     }
 697                     else
 698                     {
 699                         /* One entry for the entire water-water interaction */
 700                         if (!bDoVdW)
 701                         {
 702                             add_j_to_nblist(coul_ww, jj0);
 703                         }
 704                         else
 705                         {
 706                             add_j_to_nblist(vdwc_ww, jj0);
 707                         }
 708                     }
 709                 }
 710                 else if (iwater == esolTIP4P && jwater == esolTIP4P)
 711                 {
 712                     /* Interaction between two TIP4p molecules */
 713                     if (!bDoCoul)
 714                     {
 715                         /* VdW only - only first atoms in each water interact */
 716                         add_j_to_nblist(vdw, jj0);
 717                     }
 718                     else
 719                     {
 720                         /* One entry for the entire water-water interaction */
 721                         if (!bDoVdW)
 722                         {
 723                             add_j_to_nblist(coul_ww, jj0);
 724                         }
 725                         else
 726                         {
 727                             add_j_to_nblist(vdwc_ww, jj0);
 728                         }
 729                     }
 730                 }
 731                 else
 732                 {
 733                     /* j charge group is not water, but i is.
 734                      * Add entries to the water-other_atom lists; the geometry of the water
 735                      * molecule doesn't matter - that is taken care of in the nonbonded kernel,
 736                      * so we don't care if it is SPC or TIP4P...
 737                      */
 738
 739                     jj1 = index[jcg+1];
 740
 741                     if (!bDoVdW)
 742                     {
 743                         for (jj = jj0; (jj < jj1); jj++)
 744                         {
 745                             if (charge[jj] != 0)
 746                             {
 747                                 add_j_to_nblist(coul, jj);
 748                             }
 749                         }
 750                     }
 751                     else if (!bDoCoul)
 752                     {
 753                         for (jj = jj0; (jj < jj1); jj++)
 754                         {
 755                             if (bHaveVdW[type[jj]])
 756                             {
 757                                 add_j_to_nblist(vdw, jj);
 758                             }
 759                         }
 760                     }
 761                     else
 762                     {
 763                         /* _charge_ _groups_ interact with both coulomb and LJ */
 764                         /* Check which atoms we should add to the lists!       */
 765                         for (jj = jj0; (jj < jj1); jj++)
 766                         {
 767                             if (bHaveVdW[type[jj]])
 768                             {
 769                                 if (charge[jj] != 0)
 770                                 {
 771                                     add_j_to_nblist(vdwc, jj);
 772                                 }
 773                                 else
 774                                 {
 775                                     add_j_to_nblist(vdw, jj);
 776                                 }
 777                             }
 778                             else if (charge[jj] != 0)
 779                             {
 780                                 add_j_to_nblist(coul, jj);
 781                             }
 782                         }
 783                     }
 784                 }
 785             }
 786             close_i_nblist(vdw);
 787             close_i_nblist(coul);
 788             close_i_nblist(vdwc);
 789             close_i_nblist(coul_ww);
 790             close_i_nblist(vdwc_ww);
 791         }
 792         else
 793         {
 794             /* no solvent as i charge group */
 795             /* Loop over the atoms in the i charge group */
 796             for (i = 0; i < nicg; i++)
 797             {
 798                 i_atom  = i0+i;
 799                 gid     = GID(igid, jgid, ngid);
 800                 qi      = charge[i_atom];
 801
 802                 /* Create new i_atom for each energy group */
 803                 if (bDoVdW && bDoCoul)
 804                 {
 805                     new_i_nblist(vdwc, i_atom, shift, gid);
 806                 }
 807                 if (bDoVdW)
 808                 {
 809                     new_i_nblist(vdw, i_atom, shift, gid);
 810                 }
 811                 if (bDoCoul)
 812                 {
 813                     new_i_nblist(coul, i_atom, shift, gid);
 814                 }
 815                 bDoVdW_i  = (bDoVdW  && bHaveVdW[type[i_atom]]);
 816                 bDoCoul_i = (bDoCoul && qi != 0);
 817
 818                 if (bDoVdW_i || bDoCoul_i)
 819                 {
 820                     /* Loop over the j charge groups */
 821                     for (j = 0; (j < nj); j++)
 822                     {
 823                         jcg = jjcg[j];
 824
 825                         /* Check for large charge groups */
 826                         if (jcg == icg)
 827                         {
 828                             jj0 = i0 + i + 1;
 829                         }
 830                         else
 831                         {
 832                             jj0 = index[jcg];
 833                         }
 834
 835                         jj1 = index[jcg+1];
 836                         /* Finally loop over the atoms in the j-charge group */
 837                         for (jj = jj0; jj < jj1; jj++)
 838                         {
 839                             bNotEx = NOTEXCL(bExcl, i, jj);
 840
 841                             if (bNotEx)
 842                             {
 843                                 if (!bDoVdW_i)
 844                                 {
 845                                     if (charge[jj] != 0)
 846                                     {
 847                                         add_j_to_nblist(coul, jj);
 848                                     }
 849                                 }
 850                                 else if (!bDoCoul_i)
 851                                 {
 852                                     if (bHaveVdW[type[jj]])
 853                                     {
 854                                         add_j_to_nblist(vdw, jj);
 855                                     }
 856                                 }
 857                                 else
 858                                 {
 859                                     if (bHaveVdW[type[jj]])
 860                                     {
 861                                         if (charge[jj] != 0)
 862                                         {
 863                                             add_j_to_nblist(vdwc, jj);
 864                                         }
 865                                         else
 866                                         {
 867                                             add_j_to_nblist(vdw, jj);
 868                                         }
 869                                     }
 870                                     else if (charge[jj] != 0)
 871                                     {
 872                                         add_j_to_nblist(coul, jj);
 873                                     }
 874                                 }
 875                             }
 876                         }
 877                     }
 878                 }
 879                 close_i_nblist(vdw);
 880                 close_i_nblist(coul);
 881                 close_i_nblist(vdwc);
 882             }
 883         }
 884     }
 885     else
 886     {
 887         /* we are doing free energy */
 888         vdwc_free = &nlist[eNL_VDWQQ_FREE];
 889         vdw_free  = &nlist[eNL_VDW_FREE];
 890         coul_free = &nlist[eNL_QQ_FREE];
 891         /* Loop over the atoms in the i charge group */
 892         for (i = 0; i < nicg; i++)
 893         {
 894             i_atom  = i0+i;
 895             gid     = GID(igid, jgid, ngid);
 896             qi      = charge[i_atom];
 897             qiB     = chargeB[i_atom];
 898
 899             /* Create new i_atom for each energy group */
 900             if (bDoVdW && bDoCoul)
 901             {
 902                 new_i_nblist(vdwc, i_atom, shift, gid);
 903             }
 904             if (bDoVdW)
 905             {
 906                 new_i_nblist(vdw, i_atom, shift, gid);
 907             }
 908             if (bDoCoul)
 909             {
 910                 new_i_nblist(coul, i_atom, shift, gid);
 911             }
 912
 913             new_i_nblist(vdw_free, i_atom, shift, gid);
 914             new_i_nblist(coul_free, i_atom, shift, gid);
 915             new_i_nblist(vdwc_free, i_atom, shift, gid);
 916
 917             bDoVdW_i  = (bDoVdW  &&
 918                          (bHaveVdW[type[i_atom]] || bHaveVdW[typeB[i_atom]]));
 919             bDoCoul_i = (bDoCoul && (qi != 0 || qiB != 0));
 920             /* For TIP4P the first atom does not have a charge,
 921              * but the last three do. So we should still put an atom
 922              * without LJ but with charge in the water-atom neighborlist
 923              * for a TIP4p i charge group.
 924              * For SPC type water the first atom has LJ and charge,
 925              * so there is no such problem.
 926              */
 927             if (iwater == esolNO)
 928             {
 929                 bDoCoul_i_sol = bDoCoul_i;
 930             }
 931             else
 932             {
 933                 bDoCoul_i_sol = bDoCoul;
 934             }
 935
 936             if (bDoVdW_i || bDoCoul_i_sol)
 937             {
 938                 /* Loop over the j charge groups */
 939                 for (j = 0; (j < nj); j++)
 940                 {
 941                     jcg = jjcg[j];
 942
 943                     /* Check for large charge groups */
 944                     if (jcg == icg)
 945                     {
 946                         jj0 = i0 + i + 1;
 947                     }
 948                     else
 949                     {
 950                         jj0 = index[jcg];
 951                     }
 952
 953                     jj1 = index[jcg+1];
 954                     /* Finally loop over the atoms in the j-charge group */
 955                     bFree = bPert[i_atom];
 956                     for (jj = jj0; (jj < jj1); jj++)
 957                     {
 958                         bFreeJ = bFree || bPert[jj];
 959                         /* Complicated if, because the water H's should also
 960                          * see perturbed j-particles
 961                          */
 962                         if (iwater == esolNO || i == 0 || bFreeJ)
 963                         {
 964                             bNotEx = NOTEXCL(bExcl, i, jj);
 965
 966                             if (bNotEx)
 967                             {
 968                                 if (bFreeJ)
 969                                 {
 970                                     if (!bDoVdW_i)
 971                                     {
 972                                         if (charge[jj] != 0 || chargeB[jj] != 0)
 973                                         {
 974                                             add_j_to_nblist(coul_free, jj);
 975                                         }
 976                                     }
 977                                     else if (!bDoCoul_i)
 978                                     {
 979                                         if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
 980                                         {
 981                                             add_j_to_nblist(vdw_free, jj);
 982                                         }
 983                                     }
 984                                     else
 985                                     {
 986                                         if (bHaveVdW[type[jj]] || bHaveVdW[typeB[jj]])
 987                                         {
 988                                             if (charge[jj] != 0 || chargeB[jj] != 0)
 989                                             {
 990                                                 add_j_to_nblist(vdwc_free, jj);
 991                                             }
 992                                             else
 993                                             {
 994                                                 add_j_to_nblist(vdw_free, jj);
 995                                             }
 996                                         }
 997                                         else if (charge[jj] != 0 || chargeB[jj] != 0)
 998                                         {
 999                                             add_j_to_nblist(coul_free, jj);
1000                                         }
1001                                     }
1002                                 }
1003                                 else if (!bDoVdW_i)
1004                                 {
1005                                     /* This is done whether or not bWater is set */
1006                                     if (charge[jj] != 0)
1007                                     {
1008                                         add_j_to_nblist(coul, jj);
1009                                     }
1010                                 }
1011                                 else if (!bDoCoul_i_sol)
1012                                 {
1013                                     if (bHaveVdW[type[jj]])
1014                                     {
1015                                         add_j_to_nblist(vdw, jj);
1016                                     }
1017                                 }
1018                                 else
1019                                 {
1020                                     if (bHaveVdW[type[jj]])
1021                                     {
1022                                         if (charge[jj] != 0)
1023                                         {
1024                                             add_j_to_nblist(vdwc, jj);
1025                                         }
1026                                         else
1027                                         {
1028                                             add_j_to_nblist(vdw, jj);
1029                                         }
1030                                     }
1031                                     else if (charge[jj] != 0)
1032                                     {
1033                                         add_j_to_nblist(coul, jj);
1034                                     }
1035                                 }
1036                             }
1037                         }
1038                     }
1039                 }
1040             }
1041             close_i_nblist(vdw);
1042             close_i_nblist(coul);
1043             close_i_nblist(vdwc);
1044             close_i_nblist(vdw_free);
1045             close_i_nblist(coul_free);
1046             close_i_nblist(vdwc_free);
1047         }
1048     }
1049 }
1050
1051 static void
1052 put_in_list_qmmm(gmx_bool gmx_unused              bHaveVdW[],
1053                  int                              ngid,
1054                  t_mdatoms gmx_unused     *       md,
1055                  int                              icg,
1056                  int                              jgid,
1057                  int                              nj,
1058                  int                              jjcg[],
1059                  int                              index[],
1060                  t_excl                           bExcl[],
1061                  int                              shift,
1062                  t_forcerec                *      fr,
1063                  gmx_bool  gmx_unused             bDoVdW,
1064                  gmx_bool  gmx_unused             bDoCoul,
1065                  int       gmx_unused             solvent_opt)
1066 {
1067     t_nblist  *   coul;
1068     int           i, j, jcg, igid, gid;
1069     int           jj, jj0, jj1, i_atom;
1070     int           i0, nicg;
1071     gmx_bool      bNotEx;
1072
1073     /* Get atom range */
1074     i0     = index[icg];
1075     nicg   = index[icg+1]-i0;
1076
1077     /* Get the i charge group info */
1078     igid   = GET_CGINFO_GID(fr->cginfo[icg]);
1079
1080     coul = fr->QMMMlist;
1081
1082     /* Loop over atoms in the ith charge group */
1083     for (i = 0; i < nicg; i++)
1084     {
1085         i_atom = i0+i;
1086         gid    = GID(igid, jgid, ngid);
1087         /* Create new i_atom for each energy group */
1088         new_i_nblist(coul, i_atom, shift, gid);
1089
1090         /* Loop over the j charge groups */
1091         for (j = 0; j < nj; j++)
1092         {
1093             jcg = jjcg[j];
1094
1095             /* Charge groups cannot have QM and MM atoms simultaneously */
1096             if (jcg != icg)
1097             {
1098                 jj0 = index[jcg];
1099                 jj1 = index[jcg+1];
1100                 /* Finally loop over the atoms in the j-charge group */
1101                 for (jj = jj0; jj < jj1; jj++)
1102                 {
1103                     bNotEx = NOTEXCL(bExcl, i, jj);
1104                     if (bNotEx)
1105                     {
1106                         add_j_to_nblist(coul, jj);
1107                     }
1108                 }
1109             }
1110         }
1111         close_i_nblist(coul);
1112     }
1113 }
1114
1115 static void
1116 put_in_list_cg(gmx_bool  gmx_unused             bHaveVdW[],
1117                int                              ngid,
1118                t_mdatoms  gmx_unused    *       md,
1119                int                              icg,
1120                int                              jgid,
1121                int                              nj,
1122                int                              jjcg[],
1123                int                              index[],
1124                t_excl                           bExcl[],
1125                int                              shift,
1126                t_forcerec                *      fr,
1127                gmx_bool   gmx_unused            bDoVdW,
1128                gmx_bool   gmx_unused            bDoCoul,
1129                int        gmx_unused            solvent_opt)
1130 {
1131     int          cginfo;
1132     int          igid, gid, nbl_ind;
1133     t_nblist *   vdwc;
1134     int          j, jcg;
1135
1136     cginfo = fr->cginfo[icg];
1137
1138     igid = GET_CGINFO_GID(cginfo);
1139     gid  = GID(igid, jgid, ngid);
1140
1141     /* Unpack pointers to neighbourlist structs */
1142     if (fr->nnblists == 1)
1143     {
1144         nbl_ind = 0;
1145     }
1146     else
1147     {
1148         nbl_ind = fr->gid2nblists[gid];
1149     }
1150     vdwc = &fr->nblists[nbl_ind].nlist_sr[eNL_VDWQQ];
1151
1152     /* Make a new neighbor list for charge group icg.
1153      * Currently simply one neighbor list is made with LJ and Coulomb.
1154      * If required, zero interactions could be removed here
1155      * or in the force loop.
1156      */
1157     new_i_nblist(vdwc, index[icg], shift, gid);
1158     vdwc->iinr_end[vdwc->nri] = index[icg+1];
1159
1160     for (j = 0; (j < nj); j++)
1161     {
1162         jcg = jjcg[j];
1163         /* Skip the icg-icg pairs if all self interactions are excluded */
1164         if (!(jcg == icg && GET_CGINFO_EXCL_INTRA(cginfo)))
1165         {
1166             /* Here we add the j charge group jcg to the list,
1167              * exclusions are also added to the list.
1168              */
1169             add_j_to_nblist_cg(vdwc, index[jcg], index[jcg+1], bExcl, icg == jcg);
1170         }
1171     }
1172
1173     close_i_nblist(vdwc);
1174 }
1175
1176 static void setexcl(int start, int end, t_blocka *excl, gmx_bool b,
1177                     t_excl bexcl[])
1178 {
1179     int i, k;
1180
1181     if (b)
1182     {
1183         for (i = start; i < end; i++)
1184         {
1185             for (k = excl->index[i]; k < excl->index[i+1]; k++)
1186             {
1187                 SETEXCL(bexcl, i-start, excl->a[k]);
1188             }
1189         }
1190     }
1191     else
1192     {
1193         for (i = start; i < end; i++)
1194         {
1195             for (k = excl->index[i]; k < excl->index[i+1]; k++)
1196             {
1197                 RMEXCL(bexcl, i-start, excl->a[k]);
1198             }
1199         }
1200     }
1201 }
1202
1203 int calc_naaj(int icg, int cgtot)
1204 {
1205     int naaj;
1206
1207     if ((cgtot % 2) == 1)
1208     {
1209         /* Odd number of charge groups, easy */
1210         naaj = 1 + (cgtot/2);
1211     }
1212     else if ((cgtot % 4) == 0)
1213     {
1214         /* Multiple of four is hard */
1215         if (icg < cgtot/2)
1216         {
1217             if ((icg % 2) == 0)
1218             {
1219                 naaj = 1+(cgtot/2);
1220             }
1221             else
1222             {
1223                 naaj = cgtot/2;
1224             }
1225         }
1226         else
1227         {
1228             if ((icg % 2) == 1)
1229             {
1230                 naaj = 1+(cgtot/2);
1231             }
1232             else
1233             {
1234                 naaj = cgtot/2;
1235             }
1236         }
1237     }
1238     else
1239     {
1240         /* cgtot/2 = odd */
1241         if ((icg % 2) == 0)
1242         {
1243             naaj = 1+(cgtot/2);
1244         }
1245         else
1246         {
1247             naaj = cgtot/2;
1248         }
1249     }
1250 #ifdef DEBUG
1251     fprintf(log, "naaj=%d\n", naaj);
1252 #endif
1253
1254     return naaj;
1255 }
1256
1257 /************************************************
1258  *
1259  *  S I M P L E      C O R E     S T U F F
1260  *
1261  ************************************************/
1262
1263 static real calc_image_tric(rvec xi, rvec xj, matrix box,
1264                             rvec b_inv, int *shift)
1265 {
1266     /* This code assumes that the cut-off is smaller than
1267      * a half times the smallest diagonal element of the box.
1268      */
1269     const real h25 = 2.5;
1270     real       dx, dy, dz;
1271     real       r2;
1272     int        tx, ty, tz;
1273
1274     /* Compute diff vector */
1275     dz = xj[ZZ] - xi[ZZ];
1276     dy = xj[YY] - xi[YY];
1277     dx = xj[XX] - xi[XX];
1278
1279     /* Perform NINT operation, using trunc operation, therefore
1280      * we first add 2.5 then subtract 2 again
1281      */
1282     tz  = static_cast<int>(dz*b_inv[ZZ] + h25);
1283     tz -= 2;
1284     dz -= tz*box[ZZ][ZZ];
1285     dy -= tz*box[ZZ][YY];
1286     dx -= tz*box[ZZ][XX];
1287
1288     ty  = static_cast<int>(dy*b_inv[YY] + h25);
1289     ty -= 2;
1290     dy -= ty*box[YY][YY];
1291     dx -= ty*box[YY][XX];
1292
1293     tx  = static_cast<int>(dx*b_inv[XX]+h25);
1294     tx -= 2;
1295     dx -= tx*box[XX][XX];
1296
1297     /* Distance squared */
1298     r2 = (dx*dx) + (dy*dy) + (dz*dz);
1299
1300     *shift = XYZ2IS(tx, ty, tz);
1301
1302     return r2;
1303 }
1304
1305 static real calc_image_rect(rvec xi, rvec xj, rvec box_size,
1306                             rvec b_inv, int *shift)
1307 {
1308     const real h15 = 1.5;
1309     real       ddx, ddy, ddz;
1310     real       dx, dy, dz;
1311     real       r2;
1312     int        tx, ty, tz;
1313
1314     /* Compute diff vector */
1315     dx = xj[XX] - xi[XX];
1316     dy = xj[YY] - xi[YY];
1317     dz = xj[ZZ] - xi[ZZ];
1318
1319     /* Perform NINT operation, using trunc operation, therefore
1320      * we first add 1.5 then subtract 1 again
1321      */
1322     tx = static_cast<int>(dx*b_inv[XX] + h15);
1323     ty = static_cast<int>(dy*b_inv[YY] + h15);
1324     tz = static_cast<int>(dz*b_inv[ZZ] + h15);
1325     tx--;
1326     ty--;
1327     tz--;
1328
1329     /* Correct diff vector for translation */
1330     ddx = tx*box_size[XX] - dx;
1331     ddy = ty*box_size[YY] - dy;
1332     ddz = tz*box_size[ZZ] - dz;
1333
1334     /* Distance squared */
1335     r2 = (ddx*ddx) + (ddy*ddy) + (ddz*ddz);
1336
1337     *shift = XYZ2IS(tx, ty, tz);
1338
1339     return r2;
1340 }
1341
1342 static void add_simple(t_ns_buf * nsbuf, int nrj, int cg_j,
1343                        gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1344                        int icg, int jgid, t_block *cgs, t_excl bexcl[],
1345                        int shift, t_forcerec *fr, put_in_list_t *put_in_list)
1346 {
1347     if (nsbuf->nj + nrj > MAX_CG)
1348     {
1349         put_in_list(bHaveVdW, ngid, md, icg, jgid, nsbuf->ncg, nsbuf->jcg,
1350                     cgs->index, bexcl, shift, fr, TRUE, TRUE, fr->solvent_opt);
1351         /* Reset buffer contents */
1352         nsbuf->ncg = nsbuf->nj = 0;
1353     }
1354     nsbuf->jcg[nsbuf->ncg++] = cg_j;
1355     nsbuf->nj               += nrj;
1356 }
1357
1358 static void ns_inner_tric(rvec x[], int icg, int *i_egp_flags,
1359                           int njcg, int jcg[],
1360                           matrix box, rvec b_inv, real rcut2,
1361                           t_block *cgs, t_ns_buf **ns_buf,
1362                           gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1363                           t_excl bexcl[], t_forcerec *fr,
1364                           put_in_list_t *put_in_list)
1365 {
1366     int       shift;
1367     int       j, nrj, jgid;
1368     int      *cginfo = fr->cginfo;
1369     int       cg_j, *cgindex;
1370
1371     cgindex = cgs->index;
1372     shift   = CENTRAL;
1373     for (j = 0; (j < njcg); j++)
1374     {
1375         cg_j   = jcg[j];
1376         nrj    = cgindex[cg_j+1]-cgindex[cg_j];
1377         if (calc_image_tric(x[icg], x[cg_j], box, b_inv, &shift) < rcut2)
1378         {
1379             jgid  = GET_CGINFO_GID(cginfo[cg_j]);
1380             if (!(i_egp_flags[jgid] & EGP_EXCL))
1381             {
1382                 add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1383                            bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1384                            put_in_list);
1385             }
1386         }
1387     }
1388 }
1389
1390 static void ns_inner_rect(rvec x[], int icg, int *i_egp_flags,
1391                           int njcg, int jcg[],
1392                           gmx_bool bBox, rvec box_size, rvec b_inv, real rcut2,
1393                           t_block *cgs, t_ns_buf **ns_buf,
1394                           gmx_bool bHaveVdW[], int ngid, t_mdatoms *md,
1395                           t_excl bexcl[], t_forcerec *fr,
1396                           put_in_list_t *put_in_list)
1397 {
1398     int       shift;
1399     int       j, nrj, jgid;
1400     int      *cginfo = fr->cginfo;
1401     int       cg_j, *cgindex;
1402
1403     cgindex = cgs->index;
1404     if (bBox)
1405     {
1406         shift = CENTRAL;
1407         for (j = 0; (j < njcg); j++)
1408         {
1409             cg_j   = jcg[j];
1410             nrj    = cgindex[cg_j+1]-cgindex[cg_j];
1411             if (calc_image_rect(x[icg], x[cg_j], box_size, b_inv, &shift) < rcut2)
1412             {
1413                 jgid  = GET_CGINFO_GID(cginfo[cg_j]);
1414                 if (!(i_egp_flags[jgid] & EGP_EXCL))
1415                 {
1416                     add_simple(&ns_buf[jgid][shift], nrj, cg_j,
1417                                bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, shift, fr,
1418                                put_in_list);
1419                 }
1420             }
1421         }
1422     }
1423     else
1424     {
1425         for (j = 0; (j < njcg); j++)
1426         {
1427             cg_j   = jcg[j];
1428             nrj    = cgindex[cg_j+1]-cgindex[cg_j];
1429             if ((rcut2 == 0) || (distance2(x[icg], x[cg_j]) < rcut2))
1430             {
1431                 jgid  = GET_CGINFO_GID(cginfo[cg_j]);
1432                 if (!(i_egp_flags[jgid] & EGP_EXCL))
1433                 {
1434                     add_simple(&ns_buf[jgid][CENTRAL], nrj, cg_j,
1435                                bHaveVdW, ngid, md, icg, jgid, cgs, bexcl, CENTRAL, fr,
1436                                put_in_list);
1437                 }
1438             }
1439         }
1440     }
1441 }
1442
1443 /* ns_simple_core needs to be adapted for QMMM still 2005 */
1444
1445 static int ns_simple_core(t_forcerec *fr,
1446                           gmx_localtop_t *top,
1447                           t_mdatoms *md,
1448                           matrix box, rvec box_size,
1449                           t_excl bexcl[], int *aaj,
1450                           int ngid, t_ns_buf **ns_buf,
1451                           put_in_list_t *put_in_list, gmx_bool bHaveVdW[])
1452 {
1453     int          naaj, k;
1454     real         rlist2;
1455     int          nsearch, icg, igid, nn;
1456     int         *cginfo;
1457     t_ns_buf    *nsbuf;
1458     /* int  *i_atoms; */
1459     t_block     *cgs  = &(top->cgs);
1460     t_blocka    *excl = &(top->excls);
1461     rvec         b_inv;
1462     int          m;
1463     gmx_bool     bBox, bTriclinic;
1464     int         *i_egp_flags;
1465
1466     rlist2 = gmx::square(fr->rlist);
1467
1468     bBox = (fr->ePBC != epbcNONE);
1469     if (bBox)
1470     {
1471         for (m = 0; (m < DIM); m++)
1472         {
1473             if (gmx_numzero(box_size[m]))
1474             {
1475                 gmx_fatal(FARGS, "Dividing by zero box size!");
1476             }
1477             b_inv[m] = 1.0/box_size[m];
1478         }
1479         bTriclinic = TRICLINIC(box);
1480     }
1481     else
1482     {
1483         bTriclinic = FALSE;
1484     }
1485
1486     cginfo = fr->cginfo;
1487
1488     nsearch = 0;
1489     for (icg = fr->cg0; (icg < fr->hcg); icg++)
1490     {
1491         /*
1492            i0        = cgs->index[icg];
1493            nri       = cgs->index[icg+1]-i0;
1494            i_atoms   = &(cgs->a[i0]);
1495            i_eg_excl = fr->eg_excl + ngid*md->cENER[*i_atoms];
1496            setexcl(nri,i_atoms,excl,TRUE,bexcl);
1497          */
1498         igid        = GET_CGINFO_GID(cginfo[icg]);
1499         i_egp_flags = fr->egp_flags + ngid*igid;
1500         setexcl(cgs->index[icg], cgs->index[icg+1], excl, TRUE, bexcl);
1501
1502         naaj = calc_naaj(icg, cgs->nr);
1503         if (bTriclinic)
1504         {
1505             ns_inner_tric(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1506                           box, b_inv, rlist2, cgs, ns_buf,
1507                           bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1508         }
1509         else
1510         {
1511             ns_inner_rect(fr->cg_cm, icg, i_egp_flags, naaj, &(aaj[icg]),
1512                           bBox, box_size, b_inv, rlist2, cgs, ns_buf,
1513                           bHaveVdW, ngid, md, bexcl, fr, put_in_list);
1514         }
1515         nsearch += naaj;
1516
1517         for (nn = 0; (nn < ngid); nn++)
1518         {
1519             for (k = 0; (k < SHIFTS); k++)
1520             {
1521                 nsbuf = &(ns_buf[nn][k]);
1522                 if (nsbuf->ncg > 0)
1523                 {
1524                     put_in_list(bHaveVdW, ngid, md, icg, nn, nsbuf->ncg, nsbuf->jcg,
1525                                 cgs->index, bexcl, k, fr, TRUE, TRUE, fr->solvent_opt);
1526                     nsbuf->ncg = nsbuf->nj = 0;
1527                 }
1528             }
1529         }
1530         /* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
1531         setexcl(cgs->index[icg], cgs->index[icg+1], excl, FALSE, bexcl);
1532     }
1533     close_neighbor_lists(fr, FALSE);
1534
1535     return nsearch;
1536 }
1537
1538 /************************************************
1539  *
1540  *    N S 5     G R I D     S T U F F
1541  *
1542  ************************************************/
1543
1544 static gmx_inline void get_dx_dd(int Nx, real gridx, real rc2, int xgi, real x,
1545                                  int ncpddc, int shift_min, int shift_max,
1546                                  int *g0, int *g1, real *dcx2)
1547 {
1548     real dcx, tmp;
1549     int  g_min, g_max, shift_home;
1550
1551     if (xgi < 0)
1552     {
1553         g_min = 0;
1554         g_max = Nx - 1;
1555         *g0   = 0;
1556         *g1   = -1;
1557     }
1558     else if (xgi >= Nx)
1559     {
1560         g_min = 0;
1561         g_max = Nx - 1;
1562         *g0   = Nx;
1563         *g1   = Nx - 1;
1564     }
1565     else
1566     {
1567         if (ncpddc == 0)
1568         {
1569             g_min = 0;
1570             g_max = Nx - 1;
1571         }
1572         else
1573         {
1574             if (xgi < ncpddc)
1575             {
1576                 shift_home = 0;
1577             }
1578             else
1579             {
1580                 shift_home = -1;
1581             }
1582             g_min = (shift_min == shift_home ? 0          : ncpddc);
1583             g_max = (shift_max == shift_home ? ncpddc - 1 : Nx - 1);
1584         }
1585         if (shift_min > 0)
1586         {
1587             *g0 = g_min;
1588             *g1 = g_min - 1;
1589         }
1590         else if (shift_max < 0)
1591         {
1592             *g0 = g_max + 1;
1593             *g1 = g_max;
1594         }
1595         else
1596         {
1597             *g0       = xgi;
1598             *g1       = xgi;
1599             dcx2[xgi] = 0;
1600         }
1601     }
1602
1603     while (*g0 > g_min)
1604     {
1605         /* Check one grid cell down */
1606         dcx = ((*g0 - 1) + 1)*gridx - x;
1607         tmp = dcx*dcx;
1608         if (tmp >= rc2)
1609         {
1610             break;
1611         }
1612         (*g0)--;
1613         dcx2[*g0] = tmp;
1614     }
1615
1616     while (*g1 < g_max)
1617     {
1618         /* Check one grid cell up */
1619         dcx = (*g1 + 1)*gridx - x;
1620         tmp = dcx*dcx;
1621         if (tmp >= rc2)
1622         {
1623             break;
1624         }
1625         (*g1)++;
1626         dcx2[*g1] = tmp;
1627     }
1628 }
1629
1630
1631 #define calc_dx2(XI, YI, ZI, y) (gmx::square(XI-y[XX]) + gmx::square(YI-y[YY]) + gmx::square(ZI-y[ZZ]))
1632 #define calc_cyl_dx2(XI, YI, y) (gmx::square(XI-y[XX]) + gmx::square(YI-y[YY]))
1633 /****************************************************
1634  *
1635  *    F A S T   N E I G H B O R  S E A R C H I N G
1636  *
1637  *    Optimized neighboursearching routine using grid
1638  *    at least 1x1x1, see GROMACS manual
1639  *
1640  ****************************************************/
1641
1642
1643 static void get_cutoff2(t_forcerec *fr, real *rs2)
1644 {
1645     *rs2 = gmx::square(fr->rlist);
1646 }
1647
1648 static void init_nsgrid_lists(t_forcerec *fr, int ngid, gmx_ns_t *ns)
1649 {
1650     real rs2;
1651     int  j;
1652
1653     get_cutoff2(fr, &rs2);
1654
1655     /* Short range buffers */
1656     snew(ns->nl_sr, ngid);
1657     /* Counters */
1658     snew(ns->nsr, ngid);
1659
1660     for (j = 0; (j < ngid); j++)
1661     {
1662         snew(ns->nl_sr[j], MAX_CG);
1663     }
1664     if (debug)
1665     {
1666         fprintf(debug,
1667                 "ns5_core: rs2 = %g (nm^2)\n",
1668                 rs2);
1669     }
1670 }
1671
1672 static int nsgrid_core(t_commrec *cr, t_forcerec *fr,
1673                        matrix box, int ngid,
1674                        gmx_localtop_t *top,
1675                        t_grid *grid,
1676                        t_excl bexcl[], gmx_bool *bExcludeAlleg,
1677                        t_mdatoms *md,
1678                        put_in_list_t *put_in_list,
1679                        gmx_bool bHaveVdW[],
1680                        gmx_bool bMakeQMMMnblist)
1681 {
1682     gmx_ns_t     *ns;
1683     int         **nl_sr;
1684     int          *nsr;
1685     gmx_domdec_t *dd;
1686     t_block      *cgs    = &(top->cgs);
1687     int          *cginfo = fr->cginfo;
1688     /* int *i_atoms,*cgsindex=cgs->index; */
1689     ivec          sh0, sh1, shp;
1690     int           cell_x, cell_y, cell_z;
1691     int           d, tx, ty, tz, dx, dy, dz, cj;
1692 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
1693     int           zsh_ty, zsh_tx, ysh_tx;
1694 #endif
1695     int           dx0, dx1, dy0, dy1, dz0, dz1;
1696     int           Nx, Ny, Nz, shift = -1, j, nrj, nns, nn = -1;
1697     real          gridx, gridy, gridz, grid_x, grid_y;
1698     real         *dcx2, *dcy2, *dcz2;
1699     int           zgi, ygi, xgi;
1700     int           cg0, cg1, icg = -1, cgsnr, i0, igid, naaj, max_jcg;
1701     int           jcg0, jcg1, jjcg, cgj0, jgid;
1702     int          *grida, *gridnra, *gridind;
1703     rvec         *cgcm, grid_offset;
1704     real          r2, rs2, XI, YI, ZI, tmp1, tmp2;
1705     int          *i_egp_flags;
1706     gmx_bool      bDomDec, bTriclinicX, bTriclinicY;
1707     ivec          ncpddc;
1708
1709     ns = fr->ns;
1710
1711     bDomDec = DOMAINDECOMP(cr);
1712     dd      = cr->dd;
1713
1714     bTriclinicX = ((YY < grid->npbcdim &&
1715                     (!bDomDec || dd->nc[YY] == 1) && box[YY][XX] != 0) ||
1716                    (ZZ < grid->npbcdim &&
1717                     (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][XX] != 0));
1718     bTriclinicY =  (ZZ < grid->npbcdim &&
1719                     (!bDomDec || dd->nc[ZZ] == 1) && box[ZZ][YY] != 0);
1720
1721     cgsnr    = cgs->nr;
1722
1723     get_cutoff2(fr, &rs2);
1724
1725     nl_sr     = ns->nl_sr;
1726     nsr       = ns->nsr;
1727
1728     /* Unpack arrays */
1729     cgcm    = fr->cg_cm;
1730     Nx      = grid->n[XX];
1731     Ny      = grid->n[YY];
1732     Nz      = grid->n[ZZ];
1733     grida   = grid->a;
1734     gridind = grid->index;
1735     gridnra = grid->nra;
1736     nns     = 0;
1737
1738     gridx      = grid->cell_size[XX];
1739     gridy      = grid->cell_size[YY];
1740     gridz      = grid->cell_size[ZZ];
1741     grid_x     = 1/gridx;
1742     grid_y     = 1/gridy;
1743     copy_rvec(grid->cell_offset, grid_offset);
1744     copy_ivec(grid->ncpddc, ncpddc);
1745     dcx2       = grid->dcx2;
1746     dcy2       = grid->dcy2;
1747     dcz2       = grid->dcz2;
1748
1749 #ifdef ALLOW_OFFDIAG_LT_HALFDIAG
1750     zsh_ty = floor(-box[ZZ][YY]/box[YY][YY]+0.5);
1751     zsh_tx = floor(-box[ZZ][XX]/box[XX][XX]+0.5);
1752     ysh_tx = floor(-box[YY][XX]/box[XX][XX]+0.5);
1753     if (zsh_tx != 0 && ysh_tx != 0)
1754     {
1755         /* This could happen due to rounding, when both ratios are 0.5 */
1756         ysh_tx = 0;
1757     }
1758 #endif
1759
1760     if (fr->n_tpi)
1761     {
1762         /* We only want a list for the test particle */
1763         cg0 = cgsnr - 1;
1764     }
1765     else
1766     {
1767         cg0 = grid->icg0;
1768     }
1769     cg1 = grid->icg1;
1770
1771     /* Set the shift range */
1772     for (d = 0; d < DIM; d++)
1773     {
1774         sh0[d] = -1;
1775         sh1[d] = 1;
1776         /* Check if we need periodicity shifts.
1777          * Without PBC or with domain decomposition we don't need them.
1778          */
1779         if (d >= ePBC2npbcdim(fr->ePBC) || (bDomDec && dd->nc[d] > 1))
1780         {
1781             shp[d] = 0;
1782         }
1783         else
1784         {
1785             if (d == XX &&
1786                 box[XX][XX] - std::abs(box[YY][XX]) - std::abs(box[ZZ][XX]) < std::sqrt(rs2))
1787             {
1788                 shp[d] = 2;
1789             }
1790             else
1791             {
1792                 shp[d] = 1;
1793             }
1794         }
1795     }
1796
1797     /* Loop over charge groups */
1798     for (icg = cg0; (icg < cg1); icg++)
1799     {
1800         igid = GET_CGINFO_GID(cginfo[icg]);
1801         /* Skip this charge group if all energy groups are excluded! */
1802         if (bExcludeAlleg[igid])
1803         {
1804             continue;
1805         }
1806
1807         i0   = cgs->index[icg];
1808
1809         if (bMakeQMMMnblist)
1810         {
1811             /* Skip this charge group if it is not a QM atom while making a
1812              * QM/MM neighbourlist
1813              */
1814             if (md->bQM[i0] == FALSE)
1815             {
1816                 continue; /* MM particle, go to next particle */
1817             }
1818
1819             /* Compute the number of charge groups that fall within the control
1820              * of this one (icg)
1821              */
1822             naaj    = calc_naaj(icg, cgsnr);
1823             jcg0    = icg;
1824             jcg1    = icg + naaj;
1825             max_jcg = cgsnr;
1826         }
1827         else
1828         {
1829             /* make a normal neighbourlist */
1830
1831             if (bDomDec)
1832             {
1833                 /* Get the j charge-group and dd cell shift ranges */
1834                 dd_get_ns_ranges(cr->dd, icg, &jcg0, &jcg1, sh0, sh1);
1835                 max_jcg = 0;
1836             }
1837             else
1838             {
1839                 /* Compute the number of charge groups that fall within the control
1840                  * of this one (icg)
1841                  */
1842                 naaj = calc_naaj(icg, cgsnr);
1843                 jcg0 = icg;
1844                 jcg1 = icg + naaj;
1845
1846                 if (fr->n_tpi)
1847                 {
1848                     /* The i-particle is awlways the test particle,
1849                      * so we want all j-particles
1850                      */
1851                     max_jcg = cgsnr - 1;
1852                 }
1853                 else
1854                 {
1855                     max_jcg  = jcg1 - cgsnr;
1856                 }
1857             }
1858         }
1859
1860         i_egp_flags = fr->egp_flags + igid*ngid;
1861
1862         /* Set the exclusions for the atoms in charge group icg using a bitmask */
1863         setexcl(i0, cgs->index[icg+1], &top->excls, TRUE, bexcl);
1864
1865         ci2xyz(grid, icg, &cell_x, &cell_y, &cell_z);
1866
1867         /* Changed iicg to icg, DvdS 990115
1868          * (but see consistency check above, DvdS 990330)
1869          */
1870 #ifdef NS5DB
1871         fprintf(log, "icg=%5d, naaj=%5d, cell %d %d %d\n",
1872                 icg, naaj, cell_x, cell_y, cell_z);
1873 #endif
1874         /* Loop over shift vectors in three dimensions */
1875         for (tz = -shp[ZZ]; tz <= shp[ZZ]; tz++)
1876         {
1877             ZI = cgcm[icg][ZZ]+tz*box[ZZ][ZZ];
1878             /* Calculate range of cells in Z direction that have the shift tz */
1879             zgi = cell_z + tz*Nz;
1880             get_dx_dd(Nz, gridz, rs2, zgi, ZI-grid_offset[ZZ],
1881                       ncpddc[ZZ], sh0[ZZ], sh1[ZZ], &dz0, &dz1, dcz2);
1882             if (dz0 > dz1)
1883             {
1884                 continue;
1885             }
1886             for (ty = -shp[YY]; ty <= shp[YY]; ty++)
1887             {
1888                 YI = cgcm[icg][YY]+ty*box[YY][YY]+tz*box[ZZ][YY];
1889                 /* Calculate range of cells in Y direction that have the shift ty */
1890                 if (bTriclinicY)
1891                 {
1892                     ygi = (int)(Ny + (YI - grid_offset[YY])*grid_y) - Ny;
1893                 }
1894                 else
1895                 {
1896                     ygi = cell_y + ty*Ny;
1897                 }
1898                 get_dx_dd(Ny, gridy, rs2, ygi, YI-grid_offset[YY],
1899                           ncpddc[YY], sh0[YY], sh1[YY], &dy0, &dy1, dcy2);
1900                 if (dy0 > dy1)
1901                 {
1902                     continue;
1903                 }
1904                 for (tx = -shp[XX]; tx <= shp[XX]; tx++)
1905                 {
1906                     XI = cgcm[icg][XX]+tx*box[XX][XX]+ty*box[YY][XX]+tz*box[ZZ][XX];
1907                     /* Calculate range of cells in X direction that have the shift tx */
1908                     if (bTriclinicX)
1909                     {
1910                         xgi = (int)(Nx + (XI - grid_offset[XX])*grid_x) - Nx;
1911                     }
1912                     else
1913                     {
1914                         xgi = cell_x + tx*Nx;
1915                     }
1916                     get_dx_dd(Nx, gridx, rs2, xgi, XI-grid_offset[XX],
1917                               ncpddc[XX], sh0[XX], sh1[XX], &dx0, &dx1, dcx2);
1918                     if (dx0 > dx1)
1919                     {
1920                         continue;
1921                     }
1922                     /* Get shift vector */
1923                     shift = XYZ2IS(tx, ty, tz);
1924 #ifdef NS5DB
1925                     range_check(shift, 0, SHIFTS);
1926 #endif
1927                     for (nn = 0; (nn < ngid); nn++)
1928                     {
1929                         nsr[nn]      = 0;
1930                     }
1931 #ifdef NS5DB
1932                     fprintf(log, "shift: %2d, dx0,1: %2d,%2d, dy0,1: %2d,%2d, dz0,1: %2d,%2d\n",
1933                             shift, dx0, dx1, dy0, dy1, dz0, dz1);
1934                     fprintf(log, "cgcm: %8.3f  %8.3f  %8.3f\n", cgcm[icg][XX],
1935                             cgcm[icg][YY], cgcm[icg][ZZ]);
1936                     fprintf(log, "xi:   %8.3f  %8.3f  %8.3f\n", XI, YI, ZI);
1937 #endif
1938                     for (dx = dx0; (dx <= dx1); dx++)
1939                     {
1940                         tmp1 = rs2 - dcx2[dx];
1941                         for (dy = dy0; (dy <= dy1); dy++)
1942                         {
1943                             tmp2 = tmp1 - dcy2[dy];
1944                             if (tmp2 > 0)
1945                             {
1946                                 for (dz = dz0; (dz <= dz1); dz++)
1947                                 {
1948                                     if (tmp2 > dcz2[dz])
1949                                     {
1950                                         /* Find grid-cell cj in which possible neighbours are */
1951                                         cj   = xyz2ci(Ny, Nz, dx, dy, dz);
1952
1953                                         /* Check out how many cgs (nrj) there in this cell */
1954                                         nrj  = gridnra[cj];
1955
1956                                         /* Find the offset in the cg list */
1957                                         cgj0 = gridind[cj];
1958
1959                                         /* Check if all j's are out of range so we
1960                                          * can skip the whole cell.
1961                                          * Should save some time, especially with DD.
1962                                          */
1963                                         if (nrj == 0 ||
1964                                             (grida[cgj0] >= max_jcg &&
1965                                              (grida[cgj0] >= jcg1 || grida[cgj0+nrj-1] < jcg0)))
1966                                         {
1967                                             continue;
1968                                         }
1969
1970                                         /* Loop over cgs */
1971                                         for (j = 0; (j < nrj); j++)
1972                                         {
1973                                             jjcg = grida[cgj0+j];
1974
1975                                             /* check whether this guy is in range! */
1976                                             if ((jjcg >= jcg0 && jjcg < jcg1) ||
1977                                                 (jjcg < max_jcg))
1978                                             {
1979                                                 r2 = calc_dx2(XI, YI, ZI, cgcm[jjcg]);
1980                                                 if (r2 < rs2)
1981                                                 {
1982                                                     /* jgid = gid[cgsatoms[cgsindex[jjcg]]]; */
1983                                                     jgid = GET_CGINFO_GID(cginfo[jjcg]);
1984                                                     /* check energy group exclusions */
1985                                                     if (!(i_egp_flags[jgid] & EGP_EXCL))
1986                                                     {
1987                                                         if (nsr[jgid] >= MAX_CG)
1988                                                         {
1989                                                             /* Add to short-range list */
1990                                                             put_in_list(bHaveVdW, ngid, md, icg, jgid,
1991                                                                         nsr[jgid], nl_sr[jgid],
1992                                                                         cgs->index, /* cgsatoms, */ bexcl,
1993                                                                         shift, fr, TRUE, TRUE, fr->solvent_opt);
1994                                                             nsr[jgid] = 0;
1995                                                         }
1996                                                         nl_sr[jgid][nsr[jgid]++] = jjcg;
1997                                                     }
1998                                                 }
1999                                                 nns++;
2000                                             }
2001                                         }
2002                                     }
2003                                 }
2004                             }
2005                         }
2006                     }
2007                     /* CHECK whether there is anything left in the buffers */
2008                     for (nn = 0; (nn < ngid); nn++)
2009                     {
2010                         if (nsr[nn] > 0)
2011                         {
2012                             put_in_list(bHaveVdW, ngid, md, icg, nn, nsr[nn], nl_sr[nn],
2013                                         cgs->index, /* cgsatoms, */ bexcl,
2014                                         shift, fr, TRUE, TRUE, fr->solvent_opt);
2015                         }
2016                     }
2017                 }
2018             }
2019         }
2020         setexcl(cgs->index[icg], cgs->index[icg+1], &top->excls, FALSE, bexcl);
2021     }
2022     /* No need to perform any left-over force calculations anymore (as we used to do here)
2023      * since we now save the proper long-range lists for later evaluation.
2024      */
2025
2026     /* Close neighbourlists */
2027     close_neighbor_lists(fr, bMakeQMMMnblist);
2028
2029     return nns;
2030 }
2031
2032 void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
2033 {
2034     int i;
2035
2036     if (natoms > ns->nra_alloc)
2037     {
2038         ns->nra_alloc = over_alloc_dd(natoms);
2039         srenew(ns->bexcl, ns->nra_alloc);
2040         for (i = 0; i < ns->nra_alloc; i++)
2041         {
2042             ns->bexcl[i] = 0;
2043         }
2044     }
2045 }
2046
2047 void init_ns(FILE *fplog, const t_commrec *cr,
2048              gmx_ns_t *ns, t_forcerec *fr,
2049              const gmx_mtop_t *mtop)
2050 {
2051     int      mt, icg, nr_in_cg, maxcg, i, j, jcg, ngid, ncg;
2052     t_block *cgs;
2053
2054     /* Compute largest charge groups size (# atoms) */
2055     nr_in_cg = 1;
2056     for (mt = 0; mt < mtop->nmoltype; mt++)
2057     {
2058         cgs = &mtop->moltype[mt].cgs;
2059         for (icg = 0; (icg < cgs->nr); icg++)
2060         {
2061             nr_in_cg = std::max(nr_in_cg, (int)(cgs->index[icg+1]-cgs->index[icg]));
2062         }
2063     }
2064
2065     /* Verify whether largest charge group is <= max cg.
2066      * This is determined by the type of the local exclusion type
2067      * Exclusions are stored in bits. (If the type is not large
2068      * enough, enlarge it, unsigned char -> unsigned short -> unsigned long)
2069      */
2070     maxcg = sizeof(t_excl)*8;
2071     if (nr_in_cg > maxcg)
2072     {
2073         gmx_fatal(FARGS, "Max #atoms in a charge group: %d > %d\n",
2074                   nr_in_cg, maxcg);
2075     }
2076
2077     ngid = mtop->groups.grps[egcENER].nr;
2078     snew(ns->bExcludeAlleg, ngid);
2079     for (i = 0; i < ngid; i++)
2080     {
2081         ns->bExcludeAlleg[i] = TRUE;
2082         for (j = 0; j < ngid; j++)
2083         {
2084             if (!(fr->egp_flags[i*ngid+j] & EGP_EXCL))
2085             {
2086                 ns->bExcludeAlleg[i] = FALSE;
2087             }
2088         }
2089     }
2090
2091     if (fr->bGrid)
2092     {
2093         /* Grid search */
2094         ns->grid = init_grid(fplog, fr);
2095         init_nsgrid_lists(fr, ngid, ns);
2096     }
2097     else
2098     {
2099         /* Simple search */
2100         snew(ns->ns_buf, ngid);
2101         for (i = 0; (i < ngid); i++)
2102         {
2103             snew(ns->ns_buf[i], SHIFTS);
2104         }
2105         ncg = ncg_mtop(mtop);
2106         snew(ns->simple_aaj, 2*ncg);
2107         for (jcg = 0; (jcg < ncg); jcg++)
2108         {
2109             ns->simple_aaj[jcg]     = jcg;
2110             ns->simple_aaj[jcg+ncg] = jcg;
2111         }
2112     }
2113
2114     /* Create array that determines whether or not atoms have VdW */
2115     snew(ns->bHaveVdW, fr->ntype);
2116     for (i = 0; (i < fr->ntype); i++)
2117     {
2118         for (j = 0; (j < fr->ntype); j++)
2119         {
2120             ns->bHaveVdW[i] = (ns->bHaveVdW[i] ||
2121                                (fr->bBHAM ?
2122                                 ((BHAMA(fr->nbfp, fr->ntype, i, j) != 0) ||
2123                                  (BHAMB(fr->nbfp, fr->ntype, i, j) != 0) ||
2124                                  (BHAMC(fr->nbfp, fr->ntype, i, j) != 0)) :
2125                                 ((C6(fr->nbfp, fr->ntype, i, j) != 0) ||
2126                                  (C12(fr->nbfp, fr->ntype, i, j) != 0))));
2127         }
2128     }
2129     if (debug)
2130     {
2131         pr_bvec(debug, 0, "bHaveVdW", ns->bHaveVdW, fr->ntype, TRUE);
2132     }
2133
2134     ns->nra_alloc = 0;
2135     ns->bexcl     = NULL;
2136     if (!DOMAINDECOMP(cr))
2137     {
2138         ns_realloc_natoms(ns, mtop->natoms);
2139     }
2140
2141     ns->nblist_initialized = FALSE;
2142
2143     /* nbr list debug dump */
2144     {
2145         char *ptr = getenv("GMX_DUMP_NL");
2146         if (ptr)
2147         {
2148             ns->dump_nl = strtol(ptr, NULL, 10);
2149             if (fplog)
2150             {
2151                 fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
2152             }
2153         }
2154         else
2155         {
2156             ns->dump_nl = 0;
2157         }
2158     }
2159 }
2160
2161
2162 int search_neighbours(FILE *log, t_forcerec *fr,
2163                       matrix box,
2164                       gmx_localtop_t *top,
2165                       gmx_groups_t *groups,
2166                       t_commrec *cr,
2167                       t_nrnb *nrnb, t_mdatoms *md,
2168                       gmx_bool bFillGrid)
2169 {
2170     t_block            *cgs = &(top->cgs);
2171     rvec                box_size, grid_x0, grid_x1;
2172     int                 m, ngid;
2173     real                min_size, grid_dens;
2174     int                 nsearch;
2175     gmx_bool            bGrid;
2176     int                 start, end;
2177     gmx_ns_t           *ns;
2178     t_grid             *grid;
2179     gmx_domdec_zones_t *dd_zones;
2180     put_in_list_t      *put_in_list;
2181
2182     ns = fr->ns;
2183
2184     /* Set some local variables */
2185     bGrid = fr->bGrid;
2186     ngid  = groups->grps[egcENER].nr;
2187
2188     for (m = 0; (m < DIM); m++)
2189     {
2190         box_size[m] = box[m][m];
2191     }
2192
2193     if (fr->ePBC != epbcNONE)
2194     {
2195         if (gmx::square(fr->rlist) >= max_cutoff2(fr->ePBC, box))
2196         {
2197             gmx_fatal(FARGS, "One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.");
2198         }
2199         if (!bGrid)
2200         {
2201             min_size = std::min(box_size[XX], std::min(box_size[YY], box_size[ZZ]));
2202             if (2*fr->rlist >= min_size)
2203             {
2204                 gmx_fatal(FARGS, "One of the box diagonal elements has become smaller than twice the cut-off length.");
2205             }
2206         }
2207     }
2208
2209     if (DOMAINDECOMP(cr))
2210     {
2211         ns_realloc_natoms(ns, cgs->index[cgs->nr]);
2212     }
2213
2214     /* Reset the neighbourlists */
2215     reset_neighbor_lists(fr);
2216
2217     if (bGrid && bFillGrid)
2218     {
2219
2220         grid = ns->grid;
2221         if (DOMAINDECOMP(cr))
2222         {
2223             dd_zones = domdec_zones(cr->dd);
2224         }
2225         else
2226         {
2227             dd_zones = NULL;
2228
2229             get_nsgrid_boundaries(grid->nboundeddim, box, NULL, NULL, NULL, NULL,
2230                                   cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
2231
2232             grid_first(log, grid, NULL, NULL, box, grid_x0, grid_x1,
2233                        fr->rlist, grid_dens);
2234         }
2235
2236         start = 0;
2237         end   = cgs->nr;
2238
2239         if (DOMAINDECOMP(cr))
2240         {
2241             end = cgs->nr;
2242             fill_grid(dd_zones, grid, end, -1, end, fr->cg_cm);
2243             grid->icg0 = 0;
2244             grid->icg1 = dd_zones->izone[dd_zones->nizone-1].cg1;
2245         }
2246         else
2247         {
2248             fill_grid(NULL, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
2249             grid->icg0 = fr->cg0;
2250             grid->icg1 = fr->hcg;
2251         }
2252
2253         calc_elemnr(grid, start, end, cgs->nr);
2254         calc_ptrs(grid);
2255         grid_last(grid, start, end, cgs->nr);
2256
2257         if (gmx_debug_at)
2258         {
2259             check_grid(grid);
2260             print_grid(debug, grid);
2261         }
2262     }
2263     else if (fr->n_tpi)
2264     {
2265         /* Set the grid cell index for the test particle only.
2266          * The cell to cg index is not corrected, but that does not matter.
2267          */
2268         fill_grid(NULL, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
2269     }
2270
2271     if (!fr->ns->bCGlist)
2272     {
2273         put_in_list = put_in_list_at;
2274     }
2275     else
2276     {
2277         put_in_list = put_in_list_cg;
2278     }
2279
2280     /* Do the core! */
2281     if (bGrid)
2282     {
2283         grid    = ns->grid;
2284         nsearch = nsgrid_core(cr, fr, box, ngid, top,
2285                               grid, ns->bexcl, ns->bExcludeAlleg,
2286                               md, put_in_list, ns->bHaveVdW,
2287                               FALSE);
2288
2289         /* neighbour searching withouth QMMM! QM atoms have zero charge in
2290          * the classical calculation. The charge-charge interaction
2291          * between QM and MM atoms is handled in the QMMM core calculation
2292          * (see QMMM.c). The VDW however, we'd like to compute classically
2293          * and the QM MM atom pairs have just been put in the
2294          * corresponding neighbourlists. in case of QMMM we still need to
2295          * fill a special QMMM neighbourlist that contains all neighbours
2296          * of the QM atoms. If bQMMM is true, this list will now be made:
2297          */
2298         if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
2299         {
2300             nsearch += nsgrid_core(cr, fr, box, ngid, top,
2301                                    grid, ns->bexcl, ns->bExcludeAlleg,
2302                                    md, put_in_list_qmmm, ns->bHaveVdW,
2303                                    TRUE);
2304         }
2305     }
2306     else
2307     {
2308         nsearch = ns_simple_core(fr, top, md, box, box_size,
2309                                  ns->bexcl, ns->simple_aaj,
2310                                  ngid, ns->ns_buf, put_in_list, ns->bHaveVdW);
2311     }
2312
2313     inc_nrnb(nrnb, eNR_NS, nsearch);
2314
2315     return nsearch;
2316 }