src/gromacs/gmxpreprocess/gpp_nextnb.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "gpp_nextnb.h"
  41
  42 #include <cstdlib>
  43
  44 #include "gromacs/gmxpreprocess/grompp_impl.h"
  45 #include "gromacs/gmxpreprocess/toputil.h"
  46 #include "gromacs/topology/ifunc.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/utility/gmxassert.h"
  49 #include "gromacs/utility/smalloc.h"
  50
  51 /* #define DEBUG_NNB */
  52
  53 typedef struct {
  54     int ai, aj;
  55 } sortable;
  56
  57 static int
  58 bond_sort (const void *a, const void *b)
  59 {
  60     const sortable *sa, *sb;
  61
  62     sa = reinterpret_cast<const sortable*>(a);
  63     sb = reinterpret_cast<const sortable*>(b);
  64
  65     if (sa->ai == sb->ai)
  66     {
  67         return (sa->aj-sb->aj);
  68     }
  69     else
  70     {
  71         return (sa->ai-sb->ai);
  72     }
  73 }
  74
  75 static int
  76 compare_int (const void * a, const void * b)
  77 {
  78     return ( *reinterpret_cast<const int*>(a) - *reinterpret_cast<const int*>(b) );
  79 }
  80
  81
  82 #ifdef DEBUG
  83 #define prints(str, n, s) __prints(str, n, s)
  84 static void __prints(char *str, int n, sortable *s)
  85 {
  86     int i;
  87
  88     if (debug)
  89     {
  90         fprintf(debug, "%s\n", str);
  91         fprintf(debug, "Sortables \n");
  92         for (i = 0; (i < n); i++)
  93         {
  94             fprintf(debug, "%d\t%d\n", s[i].ai, s[i].aj);
  95         }
  96
  97         fflush(debug);
  98     }
  99 }
 100 #else
 101 #define prints(str, n, s)
 102 #endif
 103
 104 void init_nnb(t_nextnb *nnb, int nr, int nrex)
 105 {
 106     int i;
 107
 108     /* initiate nnb */
 109     nnb->nr   = nr;
 110     nnb->nrex = nrex;
 111
 112     snew(nnb->a, nr);
 113     snew(nnb->nrexcl, nr);
 114     for (i = 0; (i < nr); i++)
 115     {
 116         snew(nnb->a[i], nrex+1);
 117         snew(nnb->nrexcl[i], nrex+1);
 118     }
 119 }
 120
 121 static void add_nnb (t_nextnb *nnb, int nre, int i, int j)
 122 {
 123     srenew(nnb->a[i][nre], nnb->nrexcl[i][nre]+1);
 124     nnb->a[i][nre][nnb->nrexcl[i][nre]] = j;
 125     nnb->nrexcl[i][nre]++;
 126 }
 127
 128 void done_nnb (t_nextnb *nnb)
 129 {
 130     int i, nre;
 131
 132     for (i = 0; (i < nnb->nr); i++)
 133     {
 134         for (nre = 0; (nre <= nnb->nrex); nre++)
 135         {
 136             if (nnb->nrexcl[i][nre] > 0)
 137             {
 138                 sfree (nnb->a[i][nre]);
 139             }
 140         }
 141         sfree (nnb->nrexcl[i]);
 142         sfree (nnb->a[i]);
 143     }
 144     sfree (nnb->a);
 145     sfree (nnb->nrexcl);
 146     nnb->nr   = 0;
 147     nnb->nrex = 0;
 148 }
 149
 150 #ifdef DEBUG_NNB
 151 void __print_nnb(t_nextnb *nnb, char *s)
 152 {
 153     int i, j, k;
 154
 155     if (debug)
 156     {
 157         fprintf(debug, "%s\n", s);
 158         fprintf(debug, "nnb->nr: %d\n", nnb->nr);
 159         fprintf(debug, "nnb->nrex: %d\n", nnb->nrex);
 160         for (i = 0; (i < nnb->nr); i++)
 161         {
 162             for (j = 0; (j <= nnb->nrex); j++)
 163             {
 164                 fprintf(debug, "nrexcl[%d][%d]: %d, excl: ", i, j, nnb->nrexcl[i][j]);
 165                 for (k = 0; (k < nnb->nrexcl[i][j]); k++)
 166                 {
 167                     fprintf(debug, "%d, ", nnb->a[i][j][k]);
 168                 }
 169                 fprintf(debug, "\n");
 170             }
 171         }
 172     }
 173 }
 174 #endif
 175
 176 static void nnb2excl(t_nextnb *nnb, t_blocka *excl)
 177 {
 178     int       i, j, j_index;
 179     int       nre, nrx, nrs, nr_of_sortables;
 180     sortable *s;
 181
 182     srenew(excl->index, nnb->nr+1);
 183     excl->index[0] = 0;
 184     for (i = 0; (i < nnb->nr); i++)
 185     {
 186         /* calculate the total number of exclusions for atom i */
 187         nr_of_sortables = 0;
 188         for (nre = 0; (nre <= nnb->nrex); nre++)
 189         {
 190             nr_of_sortables += nnb->nrexcl[i][nre];
 191         }
 192
 193         /* make space for sortable array */
 194         snew(s, nr_of_sortables);
 195
 196         /* fill the sortable array and sort it */
 197         nrs = 0;
 198         for (nre = 0; (nre <= nnb->nrex); nre++)
 199         {
 200             for (nrx = 0; (nrx < nnb->nrexcl[i][nre]); nrx++)
 201             {
 202                 s[nrs].ai = i;
 203                 s[nrs].aj = nnb->a[i][nre][nrx];
 204                 nrs++;
 205             }
 206         }
 207         if (nrs != nr_of_sortables)
 208         {
 209             gmx_incons("Generating exclusions");
 210         }
 211         prints("nnb2excl before qsort", nr_of_sortables, s);
 212         if (nr_of_sortables > 1)
 213         {
 214             qsort (s, nr_of_sortables, static_cast<size_t>(sizeof(s[0])), bond_sort);
 215             prints("nnb2excl after qsort", nr_of_sortables, s);
 216         }
 217
 218         /* remove duplicate entries from the list */
 219         j_index = 0;
 220         if (nr_of_sortables > 0)
 221         {
 222             for (j = 1; (j < nr_of_sortables); j++)
 223             {
 224                 if ((s[j].ai != s[j-1].ai) || (s[j].aj != s[j-1].aj))
 225                 {
 226                     s[j_index++] = s[j-1];
 227                 }
 228             }
 229             s[j_index++] = s[j-1];
 230         }
 231         nr_of_sortables = j_index;
 232         prints("after rm-double", j_index, s);
 233
 234         /* make space for arrays */
 235         srenew(excl->a, excl->nra+nr_of_sortables);
 236
 237         /* put the sorted exclusions in the target list */
 238         for (nrs = 0; (nrs < nr_of_sortables); nrs++)
 239         {
 240             excl->a[excl->nra+nrs] = s[nrs].aj;
 241         }
 242         excl->nra       += nr_of_sortables;
 243         excl->index[i+1] = excl->nra;
 244
 245         /* cleanup temporary space */
 246         sfree (s);
 247     }
 248 }
 249
 250 /*! \brief Return true of neighbor is already present in some exclusion level
 251  *
 252  * To avoid exploding complexity when processing exclusions for highly
 253  * connected molecules with lots of exclusions, this routine is used to
 254  * check whether a particular neighbor has already been excluded at any lower
 255  * bond distance, in which case we should not add it to avoid creating loops.
 256  *
 257  * \param nnb            Valid initialized next-neighbor structure
 258  * \param atom           The host atom whose neighbors we are searching
 259  * \param highest_order  The highest-rank neighbor list to search.
 260  * \param query          Atom index to look for
 261  *
 262  * \return True if query is present as an exclusion of up to highest_order
 263  *         (inclusive) from atom. For instance, if highest_order is 2,
 264  *         the routine will return true if the query atom is already listed as
 265  *         first or second neighbor (exclusion) in nnb.
 266  */
 267 static bool
 268 atom_is_present_in_nnb(const t_nextnb *   nnb,
 269                        int                atom,
 270                        int                highest_order,
 271                        int                query)
 272 {
 273     GMX_RELEASE_ASSERT(highest_order < nnb->nrex, "Inconsistent nnb seach parameters");
 274
 275     for (int order = 0; order <= highest_order; order++)
 276     {
 277         for (int m = 0; m < nnb->nrexcl[atom][order]; m++)
 278         {
 279             if (nnb->a[atom][order][m] == query)
 280             {
 281                 return true;
 282             }
 283         }
 284     }
 285     return false;
 286 }
 287
 288 static void do_gen(int       nrbonds, /* total number of bonds in s     */
 289                    sortable *s,       /* bidirectional list of bonds    */
 290                    t_nextnb *nnb)     /* the tmp storage for excl     */
 291 /* Assume excl is initalised and s[] contains all bonds bidirectional */
 292 {
 293     int i, j, k, n, nb;
 294
 295     /* exclude self */
 296     for (i = 0; (i < nnb->nr); i++)
 297     {
 298         add_nnb(nnb, 0, i, i);
 299     }
 300     print_nnb(nnb, "After exclude self");
 301
 302     /* exclude all the bonded atoms */
 303     if (nnb->nrex > 0)
 304     {
 305         for (i = 0; (i < nrbonds); i++)
 306         {
 307             add_nnb(nnb, 1, s[i].ai, s[i].aj);
 308         }
 309     }
 310     print_nnb(nnb, "After exclude bonds");
 311
 312     /* for the nr of exclusions per atom */
 313     for (n = 1; (n < nnb->nrex); n++)
 314     {
 315         /* now for all atoms */
 316         for (i = 0; (i < nnb->nr); i++)
 317         {
 318             /* for all directly bonded atoms of atom i */
 319             for (j = 0; (j < nnb->nrexcl[i][1]); j++)
 320             {
 321
 322                 /* store the 1st neighbour in nb */
 323                 nb = nnb->a[i][1][j];
 324
 325                 /* store all atoms in nb's n-th list into i's n+1-th list */
 326                 for (k = 0; (k < nnb->nrexcl[nb][n]); k++)
 327                 {
 328                     // Only add if it is not already present as a closer neighbor
 329                     // to avoid exploding complexity for highly connected molecules
 330                     // with high exclusion order
 331                     if (!atom_is_present_in_nnb(nnb, i, n, nnb->a[nb][n][k]))
 332                     {
 333                         add_nnb(nnb, n+1, i, nnb->a[nb][n][k]);
 334                     }
 335                 }
 336             }
 337         }
 338     }
 339     print_nnb(nnb, "After exclude rest");
 340
 341 }
 342
 343 static void add_b(InteractionsOfType *bonds, int *nrf, sortable *s)
 344 {
 345     int i = 0;
 346     for (const auto &bond : bonds->interactionTypes)
 347     {
 348         int ai = bond.ai();
 349         int aj = bond.aj();
 350         if ((ai < 0) || (aj < 0))
 351         {
 352             gmx_fatal(FARGS, "Impossible atom numbers in bond %d: ai=%d, aj=%d",
 353                       i, ai, aj);
 354         }
 355         /* Add every bond twice */
 356         s[(*nrf)].ai   = ai;
 357         s[(*nrf)++].aj = aj;
 358         s[(*nrf)].aj   = ai;
 359         s[(*nrf)++].ai = aj;
 360         i++;
 361     }
 362 }
 363
 364 void gen_nnb(t_nextnb *nnb, gmx::ArrayRef<InteractionsOfType> plist)
 365 {
 366     sortable *s;
 367     int       nrbonds, nrf;
 368
 369     nrbonds = 0;
 370     for (int i = 0; (i < F_NRE); i++)
 371     {
 372         if (IS_CHEMBOND(i))
 373         {
 374             /* we need every bond twice (bidirectional) */
 375             nrbonds += 2*plist[i].size();
 376         }
 377     }
 378
 379     snew(s, nrbonds);
 380
 381     nrf = 0;
 382     for (int i = 0; (i < F_NRE); i++)
 383     {
 384         if (IS_CHEMBOND(i))
 385         {
 386             add_b(&plist[i], &nrf, s);
 387         }
 388     }
 389
 390     /* now sort the bonds */
 391     prints("gen_excl before qsort", nrbonds, s);
 392     if (nrbonds > 1)
 393     {
 394         qsort(s, nrbonds, static_cast<size_t>(sizeof(sortable)), bond_sort);
 395         prints("gen_excl after qsort", nrbonds, s);
 396     }
 397
 398     do_gen(nrbonds, s, nnb);
 399     sfree(s);
 400 }
 401
 402 static void
 403 sort_and_purge_nnb(t_nextnb *nnb)
 404 {
 405     int  i, j, k, m, n, cnt, prev, idx;
 406     bool found;
 407
 408     for (i = 0; (i < nnb->nr); i++)
 409     {
 410         for (n = 0; (n <= nnb->nrex); n++)
 411         {
 412             /* Sort atoms in this list */
 413             qsort(nnb->a[i][n], nnb->nrexcl[i][n], sizeof(int), compare_int);
 414
 415             cnt  = 0;
 416             prev = -1;
 417             for (j = 0; j < nnb->nrexcl[i][n]; j++)
 418             {
 419                 idx = nnb->a[i][n][j];
 420
 421                 found = false;
 422                 for (m = 0; m < n && !found; m++)
 423                 {
 424                     for (k = 0; k < nnb->nrexcl[i][m] && !found; k++)
 425                     {
 426                         found = idx == nnb->a[i][m][k];
 427                     }
 428                 }
 429
 430                 if (!found && nnb->a[i][n][j] != prev)
 431                 {
 432                     nnb->a[i][n][cnt] = nnb->a[i][n][j];
 433                     prev              = nnb->a[i][n][cnt];
 434                     cnt++;
 435                 }
 436             }
 437             nnb->nrexcl[i][n] = cnt;
 438         }
 439     }
 440 }
 441
 442
 443 void generate_excl (int nrexcl,
 444                     int nratoms,
 445                     gmx::ArrayRef<InteractionsOfType> plist, t_nextnb *nnb, t_blocka *excl)
 446 {
 447     if (nrexcl < 0)
 448     {
 449         gmx_fatal(FARGS, "Can't have %d exclusions...", nrexcl);
 450     }
 451     init_nnb(nnb, nratoms, nrexcl);
 452     gen_nnb(nnb, plist);
 453     excl->nr = nratoms;
 454     sort_and_purge_nnb(nnb);
 455     nnb2excl (nnb, excl);
 456 }