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 <stdlib.h>
  43
  44 #include "gromacs/gmxpreprocess/toputil.h"
  45 #include "gromacs/topology/ifunc.h"
  46 #include "gromacs/utility/fatalerror.h"
  47 #include "gromacs/utility/smalloc.h"
  48
  49 /* #define DEBUG_NNB */
  50
  51 typedef struct {
  52     int ai, aj;
  53 } sortable;
  54
  55 static int
  56 bond_sort (const void *a, const void *b)
  57 {
  58     sortable *sa, *sb;
  59
  60     sa = (sortable *) a;
  61     sb = (sortable *) b;
  62
  63     if (sa->ai == sb->ai)
  64     {
  65         return (sa->aj-sb->aj);
  66     }
  67     else
  68     {
  69         return (sa->ai-sb->ai);
  70     }
  71 }
  72
  73 static int
  74 compare_int (const void * a, const void * b)
  75 {
  76     return ( *(int*)a - *(int*)b );
  77 }
  78
  79
  80 #ifdef DEBUG
  81 #define prints(str, n, s) __prints(str, n, s)
  82 static void __prints(char *str, int n, sortable *s)
  83 {
  84     int i;
  85
  86     if (debug)
  87     {
  88         fprintf(debug, "%s\n", str);
  89         fprintf(debug, "Sortables \n");
  90         for (i = 0; (i < n); i++)
  91         {
  92             fprintf(debug, "%d\t%d\n", s[i].ai, s[i].aj);
  93         }
  94
  95         fflush(debug);
  96     }
  97 }
  98 #else
  99 #define prints(str, n, s)
 100 #endif
 101
 102 void init_nnb(t_nextnb *nnb, int nr, int nrex)
 103 {
 104     int i;
 105
 106     /* initiate nnb */
 107     nnb->nr   = nr;
 108     nnb->nrex = nrex;
 109
 110     snew(nnb->a, nr);
 111     snew(nnb->nrexcl, nr);
 112     for (i = 0; (i < nr); i++)
 113     {
 114         snew(nnb->a[i], nrex+1);
 115         snew(nnb->nrexcl[i], nrex+1);
 116     }
 117 }
 118
 119 static void add_nnb (t_nextnb *nnb, int nre, int i, int j)
 120 {
 121     srenew(nnb->a[i][nre], nnb->nrexcl[i][nre]+1);
 122     nnb->a[i][nre][nnb->nrexcl[i][nre]] = j;
 123     nnb->nrexcl[i][nre]++;
 124 }
 125
 126 void done_nnb (t_nextnb *nnb)
 127 {
 128     int i, nre;
 129
 130     for (i = 0; (i < nnb->nr); i++)
 131     {
 132         for (nre = 0; (nre <= nnb->nrex); nre++)
 133         {
 134             if (nnb->nrexcl[i][nre] > 0)
 135             {
 136                 sfree (nnb->a[i][nre]);
 137             }
 138         }
 139         sfree (nnb->nrexcl[i]);
 140         sfree (nnb->a[i]);
 141     }
 142     sfree (nnb->a);
 143     sfree (nnb->nrexcl);
 144     nnb->nr   = 0;
 145     nnb->nrex = 0;
 146 }
 147
 148 #ifdef DEBUG_NNB
 149 void __print_nnb(t_nextnb *nnb, char *s)
 150 {
 151     int i, j, k;
 152
 153     if (debug)
 154     {
 155         fprintf(debug, "%s\n", s);
 156         fprintf(debug, "nnb->nr: %d\n", nnb->nr);
 157         fprintf(debug, "nnb->nrex: %d\n", nnb->nrex);
 158         for (i = 0; (i < nnb->nr); i++)
 159         {
 160             for (j = 0; (j <= nnb->nrex); j++)
 161             {
 162                 fprintf(debug, "nrexcl[%d][%d]: %d, excl: ", i, j, nnb->nrexcl[i][j]);
 163                 for (k = 0; (k < nnb->nrexcl[i][j]); k++)
 164                 {
 165                     fprintf(debug, "%d, ", nnb->a[i][j][k]);
 166                 }
 167                 fprintf(debug, "\n");
 168             }
 169         }
 170     }
 171 }
 172 #endif
 173
 174 static void nnb2excl(t_nextnb *nnb, t_blocka *excl)
 175 {
 176     int       i, j, j_index;
 177     int       nre, nrx, nrs, nr_of_sortables;
 178     sortable *s;
 179
 180     srenew(excl->index, nnb->nr+1);
 181     excl->index[0] = 0;
 182     for (i = 0; (i < nnb->nr); i++)
 183     {
 184         /* calculate the total number of exclusions for atom i */
 185         nr_of_sortables = 0;
 186         for (nre = 0; (nre <= nnb->nrex); nre++)
 187         {
 188             nr_of_sortables += nnb->nrexcl[i][nre];
 189         }
 190
 191         if (debug)
 192         {
 193             fprintf(debug, "nr_of_sortables: %d\n", nr_of_sortables);
 194         }
 195         /* make space for sortable array */
 196         snew(s, nr_of_sortables);
 197
 198         /* fill the sortable array and sort it */
 199         nrs = 0;
 200         for (nre = 0; (nre <= nnb->nrex); nre++)
 201         {
 202             for (nrx = 0; (nrx < nnb->nrexcl[i][nre]); nrx++)
 203             {
 204                 s[nrs].ai = i;
 205                 s[nrs].aj = nnb->a[i][nre][nrx];
 206                 nrs++;
 207             }
 208         }
 209         if (nrs != nr_of_sortables)
 210         {
 211             gmx_incons("Generating exclusions");
 212         }
 213         prints("nnb2excl before qsort", nr_of_sortables, s);
 214         if (nr_of_sortables > 1)
 215         {
 216             qsort ((void *)s, nr_of_sortables, (size_t)sizeof(s[0]), bond_sort);
 217             prints("nnb2excl after qsort", nr_of_sortables, s);
 218         }
 219
 220         /* remove duplicate entries from the list */
 221         j_index = 0;
 222         if (nr_of_sortables > 0)
 223         {
 224             for (j = 1; (j < nr_of_sortables); j++)
 225             {
 226                 if ((s[j].ai != s[j-1].ai) || (s[j].aj != s[j-1].aj))
 227                 {
 228                     s[j_index++] = s[j-1];
 229                 }
 230             }
 231             s[j_index++] = s[j-1];
 232         }
 233         nr_of_sortables = j_index;
 234         prints("after rm-double", j_index, s);
 235
 236         /* make space for arrays */
 237         srenew(excl->a, excl->nra+nr_of_sortables);
 238
 239         /* put the sorted exclusions in the target list */
 240         for (nrs = 0; (nrs < nr_of_sortables); nrs++)
 241         {
 242             excl->a[excl->nra+nrs] = s[nrs].aj;
 243         }
 244         excl->nra       += nr_of_sortables;
 245         excl->index[i+1] = excl->nra;
 246
 247         /* cleanup temporary space */
 248         sfree (s);
 249     }
 250     if (debug)
 251     {
 252         print_blocka(debug, "Exclusions", "Atom", "Excluded", excl);
 253     }
 254 }
 255
 256 static void do_gen(int       nrbonds, /* total number of bonds in s     */
 257                    sortable *s,       /* bidirectional list of bonds    */
 258                    t_nextnb *nnb)     /* the tmp storage for excl     */
 259 /* Assume excl is initalised and s[] contains all bonds bidirectional */
 260 {
 261     int i, j, k, n, nb;
 262
 263     /* exclude self */
 264     for (i = 0; (i < nnb->nr); i++)
 265     {
 266         add_nnb(nnb, 0, i, i);
 267     }
 268     print_nnb(nnb, "After exclude self");
 269
 270     /* exclude all the bonded atoms */
 271     if (nnb->nrex > 0)
 272     {
 273         for (i = 0; (i < nrbonds); i++)
 274         {
 275             add_nnb(nnb, 1, s[i].ai, s[i].aj);
 276         }
 277     }
 278     print_nnb(nnb, "After exclude bonds");
 279
 280     /* for the nr of exclusions per atom */
 281     for (n = 1; (n < nnb->nrex); n++)
 282     {
 283         /* now for all atoms */
 284         for (i = 0; (i < nnb->nr); i++)
 285         {
 286             /* for all directly bonded atoms of atom i */
 287             for (j = 0; (j < nnb->nrexcl[i][1]); j++)
 288             {
 289
 290                 /* store the 1st neighbour in nb */
 291                 nb = nnb->a[i][1][j];
 292
 293                 /* store all atoms in nb's n-th list into i's n+1-th list */
 294                 for (k = 0; (k < nnb->nrexcl[nb][n]); k++)
 295                 {
 296                     if (i != nnb->a[nb][n][k])
 297                     {
 298                         add_nnb(nnb, n+1, i, nnb->a[nb][n][k]);
 299                     }
 300                 }
 301             }
 302         }
 303     }
 304     print_nnb(nnb, "After exclude rest");
 305
 306 }
 307
 308 static void add_b(t_params *bonds, int *nrf, sortable *s)
 309 {
 310     int i;
 311     int ai, aj;
 312
 313     for (i = 0; (i < bonds->nr); i++)
 314     {
 315         ai = bonds->param[i].ai();
 316         aj = bonds->param[i].aj();
 317         if ((ai < 0) || (aj < 0))
 318         {
 319             gmx_fatal(FARGS, "Impossible atom numbers in bond %d: ai=%d, aj=%d",
 320                       i, ai, aj);
 321         }
 322         /* Add every bond twice */
 323         s[(*nrf)].ai   = ai;
 324         s[(*nrf)++].aj = aj;
 325         s[(*nrf)].aj   = ai;
 326         s[(*nrf)++].ai = aj;
 327     }
 328 }
 329
 330 void gen_nnb(t_nextnb *nnb, t_params plist[])
 331 {
 332     sortable *s;
 333     int       i, nrbonds, nrf;
 334
 335     nrbonds = 0;
 336     for (i = 0; (i < F_NRE); i++)
 337     {
 338         if (IS_CHEMBOND(i))
 339         {
 340             /* we need every bond twice (bidirectional) */
 341             nrbonds += 2*plist[i].nr;
 342         }
 343     }
 344
 345     snew(s, nrbonds);
 346
 347     nrf = 0;
 348     for (i = 0; (i < F_NRE); i++)
 349     {
 350         if (IS_CHEMBOND(i))
 351         {
 352             add_b(&plist[i], &nrf, s);
 353         }
 354     }
 355
 356     /* now sort the bonds */
 357     prints("gen_excl before qsort", nrbonds, s);
 358     if (nrbonds > 1)
 359     {
 360         qsort((void *) s, nrbonds, (size_t)sizeof(sortable), bond_sort);
 361         prints("gen_excl after qsort", nrbonds, s);
 362     }
 363
 364     do_gen(nrbonds, s, nnb);
 365     sfree(s);
 366 }
 367
 368 static void
 369 sort_and_purge_nnb(t_nextnb *nnb)
 370 {
 371     int i, j, k, m, n, cnt, found, prev, idx;
 372
 373     for (i = 0; (i < nnb->nr); i++)
 374     {
 375         for (n = 0; (n <= nnb->nrex); n++)
 376         {
 377             /* Sort atoms in this list */
 378             qsort(nnb->a[i][n], nnb->nrexcl[i][n], sizeof(int), compare_int);
 379
 380             cnt  = 0;
 381             prev = -1;
 382             for (j = 0; j < nnb->nrexcl[i][n]; j++)
 383             {
 384                 idx = nnb->a[i][n][j];
 385
 386                 found = 0;
 387                 for (m = 0; m < n && !found; m++)
 388                 {
 389                     for (k = 0; k < nnb->nrexcl[i][m] && !found; k++)
 390                     {
 391                         found = (idx == nnb->a[i][m][k]);
 392                     }
 393                 }
 394
 395                 if (!found && nnb->a[i][n][j] != prev)
 396                 {
 397                     nnb->a[i][n][cnt] = nnb->a[i][n][j];
 398                     prev              = nnb->a[i][n][cnt];
 399                     cnt++;
 400                 }
 401             }
 402             nnb->nrexcl[i][n] = cnt;
 403         }
 404     }
 405 }
 406
 407
 408 void generate_excl (int nrexcl, int nratoms, t_params plist[], t_nextnb *nnb, t_blocka *excl)
 409 {
 410     if (nrexcl < 0)
 411     {
 412         gmx_fatal(FARGS, "Can't have %d exclusions...", nrexcl);
 413     }
 414     init_nnb(nnb, nratoms, nrexcl);
 415     gen_nnb(nnb, plist);
 416     excl->nr = nratoms;
 417     sort_and_purge_nnb(nnb);
 418     nnb2excl (nnb, excl);
 419 }