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37 /* This file is completely threadsafe - keep it that way! */
44 /* #define DEBUG_NNB */
45 #include "gpp_nextnb.h"
48 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/utility/smalloc.h"
56 bond_sort (const void *a, const void *b)
65 return (sa->aj-sb->aj);
69 return (sa->ai-sb->ai);
74 compare_int (const void * a, const void * b)
76 return ( *(int*)a - *(int*)b );
81 #define prints(str, n, s) __prints(str, n, s)
82 static void __prints(char *str, int n, sortable *s)
88 fprintf(debug, "%s\n", str);
89 fprintf(debug, "Sortables \n");
90 for (i = 0; (i < n); i++)
92 fprintf(debug, "%d\t%d\n", s[i].ai, s[i].aj);
99 #define prints(str, n, s)
102 void init_nnb(t_nextnb *nnb, int nr, int nrex)
111 snew(nnb->nrexcl, nr);
112 for (i = 0; (i < nr); i++)
114 snew(nnb->a[i], nrex+1);
115 snew(nnb->nrexcl[i], nrex+1);
119 static void add_nnb (t_nextnb *nnb, int nre, int i, int j)
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]++;
126 void done_nnb (t_nextnb *nnb)
130 for (i = 0; (i < nnb->nr); i++)
132 for (nre = 0; (nre <= nnb->nrex); nre++)
134 if (nnb->nrexcl[i][nre] > 0)
136 sfree (nnb->a[i][nre]);
139 sfree (nnb->nrexcl[i]);
149 void __print_nnb(t_nextnb *nnb, char *s)
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++)
160 for (j = 0; (j <= nnb->nrex); j++)
162 fprintf(debug, "nrexcl[%d][%d]: %d, excl: ", i, j, nnb->nrexcl[i][j]);
163 for (k = 0; (k < nnb->nrexcl[i][j]); k++)
165 fprintf(debug, "%d, ", nnb->a[i][j][k]);
167 fprintf(debug, "\n");
174 static void nnb2excl(t_nextnb *nnb, t_blocka *excl)
177 int nre, nrx, nrs, nr_of_sortables;
180 srenew(excl->index, nnb->nr+1);
182 for (i = 0; (i < nnb->nr); i++)
184 /* calculate the total number of exclusions for atom i */
186 for (nre = 0; (nre <= nnb->nrex); nre++)
188 nr_of_sortables += nnb->nrexcl[i][nre];
193 fprintf(debug, "nr_of_sortables: %d\n", nr_of_sortables);
195 /* make space for sortable array */
196 snew(s, nr_of_sortables);
198 /* fill the sortable array and sort it */
200 for (nre = 0; (nre <= nnb->nrex); nre++)
202 for (nrx = 0; (nrx < nnb->nrexcl[i][nre]); nrx++)
205 s[nrs].aj = nnb->a[i][nre][nrx];
209 if (nrs != nr_of_sortables)
211 gmx_incons("Generating exclusions");
213 prints("nnb2excl before qsort", nr_of_sortables, s);
214 if (nr_of_sortables > 1)
216 qsort ((void *)s, nr_of_sortables, (size_t)sizeof(s[0]), bond_sort);
217 prints("nnb2excl after qsort", nr_of_sortables, s);
220 /* remove duplicate entries from the list */
222 if (nr_of_sortables > 0)
224 for (j = 1; (j < nr_of_sortables); j++)
226 if ((s[j].ai != s[j-1].ai) || (s[j].aj != s[j-1].aj))
228 s[j_index++] = s[j-1];
231 s[j_index++] = s[j-1];
233 nr_of_sortables = j_index;
234 prints("after rm-double", j_index, s);
236 /* make space for arrays */
237 srenew(excl->a, excl->nra+nr_of_sortables);
239 /* put the sorted exclusions in the target list */
240 for (nrs = 0; (nrs < nr_of_sortables); nrs++)
242 excl->a[excl->nra+nrs] = s[nrs].aj;
244 excl->nra += nr_of_sortables;
245 excl->index[i+1] = excl->nra;
247 /* cleanup temporary space */
252 print_blocka(debug, "Exclusions", "Atom", "Excluded", excl);
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 */
264 for (i = 0; (i < nnb->nr); i++)
266 add_nnb(nnb, 0, i, i);
268 print_nnb(nnb, "After exclude self");
270 /* exclude all the bonded atoms */
273 for (i = 0; (i < nrbonds); i++)
275 add_nnb(nnb, 1, s[i].ai, s[i].aj);
278 print_nnb(nnb, "After exclude bonds");
280 /* for the nr of exclusions per atom */
281 for (n = 1; (n < nnb->nrex); n++)
283 /* now for all atoms */
284 for (i = 0; (i < nnb->nr); i++)
286 /* for all directly bonded atoms of atom i */
287 for (j = 0; (j < nnb->nrexcl[i][1]); j++)
290 /* store the 1st neighbour in nb */
291 nb = nnb->a[i][1][j];
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++)
296 if (i != nnb->a[nb][n][k])
298 add_nnb(nnb, n+1, i, nnb->a[nb][n][k]);
304 print_nnb(nnb, "After exclude rest");
308 static void add_b(t_params *bonds, int *nrf, sortable *s)
313 for (i = 0; (i < bonds->nr); i++)
315 ai = bonds->param[i].AI;
316 aj = bonds->param[i].AJ;
317 if ((ai < 0) || (aj < 0))
319 gmx_fatal(FARGS, "Impossible atom numbers in bond %d: ai=%d, aj=%d",
322 /* Add every bond twice */
330 void gen_nnb(t_nextnb *nnb, t_params plist[])
336 for (i = 0; (i < F_NRE); i++)
340 /* we need every bond twice (bidirectional) */
341 nrbonds += 2*plist[i].nr;
348 for (i = 0; (i < F_NRE); i++)
352 add_b(&plist[i], &nrf, s);
356 /* now sort the bonds */
357 prints("gen_excl before qsort", nrbonds, s);
360 qsort((void *) s, nrbonds, (size_t)sizeof(sortable), bond_sort);
361 prints("gen_excl after qsort", nrbonds, s);
364 do_gen(nrbonds, s, nnb);
369 sort_and_purge_nnb(t_nextnb *nnb)
371 int i, j, k, m, n, cnt, found, prev, idx;
373 for (i = 0; (i < nnb->nr); i++)
375 for (n = 0; (n <= nnb->nrex); n++)
377 /* Sort atoms in this list */
378 qsort(nnb->a[i][n], nnb->nrexcl[i][n], sizeof(int), compare_int);
382 for (j = 0; j < nnb->nrexcl[i][n]; j++)
384 idx = nnb->a[i][n][j];
387 for (m = 0; m < n && !found; m++)
389 for (k = 0; k < nnb->nrexcl[i][m] && !found; k++)
391 found = (idx == nnb->a[i][m][k]);
395 if (!found && nnb->a[i][n][j] != prev)
397 nnb->a[i][n][cnt] = nnb->a[i][n][j];
398 prev = nnb->a[i][n][cnt];
402 nnb->nrexcl[i][n] = cnt;
408 void generate_excl (int nrexcl, int nratoms, t_params plist[], t_nextnb *nnb, t_blocka *excl)
414 gmx_fatal(FARGS, "Can't have %d exclusions...", nrexcl);
416 init_nnb(nnb, nratoms, nrexcl);
419 sort_and_purge_nnb(nnb);
420 nnb2excl (nnb, excl);