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48 #include "gmx_fatal.h"
54 static int sid_comp(const void *a, const void *b)
65 return (sa->atom-sb->atom);
73 static int mk_grey(egCol egc[], t_graph *g, int *AtomI,
74 int maxsid, t_sid sid[])
76 int j, ng, ai, aj, g0;
82 /* Loop over all the bonds */
83 for (j = 0; (j < g->nedge[ai]); j++)
85 aj = g->edge[ai][j]-g0;
86 /* If there is a white one, make it gray and set pbc */
87 if (egc[aj] == egcolWhite)
95 /* Check whether this one has been set before... */
96 range_check(aj+g0, 0, maxsid);
97 range_check(ai+g0, 0, maxsid);
98 if (sid[aj+g0].sid != -1)
100 gmx_fatal(FARGS, "sid[%d]=%d, sid[%d]=%d, file %s, line %d",
101 ai, sid[ai+g0].sid, aj, sid[aj+g0].sid, __FILE__, __LINE__);
105 sid[aj+g0].sid = sid[ai+g0].sid;
106 sid[aj+g0].atom = aj+g0;
114 static int first_colour(int fC, egCol Col, t_graph *g, egCol egc[])
115 /* Return the first node with colour Col starting at fC.
116 * return -1 if none found.
121 for (i = fC; (i < g->nnodes); i++)
123 if ((g->nedge[i] > 0) && (egc[i] == Col))
132 static int mk_sblocks(FILE *fp, t_graph *g, int maxsid, t_sid sid[])
135 int nW, nG, nB; /* Number of Grey, Black, White */
136 int fW, fG; /* First of each category */
137 egCol *egc = NULL; /* The colour of each node */
157 /* We even have a loop invariant:
158 * nW+nG+nB == g->nbound
163 fprintf(fp, "Walking down the molecule graph to make constraint-blocks\n");
168 /* Find the first white, this will allways be a larger
169 * number than before, because no nodes are made white
172 if ((fW = first_colour(fW, egcolWhite, g, egc)) == -1)
174 gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
177 /* Make the first white node grey, and set the block number */
179 range_check(fW+g0, 0, maxsid);
180 sid[fW+g0].sid = nblock++;
184 /* Initial value for the first grey */
189 fprintf(debug, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n",
190 nW, nG, nB, nW+nG+nB);
195 if ((fG = first_colour(fG, egcolGrey, g, egc)) == -1)
197 gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
200 /* Make the first grey node black */
201 egc[fG] = egcolBlack;
205 /* Make all the neighbours of this black node grey
206 * and set their block number
208 ng = mk_grey(egc, g, &fG, maxsid, sid);
209 /* ng is the number of white nodes made grey */
218 fprintf(debug, "Found %d shake blocks\n", nblock);
226 int first, last, sid;
229 static int ms_comp(const void *a, const void *b)
231 t_merge_sid *ma = (t_merge_sid *)a;
232 t_merge_sid *mb = (t_merge_sid *)b;
235 d = ma->first-mb->first;
238 return ma->last-mb->last;
246 static int merge_sid(int at_start, int at_end, int nsid, t_sid sid[],
249 int i, j, k, n, isid, ndel;
253 /* We try to remdy the following problem:
254 * Atom: 1 2 3 4 5 6 7 8 9 10
255 * Sid: 0 -1 1 0 -1 1 1 1 1 1
258 /* Determine first and last atom in each shake ID */
261 for (k = 0; (k < nsid); k++)
263 ms[k].first = at_end+1;
267 for (i = at_start; (i < at_end); i++)
270 range_check(isid, -1, nsid);
273 ms[isid].first = min(ms[isid].first, sid[i].atom);
274 ms[isid].last = max(ms[isid].last, sid[i].atom);
277 qsort(ms, nsid, sizeof(ms[0]), ms_comp);
279 /* Now merge the overlapping ones */
281 for (k = 0; (k < nsid); )
283 for (j = k+1; (j < nsid); )
285 if (ms[j].first <= ms[k].last)
287 ms[k].last = max(ms[k].last, ms[j].last);
288 ms[k].first = min(ms[k].first, ms[j].first);
304 for (k = 0; (k < nsid); k++)
306 while ((k < nsid-1) && (ms[k].sid == -1))
308 for (j = k+1; (j < nsid); j++)
310 memcpy(&(ms[j-1]), &(ms[j]), sizeof(ms[0]));
316 for (k = at_start; (k < at_end); k++)
322 sblock->nalloc_index = sblock->nr+1;
323 snew(sblock->index, sblock->nalloc_index);
324 sblock->nra = at_end - at_start;
325 sblock->nalloc_a = sblock->nra;
326 snew(sblock->a, sblock->nalloc_a);
327 sblock->index[0] = 0;
328 for (k = n = 0; (k < nsid); k++)
330 sblock->index[k+1] = sblock->index[k] + ms[k].last - ms[k].first+1;
331 for (j = ms[k].first; (j <= ms[k].last); j++)
333 range_check(n, 0, sblock->nra);
335 range_check(j, 0, at_end);
336 if (sid[j].sid == -1)
342 fprintf(stderr, "Double sids (%d, %d) for atom %d\n", sid[j].sid, k, j);
347 /* Removed 2007-09-04
348 sblock->index[k+1] = natoms;
349 for(k=0; (k<natoms); k++)
350 if (sid[k].sid == -1)
355 assert(sblock->index[k] == sblock->nra);
361 void gen_sblocks(FILE *fp, int at_start, int at_end,
362 t_idef *idef, t_blocka *sblock,
366 int i, i0, j, k, istart, n;
370 g = mk_graph(NULL, idef, at_start, at_end, TRUE, bSettle);
373 p_graph(debug, "Graaf Dracula", g);
376 for (i = at_start; (i < at_end); i++)
381 nsid = mk_sblocks(fp, g, at_end, sid);
388 /* Now sort the shake blocks... */
389 qsort(sid+at_start, at_end-at_start, (size_t)sizeof(sid[0]), sid_comp);
393 fprintf(debug, "Sorted shake block\n");
394 for (i = at_start; (i < at_end); i++)
396 fprintf(debug, "sid[%5d] = atom:%5d sid:%5d\n", i, sid[i].atom, sid[i].sid);
399 /* Now check how many are NOT -1, i.e. how many have to be shaken */
400 for (i0 = at_start; (i0 < at_end); i0++)
402 if (sid[i0].sid > -1)
408 /* Now we have the sids that have to be shaken. We'll check the min and
409 * max atom numbers and this determines the shake block. DvdS 2007-07-19.
410 * For the purpose of making boundaries all atoms in between need to be
411 * part of the shake block too. There may be cases where blocks overlap
412 * and they will have to be merged.
414 nsid = merge_sid(at_start, at_end, nsid, sid, sblock);
415 /* Now sort the shake blocks again... */
416 /*qsort(sid,natoms,(size_t)sizeof(sid[0]),sid_comp);*/
418 /* Fill the sblock struct */
419 /* sblock->nr = nsid;
420 sblock->nra = natoms;
421 srenew(sblock->a,sblock->nra);
422 srenew(sblock->index,sblock->nr+1);
427 sblock->index[n++]=k;
429 istart = sid[i].atom;
430 while ((i<natoms-1) && (sid[i+1].sid == isid))
432 /* After while: we found a new block, or are thru with the atoms */
433 /* for(j=istart; (j<=sid[i].atom); j++,k++)
435 sblock->index[n] = k;
439 gmx_fatal(FARGS,"Death Horror: nsid = %d, n= %d",nsid,n);
445 /* Due to unknown reason this free generates a problem sometimes */
450 fprintf(debug, "Done gen_sblocks\n");