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47 #include "gromacs/pbcutil/mshift.h"
48 #include "gromacs/topology/block.h"
49 #include "gromacs/topology/idef.h"
50 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/utility/smalloc.h"
57 static int sid_comp(const void *a, const void *b)
68 return (sa->atom-sb->atom);
76 static int mk_grey(egCol egc[], t_graph *g, int *AtomI,
77 int maxsid, t_sid sid[])
79 int j, ng, ai, aj, g0;
85 /* Loop over all the bonds */
86 for (j = 0; (j < g->nedge[ai]); j++)
88 aj = g->edge[ai][j]-g0;
89 /* If there is a white one, make it gray and set pbc */
90 if (egc[aj] == egcolWhite)
98 /* Check whether this one has been set before... */
99 range_check(aj+g0, 0, maxsid);
100 range_check(ai+g0, 0, maxsid);
101 if (sid[aj+g0].sid != -1)
103 gmx_fatal(FARGS, "sid[%d]=%d, sid[%d]=%d, file %s, line %d",
104 ai, sid[ai+g0].sid, aj, sid[aj+g0].sid, __FILE__, __LINE__);
108 sid[aj+g0].sid = sid[ai+g0].sid;
109 sid[aj+g0].atom = aj+g0;
117 static int first_colour(int fC, egCol Col, t_graph *g, egCol egc[])
118 /* Return the first node with colour Col starting at fC.
119 * return -1 if none found.
124 for (i = fC; (i < g->nnodes); i++)
126 if ((g->nedge[i] > 0) && (egc[i] == Col))
135 static int mk_sblocks(FILE *fp, t_graph *g, int maxsid, t_sid sid[])
138 int nW, nG, nB; /* Number of Grey, Black, White */
139 int fW, fG; /* First of each category */
140 egCol *egc = NULL; /* The colour of each node */
160 /* We even have a loop invariant:
161 * nW+nG+nB == g->nbound
166 fprintf(fp, "Walking down the molecule graph to make constraint-blocks\n");
171 /* Find the first white, this will allways be a larger
172 * number than before, because no nodes are made white
175 if ((fW = first_colour(fW, egcolWhite, g, egc)) == -1)
177 gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
180 /* Make the first white node grey, and set the block number */
182 range_check(fW+g0, 0, maxsid);
183 sid[fW+g0].sid = nblock++;
187 /* Initial value for the first grey */
192 fprintf(debug, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n",
193 nW, nG, nB, nW+nG+nB);
198 if ((fG = first_colour(fG, egcolGrey, g, egc)) == -1)
200 gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
203 /* Make the first grey node black */
204 egc[fG] = egcolBlack;
208 /* Make all the neighbours of this black node grey
209 * and set their block number
211 ng = mk_grey(egc, g, &fG, maxsid, sid);
212 /* ng is the number of white nodes made grey */
221 fprintf(debug, "Found %d shake blocks\n", nblock);
229 int first, last, sid;
232 static int ms_comp(const void *a, const void *b)
234 t_merge_sid *ma = (t_merge_sid *)a;
235 t_merge_sid *mb = (t_merge_sid *)b;
238 d = ma->first-mb->first;
241 return ma->last-mb->last;
249 static int merge_sid(int at_start, int at_end, int nsid, t_sid sid[],
252 int i, j, k, n, isid, ndel;
256 /* We try to remdy the following problem:
257 * Atom: 1 2 3 4 5 6 7 8 9 10
258 * Sid: 0 -1 1 0 -1 1 1 1 1 1
261 /* Determine first and last atom in each shake ID */
264 for (k = 0; (k < nsid); k++)
266 ms[k].first = at_end+1;
270 for (i = at_start; (i < at_end); i++)
273 range_check(isid, -1, nsid);
276 ms[isid].first = min(ms[isid].first, sid[i].atom);
277 ms[isid].last = max(ms[isid].last, sid[i].atom);
280 qsort(ms, nsid, sizeof(ms[0]), ms_comp);
282 /* Now merge the overlapping ones */
284 for (k = 0; (k < nsid); )
286 for (j = k+1; (j < nsid); )
288 if (ms[j].first <= ms[k].last)
290 ms[k].last = max(ms[k].last, ms[j].last);
291 ms[k].first = min(ms[k].first, ms[j].first);
307 for (k = 0; (k < nsid); k++)
309 while ((k < nsid-1) && (ms[k].sid == -1))
311 for (j = k+1; (j < nsid); j++)
313 memcpy(&(ms[j-1]), &(ms[j]), sizeof(ms[0]));
319 for (k = at_start; (k < at_end); k++)
325 sblock->nalloc_index = sblock->nr+1;
326 snew(sblock->index, sblock->nalloc_index);
327 sblock->nra = at_end - at_start;
328 sblock->nalloc_a = sblock->nra;
329 snew(sblock->a, sblock->nalloc_a);
330 sblock->index[0] = 0;
331 for (k = n = 0; (k < nsid); k++)
333 sblock->index[k+1] = sblock->index[k] + ms[k].last - ms[k].first+1;
334 for (j = ms[k].first; (j <= ms[k].last); j++)
336 range_check(n, 0, sblock->nra);
338 range_check(j, 0, at_end);
339 if (sid[j].sid == -1)
345 fprintf(stderr, "Double sids (%d, %d) for atom %d\n", sid[j].sid, k, j);
350 /* Removed 2007-09-04
351 sblock->index[k+1] = natoms;
352 for(k=0; (k<natoms); k++)
353 if (sid[k].sid == -1)
358 assert(sblock->index[k] == sblock->nra);
364 void gen_sblocks(FILE *fp, int at_start, int at_end,
365 t_idef *idef, t_blocka *sblock,
369 int i, i0, j, k, istart, n;
373 g = mk_graph(NULL, idef, at_start, at_end, TRUE, bSettle);
376 p_graph(debug, "Graaf Dracula", g);
379 for (i = at_start; (i < at_end); i++)
384 nsid = mk_sblocks(fp, g, at_end, sid);
391 /* Now sort the shake blocks... */
392 qsort(sid+at_start, at_end-at_start, (size_t)sizeof(sid[0]), sid_comp);
396 fprintf(debug, "Sorted shake block\n");
397 for (i = at_start; (i < at_end); i++)
399 fprintf(debug, "sid[%5d] = atom:%5d sid:%5d\n", i, sid[i].atom, sid[i].sid);
402 /* Now check how many are NOT -1, i.e. how many have to be shaken */
403 for (i0 = at_start; (i0 < at_end); i0++)
405 if (sid[i0].sid > -1)
411 /* Now we have the sids that have to be shaken. We'll check the min and
412 * max atom numbers and this determines the shake block. DvdS 2007-07-19.
413 * For the purpose of making boundaries all atoms in between need to be
414 * part of the shake block too. There may be cases where blocks overlap
415 * and they will have to be merged.
417 nsid = merge_sid(at_start, at_end, nsid, sid, sblock);
418 /* Now sort the shake blocks again... */
419 /*qsort(sid,natoms,(size_t)sizeof(sid[0]),sid_comp);*/
421 /* Fill the sblock struct */
422 /* sblock->nr = nsid;
423 sblock->nra = natoms;
424 srenew(sblock->a,sblock->nra);
425 srenew(sblock->index,sblock->nr+1);
430 sblock->index[n++]=k;
432 istart = sid[i].atom;
433 while ((i<natoms-1) && (sid[i+1].sid == isid))
435 /* After while: we found a new block, or are thru with the atoms */
436 /* for(j=istart; (j<=sid[i].atom); j++,k++)
438 sblock->index[n] = k;
442 gmx_fatal(FARGS,"Death Horror: nsid = %d, n= %d",nsid,n);
448 /* Due to unknown reason this free generates a problem sometimes */
453 fprintf(debug, "Done gen_sblocks\n");