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49 #include "gromacs/pbcutil/mshift.h"
50 #include "gromacs/topology/block.h"
51 #include "gromacs/topology/idef.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/smalloc.h"
59 static int sid_comp(const void *a, const void *b)
70 return (sa->atom-sb->atom);
78 static int mk_grey(egCol egc[], t_graph *g, int *AtomI,
79 int maxsid, t_sid sid[])
81 int j, ng, ai, aj, g0;
87 /* Loop over all the bonds */
88 for (j = 0; (j < g->nedge[ai]); j++)
90 aj = g->edge[ai][j]-g0;
91 /* If there is a white one, make it gray and set pbc */
92 if (egc[aj] == egcolWhite)
100 /* Check whether this one has been set before... */
101 range_check(aj+g0, 0, maxsid);
102 range_check(ai+g0, 0, maxsid);
103 if (sid[aj+g0].sid != -1)
105 gmx_fatal(FARGS, "sid[%d]=%d, sid[%d]=%d, file %s, line %d",
106 ai, sid[ai+g0].sid, aj, sid[aj+g0].sid, __FILE__, __LINE__);
110 sid[aj+g0].sid = sid[ai+g0].sid;
111 sid[aj+g0].atom = aj+g0;
119 static int first_colour(int fC, egCol Col, t_graph *g, egCol egc[])
120 /* Return the first node with colour Col starting at fC.
121 * return -1 if none found.
126 for (i = fC; (i < g->nnodes); i++)
128 if ((g->nedge[i] > 0) && (egc[i] == Col))
137 static int mk_sblocks(FILE *fp, t_graph *g, int maxsid, t_sid sid[])
140 int nW, nG, nB; /* Number of Grey, Black, White */
141 int fW, fG; /* First of each category */
142 egCol *egc = NULL; /* The colour of each node */
162 /* We even have a loop invariant:
163 * nW+nG+nB == g->nbound
168 fprintf(fp, "Walking down the molecule graph to make constraint-blocks\n");
173 /* Find the first white, this will allways be a larger
174 * number than before, because no nodes are made white
177 if ((fW = first_colour(fW, egcolWhite, g, egc)) == -1)
179 gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
182 /* Make the first white node grey, and set the block number */
184 range_check(fW+g0, 0, maxsid);
185 sid[fW+g0].sid = nblock++;
189 /* Initial value for the first grey */
194 fprintf(debug, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n",
195 nW, nG, nB, nW+nG+nB);
200 if ((fG = first_colour(fG, egcolGrey, g, egc)) == -1)
202 gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
205 /* Make the first grey node black */
206 egc[fG] = egcolBlack;
210 /* Make all the neighbours of this black node grey
211 * and set their block number
213 ng = mk_grey(egc, g, &fG, maxsid, sid);
214 /* ng is the number of white nodes made grey */
223 fprintf(debug, "Found %d shake blocks\n", nblock);
231 int first, last, sid;
234 static int ms_comp(const void *a, const void *b)
236 t_merge_sid *ma = (t_merge_sid *)a;
237 t_merge_sid *mb = (t_merge_sid *)b;
240 d = ma->first-mb->first;
243 return ma->last-mb->last;
251 static int merge_sid(int at_start, int at_end, int nsid, t_sid sid[],
254 int i, j, k, n, isid, ndel;
258 /* We try to remdy the following problem:
259 * Atom: 1 2 3 4 5 6 7 8 9 10
260 * Sid: 0 -1 1 0 -1 1 1 1 1 1
263 /* Determine first and last atom in each shake ID */
266 for (k = 0; (k < nsid); k++)
268 ms[k].first = at_end+1;
272 for (i = at_start; (i < at_end); i++)
275 range_check(isid, -1, nsid);
278 ms[isid].first = min(ms[isid].first, sid[i].atom);
279 ms[isid].last = max(ms[isid].last, sid[i].atom);
282 qsort(ms, nsid, sizeof(ms[0]), ms_comp);
284 /* Now merge the overlapping ones */
286 for (k = 0; (k < nsid); )
288 for (j = k+1; (j < nsid); )
290 if (ms[j].first <= ms[k].last)
292 ms[k].last = max(ms[k].last, ms[j].last);
293 ms[k].first = min(ms[k].first, ms[j].first);
309 for (k = 0; (k < nsid); k++)
311 while ((k < nsid-1) && (ms[k].sid == -1))
313 for (j = k+1; (j < nsid); j++)
315 memcpy(&(ms[j-1]), &(ms[j]), sizeof(ms[0]));
321 for (k = at_start; (k < at_end); k++)
327 sblock->nalloc_index = sblock->nr+1;
328 snew(sblock->index, sblock->nalloc_index);
329 sblock->nra = at_end - at_start;
330 sblock->nalloc_a = sblock->nra;
331 snew(sblock->a, sblock->nalloc_a);
332 sblock->index[0] = 0;
333 for (k = n = 0; (k < nsid); k++)
335 sblock->index[k+1] = sblock->index[k] + ms[k].last - ms[k].first+1;
336 for (j = ms[k].first; (j <= ms[k].last); j++)
338 range_check(n, 0, sblock->nra);
340 range_check(j, 0, at_end);
341 if (sid[j].sid == -1)
347 fprintf(stderr, "Double sids (%d, %d) for atom %d\n", sid[j].sid, k, j);
352 /* Removed 2007-09-04
353 sblock->index[k+1] = natoms;
354 for(k=0; (k<natoms); k++)
355 if (sid[k].sid == -1)
360 assert(sblock->index[k] == sblock->nra);
366 void gen_sblocks(FILE *fp, int at_start, int at_end,
367 t_idef *idef, t_blocka *sblock,
371 int i, i0, j, k, istart, n;
375 g = mk_graph(NULL, idef, at_start, at_end, TRUE, bSettle);
378 p_graph(debug, "Graaf Dracula", g);
381 for (i = at_start; (i < at_end); i++)
386 nsid = mk_sblocks(fp, g, at_end, sid);
393 /* Now sort the shake blocks... */
394 qsort(sid+at_start, at_end-at_start, (size_t)sizeof(sid[0]), sid_comp);
398 fprintf(debug, "Sorted shake block\n");
399 for (i = at_start; (i < at_end); i++)
401 fprintf(debug, "sid[%5d] = atom:%5d sid:%5d\n", i, sid[i].atom, sid[i].sid);
404 /* Now check how many are NOT -1, i.e. how many have to be shaken */
405 for (i0 = at_start; (i0 < at_end); i0++)
407 if (sid[i0].sid > -1)
413 /* Now we have the sids that have to be shaken. We'll check the min and
414 * max atom numbers and this determines the shake block. DvdS 2007-07-19.
415 * For the purpose of making boundaries all atoms in between need to be
416 * part of the shake block too. There may be cases where blocks overlap
417 * and they will have to be merged.
419 nsid = merge_sid(at_start, at_end, nsid, sid, sblock);
420 /* Now sort the shake blocks again... */
421 /*qsort(sid,natoms,(size_t)sizeof(sid[0]),sid_comp);*/
423 /* Fill the sblock struct */
424 /* sblock->nr = nsid;
425 sblock->nra = natoms;
426 srenew(sblock->a,sblock->nra);
427 srenew(sblock->index,sblock->nr+1);
432 sblock->index[n++]=k;
434 istart = sid[i].atom;
435 while ((i<natoms-1) && (sid[i+1].sid == isid))
437 /* After while: we found a new block, or are thru with the atoms */
438 /* for(j=istart; (j<=sid[i].atom); j++,k++)
440 sblock->index[n] = k;
444 gmx_fatal(FARGS,"Death Horror: nsid = %d, n= %d",nsid,n);
450 /* Due to unknown reason this free generates a problem sometimes */
455 fprintf(debug, "Done gen_sblocks\n");