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46 #include "gromacs/pbcutil/mshift.h"
47 #include "gromacs/topology/block.h"
48 #include "gromacs/topology/idef.h"
49 #include "gromacs/utility/fatalerror.h"
50 #include "gromacs/utility/gmxassert.h"
51 #include "gromacs/utility/smalloc.h"
58 static bool sid_comp(const t_sid& sa, const t_sid& sb)
62 return sa.atom < sb.atom;
66 return sa.sid < sb.sid;
70 static int mk_grey(egCol egc[], t_graph* g, int* AtomI, int maxsid, t_sid sid[])
72 int j, ng, ai, aj, g0;
78 /* Loop over all the bonds */
79 for (j = 0; (j < g->nedge[ai]); j++)
81 aj = g->edge[ai][j] - g0;
82 /* If there is a white one, make it gray and set pbc */
83 if (egc[aj] == egcolWhite)
91 /* Check whether this one has been set before... */
92 range_check(aj + g0, 0, maxsid);
93 range_check(ai + g0, 0, maxsid);
94 if (sid[aj + g0].sid != -1)
96 gmx_fatal(FARGS, "sid[%d]=%d, sid[%d]=%d, file %s, line %d", ai, sid[ai + g0].sid,
97 aj, sid[aj + g0].sid, __FILE__, __LINE__);
101 sid[aj + g0].sid = sid[ai + g0].sid;
102 sid[aj + g0].atom = aj + g0;
110 static int first_colour(int fC, egCol Col, t_graph* g, const egCol egc[])
111 /* Return the first node with colour Col starting at fC.
112 * return -1 if none found.
117 for (i = fC; (i < g->nnodes); i++)
119 if ((g->nedge[i] > 0) && (egc[i] == Col))
128 static int mk_sblocks(FILE* fp, t_graph* g, int maxsid, t_sid sid[])
131 int nW, nG, nB; /* Number of Grey, Black, White */
132 int fW, fG; /* First of each category */
133 egCol* egc = nullptr; /* The colour of each node */
153 /* We even have a loop invariant:
154 * nW+nG+nB == g->nbound
159 fprintf(fp, "Walking down the molecule graph to make constraint-blocks\n");
164 /* Find the first white, this will allways be a larger
165 * number than before, because no nodes are made white
168 if ((fW = first_colour(fW, egcolWhite, g, egc)) == -1)
170 gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
173 /* Make the first white node grey, and set the block number */
175 range_check(fW + g0, 0, maxsid);
176 sid[fW + g0].sid = nblock++;
180 /* Initial value for the first grey */
185 fprintf(debug, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n", nW, nG, nB, nW + nG + nB);
190 if ((fG = first_colour(fG, egcolGrey, g, egc)) == -1)
192 gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
195 /* Make the first grey node black */
196 egc[fG] = egcolBlack;
200 /* Make all the neighbours of this black node grey
201 * and set their block number
203 ng = mk_grey(egc, g, &fG, maxsid, sid);
204 /* ng is the number of white nodes made grey */
213 fprintf(debug, "Found %d shake blocks\n", nblock);
222 int first, last, sid;
225 static int ms_comp(const void* a, const void* b)
227 const t_merge_sid* ma = reinterpret_cast<const t_merge_sid*>(a);
228 const t_merge_sid* mb = reinterpret_cast<const t_merge_sid*>(b);
231 d = ma->first - mb->first;
234 return ma->last - mb->last;
242 static int merge_sid(int at_start, int at_end, int nsid, t_sid sid[], t_blocka* sblock)
244 int i, j, k, n, isid, ndel;
247 /* We try to remdy the following problem:
248 * Atom: 1 2 3 4 5 6 7 8 9 10
249 * Sid: 0 -1 1 0 -1 1 1 1 1 1
252 /* Determine first and last atom in each shake ID */
255 for (k = 0; (k < nsid); k++)
257 ms[k].first = at_end + 1;
261 for (i = at_start; (i < at_end); i++)
264 range_check(isid, -1, nsid);
267 ms[isid].first = std::min(ms[isid].first, sid[i].atom);
268 ms[isid].last = std::max(ms[isid].last, sid[i].atom);
271 qsort(ms, nsid, sizeof(ms[0]), ms_comp);
273 /* Now merge the overlapping ones */
275 for (k = 0; (k < nsid);)
277 for (j = k + 1; (j < nsid);)
279 if (ms[j].first <= ms[k].last)
281 ms[k].last = std::max(ms[k].last, ms[j].last);
282 ms[k].first = std::min(ms[k].first, ms[j].first);
298 for (k = 0; (k < nsid); k++)
300 while ((k < nsid - 1) && (ms[k].sid == -1))
302 for (j = k + 1; (j < nsid); j++)
304 std::memcpy(&(ms[j - 1]), &(ms[j]), sizeof(ms[0]));
310 for (k = at_start; (k < at_end); k++)
316 sblock->nalloc_index = sblock->nr + 1;
317 snew(sblock->index, sblock->nalloc_index);
318 sblock->nra = at_end - at_start;
319 sblock->nalloc_a = sblock->nra;
320 snew(sblock->a, sblock->nalloc_a);
321 sblock->index[0] = 0;
322 for (k = n = 0; (k < nsid); k++)
324 sblock->index[k + 1] = sblock->index[k] + ms[k].last - ms[k].first + 1;
325 for (j = ms[k].first; (j <= ms[k].last); j++)
327 range_check(n, 0, sblock->nra);
329 range_check(j, 0, at_end);
330 if (sid[j].sid == -1)
336 fprintf(stderr, "Double sids (%d, %d) for atom %d\n", sid[j].sid, k, j);
342 GMX_RELEASE_ASSERT(sblock->index[k] == sblock->nra, "Internal inconsistency; sid merge failed");
349 void gen_sblocks(FILE* fp, int at_start, int at_end, const t_idef* idef, t_blocka* sblock, gmx_bool bSettle)
356 g = mk_graph(nullptr, idef, at_start, at_end, TRUE, bSettle);
359 p_graph(debug, "Graaf Dracula", g);
362 for (i = at_start; (i < at_end); i++)
367 nsid = mk_sblocks(fp, g, at_end, sid);
374 /* Now sort the shake blocks... */
375 std::sort(sid + at_start, sid + at_end, sid_comp);
379 fprintf(debug, "Sorted shake block\n");
380 for (i = at_start; (i < at_end); i++)
382 fprintf(debug, "sid[%5d] = atom:%5d sid:%5d\n", i, sid[i].atom, sid[i].sid);
385 /* Now check how many are NOT -1, i.e. how many have to be shaken */
386 for (i0 = at_start; (i0 < at_end); i0++)
388 if (sid[i0].sid > -1)
394 /* Now we have the sids that have to be shaken. We'll check the min and
395 * max atom numbers and this determines the shake block. DvdS 2007-07-19.
396 * For the purpose of making boundaries all atoms in between need to be
397 * part of the shake block too. There may be cases where blocks overlap
398 * and they will have to be merged.
400 merge_sid(at_start, at_end, nsid, sid, sblock);
402 /* Due to unknown reason this free generates a problem sometimes */
407 fprintf(debug, "Done gen_sblocks\n");