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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/gmxassert.h"
52 #include "gromacs/utility/smalloc.h"
59 static bool sid_comp(const t_sid& sa, const t_sid& sb)
63 return sa.atom < sb.atom;
67 return sa.sid < sb.sid;
71 static int mk_grey(egCol egc[], t_graph* g, int* AtomI, int maxsid, t_sid sid[])
73 int j, ng, ai, aj, g0;
79 /* Loop over all the bonds */
80 for (j = 0; (j < g->nedge[ai]); j++)
82 aj = g->edge[ai][j] - g0;
83 /* If there is a white one, make it gray and set pbc */
84 if (egc[aj] == egcolWhite)
92 /* Check whether this one has been set before... */
93 range_check(aj + g0, 0, maxsid);
94 range_check(ai + g0, 0, maxsid);
95 if (sid[aj + g0].sid != -1)
97 gmx_fatal(FARGS, "sid[%d]=%d, sid[%d]=%d, file %s, line %d", ai, sid[ai + g0].sid,
98 aj, sid[aj + g0].sid, __FILE__, __LINE__);
102 sid[aj + g0].sid = sid[ai + g0].sid;
103 sid[aj + g0].atom = aj + g0;
111 static int first_colour(int fC, egCol Col, t_graph* g, const egCol egc[])
112 /* Return the first node with colour Col starting at fC.
113 * return -1 if none found.
118 for (i = fC; (i < g->nnodes); i++)
120 if ((g->nedge[i] > 0) && (egc[i] == Col))
129 static int mk_sblocks(FILE* fp, t_graph* g, int maxsid, t_sid sid[])
132 int nW, nG, nB; /* Number of Grey, Black, White */
133 int fW, fG; /* First of each category */
134 egCol* egc = nullptr; /* The colour of each node */
154 /* We even have a loop invariant:
155 * nW+nG+nB == g->nbound
160 fprintf(fp, "Walking down the molecule graph to make constraint-blocks\n");
165 /* Find the first white, this will allways be a larger
166 * number than before, because no nodes are made white
169 if ((fW = first_colour(fW, egcolWhite, g, egc)) == -1)
171 gmx_fatal(FARGS, "No WHITE nodes found while nW=%d\n", nW);
174 /* Make the first white node grey, and set the block number */
176 range_check(fW + g0, 0, maxsid);
177 sid[fW + g0].sid = nblock++;
181 /* Initial value for the first grey */
186 fprintf(debug, "Starting G loop (nW=%d, nG=%d, nB=%d, total %d)\n", nW, nG, nB, nW + nG + nB);
191 if ((fG = first_colour(fG, egcolGrey, g, egc)) == -1)
193 gmx_fatal(FARGS, "No GREY nodes found while nG=%d\n", nG);
196 /* Make the first grey node black */
197 egc[fG] = egcolBlack;
201 /* Make all the neighbours of this black node grey
202 * and set their block number
204 ng = mk_grey(egc, g, &fG, maxsid, sid);
205 /* ng is the number of white nodes made grey */
214 fprintf(debug, "Found %d shake blocks\n", nblock);
223 int first, last, sid;
226 static int ms_comp(const void* a, const void* b)
228 const t_merge_sid* ma = reinterpret_cast<const t_merge_sid*>(a);
229 const t_merge_sid* mb = reinterpret_cast<const t_merge_sid*>(b);
232 d = ma->first - mb->first;
235 return ma->last - mb->last;
243 static int merge_sid(int at_start, int at_end, int nsid, t_sid sid[], t_blocka* sblock)
245 int i, j, k, n, isid, ndel;
248 /* We try to remdy the following problem:
249 * Atom: 1 2 3 4 5 6 7 8 9 10
250 * Sid: 0 -1 1 0 -1 1 1 1 1 1
253 /* Determine first and last atom in each shake ID */
256 for (k = 0; (k < nsid); k++)
258 ms[k].first = at_end + 1;
262 for (i = at_start; (i < at_end); i++)
265 range_check(isid, -1, nsid);
268 ms[isid].first = std::min(ms[isid].first, sid[i].atom);
269 ms[isid].last = std::max(ms[isid].last, sid[i].atom);
272 qsort(ms, nsid, sizeof(ms[0]), ms_comp);
274 /* Now merge the overlapping ones */
276 for (k = 0; (k < nsid);)
278 for (j = k + 1; (j < nsid);)
280 if (ms[j].first <= ms[k].last)
282 ms[k].last = std::max(ms[k].last, ms[j].last);
283 ms[k].first = std::min(ms[k].first, ms[j].first);
299 for (k = 0; (k < nsid); k++)
301 while ((k < nsid - 1) && (ms[k].sid == -1))
303 for (j = k + 1; (j < nsid); j++)
305 std::memcpy(&(ms[j - 1]), &(ms[j]), sizeof(ms[0]));
311 for (k = at_start; (k < at_end); k++)
317 sblock->nalloc_index = sblock->nr + 1;
318 snew(sblock->index, sblock->nalloc_index);
319 sblock->nra = at_end - at_start;
320 sblock->nalloc_a = sblock->nra;
321 snew(sblock->a, sblock->nalloc_a);
322 sblock->index[0] = 0;
323 for (k = n = 0; (k < nsid); k++)
325 sblock->index[k + 1] = sblock->index[k] + ms[k].last - ms[k].first + 1;
326 for (j = ms[k].first; (j <= ms[k].last); j++)
328 range_check(n, 0, sblock->nra);
330 range_check(j, 0, at_end);
331 if (sid[j].sid == -1)
337 fprintf(stderr, "Double sids (%d, %d) for atom %d\n", sid[j].sid, k, j);
343 GMX_RELEASE_ASSERT(sblock->index[k] == sblock->nra, "Internal inconsistency; sid merge failed");
350 void gen_sblocks(FILE* fp, int at_start, int at_end, const t_idef* idef, t_blocka* sblock, gmx_bool bSettle)
357 g = mk_graph(nullptr, idef, at_start, at_end, TRUE, bSettle);
360 p_graph(debug, "Graaf Dracula", g);
363 for (i = at_start; (i < at_end); i++)
368 nsid = mk_sblocks(fp, g, at_end, sid);
375 /* Now sort the shake blocks... */
376 std::sort(sid + at_start, sid + at_end, sid_comp);
380 fprintf(debug, "Sorted shake block\n");
381 for (i = at_start; (i < at_end); i++)
383 fprintf(debug, "sid[%5d] = atom:%5d sid:%5d\n", i, sid[i].atom, sid[i].sid);
386 /* Now check how many are NOT -1, i.e. how many have to be shaken */
387 for (i0 = at_start; (i0 < at_end); i0++)
389 if (sid[i0].sid > -1)
395 /* Now we have the sids that have to be shaken. We'll check the min and
396 * max atom numbers and this determines the shake block. DvdS 2007-07-19.
397 * For the purpose of making boundaries all atoms in between need to be
398 * part of the shake block too. There may be cases where blocks overlap
399 * and they will have to be merged.
401 merge_sid(at_start, at_end, nsid, sid, sblock);
403 /* Due to unknown reason this free generates a problem sometimes */
408 fprintf(debug, "Done gen_sblocks\n");