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45 #include "gromacs/math/vecdump.h"
46 #include "gromacs/topology/atoms.h"
47 #include "gromacs/topology/idef.h"
48 #include "gromacs/topology/ifunc.h"
49 #include "gromacs/topology/symtab.h"
50 #include "gromacs/utility/compare.h"
51 #include "gromacs/utility/gmxassert.h"
52 #include "gromacs/utility/smalloc.h"
53 #include "gromacs/utility/strconvert.h"
54 #include "gromacs/utility/txtdump.h"
56 const char *gtypes[egcNR+1] = {
57 "T-Coupling", "Energy Mon.", "Acceleration", "Freeze",
58 "User1", "User2", "VCM", "Compressed X", "Or. Res. Fit", "QMMM", nullptr
61 static void init_groups(gmx_groups_t *groups)
64 groups->grpname = nullptr;
65 for (int g = 0; g < egcNR; g++)
67 groups->grps[g].nr = 0;
68 groups->grps[g].nm_ind = nullptr;
69 groups->ngrpnr[g] = 0;
70 groups->grpnr[g] = nullptr;
75 void init_mtop(gmx_mtop_t *mtop)
79 // TODO: Move to ffparams when that is converted to C++
80 mtop->ffparams.functype = nullptr;
81 mtop->ffparams.iparams = nullptr;
82 mtop->ffparams.cmap_grid.ngrid = 0;
83 mtop->ffparams.cmap_grid.grid_spacing = 0;
84 mtop->ffparams.cmap_grid.cmapdata = nullptr;
85 mtop->ffparams.ntypes = 0;
87 mtop->moltype.clear();
88 mtop->molblock.clear();
89 mtop->bIntermolecularInteractions = FALSE;
90 mtop->intermolecular_ilist = nullptr;
93 mtop->maxres_renum = 0;
95 init_atomtypes(&mtop->atomtypes);
96 init_groups(&mtop->groups);
97 open_symtab(&mtop->symtab);
100 void init_top(t_topology *top)
103 init_atom(&(top->atoms));
104 init_atomtypes(&(top->atomtypes));
105 init_block(&top->cgs);
106 init_block(&top->mols);
107 init_blocka(&top->excls);
108 open_symtab(&top->symtab);
112 gmx_moltype_t::gmx_moltype_t() :
117 init_t_atoms(&atoms, 0, FALSE);
119 for (int ftype = 0; ftype < F_NRE; ftype++)
122 ilist[ftype].nr_nonperturbed = 0;
123 ilist[ftype].iatoms = nullptr;
124 ilist[ftype].nalloc = 0;
128 gmx_moltype_t::~gmx_moltype_t()
134 for (int f = 0; f < F_NRE; f++)
136 sfree(ilist[f].iatoms);
141 void done_gmx_groups_t(gmx_groups_t *g)
145 for (i = 0; (i < egcNR); i++)
147 if (nullptr != g->grps[i].nm_ind)
149 sfree(g->grps[i].nm_ind);
150 g->grps[i].nm_ind = nullptr;
152 if (nullptr != g->grpnr[i])
155 g->grpnr[i] = nullptr;
158 /* The contents of this array is in symtab, don't free it here */
162 gmx_mtop_t::gmx_mtop_t()
167 gmx_mtop_t::~gmx_mtop_t()
169 done_symtab(&symtab);
171 sfree(ffparams.functype);
172 sfree(ffparams.iparams);
173 for (int i = 0; i < ffparams.cmap_grid.ngrid; i++)
175 sfree(ffparams.cmap_grid.cmapdata[i].cmap);
177 sfree(ffparams.cmap_grid.cmapdata);
181 done_atomtypes(&atomtypes);
182 done_gmx_groups_t(&groups);
185 void done_top(t_topology *top)
187 sfree(top->idef.functype);
188 sfree(top->idef.iparams);
189 sfree(top->idef.cmap_grid.cmapdata);
190 for (int f = 0; f < F_NRE; ++f)
192 sfree(top->idef.il[f].iatoms);
193 top->idef.il[f].iatoms = nullptr;
194 top->idef.il[f].nalloc = 0;
197 done_atom(&(top->atoms));
200 done_atomtypes(&(top->atomtypes));
202 done_symtab(&(top->symtab));
203 done_block(&(top->cgs));
204 done_block(&(top->mols));
205 done_blocka(&(top->excls));
208 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
214 for (int f = 0; f < F_NRE; ++f)
216 sfree(top->idef.il[f].iatoms);
217 top->idef.il[f].iatoms = nullptr;
218 top->idef.il[f].nalloc = 0;
220 done_atom(&top->atoms);
221 done_block(&top->cgs);
222 done_blocka(&top->excls);
223 done_block(&top->mols);
224 done_symtab(&top->symtab);
225 open_symtab(&mtop->symtab);
226 sfree(top->idef.functype);
227 sfree(top->idef.iparams);
228 sfree(top->idef.cmap_grid.cmapdata);
229 done_atomtypes(&(top->atomtypes));
232 // Note that the rest of mtop will be freed by the destructor
236 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop)
242 return mtop->moltype.empty() || mtop->moltype[0].atoms.haveMass;
245 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop)
251 return mtop->moltype.empty() || mtop->moltype[0].atoms.haveCharge;
254 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop)
260 return mtop->moltype.empty() || mtop->moltype[0].atoms.haveType;
263 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop)
269 return mtop->moltype.empty() || mtop->moltype[0].atoms.havePdbInfo;
272 static void pr_grps(FILE *fp, const char *title, const t_grps grps[], char **grpname[])
276 for (i = 0; (i < egcNR); i++)
278 fprintf(fp, "%s[%-12s] nr=%d, name=[", title, gtypes[i], grps[i].nr);
279 for (j = 0; (j < grps[i].nr); j++)
281 fprintf(fp, " %s", *(grpname[grps[i].nm_ind[j]]));
287 static void pr_groups(FILE *fp, int indent,
288 const gmx_groups_t *groups,
289 gmx_bool bShowNumbers)
293 pr_grps(fp, "grp", groups->grps, groups->grpname);
294 pr_strings(fp, indent, "grpname", groups->grpname, groups->ngrpname, bShowNumbers);
296 pr_indent(fp, indent);
297 fprintf(fp, "groups ");
298 for (g = 0; g < egcNR; g++)
300 printf(" %5.5s", gtypes[g]);
304 pr_indent(fp, indent);
305 fprintf(fp, "allocated ");
307 for (g = 0; g < egcNR; g++)
309 printf(" %5d", groups->ngrpnr[g]);
310 nat_max = std::max(nat_max, groups->ngrpnr[g]);
316 pr_indent(fp, indent);
317 fprintf(fp, "groupnr[%5s] =", "*");
318 for (g = 0; g < egcNR; g++)
320 fprintf(fp, " %3d ", 0);
326 for (i = 0; i < nat_max; i++)
328 pr_indent(fp, indent);
329 fprintf(fp, "groupnr[%5d] =", i);
330 for (g = 0; g < egcNR; g++)
333 groups->grpnr[g] ? groups->grpnr[g][i] : 0);
340 static void pr_moltype(FILE *fp, int indent, const char *title,
341 const gmx_moltype_t *molt, int n,
342 const gmx_ffparams_t *ffparams,
343 gmx_bool bShowNumbers, gmx_bool bShowParameters)
347 indent = pr_title_n(fp, indent, title, n);
348 pr_indent(fp, indent);
349 fprintf(fp, "name=\"%s\"\n", *(molt->name));
350 pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
351 pr_block(fp, indent, "cgs", &molt->cgs, bShowNumbers);
352 pr_blocka(fp, indent, "excls", &molt->excls, bShowNumbers);
353 for (j = 0; (j < F_NRE); j++)
355 pr_ilist(fp, indent, interaction_function[j].longname,
356 ffparams->functype, &molt->ilist[j],
357 bShowNumbers, bShowParameters, ffparams->iparams);
361 static void pr_molblock(FILE *fp, int indent, const char *title,
362 const gmx_molblock_t *molb, int n,
363 const std::vector<gmx_moltype_t> &molt)
365 indent = pr_title_n(fp, indent, title, n);
366 pr_indent(fp, indent);
367 fprintf(fp, "%-20s = %d \"%s\"\n",
368 "moltype", molb->type, *(molt[molb->type].name));
369 pr_int(fp, indent, "#molecules", molb->nmol);
370 pr_int(fp, indent, "#posres_xA", molb->posres_xA.size());
371 if (!molb->posres_xA.empty())
373 pr_rvecs(fp, indent, "posres_xA", as_rvec_array(molb->posres_xA.data()), molb->posres_xA.size());
375 pr_int(fp, indent, "#posres_xB", molb->posres_xB.size());
376 if (!molb->posres_xB.empty())
378 pr_rvecs(fp, indent, "posres_xB", as_rvec_array(molb->posres_xB.data()), molb->posres_xB.size());
382 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
383 gmx_bool bShowNumbers, gmx_bool bShowParameters)
385 if (available(fp, mtop, indent, title))
387 indent = pr_title(fp, indent, title);
388 pr_indent(fp, indent);
389 fprintf(fp, "name=\"%s\"\n", *(mtop->name));
390 pr_int(fp, indent, "#atoms", mtop->natoms);
391 pr_int(fp, indent, "#molblock", mtop->molblock.size());
392 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
394 pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
396 pr_str(fp, indent, "bIntermolecularInteractions",
397 gmx::boolToString(mtop->bIntermolecularInteractions));
398 if (mtop->bIntermolecularInteractions)
400 for (int j = 0; j < F_NRE; j++)
402 pr_ilist(fp, indent, interaction_function[j].longname,
403 mtop->ffparams.functype,
404 &mtop->intermolecular_ilist[j],
405 bShowNumbers, bShowParameters, mtop->ffparams.iparams);
408 pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
409 pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
410 for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
412 pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
413 &mtop->ffparams, bShowNumbers, bShowParameters);
415 pr_groups(fp, indent, &mtop->groups, bShowNumbers);
419 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
420 gmx_bool bShowNumbers, gmx_bool bShowParameters)
422 if (available(fp, top, indent, title))
424 indent = pr_title(fp, indent, title);
425 pr_indent(fp, indent);
426 fprintf(fp, "name=\"%s\"\n", *(top->name));
427 pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
428 pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
429 pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
430 pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
431 pr_str(fp, indent, "bIntermolecularInteractions",
432 gmx::boolToString(top->bIntermolecularInteractions));
433 pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
434 pr_idef(fp, indent, "idef", &top->idef, bShowNumbers, bShowParameters);
438 static void cmp_ilist(FILE *fp, int ftype, const t_ilist *il1, const t_ilist *il2)
443 fprintf(fp, "comparing ilist %s\n", interaction_function[ftype].name);
444 sprintf(buf, "%s->nr", interaction_function[ftype].name);
445 cmp_int(fp, buf, -1, il1->nr, il2->nr);
446 sprintf(buf, "%s->iatoms", interaction_function[ftype].name);
447 if (((il1->nr > 0) && (!il1->iatoms)) ||
448 ((il2->nr > 0) && (!il2->iatoms)) ||
449 ((il1->nr != il2->nr)))
451 fprintf(fp, "Comparing radically different topologies - %s is different\n",
456 for (i = 0; (i < il1->nr); i++)
458 cmp_int(fp, buf, i, il1->iatoms[i], il2->iatoms[i]);
463 static void cmp_iparm(FILE *fp, const char *s, t_functype ft,
464 const t_iparams &ip1, const t_iparams &ip2, real ftol, real abstol)
470 for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
472 bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], ftol, abstol);
476 fprintf(fp, "%s1: ", s);
477 pr_iparams(fp, ft, &ip1);
478 fprintf(fp, "%s2: ", s);
479 pr_iparams(fp, ft, &ip2);
483 static void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft,
484 const t_iparams &ip1, real ftol, real abstol)
486 int nrfpA, nrfpB, p0, i;
489 /* Normally the first parameter is perturbable */
491 nrfpA = interaction_function[ft].nrfpA;
492 nrfpB = interaction_function[ft].nrfpB;
497 else if (interaction_function[ft].flags & IF_TABULATED)
499 /* For tabulated interactions only the second parameter is perturbable */
504 for (i = 0; i < nrfpB && !bDiff; i++)
506 bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], ftol, abstol);
510 fprintf(fp, "%s: ", s);
511 pr_iparams(fp, ft, &ip1);
515 static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real ftol, real abstol)
517 cmp_int(fp, "cmap ngrid", -1, cmap1->ngrid, cmap2->ngrid);
518 cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
519 if (cmap1->ngrid == cmap2->ngrid &&
520 cmap1->grid_spacing == cmap2->grid_spacing)
524 for (g = 0; g < cmap1->ngrid; g++)
528 fprintf(fp, "comparing cmap %d\n", g);
530 for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
532 cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], ftol, abstol);
538 static void cmp_idef(FILE *fp, const t_idef *id1, const t_idef *id2, real ftol, real abstol)
541 char buf1[64], buf2[64];
543 fprintf(fp, "comparing idef\n");
546 cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes);
547 cmp_int(fp, "idef->atnr", -1, id1->atnr, id2->atnr);
548 for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++)
550 sprintf(buf1, "idef->functype[%d]", i);
551 sprintf(buf2, "idef->iparam[%d]", i);
552 cmp_int(fp, buf1, i, (int)id1->functype[i], (int)id2->functype[i]);
553 cmp_iparm(fp, buf2, id1->functype[i],
554 id1->iparams[i], id2->iparams[i], ftol, abstol);
556 cmp_real(fp, "fudgeQQ", -1, id1->fudgeQQ, id2->fudgeQQ, ftol, abstol);
557 cmp_cmap(fp, &id1->cmap_grid, &id2->cmap_grid, ftol, abstol);
558 for (i = 0; (i < F_NRE); i++)
560 cmp_ilist(fp, i, &(id1->il[i]), &(id2->il[i]));
565 for (i = 0; (i < id1->ntypes); i++)
567 cmp_iparm_AB(fp, "idef->iparam", id1->functype[i], id1->iparams[i], ftol, abstol);
572 static void cmp_block(FILE *fp, const t_block *b1, const t_block *b2, const char *s)
576 fprintf(fp, "comparing block %s\n", s);
577 sprintf(buf, "%s.nr", s);
578 cmp_int(fp, buf, -1, b1->nr, b2->nr);
581 static void cmp_blocka(FILE *fp, const t_blocka *b1, const t_blocka *b2, const char *s)
585 fprintf(fp, "comparing blocka %s\n", s);
586 sprintf(buf, "%s.nr", s);
587 cmp_int(fp, buf, -1, b1->nr, b2->nr);
588 sprintf(buf, "%s.nra", s);
589 cmp_int(fp, buf, -1, b1->nra, b2->nra);
592 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol)
594 fprintf(fp, "comparing top\n");
597 cmp_idef(fp, &(t1->idef), &(t2->idef), ftol, abstol);
598 cmp_atoms(fp, &(t1->atoms), &(t2->atoms), ftol, abstol);
599 cmp_block(fp, &t1->cgs, &t2->cgs, "cgs");
600 cmp_block(fp, &t1->mols, &t2->mols, "mols");
601 cmp_bool(fp, "bIntermolecularInteractions", -1, t1->bIntermolecularInteractions, t2->bIntermolecularInteractions);
602 cmp_blocka(fp, &t1->excls, &t2->excls, "excls");
606 cmp_idef(fp, &(t1->idef), nullptr, ftol, abstol);
607 cmp_atoms(fp, &(t1->atoms), nullptr, ftol, abstol);
611 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
612 int natoms0, int natoms1)
617 fprintf(fp, "comparing groups\n");
619 for (i = 0; i < egcNR; i++)
621 sprintf(buf, "grps[%d].nr", i);
622 cmp_int(fp, buf, -1, g0->grps[i].nr, g1->grps[i].nr);
623 if (g0->grps[i].nr == g1->grps[i].nr)
625 for (j = 0; j < g0->grps[i].nr; j++)
627 sprintf(buf, "grps[%d].name[%d]", i, j);
629 *g0->grpname[g0->grps[i].nm_ind[j]],
630 *g1->grpname[g1->grps[i].nm_ind[j]]);
633 cmp_int(fp, "ngrpnr", i, g0->ngrpnr[i], g1->ngrpnr[i]);
634 if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 &&
635 (g0->grpnr[i] != nullptr || g1->grpnr[i] != nullptr))
637 for (j = 0; j < natoms0; j++)
639 cmp_int(fp, gtypes[i], j, ggrpnr(g0, i, j), ggrpnr(g1, i, j));
643 /* We have compared the names in the groups lists,
644 * so we can skip the grpname list comparison.