src/gromacs/topology/topology.cpp

   1 /*
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  37 #include "gmxpre.h"
  38
  39 #include "topology.h"
  40
  41 #include <cstdio>
  42
  43 #include <algorithm>
  44
  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/smalloc.h"
  52 #include "gromacs/utility/stringutil.h"
  53 #include "gromacs/utility/txtdump.h"
  54
  55 const char *gtypes[egcNR+1] = {
  56     "T-Coupling", "Energy Mon.", "Acceleration", "Freeze",
  57     "User1", "User2", "VCM", "Compressed X", "Or. Res. Fit", "QMMM", NULL
  58 };
  59
  60 static void init_groups(gmx_groups_t *groups)
  61 {
  62     groups->ngrpname = 0;
  63     groups->grpname  = NULL;
  64     for (int g = 0; g < egcNR; g++)
  65     {
  66         groups->grps[g].nm_ind = NULL;
  67         groups->ngrpnr[g]      = 0;
  68         groups->grpnr[g]       = NULL;
  69     }
  70
  71 }
  72
  73 void init_mtop(gmx_mtop_t *mtop)
  74 {
  75     mtop->name         = NULL;
  76     mtop->nmoltype     = 0;
  77     mtop->moltype      = NULL;
  78     mtop->nmolblock    = 0;
  79     mtop->molblock     = NULL;
  80     mtop->maxres_renum = 0;
  81     mtop->maxresnr     = -1;
  82     init_groups(&mtop->groups);
  83     init_block(&mtop->mols);
  84     open_symtab(&mtop->symtab);
  85 }
  86
  87 void init_top(t_topology *top)
  88 {
  89     top->name = NULL;
  90     init_atom(&(top->atoms));
  91     init_atomtypes(&(top->atomtypes));
  92     init_block(&top->cgs);
  93     init_block(&top->mols);
  94     init_blocka(&top->excls);
  95     open_symtab(&top->symtab);
  96 }
  97
  98
  99 void done_moltype(gmx_moltype_t *molt)
 100 {
 101     done_atom(&molt->atoms);
 102     done_block(&molt->cgs);
 103     done_blocka(&molt->excls);
 104
 105     for (int f = 0; f < F_NRE; f++)
 106     {
 107         sfree(molt->ilist[f].iatoms);
 108         molt->ilist[f].nalloc = 0;
 109     }
 110 }
 111
 112 void done_molblock(gmx_molblock_t *molb)
 113 {
 114     if (molb->nposres_xA > 0)
 115     {
 116         molb->nposres_xA = 0;
 117         sfree(molb->posres_xA);
 118     }
 119     if (molb->nposres_xB > 0)
 120     {
 121         molb->nposres_xB = 0;
 122         sfree(molb->posres_xB);
 123     }
 124 }
 125
 126 void done_gmx_groups_t(gmx_groups_t *g)
 127 {
 128     int i;
 129
 130     for (i = 0; (i < egcNR); i++)
 131     {
 132         if (NULL != g->grps[i].nm_ind)
 133         {
 134             sfree(g->grps[i].nm_ind);
 135             g->grps[i].nm_ind = NULL;
 136         }
 137         if (NULL != g->grpnr[i])
 138         {
 139             sfree(g->grpnr[i]);
 140             g->grpnr[i] = NULL;
 141         }
 142     }
 143     /* The contents of this array is in symtab, don't free it here */
 144     sfree(g->grpname);
 145 }
 146
 147 void done_mtop(gmx_mtop_t *mtop)
 148 {
 149     done_symtab(&mtop->symtab);
 150
 151     sfree(mtop->ffparams.functype);
 152     sfree(mtop->ffparams.iparams);
 153
 154     for (int i = 0; i < mtop->nmoltype; i++)
 155     {
 156         done_moltype(&mtop->moltype[i]);
 157     }
 158     sfree(mtop->moltype);
 159     for (int i = 0; i < mtop->nmolblock; i++)
 160     {
 161         done_molblock(&mtop->molblock[i]);
 162     }
 163     sfree(mtop->molblock);
 164     done_atomtypes(&mtop->atomtypes);
 165     done_gmx_groups_t(&mtop->groups);
 166     done_block(&mtop->mols);
 167 }
 168
 169 void done_top(t_topology *top)
 170 {
 171     sfree(top->idef.functype);
 172     sfree(top->idef.iparams);
 173     for (int f = 0; f < F_NRE; ++f)
 174     {
 175         sfree(top->idef.il[f].iatoms);
 176         top->idef.il[f].iatoms = NULL;
 177         top->idef.il[f].nalloc = 0;
 178     }
 179
 180     done_atom(&(top->atoms));
 181
 182     /* For GB */
 183     done_atomtypes(&(top->atomtypes));
 184
 185     done_symtab(&(top->symtab));
 186     done_block(&(top->cgs));
 187     done_block(&(top->mols));
 188     done_blocka(&(top->excls));
 189 }
 190
 191 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
 192 {
 193     if (mtop != nullptr)
 194     {
 195         if (top != nullptr)
 196         {
 197             for (int f = 0; f < F_NRE; ++f)
 198             {
 199                 sfree(top->idef.il[f].iatoms);
 200                 top->idef.il[f].iatoms = NULL;
 201                 top->idef.il[f].nalloc = 0;
 202             }
 203             done_atom(&top->atoms);
 204             done_block(&top->cgs);
 205             done_blocka(&top->excls);
 206             done_symtab(&top->symtab);
 207             open_symtab(&mtop->symtab);
 208         }
 209         done_mtop(mtop);
 210     }
 211 }
 212
 213 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop)
 214 {
 215     if (mtop == nullptr)
 216     {
 217         return false;
 218     }
 219     return mtop->nmoltype == 0 || mtop->moltype[0].atoms.haveMass;
 220 }
 221
 222 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop)
 223 {
 224     if (mtop == nullptr)
 225     {
 226         return false;
 227     }
 228     return mtop->nmoltype == 0 || mtop->moltype[0].atoms.haveCharge;
 229 }
 230
 231 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop)
 232 {
 233     if (mtop == nullptr)
 234     {
 235         return false;
 236     }
 237     return mtop->nmoltype == 0 || mtop->moltype[0].atoms.haveType;
 238 }
 239
 240 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop)
 241 {
 242     if (mtop == nullptr)
 243     {
 244         return false;
 245     }
 246     return mtop->nmoltype == 0 || mtop->moltype[0].atoms.havePdbInfo;
 247 }
 248
 249 static void pr_grps(FILE *fp, const char *title, const t_grps grps[], char **grpname[])
 250 {
 251     int i, j;
 252
 253     for (i = 0; (i < egcNR); i++)
 254     {
 255         fprintf(fp, "%s[%-12s] nr=%d, name=[", title, gtypes[i], grps[i].nr);
 256         for (j = 0; (j < grps[i].nr); j++)
 257         {
 258             fprintf(fp, " %s", *(grpname[grps[i].nm_ind[j]]));
 259         }
 260         fprintf(fp, "]\n");
 261     }
 262 }
 263
 264 static void pr_groups(FILE *fp, int indent,
 265                       const gmx_groups_t *groups,
 266                       gmx_bool bShowNumbers)
 267 {
 268     int nat_max, i, g;
 269
 270     pr_grps(fp, "grp", groups->grps, groups->grpname);
 271     pr_strings(fp, indent, "grpname", groups->grpname, groups->ngrpname, bShowNumbers);
 272
 273     pr_indent(fp, indent);
 274     fprintf(fp, "groups          ");
 275     for (g = 0; g < egcNR; g++)
 276     {
 277         printf(" %5.5s", gtypes[g]);
 278     }
 279     printf("\n");
 280
 281     pr_indent(fp, indent);
 282     fprintf(fp, "allocated       ");
 283     nat_max = 0;
 284     for (g = 0; g < egcNR; g++)
 285     {
 286         printf(" %5d", groups->ngrpnr[g]);
 287         nat_max = std::max(nat_max, groups->ngrpnr[g]);
 288     }
 289     printf("\n");
 290
 291     if (nat_max == 0)
 292     {
 293         pr_indent(fp, indent);
 294         fprintf(fp, "groupnr[%5s] =", "*");
 295         for (g = 0; g < egcNR; g++)
 296         {
 297             fprintf(fp, "  %3d ", 0);
 298         }
 299         fprintf(fp, "\n");
 300     }
 301     else
 302     {
 303         for (i = 0; i < nat_max; i++)
 304         {
 305             pr_indent(fp, indent);
 306             fprintf(fp, "groupnr[%5d] =", i);
 307             for (g = 0; g < egcNR; g++)
 308             {
 309                 fprintf(fp, "  %3d ",
 310                         groups->grpnr[g] ? groups->grpnr[g][i] : 0);
 311             }
 312             fprintf(fp, "\n");
 313         }
 314     }
 315 }
 316
 317 static void pr_moltype(FILE *fp, int indent, const char *title,
 318                        const gmx_moltype_t *molt, int n,
 319                        const gmx_ffparams_t *ffparams,
 320                        gmx_bool bShowNumbers)
 321 {
 322     int j;
 323
 324     indent = pr_title_n(fp, indent, title, n);
 325     pr_indent(fp, indent);
 326     fprintf(fp, "name=\"%s\"\n", *(molt->name));
 327     pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
 328     pr_block(fp, indent, "cgs", &molt->cgs, bShowNumbers);
 329     pr_blocka(fp, indent, "excls", &molt->excls, bShowNumbers);
 330     for (j = 0; (j < F_NRE); j++)
 331     {
 332         pr_ilist(fp, indent, interaction_function[j].longname,
 333                  ffparams->functype, &molt->ilist[j], bShowNumbers);
 334     }
 335 }
 336
 337 static void pr_molblock(FILE *fp, int indent, const char *title,
 338                         const gmx_molblock_t *molb, int n,
 339                         const gmx_moltype_t *molt)
 340 {
 341     indent = pr_title_n(fp, indent, title, n);
 342     pr_indent(fp, indent);
 343     fprintf(fp, "%-20s = %d \"%s\"\n",
 344             "moltype", molb->type, *(molt[molb->type].name));
 345     pr_int(fp, indent, "#molecules", molb->nmol);
 346     pr_int(fp, indent, "#atoms_mol", molb->natoms_mol);
 347     pr_int(fp, indent, "#posres_xA", molb->nposres_xA);
 348     if (molb->nposres_xA > 0)
 349     {
 350         pr_rvecs(fp, indent, "posres_xA", molb->posres_xA, molb->nposres_xA);
 351     }
 352     pr_int(fp, indent, "#posres_xB", molb->nposres_xB);
 353     if (molb->nposres_xB > 0)
 354     {
 355         pr_rvecs(fp, indent, "posres_xB", molb->posres_xB, molb->nposres_xB);
 356     }
 357 }
 358
 359 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 360              gmx_bool bShowNumbers)
 361 {
 362     int mt, mb, j;
 363
 364     if (available(fp, mtop, indent, title))
 365     {
 366         indent = pr_title(fp, indent, title);
 367         pr_indent(fp, indent);
 368         fprintf(fp, "name=\"%s\"\n", *(mtop->name));
 369         pr_int(fp, indent, "#atoms", mtop->natoms);
 370         pr_int(fp, indent, "#molblock", mtop->nmolblock);
 371         for (mb = 0; mb < mtop->nmolblock; mb++)
 372         {
 373             pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
 374         }
 375         pr_str(fp, indent, "bIntermolecularInteractions",
 376                gmx::boolToString(mtop->bIntermolecularInteractions));
 377         if (mtop->bIntermolecularInteractions)
 378         {
 379             for (j = 0; (j < F_NRE); j++)
 380             {
 381                 pr_ilist(fp, indent, interaction_function[j].longname,
 382                          mtop->ffparams.functype,
 383                          &mtop->intermolecular_ilist[j], bShowNumbers);
 384             }
 385         }
 386         pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
 387         pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
 388         for (mt = 0; mt < mtop->nmoltype; mt++)
 389         {
 390             pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
 391                        &mtop->ffparams, bShowNumbers);
 392         }
 393         pr_groups(fp, indent, &mtop->groups, bShowNumbers);
 394     }
 395 }
 396
 397 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers)
 398 {
 399     if (available(fp, top, indent, title))
 400     {
 401         indent = pr_title(fp, indent, title);
 402         pr_indent(fp, indent);
 403         fprintf(fp, "name=\"%s\"\n", *(top->name));
 404         pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
 405         pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
 406         pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
 407         pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
 408         pr_str(fp, indent, "bIntermolecularInteractions",
 409                gmx::boolToString(top->bIntermolecularInteractions));
 410         pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
 411         pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
 412     }
 413 }
 414
 415 static void cmp_ilist(FILE *fp, int ftype, const t_ilist *il1, const t_ilist *il2)
 416 {
 417     int  i;
 418     char buf[256];
 419
 420     fprintf(fp, "comparing ilist %s\n", interaction_function[ftype].name);
 421     sprintf(buf, "%s->nr", interaction_function[ftype].name);
 422     cmp_int(fp, buf, -1, il1->nr, il2->nr);
 423     sprintf(buf, "%s->iatoms", interaction_function[ftype].name);
 424     if (((il1->nr > 0) && (!il1->iatoms)) ||
 425         ((il2->nr > 0) && (!il2->iatoms)) ||
 426         ((il1->nr != il2->nr)))
 427     {
 428         fprintf(fp, "Comparing radically different topologies - %s is different\n",
 429                 buf);
 430     }
 431     else
 432     {
 433         for (i = 0; (i < il1->nr); i++)
 434         {
 435             cmp_int(fp, buf, i, il1->iatoms[i], il2->iatoms[i]);
 436         }
 437     }
 438 }
 439
 440 static void cmp_iparm(FILE *fp, const char *s, t_functype ft,
 441                       const t_iparams &ip1, const t_iparams &ip2, real ftol, real abstol)
 442 {
 443     int      i;
 444     gmx_bool bDiff;
 445
 446     bDiff = FALSE;
 447     for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
 448     {
 449         bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], ftol, abstol);
 450     }
 451     if (bDiff)
 452     {
 453         fprintf(fp, "%s1: ", s);
 454         pr_iparams(fp, ft, &ip1);
 455         fprintf(fp, "%s2: ", s);
 456         pr_iparams(fp, ft, &ip2);
 457     }
 458 }
 459
 460 static void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft,
 461                          const t_iparams &ip1, real ftol, real abstol)
 462 {
 463     int      nrfpA, nrfpB, p0, i;
 464     gmx_bool bDiff;
 465
 466     /* Normally the first parameter is perturbable */
 467     p0    = 0;
 468     nrfpA = interaction_function[ft].nrfpA;
 469     nrfpB = interaction_function[ft].nrfpB;
 470     if (ft == F_PDIHS)
 471     {
 472         nrfpB = 2;
 473     }
 474     else if (interaction_function[ft].flags & IF_TABULATED)
 475     {
 476         /* For tabulated interactions only the second parameter is perturbable */
 477         p0    = 1;
 478         nrfpB = 1;
 479     }
 480     bDiff = FALSE;
 481     for (i = 0; i < nrfpB && !bDiff; i++)
 482     {
 483         bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], ftol, abstol);
 484     }
 485     if (bDiff)
 486     {
 487         fprintf(fp, "%s: ", s);
 488         pr_iparams(fp, ft, &ip1);
 489     }
 490 }
 491
 492 static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real ftol, real abstol)
 493 {
 494     cmp_int(fp, "cmap ngrid", -1, cmap1->ngrid, cmap2->ngrid);
 495     cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
 496     if (cmap1->ngrid == cmap2->ngrid &&
 497         cmap1->grid_spacing == cmap2->grid_spacing)
 498     {
 499         int g;
 500
 501         for (g = 0; g < cmap1->ngrid; g++)
 502         {
 503             int i;
 504
 505             fprintf(fp, "comparing cmap %d\n", g);
 506
 507             for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
 508             {
 509                 cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], ftol, abstol);
 510             }
 511         }
 512     }
 513 }
 514
 515 static void cmp_idef(FILE *fp, const t_idef *id1, const t_idef *id2, real ftol, real abstol)
 516 {
 517     int  i;
 518     char buf1[64], buf2[64];
 519
 520     fprintf(fp, "comparing idef\n");
 521     if (id2)
 522     {
 523         cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes);
 524         cmp_int(fp, "idef->atnr",  -1, id1->atnr, id2->atnr);
 525         for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++)
 526         {
 527             sprintf(buf1, "idef->functype[%d]", i);
 528             sprintf(buf2, "idef->iparam[%d]", i);
 529             cmp_int(fp, buf1, i, (int)id1->functype[i], (int)id2->functype[i]);
 530             cmp_iparm(fp, buf2, id1->functype[i],
 531                       id1->iparams[i], id2->iparams[i], ftol, abstol);
 532         }
 533         cmp_real(fp, "fudgeQQ", -1, id1->fudgeQQ, id2->fudgeQQ, ftol, abstol);
 534         cmp_cmap(fp, &id1->cmap_grid, &id2->cmap_grid, ftol, abstol);
 535         for (i = 0; (i < F_NRE); i++)
 536         {
 537             cmp_ilist(fp, i, &(id1->il[i]), &(id2->il[i]));
 538         }
 539     }
 540     else
 541     {
 542         for (i = 0; (i < id1->ntypes); i++)
 543         {
 544             cmp_iparm_AB(fp, "idef->iparam", id1->functype[i], id1->iparams[i], ftol, abstol);
 545         }
 546     }
 547 }
 548
 549 static void cmp_block(FILE *fp, const t_block *b1, const t_block *b2, const char *s)
 550 {
 551     char buf[32];
 552
 553     fprintf(fp, "comparing block %s\n", s);
 554     sprintf(buf, "%s.nr", s);
 555     cmp_int(fp, buf, -1, b1->nr, b2->nr);
 556 }
 557
 558 static void cmp_blocka(FILE *fp, const t_blocka *b1, const t_blocka *b2, const char *s)
 559 {
 560     char buf[32];
 561
 562     fprintf(fp, "comparing blocka %s\n", s);
 563     sprintf(buf, "%s.nr", s);
 564     cmp_int(fp, buf, -1, b1->nr, b2->nr);
 565     sprintf(buf, "%s.nra", s);
 566     cmp_int(fp, buf, -1, b1->nra, b2->nra);
 567 }
 568
 569 void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol)
 570 {
 571     fprintf(fp, "comparing top\n");
 572     if (t2)
 573     {
 574         cmp_idef(fp, &(t1->idef), &(t2->idef), ftol, abstol);
 575         cmp_atoms(fp, &(t1->atoms), &(t2->atoms), ftol, abstol);
 576         cmp_block(fp, &t1->cgs, &t2->cgs, "cgs");
 577         cmp_block(fp, &t1->mols, &t2->mols, "mols");
 578         cmp_bool(fp, "bIntermolecularInteractions", -1, t1->bIntermolecularInteractions, t2->bIntermolecularInteractions);
 579         cmp_blocka(fp, &t1->excls, &t2->excls, "excls");
 580     }
 581     else
 582     {
 583         cmp_idef(fp, &(t1->idef), NULL, ftol, abstol);
 584         cmp_atoms(fp, &(t1->atoms), NULL, ftol, abstol);
 585     }
 586 }
 587
 588 void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
 589                 int natoms0, int natoms1)
 590 {
 591     int  i, j;
 592     char buf[32];
 593
 594     fprintf(fp, "comparing groups\n");
 595
 596     for (i = 0; i < egcNR; i++)
 597     {
 598         sprintf(buf, "grps[%d].nr", i);
 599         cmp_int(fp, buf, -1, g0->grps[i].nr, g1->grps[i].nr);
 600         if (g0->grps[i].nr == g1->grps[i].nr)
 601         {
 602             for (j = 0; j < g0->grps[i].nr; j++)
 603             {
 604                 sprintf(buf, "grps[%d].name[%d]", i, j);
 605                 cmp_str(fp, buf, -1,
 606                         *g0->grpname[g0->grps[i].nm_ind[j]],
 607                         *g1->grpname[g1->grps[i].nm_ind[j]]);
 608             }
 609         }
 610         cmp_int(fp, "ngrpnr", i, g0->ngrpnr[i], g1->ngrpnr[i]);
 611         if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 &&
 612             (g0->grpnr[i] != NULL || g1->grpnr[i] != NULL))
 613         {
 614             for (j = 0; j < natoms0; j++)
 615             {
 616                 cmp_int(fp, gtypes[i], j, ggrpnr(g0, i, j), ggrpnr(g1, i, j));
 617             }
 618         }
 619     }
 620     /* We have compared the names in the groups lists,
 621      * so we can skip the grpname list comparison.
 622      */
 623 }