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/arrayref.h"
  51 #include "gromacs/utility/compare.h"
  52 #include "gromacs/utility/gmxassert.h"
  53 #include "gromacs/utility/smalloc.h"
  54 #include "gromacs/utility/strconvert.h"
  55 #include "gromacs/utility/txtdump.h"
  56
  57 gmx::EnumerationArray<SimulationAtomGroupType, const char *>
  58 c_simulationAtomGroupTypeShortNames
  59     = { {
  60             "T-Coupling",
  61             "Energy Mon.",
  62             "Acceleration",
  63             "Freeze",
  64             "User1",
  65             "User2",
  66             "VCM",
  67             "Compressed X",
  68             "Or. Res. Fit",
  69             "QMMM"
  70         } };
  71
  72 const char *shortName(SimulationAtomGroupType type)
  73 {
  74     return c_simulationAtomGroupTypeShortNames[type];
  75 }
  76
  77 SimulationGroups::SimulationGroups()
  78 {
  79     for (auto group : keysOf(groups))
  80     {
  81         groups[group].nr     = 0;
  82         groups[group].nm_ind = nullptr;
  83     }
  84
  85 }
  86
  87 void init_top(t_topology *top)
  88 {
  89     top->name = nullptr;
  90     init_idef(&top->idef);
  91     init_atom(&(top->atoms));
  92     init_atomtypes(&(top->atomtypes));
  93     init_block(&top->cgs);
  94     init_block(&top->mols);
  95     init_blocka(&top->excls);
  96     open_symtab(&top->symtab);
  97 }
  98
  99
 100 gmx_moltype_t::gmx_moltype_t() :
 101     name(nullptr),
 102     cgs(),
 103     excls()
 104 {
 105     init_t_atoms(&atoms, 0, FALSE);
 106 }
 107
 108 gmx_moltype_t::~gmx_moltype_t()
 109 {
 110     done_atom(&atoms);
 111     done_block(&cgs);
 112     done_blocka(&excls);
 113 }
 114
 115 SimulationGroups::~SimulationGroups()
 116 {
 117     for (auto group : keysOf(groups))
 118     {
 119         if (nullptr != groups[group].nm_ind)
 120         {
 121             sfree(groups[group].nm_ind);
 122             groups[group].nm_ind = nullptr;
 123         }
 124     }
 125 }
 126
 127 gmx_mtop_t::gmx_mtop_t()
 128 {
 129     init_atomtypes(&atomtypes);
 130     open_symtab(&symtab);
 131 }
 132
 133 gmx_mtop_t::~gmx_mtop_t()
 134 {
 135     done_symtab(&symtab);
 136
 137     moltype.clear();
 138     molblock.clear();
 139     done_atomtypes(&atomtypes);
 140 }
 141
 142 void done_top(t_topology *top)
 143 {
 144     done_idef(&top->idef);
 145     done_atom(&(top->atoms));
 146
 147     /* For GB */
 148     done_atomtypes(&(top->atomtypes));
 149
 150     done_symtab(&(top->symtab));
 151     done_block(&(top->cgs));
 152     done_block(&(top->mols));
 153     done_blocka(&(top->excls));
 154 }
 155
 156 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
 157 {
 158     if (mtop != nullptr)
 159     {
 160         if (top != nullptr)
 161         {
 162             done_idef(&top->idef);
 163             done_atom(&top->atoms);
 164             done_block(&top->cgs);
 165             done_blocka(&top->excls);
 166             done_block(&top->mols);
 167             done_symtab(&top->symtab);
 168             open_symtab(&mtop->symtab);
 169             done_atomtypes(&(top->atomtypes));
 170         }
 171
 172         // Note that the rest of mtop will be freed by the destructor
 173     }
 174 }
 175
 176 gmx_localtop_t::gmx_localtop_t()
 177 {
 178     init_block_null(&cgs);
 179     init_blocka_null(&excls);
 180     init_idef(&idef);
 181     init_atomtypes(&atomtypes);
 182 }
 183
 184 gmx_localtop_t::~gmx_localtop_t()
 185 {
 186     if (!useInDomainDecomp_)
 187     {
 188         done_idef(&idef);
 189         done_block(&cgs);
 190         done_blocka(&excls);
 191         done_atomtypes(&atomtypes);
 192     }
 193 }
 194
 195 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop)
 196 {
 197     if (mtop == nullptr)
 198     {
 199         return false;
 200     }
 201     return mtop->moltype.empty() || mtop->moltype[0].atoms.haveMass;
 202 }
 203
 204 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop)
 205 {
 206     if (mtop == nullptr)
 207     {
 208         return false;
 209     }
 210     return mtop->moltype.empty() || mtop->moltype[0].atoms.haveCharge;
 211 }
 212
 213 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t &mtop)
 214 {
 215     for (const gmx_moltype_t &moltype : mtop.moltype)
 216     {
 217         const t_atoms &atoms = moltype.atoms;
 218         if (atoms.haveBState)
 219         {
 220             for (int a = 0; a < atoms.nr; a++)
 221             {
 222                 if (atoms.atom[a].q != atoms.atom[a].qB)
 223                 {
 224                     return true;
 225                 }
 226             }
 227         }
 228     }
 229     return false;
 230 }
 231
 232 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop)
 233 {
 234     if (mtop == nullptr)
 235     {
 236         return false;
 237     }
 238     return mtop->moltype.empty() || mtop->moltype[0].atoms.haveType;
 239 }
 240
 241 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop)
 242 {
 243     if (mtop == nullptr)
 244     {
 245         return false;
 246     }
 247     return mtop->moltype.empty() || mtop->moltype[0].atoms.havePdbInfo;
 248 }
 249
 250 static void pr_grps(FILE                       *fp,
 251                     const char                 *title,
 252                     gmx::ArrayRef<const t_grps> grps,
 253                     char                     ***grpname)
 254 {
 255     int index = 0;
 256     for (const auto &group : grps)
 257     {
 258         fprintf(fp, "%s[%-12s] nr=%d, name=[", title, c_simulationAtomGroupTypeShortNames[index], group.nr);
 259         for (int j = 0; (j < group.nr); j++)
 260         {
 261             fprintf(fp, " %s", *(grpname[group.nm_ind[j]]));
 262         }
 263         fprintf(fp, "]\n");
 264         index++;
 265     }
 266 }
 267
 268 static void pr_groups(FILE *fp, int indent,
 269                       const SimulationGroups &groups,
 270                       gmx_bool bShowNumbers)
 271 {
 272     pr_grps(fp,
 273             "grp",
 274             groups.groups,
 275             const_cast<char ***>(groups.groupNames.data()));
 276     pr_strings(fp, indent, "grpname", const_cast<char ***>(groups.groupNames.data()), groups.groupNames.size(), bShowNumbers);
 277
 278     pr_indent(fp, indent);
 279     fprintf(fp, "groups          ");
 280     for (const auto &group : c_simulationAtomGroupTypeShortNames)
 281     {
 282         printf(" %5.5s", group);
 283     }
 284     printf("\n");
 285
 286     pr_indent(fp, indent);
 287     fprintf(fp, "allocated       ");
 288     int nat_max = 0;
 289     for (auto group : keysOf(groups.groups))
 290     {
 291         printf(" %5d", groups.numberOfGroupNumbers(group));
 292         nat_max = std::max(nat_max, groups.numberOfGroupNumbers(group));
 293     }
 294     printf("\n");
 295
 296     if (nat_max == 0)
 297     {
 298         pr_indent(fp, indent);
 299         fprintf(fp, "groupnr[%5s] =", "*");
 300         for (auto gmx_unused group : keysOf(groups.groups))
 301         {
 302             fprintf(fp, "  %3d ", 0);
 303         }
 304         fprintf(fp, "\n");
 305     }
 306     else
 307     {
 308         for (int i = 0; i < nat_max; i++)
 309         {
 310             pr_indent(fp, indent);
 311             fprintf(fp, "groupnr[%5d] =", i);
 312             for (auto group : keysOf(groups.groups))
 313             {
 314                 fprintf(fp, "  %3d ",
 315                         !groups.groupNumbers[group].empty() ?
 316                         groups.groupNumbers[group][i] : 0);
 317             }
 318             fprintf(fp, "\n");
 319         }
 320     }
 321 }
 322
 323 static void pr_moltype(FILE *fp, int indent, const char *title,
 324                        const gmx_moltype_t *molt, int n,
 325                        const gmx_ffparams_t *ffparams,
 326                        gmx_bool bShowNumbers, gmx_bool bShowParameters)
 327 {
 328     int j;
 329
 330     indent = pr_title_n(fp, indent, title, n);
 331     pr_indent(fp, indent);
 332     fprintf(fp, "name=\"%s\"\n", *(molt->name));
 333     pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
 334     pr_block(fp, indent, "cgs", &molt->cgs, bShowNumbers);
 335     pr_blocka(fp, indent, "excls", &molt->excls, bShowNumbers);
 336     for (j = 0; (j < F_NRE); j++)
 337     {
 338         pr_ilist(fp, indent, interaction_function[j].longname,
 339                  ffparams->functype.data(), molt->ilist[j],
 340                  bShowNumbers, bShowParameters, ffparams->iparams.data());
 341     }
 342 }
 343
 344 static void pr_molblock(FILE *fp, int indent, const char *title,
 345                         const gmx_molblock_t *molb, int n,
 346                         const std::vector<gmx_moltype_t> &molt)
 347 {
 348     indent = pr_title_n(fp, indent, title, n);
 349     pr_indent(fp, indent);
 350     fprintf(fp, "%-20s = %d \"%s\"\n",
 351             "moltype", molb->type, *(molt[molb->type].name));
 352     pr_int(fp, indent, "#molecules", molb->nmol);
 353     pr_int(fp, indent, "#posres_xA", molb->posres_xA.size());
 354     if (!molb->posres_xA.empty())
 355     {
 356         pr_rvecs(fp, indent, "posres_xA", as_rvec_array(molb->posres_xA.data()), molb->posres_xA.size());
 357     }
 358     pr_int(fp, indent, "#posres_xB", molb->posres_xB.size());
 359     if (!molb->posres_xB.empty())
 360     {
 361         pr_rvecs(fp, indent, "posres_xB", as_rvec_array(molb->posres_xB.data()), molb->posres_xB.size());
 362     }
 363 }
 364
 365 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 366              gmx_bool bShowNumbers, gmx_bool bShowParameters)
 367 {
 368     if (available(fp, mtop, indent, title))
 369     {
 370         indent = pr_title(fp, indent, title);
 371         pr_indent(fp, indent);
 372         fprintf(fp, "name=\"%s\"\n", *(mtop->name));
 373         pr_int(fp, indent, "#atoms", mtop->natoms);
 374         pr_int(fp, indent, "#molblock", mtop->molblock.size());
 375         for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
 376         {
 377             pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
 378         }
 379         pr_str(fp, indent, "bIntermolecularInteractions",
 380                gmx::boolToString(mtop->bIntermolecularInteractions));
 381         if (mtop->bIntermolecularInteractions)
 382         {
 383             for (int j = 0; j < F_NRE; j++)
 384             {
 385                 pr_ilist(fp, indent, interaction_function[j].longname,
 386                          mtop->ffparams.functype.data(),
 387                          (*mtop->intermolecular_ilist)[j],
 388                          bShowNumbers, bShowParameters, mtop->ffparams.iparams.data());
 389             }
 390         }
 391         pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
 392         pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
 393         for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 394         {
 395             pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
 396                        &mtop->ffparams, bShowNumbers, bShowParameters);
 397         }
 398         pr_groups(fp, indent, mtop->groups, bShowNumbers);
 399     }
 400 }
 401
 402 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 403             gmx_bool bShowNumbers, gmx_bool bShowParameters)
 404 {
 405     if (available(fp, top, indent, title))
 406     {
 407         indent = pr_title(fp, indent, title);
 408         pr_indent(fp, indent);
 409         fprintf(fp, "name=\"%s\"\n", *(top->name));
 410         pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
 411         pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
 412         pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
 413         pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
 414         pr_str(fp, indent, "bIntermolecularInteractions",
 415                gmx::boolToString(top->bIntermolecularInteractions));
 416         pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
 417         pr_idef(fp, indent, "idef", &top->idef, bShowNumbers, bShowParameters);
 418     }
 419 }
 420
 421 static void cmp_iparm(FILE *fp, const char *s, t_functype ft,
 422                       const t_iparams &ip1, const t_iparams &ip2, real relativeTolerance, real absoluteTolerance)
 423 {
 424     int      i;
 425     gmx_bool bDiff;
 426
 427     bDiff = FALSE;
 428     for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
 429     {
 430         bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], relativeTolerance, absoluteTolerance);
 431     }
 432     if (bDiff)
 433     {
 434         fprintf(fp, "%s1: ", s);
 435         pr_iparams(fp, ft, &ip1);
 436         fprintf(fp, "%s2: ", s);
 437         pr_iparams(fp, ft, &ip2);
 438     }
 439 }
 440
 441 static void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft,
 442                          const t_iparams &ip1, real relativeTolerance, real absoluteTolerance)
 443 {
 444     int      nrfpA, nrfpB, p0, i;
 445     gmx_bool bDiff;
 446
 447     /* Normally the first parameter is perturbable */
 448     p0    = 0;
 449     nrfpA = interaction_function[ft].nrfpA;
 450     nrfpB = interaction_function[ft].nrfpB;
 451     if (ft == F_PDIHS)
 452     {
 453         nrfpB = 2;
 454     }
 455     else if (interaction_function[ft].flags & IF_TABULATED)
 456     {
 457         /* For tabulated interactions only the second parameter is perturbable */
 458         p0    = 1;
 459         nrfpB = 1;
 460     }
 461     bDiff = FALSE;
 462     for (i = 0; i < nrfpB && !bDiff; i++)
 463     {
 464         bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], relativeTolerance, absoluteTolerance);
 465     }
 466     if (bDiff)
 467     {
 468         fprintf(fp, "%s: ", s);
 469         pr_iparams(fp, ft, &ip1);
 470     }
 471 }
 472
 473 static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real relativeTolerance, real absoluteTolerance)
 474 {
 475     int cmap1_ngrid = (cmap1 ? cmap1->cmapdata.size() : 0);
 476     int cmap2_ngrid = (cmap2 ? cmap2->cmapdata.size() : 0);
 477
 478     cmp_int(fp, "cmap ngrid", -1, cmap1_ngrid, cmap2_ngrid);
 479
 480     if (cmap1 == nullptr || cmap2 == nullptr)
 481     {
 482         return;
 483     }
 484
 485     cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
 486     if (cmap1->cmapdata.size() == cmap2->cmapdata.size() &&
 487         cmap1->grid_spacing == cmap2->grid_spacing)
 488     {
 489         for (size_t g = 0; g < cmap1->cmapdata.size(); g++)
 490         {
 491             int i;
 492
 493             fprintf(fp, "comparing cmap %zu\n", g);
 494
 495             for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
 496             {
 497                 cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], relativeTolerance, absoluteTolerance);
 498             }
 499         }
 500     }
 501 }
 502
 503 static void cmp_block(FILE *fp, const t_block *b1, const t_block *b2, const char *s)
 504 {
 505     char buf[32];
 506
 507     fprintf(fp, "comparing block %s\n", s);
 508     sprintf(buf, "%s.nr", s);
 509     cmp_int(fp, buf, -1, b1->nr, b2->nr);
 510 }
 511
 512 static void cmp_blocka(FILE *fp, const t_blocka *b1, const t_blocka *b2, const char *s)
 513 {
 514     char buf[32];
 515
 516     fprintf(fp, "comparing blocka %s\n", s);
 517     sprintf(buf, "%s.nr", s);
 518     cmp_int(fp, buf, -1, b1->nr, b2->nr);
 519     sprintf(buf, "%s.nra", s);
 520     cmp_int(fp, buf, -1, b1->nra, b2->nra);
 521 }
 522
 523 static void compareFfparams(FILE *fp, const gmx_ffparams_t &ff1, const gmx_ffparams_t &ff2, real relativeTolerance, real absoluteTolerance)
 524 {
 525     fprintf(fp, "comparing force field parameters\n");
 526     cmp_int(fp, "numTypes", -1, ff1.numTypes(), ff2.numTypes());
 527     cmp_int(fp, "atnr", -1, ff1.atnr, ff1.atnr);
 528     cmp_double(fp, "reppow", -1, ff1.reppow, ff2.reppow, relativeTolerance, absoluteTolerance);
 529     cmp_real(fp, "fudgeQQ", -1, ff1.fudgeQQ, ff2.fudgeQQ, relativeTolerance, absoluteTolerance);
 530     cmp_cmap(fp, &ff1.cmap_grid, &ff2.cmap_grid, relativeTolerance, absoluteTolerance);
 531     for (int i = 0; i < std::min(ff1.numTypes(), ff2.numTypes()); i++)
 532     {
 533         std::string buf = gmx::formatString("ffparams->functype[%d]", i);
 534         cmp_int(fp, buf.c_str(), i, ff1.functype[i], ff2.functype[i]);
 535         buf = gmx::formatString("ffparams->iparams[%d]", i);
 536         cmp_iparm(fp, buf.c_str(), ff1.functype[i], ff1.iparams[i], ff2.iparams[i], relativeTolerance, absoluteTolerance);
 537     }
 538
 539 }
 540
 541 static void compareFfparamAB(FILE *fp, const gmx_ffparams_t &ff1, real relativeTolerance,   real absoluteTolerance)
 542 {
 543     fprintf(fp, "comparing free energy parameters\n");
 544     for (int i = 0; i < ff1.numTypes(); i++)
 545     {
 546         std::string buf = gmx::formatString("ffparams->iparams[%d]", i);
 547         cmp_iparm_AB(fp, buf.c_str(), ff1.functype[i], ff1.iparams[i], relativeTolerance, absoluteTolerance);
 548     }
 549 }
 550 static void compareInteractionLists(FILE *fp, const InteractionLists *il1, const InteractionLists *il2)
 551 {
 552     fprintf(fp, "comparing InteractionLists\n");
 553     if ((il1 || il2) && (!il1 || !il2))
 554     {
 555         fprintf(fp, "InteractionLists are present in topology %d but not in the other\n", il1 ? 1 : 2);
 556     }
 557     if (il1 && il2)
 558     {
 559         for (int i = 0; i < F_NRE; i++)
 560         {
 561             cmp_int(fp, "InteractionList size", i, il1->at(i).size(), il2->at(i).size());
 562             int nr = std::min(il1->at(i).size(), il2->at(i).size());
 563             for (int j = 0; j < nr; j++)
 564             {
 565                 cmp_int(fp, "InteractionList entry", j, il1->at(i).iatoms.at(j), il2->at(i).iatoms.at(j));
 566             }
 567         }
 568     }
 569 }
 570
 571 static void compareMoltypes(FILE *fp, gmx::ArrayRef<const gmx_moltype_t> mt1, gmx::ArrayRef<const gmx_moltype_t> mt2, real relativeTolerance, real absoluteTolerance)
 572 {
 573     fprintf(fp, "comparing molecule types\n");
 574     cmp_int(fp, "moltype size", -1, mt1.size(), mt2.size());
 575     for (int i = 0; i < std::min(mt1.ssize(), mt2.ssize()); i++)
 576     {
 577         cmp_str(fp, "Name", i, *mt1[i].name, *mt2[i].name);
 578         compareAtoms(fp, &mt1[i].atoms, &mt2[i].atoms, relativeTolerance, absoluteTolerance);
 579         compareInteractionLists(fp, &mt1[i].ilist, &mt2[i].ilist);
 580         std::string buf = gmx::formatString("cgs[%d]", i);
 581         cmp_block(fp, &mt1[i].cgs, &mt2[i].cgs, buf.c_str());
 582         buf = gmx::formatString("excls[%d]", i);
 583         cmp_blocka(fp, &mt1[i].excls, &mt2[i].excls, buf.c_str());
 584     }
 585 }
 586
 587 static void compareMoletypeAB(FILE *fp, gmx::ArrayRef<const gmx_moltype_t> mt1, real relativeTolerance, real absoluteTolerance)
 588 {
 589     fprintf(fp, "comparing free energy molecule types\n");
 590     for (int i = 0; i < mt1.ssize(); i++)
 591     {
 592         compareAtoms(fp, &mt1[i].atoms, nullptr, relativeTolerance, absoluteTolerance);
 593     }
 594 }
 595 static void compareMolblocks(FILE *fp, gmx::ArrayRef<const gmx_molblock_t> mb1, gmx::ArrayRef<const gmx_molblock_t> mb2)
 596 {
 597     fprintf(fp, "comparing molecule blocks\n");
 598     cmp_int(fp, "molblock size", -1, mb1.size(), mb2.size());
 599     int nr = std::min(mb1.size(), mb2.size());
 600     for (int i = 0; i < nr; i++)
 601     {
 602         cmp_int(fp, "type", i, mb1[i].type, mb2[i].type);
 603         cmp_int(fp, "nmol", i, mb1[i].nmol, mb2[i].nmol);
 604         // Only checking size of restraint vectors for now
 605         cmp_int(fp, "posres_xA size", i, mb1[i].posres_xA.size(), mb2[i].posres_xA.size());
 606         cmp_int(fp, "posres_xB size", i, mb1[i].posres_xB.size(), mb2[i].posres_xB.size());
 607     }
 608
 609 }
 610
 611 static void compareAtomtypes(FILE *fp, const t_atomtypes &at1, const t_atomtypes &at2)
 612 {
 613     fprintf(fp, "comparing atomtypes\n");
 614     cmp_int(fp, "nr", -1, at1.nr, at2.nr);
 615     int nr = std::min(at1.nr, at2.nr);
 616     for (int i = 0; i < nr; i++)
 617     {
 618         cmp_int(fp, "atomtype", i, at1.atomnumber[i], at2.atomnumber[i]);
 619     }
 620 }
 621
 622 static void compareIntermolecularExclusions(FILE *fp, gmx::ArrayRef<const int> ime1, gmx::ArrayRef<const int> ime2)
 623 {
 624     fprintf(fp, "comparing intermolecular exclusions\n");
 625     cmp_int(fp, "exclusion number", -1, ime1.size(), ime2.size());
 626     int nr = std::min(ime1.size(), ime2.size());
 627     for (int i = 0; i < nr; i++)
 628     {
 629         cmp_int(fp, "exclusion", i, ime1[i], ime2[i]);
 630     }
 631 }
 632
 633 static void compareBlockIndices(FILE *fp, gmx::ArrayRef<const MoleculeBlockIndices> mbi1, gmx::ArrayRef<const MoleculeBlockIndices> mbi2)
 634 {
 635     fprintf(fp, "comparing moleculeBlockIndices\n");
 636     cmp_int(fp, "size", -1, mbi1.size(), mbi2.size());
 637     int nr = std::min(mbi1.size(), mbi2.size());
 638     for (int i = 0; i < nr; i++)
 639     {
 640         cmp_int(fp, "numAtomsPerMolecule", i, mbi1[i].numAtomsPerMolecule, mbi2[i].numAtomsPerMolecule);
 641         cmp_int(fp, "globalAtomStart", i, mbi1[i].globalAtomStart, mbi2[i].globalAtomStart);
 642         cmp_int(fp, "globalAtomEnd", i, mbi1[i].globalAtomEnd, mbi2[i].globalAtomEnd);
 643         cmp_int(fp, "globalResidueStart", i, mbi1[i].globalResidueStart, mbi2[i].globalResidueStart);
 644         cmp_int(fp, "moleculeIndexStart", i, mbi1[i].moleculeIndexStart, mbi2[i].moleculeIndexStart);
 645     }
 646 }
 647
 648 void compareMtop(FILE *fp, const gmx_mtop_t &mtop1, const gmx_mtop_t &mtop2, real relativeTolerance, real absoluteTolerance)
 649 {
 650     fprintf(fp, "comparing mtop topology\n");
 651     cmp_str(fp, "Name", -1, *mtop1.name, *mtop2.name);
 652     cmp_int(fp, "natoms", -1, mtop1.natoms, mtop2.natoms);
 653     cmp_int(fp, "maxres_renum", -1, mtop1.maxres_renum, mtop2.maxres_renum);
 654     cmp_int(fp, "maxresnr", -1, mtop1.maxresnr, mtop2.maxresnr);
 655     cmp_bool(fp, "bIntermolecularInteractions", -1, mtop1.bIntermolecularInteractions, mtop2.bIntermolecularInteractions);
 656     cmp_bool(fp, "haveMoleculeIndices", -1, mtop1.haveMoleculeIndices, mtop2.haveMoleculeIndices);
 657
 658     compareFfparams(fp, mtop1.ffparams, mtop2.ffparams, relativeTolerance, absoluteTolerance);
 659     compareMoltypes(fp, mtop1.moltype, mtop2.moltype, relativeTolerance, absoluteTolerance);
 660     compareMolblocks(fp, mtop1.molblock, mtop2.molblock);
 661     compareInteractionLists(fp, mtop1.intermolecular_ilist.get(), mtop2.intermolecular_ilist.get());
 662     compareAtomtypes(fp, mtop1.atomtypes, mtop2.atomtypes);
 663     compareAtomGroups(fp, mtop1.groups, mtop2.groups, mtop1.natoms, mtop2.natoms);
 664     compareIntermolecularExclusions(fp, mtop1.intermolecularExclusionGroup, mtop2.intermolecularExclusionGroup);
 665     compareBlockIndices(fp, mtop1.moleculeBlockIndices, mtop2.moleculeBlockIndices);
 666 }
 667
 668 void compareMtopAB(FILE *fp, const gmx_mtop_t &mtop1, real relativeTolerance, real absoluteTolerance)
 669 {
 670     fprintf(fp, "comparing topAB\n");
 671     compareFfparamAB(fp, mtop1.ffparams, relativeTolerance, absoluteTolerance);
 672     compareMoletypeAB(fp, mtop1.moltype, relativeTolerance, absoluteTolerance);
 673 }
 674
 675 void compareAtomGroups(FILE *fp, const SimulationGroups &g0, const SimulationGroups &g1,
 676                        int natoms0, int natoms1)
 677 {
 678     fprintf(fp, "comparing groups\n");
 679
 680     for (auto group : keysOf(g0.groups))
 681     {
 682         std::string buf = gmx::formatString("grps[%d].nr", static_cast<int>(group));
 683         cmp_int(fp, buf.c_str(), -1, g0.groups[group].nr, g1.groups[group].nr);
 684         if (g0.groups[group].nr == g1.groups[group].nr)
 685         {
 686             for (int j = 0; j < g0.groups[group].nr; j++)
 687             {
 688                 buf = gmx::formatString("grps[%d].name[%d]", static_cast<int>(group), j);
 689                 cmp_str(fp, buf.c_str(), -1,
 690                         *g0.groupNames[g0.groups[group].nm_ind[j]],
 691                         *g1.groupNames[g1.groups[group].nm_ind[j]]);
 692             }
 693         }
 694         cmp_int(fp, "ngrpnr", static_cast<int>(group), g0.numberOfGroupNumbers(group), g1.numberOfGroupNumbers(group));
 695         if (g0.numberOfGroupNumbers(group) == g1.numberOfGroupNumbers(group) && natoms0 == natoms1 &&
 696             (!g0.groupNumbers[group].empty() || !g1.groupNumbers[group].empty()))
 697         {
 698             for (int j = 0; j < natoms0; j++)
 699             {
 700                 cmp_int(fp, c_simulationAtomGroupTypeShortNames[group], j, getGroupType(g0, group, j), getGroupType(g1, group, j));
 701             }
 702         }
 703     }
 704     /* We have compared the names in the groups lists,
 705      * so we can skip the grpname list comparison.
 706      */
 707 }
 708
 709 int getGroupType(const SimulationGroups &group, SimulationAtomGroupType type, int atom)
 710 {
 711     return (group.groupNumbers[type].empty() ? 0 : group.groupNumbers[type][atom]);
 712 }
 713
 714 void copy_moltype(const gmx_moltype_t *src, gmx_moltype_t *dst)
 715 {
 716     dst->name = src->name;
 717     copy_blocka(&src->excls, &dst->excls);
 718     copy_block(&src->cgs, &dst->cgs);
 719     t_atoms *atomsCopy = copy_t_atoms(&src->atoms);
 720     dst->atoms = *atomsCopy;
 721     sfree(atomsCopy);
 722
 723     for (int i = 0; i < F_NRE; ++i)
 724     {
 725         dst->ilist[i] = src->ilist[i];
 726     }
 727 }