src/gromacs/topology/topology.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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 static 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 void init_top(t_topology *top)
  78 {
  79     top->name = nullptr;
  80     init_idef(&top->idef);
  81     init_atom(&(top->atoms));
  82     init_atomtypes(&(top->atomtypes));
  83     init_block(&top->cgs);
  84     init_block(&top->mols);
  85     init_blocka(&top->excls);
  86     open_symtab(&top->symtab);
  87 }
  88
  89
  90 gmx_moltype_t::gmx_moltype_t() :
  91     name(nullptr),
  92     cgs(),
  93     excls()
  94 {
  95     init_t_atoms(&atoms, 0, FALSE);
  96 }
  97
  98 gmx_moltype_t::~gmx_moltype_t()
  99 {
 100     done_atom(&atoms);
 101     done_block(&cgs);
 102     done_blocka(&excls);
 103 }
 104
 105 gmx_mtop_t::gmx_mtop_t()
 106 {
 107     init_atomtypes(&atomtypes);
 108     open_symtab(&symtab);
 109 }
 110
 111 gmx_mtop_t::~gmx_mtop_t()
 112 {
 113     done_symtab(&symtab);
 114
 115     moltype.clear();
 116     molblock.clear();
 117     done_atomtypes(&atomtypes);
 118 }
 119
 120 void done_top(t_topology *top)
 121 {
 122     done_idef(&top->idef);
 123     done_atom(&(top->atoms));
 124
 125     /* For GB */
 126     done_atomtypes(&(top->atomtypes));
 127
 128     done_symtab(&(top->symtab));
 129     done_block(&(top->cgs));
 130     done_block(&(top->mols));
 131     done_blocka(&(top->excls));
 132 }
 133
 134 void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
 135 {
 136     if (mtop != nullptr)
 137     {
 138         if (top != nullptr)
 139         {
 140             done_idef(&top->idef);
 141             done_atom(&top->atoms);
 142             done_block(&top->cgs);
 143             done_blocka(&top->excls);
 144             done_block(&top->mols);
 145             done_symtab(&top->symtab);
 146             open_symtab(&mtop->symtab);
 147             done_atomtypes(&(top->atomtypes));
 148         }
 149
 150         // Note that the rest of mtop will be freed by the destructor
 151     }
 152 }
 153
 154 gmx_localtop_t::gmx_localtop_t()
 155 {
 156     init_blocka_null(&excls);
 157     init_idef(&idef);
 158     init_atomtypes(&atomtypes);
 159 }
 160
 161 gmx_localtop_t::~gmx_localtop_t()
 162 {
 163     if (!useInDomainDecomp_)
 164     {
 165         done_idef(&idef);
 166         done_blocka(&excls);
 167         done_atomtypes(&atomtypes);
 168     }
 169 }
 170
 171 bool gmx_mtop_has_masses(const gmx_mtop_t *mtop)
 172 {
 173     if (mtop == nullptr)
 174     {
 175         return false;
 176     }
 177     return mtop->moltype.empty() || mtop->moltype[0].atoms.haveMass;
 178 }
 179
 180 bool gmx_mtop_has_charges(const gmx_mtop_t *mtop)
 181 {
 182     if (mtop == nullptr)
 183     {
 184         return false;
 185     }
 186     return mtop->moltype.empty() || mtop->moltype[0].atoms.haveCharge;
 187 }
 188
 189 bool gmx_mtop_has_perturbed_charges(const gmx_mtop_t &mtop)
 190 {
 191     for (const gmx_moltype_t &moltype : mtop.moltype)
 192     {
 193         const t_atoms &atoms = moltype.atoms;
 194         if (atoms.haveBState)
 195         {
 196             for (int a = 0; a < atoms.nr; a++)
 197             {
 198                 if (atoms.atom[a].q != atoms.atom[a].qB)
 199                 {
 200                     return true;
 201                 }
 202             }
 203         }
 204     }
 205     return false;
 206 }
 207
 208 bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop)
 209 {
 210     if (mtop == nullptr)
 211     {
 212         return false;
 213     }
 214     return mtop->moltype.empty() || mtop->moltype[0].atoms.haveType;
 215 }
 216
 217 bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop)
 218 {
 219     if (mtop == nullptr)
 220     {
 221         return false;
 222     }
 223     return mtop->moltype.empty() || mtop->moltype[0].atoms.havePdbInfo;
 224 }
 225
 226 static void pr_grps(FILE                                 *fp,
 227                     const char                           *title,
 228                     gmx::ArrayRef<const AtomGroupIndices> grps,
 229                     char                               ***grpname)
 230 {
 231     int index = 0;
 232     for (const auto &group : grps)
 233     {
 234         fprintf(fp, "%s[%-12s] nr=%zu, name=[", title, c_simulationAtomGroupTypeShortNames[index], group.size());
 235         for (const auto &entry : group)
 236         {
 237             fprintf(fp, " %s", *(grpname[entry]));
 238         }
 239         fprintf(fp, "]\n");
 240         index++;
 241     }
 242 }
 243
 244 static void pr_groups(FILE *fp, int indent,
 245                       const SimulationGroups &groups,
 246                       gmx_bool bShowNumbers)
 247 {
 248     pr_grps(fp,
 249             "grp",
 250             groups.groups,
 251             const_cast<char ***>(groups.groupNames.data()));
 252     pr_strings(fp, indent, "grpname", const_cast<char ***>(groups.groupNames.data()), groups.groupNames.size(), bShowNumbers);
 253
 254     pr_indent(fp, indent);
 255     fprintf(fp, "groups          ");
 256     for (const auto &group : c_simulationAtomGroupTypeShortNames)
 257     {
 258         printf(" %5.5s", group);
 259     }
 260     printf("\n");
 261
 262     pr_indent(fp, indent);
 263     fprintf(fp, "allocated       ");
 264     int nat_max = 0;
 265     for (auto group : keysOf(groups.groups))
 266     {
 267         printf(" %5d", groups.numberOfGroupNumbers(group));
 268         nat_max = std::max(nat_max, groups.numberOfGroupNumbers(group));
 269     }
 270     printf("\n");
 271
 272     if (nat_max == 0)
 273     {
 274         pr_indent(fp, indent);
 275         fprintf(fp, "groupnr[%5s] =", "*");
 276         for (auto gmx_unused group : keysOf(groups.groups))
 277         {
 278             fprintf(fp, "  %3d ", 0);
 279         }
 280         fprintf(fp, "\n");
 281     }
 282     else
 283     {
 284         for (int i = 0; i < nat_max; i++)
 285         {
 286             pr_indent(fp, indent);
 287             fprintf(fp, "groupnr[%5d] =", i);
 288             for (auto group : keysOf(groups.groups))
 289             {
 290                 fprintf(fp, "  %3d ",
 291                         !groups.groupNumbers[group].empty() ?
 292                         groups.groupNumbers[group][i] : 0);
 293             }
 294             fprintf(fp, "\n");
 295         }
 296     }
 297 }
 298
 299 static void pr_moltype(FILE *fp, int indent, const char *title,
 300                        const gmx_moltype_t *molt, int n,
 301                        const gmx_ffparams_t *ffparams,
 302                        gmx_bool bShowNumbers, gmx_bool bShowParameters)
 303 {
 304     int j;
 305
 306     indent = pr_title_n(fp, indent, title, n);
 307     pr_indent(fp, indent);
 308     fprintf(fp, "name=\"%s\"\n", *(molt->name));
 309     pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
 310     pr_block(fp, indent, "cgs", &molt->cgs, bShowNumbers);
 311     pr_blocka(fp, indent, "excls", &molt->excls, bShowNumbers);
 312     for (j = 0; (j < F_NRE); j++)
 313     {
 314         pr_ilist(fp, indent, interaction_function[j].longname,
 315                  ffparams->functype.data(), molt->ilist[j],
 316                  bShowNumbers, bShowParameters, ffparams->iparams.data());
 317     }
 318 }
 319
 320 static void pr_molblock(FILE *fp, int indent, const char *title,
 321                         const gmx_molblock_t *molb, int n,
 322                         const std::vector<gmx_moltype_t> &molt)
 323 {
 324     indent = pr_title_n(fp, indent, title, n);
 325     pr_indent(fp, indent);
 326     fprintf(fp, "%-20s = %d \"%s\"\n",
 327             "moltype", molb->type, *(molt[molb->type].name));
 328     pr_int(fp, indent, "#molecules", molb->nmol);
 329     pr_int(fp, indent, "#posres_xA", molb->posres_xA.size());
 330     if (!molb->posres_xA.empty())
 331     {
 332         pr_rvecs(fp, indent, "posres_xA", as_rvec_array(molb->posres_xA.data()), molb->posres_xA.size());
 333     }
 334     pr_int(fp, indent, "#posres_xB", molb->posres_xB.size());
 335     if (!molb->posres_xB.empty())
 336     {
 337         pr_rvecs(fp, indent, "posres_xB", as_rvec_array(molb->posres_xB.data()), molb->posres_xB.size());
 338     }
 339 }
 340
 341 void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
 342              gmx_bool bShowNumbers, gmx_bool bShowParameters)
 343 {
 344     if (available(fp, mtop, indent, title))
 345     {
 346         indent = pr_title(fp, indent, title);
 347         pr_indent(fp, indent);
 348         fprintf(fp, "name=\"%s\"\n", *(mtop->name));
 349         pr_int(fp, indent, "#atoms", mtop->natoms);
 350         pr_int(fp, indent, "#molblock", mtop->molblock.size());
 351         for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
 352         {
 353             pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
 354         }
 355         pr_str(fp, indent, "bIntermolecularInteractions",
 356                gmx::boolToString(mtop->bIntermolecularInteractions));
 357         if (mtop->bIntermolecularInteractions)
 358         {
 359             for (int j = 0; j < F_NRE; j++)
 360             {
 361                 pr_ilist(fp, indent, interaction_function[j].longname,
 362                          mtop->ffparams.functype.data(),
 363                          (*mtop->intermolecular_ilist)[j],
 364                          bShowNumbers, bShowParameters, mtop->ffparams.iparams.data());
 365             }
 366         }
 367         pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
 368         pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
 369         for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 370         {
 371             pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
 372                        &mtop->ffparams, bShowNumbers, bShowParameters);
 373         }
 374         pr_groups(fp, indent, mtop->groups, bShowNumbers);
 375     }
 376 }
 377
 378 void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
 379             gmx_bool bShowNumbers, gmx_bool bShowParameters)
 380 {
 381     if (available(fp, top, indent, title))
 382     {
 383         indent = pr_title(fp, indent, title);
 384         pr_indent(fp, indent);
 385         fprintf(fp, "name=\"%s\"\n", *(top->name));
 386         pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
 387         pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
 388         pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
 389         pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
 390         pr_str(fp, indent, "bIntermolecularInteractions",
 391                gmx::boolToString(top->bIntermolecularInteractions));
 392         pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
 393         pr_idef(fp, indent, "idef", &top->idef, bShowNumbers, bShowParameters);
 394     }
 395 }
 396
 397 static void cmp_iparm(FILE *fp, const char *s, t_functype ft,
 398                       const t_iparams &ip1, const t_iparams &ip2, real relativeTolerance, real absoluteTolerance)
 399 {
 400     int      i;
 401     gmx_bool bDiff;
 402
 403     bDiff = FALSE;
 404     for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
 405     {
 406         bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], relativeTolerance, absoluteTolerance);
 407     }
 408     if (bDiff)
 409     {
 410         fprintf(fp, "%s1: ", s);
 411         pr_iparams(fp, ft, &ip1);
 412         fprintf(fp, "%s2: ", s);
 413         pr_iparams(fp, ft, &ip2);
 414     }
 415 }
 416
 417 static void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft,
 418                          const t_iparams &ip1, real relativeTolerance, real absoluteTolerance)
 419 {
 420     int      nrfpA, nrfpB, p0, i;
 421     gmx_bool bDiff;
 422
 423     /* Normally the first parameter is perturbable */
 424     p0    = 0;
 425     nrfpA = interaction_function[ft].nrfpA;
 426     nrfpB = interaction_function[ft].nrfpB;
 427     if (ft == F_PDIHS)
 428     {
 429         nrfpB = 2;
 430     }
 431     else if (interaction_function[ft].flags & IF_TABULATED)
 432     {
 433         /* For tabulated interactions only the second parameter is perturbable */
 434         p0    = 1;
 435         nrfpB = 1;
 436     }
 437     bDiff = FALSE;
 438     for (i = 0; i < nrfpB && !bDiff; i++)
 439     {
 440         bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], relativeTolerance, absoluteTolerance);
 441     }
 442     if (bDiff)
 443     {
 444         fprintf(fp, "%s: ", s);
 445         pr_iparams(fp, ft, &ip1);
 446     }
 447 }
 448
 449 static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real relativeTolerance, real absoluteTolerance)
 450 {
 451     int cmap1_ngrid = (cmap1 ? cmap1->cmapdata.size() : 0);
 452     int cmap2_ngrid = (cmap2 ? cmap2->cmapdata.size() : 0);
 453
 454     cmp_int(fp, "cmap ngrid", -1, cmap1_ngrid, cmap2_ngrid);
 455
 456     if (cmap1 == nullptr || cmap2 == nullptr)
 457     {
 458         return;
 459     }
 460
 461     cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
 462     if (cmap1->cmapdata.size() == cmap2->cmapdata.size() &&
 463         cmap1->grid_spacing == cmap2->grid_spacing)
 464     {
 465         for (size_t g = 0; g < cmap1->cmapdata.size(); g++)
 466         {
 467             int i;
 468
 469             fprintf(fp, "comparing cmap %zu\n", g);
 470
 471             for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
 472             {
 473                 cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], relativeTolerance, absoluteTolerance);
 474             }
 475         }
 476     }
 477 }
 478
 479 static void cmp_block(FILE *fp, const t_block *b1, const t_block *b2, const char *s)
 480 {
 481     char buf[32];
 482
 483     fprintf(fp, "comparing block %s\n", s);
 484     sprintf(buf, "%s.nr", s);
 485     cmp_int(fp, buf, -1, b1->nr, b2->nr);
 486 }
 487
 488 static void cmp_blocka(FILE *fp, const t_blocka *b1, const t_blocka *b2, const char *s)
 489 {
 490     char buf[32];
 491
 492     fprintf(fp, "comparing blocka %s\n", s);
 493     sprintf(buf, "%s.nr", s);
 494     cmp_int(fp, buf, -1, b1->nr, b2->nr);
 495     sprintf(buf, "%s.nra", s);
 496     cmp_int(fp, buf, -1, b1->nra, b2->nra);
 497 }
 498
 499 static void compareFfparams(FILE *fp, const gmx_ffparams_t &ff1, const gmx_ffparams_t &ff2, real relativeTolerance, real absoluteTolerance)
 500 {
 501     fprintf(fp, "comparing force field parameters\n");
 502     cmp_int(fp, "numTypes", -1, ff1.numTypes(), ff2.numTypes());
 503     cmp_int(fp, "atnr", -1, ff1.atnr, ff1.atnr);
 504     cmp_double(fp, "reppow", -1, ff1.reppow, ff2.reppow, relativeTolerance, absoluteTolerance);
 505     cmp_real(fp, "fudgeQQ", -1, ff1.fudgeQQ, ff2.fudgeQQ, relativeTolerance, absoluteTolerance);
 506     cmp_cmap(fp, &ff1.cmap_grid, &ff2.cmap_grid, relativeTolerance, absoluteTolerance);
 507     for (int i = 0; i < std::min(ff1.numTypes(), ff2.numTypes()); i++)
 508     {
 509         std::string buf = gmx::formatString("ffparams->functype[%d]", i);
 510         cmp_int(fp, buf.c_str(), i, ff1.functype[i], ff2.functype[i]);
 511         buf = gmx::formatString("ffparams->iparams[%d]", i);
 512         cmp_iparm(fp, buf.c_str(), ff1.functype[i], ff1.iparams[i], ff2.iparams[i], relativeTolerance, absoluteTolerance);
 513     }
 514
 515 }
 516
 517 static void compareFfparamAB(FILE *fp, const gmx_ffparams_t &ff1, real relativeTolerance,   real absoluteTolerance)
 518 {
 519     fprintf(fp, "comparing free energy parameters\n");
 520     for (int i = 0; i < ff1.numTypes(); i++)
 521     {
 522         std::string buf = gmx::formatString("ffparams->iparams[%d]", i);
 523         cmp_iparm_AB(fp, buf.c_str(), ff1.functype[i], ff1.iparams[i], relativeTolerance, absoluteTolerance);
 524     }
 525 }
 526 static void compareInteractionLists(FILE *fp, const InteractionLists *il1, const InteractionLists *il2)
 527 {
 528     fprintf(fp, "comparing InteractionLists\n");
 529     if ((il1 || il2) && (!il1 || !il2))
 530     {
 531         fprintf(fp, "InteractionLists are present in topology %d but not in the other\n", il1 ? 1 : 2);
 532     }
 533     if (il1 && il2)
 534     {
 535         for (int i = 0; i < F_NRE; i++)
 536         {
 537             cmp_int(fp, "InteractionList size", i, il1->at(i).size(), il2->at(i).size());
 538             int nr = std::min(il1->at(i).size(), il2->at(i).size());
 539             for (int j = 0; j < nr; j++)
 540             {
 541                 cmp_int(fp, "InteractionList entry", j, il1->at(i).iatoms.at(j), il2->at(i).iatoms.at(j));
 542             }
 543         }
 544     }
 545 }
 546
 547 static void compareMoltypes(FILE *fp, gmx::ArrayRef<const gmx_moltype_t> mt1, gmx::ArrayRef<const gmx_moltype_t> mt2, real relativeTolerance, real absoluteTolerance)
 548 {
 549     fprintf(fp, "comparing molecule types\n");
 550     cmp_int(fp, "moltype size", -1, mt1.size(), mt2.size());
 551     for (int i = 0; i < std::min(mt1.ssize(), mt2.ssize()); i++)
 552     {
 553         cmp_str(fp, "Name", i, *mt1[i].name, *mt2[i].name);
 554         compareAtoms(fp, &mt1[i].atoms, &mt2[i].atoms, relativeTolerance, absoluteTolerance);
 555         compareInteractionLists(fp, &mt1[i].ilist, &mt2[i].ilist);
 556         std::string buf = gmx::formatString("cgs[%d]", i);
 557         cmp_block(fp, &mt1[i].cgs, &mt2[i].cgs, buf.c_str());
 558         buf = gmx::formatString("excls[%d]", i);
 559         cmp_blocka(fp, &mt1[i].excls, &mt2[i].excls, buf.c_str());
 560     }
 561 }
 562
 563 static void compareMoletypeAB(FILE *fp, gmx::ArrayRef<const gmx_moltype_t> mt1, real relativeTolerance, real absoluteTolerance)
 564 {
 565     fprintf(fp, "comparing free energy molecule types\n");
 566     for (int i = 0; i < mt1.ssize(); i++)
 567     {
 568         compareAtoms(fp, &mt1[i].atoms, nullptr, relativeTolerance, absoluteTolerance);
 569     }
 570 }
 571 static void compareMolblocks(FILE *fp, gmx::ArrayRef<const gmx_molblock_t> mb1, gmx::ArrayRef<const gmx_molblock_t> mb2)
 572 {
 573     fprintf(fp, "comparing molecule blocks\n");
 574     cmp_int(fp, "molblock size", -1, mb1.size(), mb2.size());
 575     int nr = std::min(mb1.size(), mb2.size());
 576     for (int i = 0; i < nr; i++)
 577     {
 578         cmp_int(fp, "type", i, mb1[i].type, mb2[i].type);
 579         cmp_int(fp, "nmol", i, mb1[i].nmol, mb2[i].nmol);
 580         // Only checking size of restraint vectors for now
 581         cmp_int(fp, "posres_xA size", i, mb1[i].posres_xA.size(), mb2[i].posres_xA.size());
 582         cmp_int(fp, "posres_xB size", i, mb1[i].posres_xB.size(), mb2[i].posres_xB.size());
 583     }
 584
 585 }
 586
 587 static void compareAtomtypes(FILE *fp, const t_atomtypes &at1, const t_atomtypes &at2)
 588 {
 589     fprintf(fp, "comparing atomtypes\n");
 590     cmp_int(fp, "nr", -1, at1.nr, at2.nr);
 591     int nr = std::min(at1.nr, at2.nr);
 592     for (int i = 0; i < nr; i++)
 593     {
 594         cmp_int(fp, "atomtype", i, at1.atomnumber[i], at2.atomnumber[i]);
 595     }
 596 }
 597
 598 static void compareIntermolecularExclusions(FILE *fp, gmx::ArrayRef<const int> ime1, gmx::ArrayRef<const int> ime2)
 599 {
 600     fprintf(fp, "comparing intermolecular exclusions\n");
 601     cmp_int(fp, "exclusion number", -1, ime1.size(), ime2.size());
 602     int nr = std::min(ime1.size(), ime2.size());
 603     for (int i = 0; i < nr; i++)
 604     {
 605         cmp_int(fp, "exclusion", i, ime1[i], ime2[i]);
 606     }
 607 }
 608
 609 static void compareBlockIndices(FILE *fp, gmx::ArrayRef<const MoleculeBlockIndices> mbi1, gmx::ArrayRef<const MoleculeBlockIndices> mbi2)
 610 {
 611     fprintf(fp, "comparing moleculeBlockIndices\n");
 612     cmp_int(fp, "size", -1, mbi1.size(), mbi2.size());
 613     int nr = std::min(mbi1.size(), mbi2.size());
 614     for (int i = 0; i < nr; i++)
 615     {
 616         cmp_int(fp, "numAtomsPerMolecule", i, mbi1[i].numAtomsPerMolecule, mbi2[i].numAtomsPerMolecule);
 617         cmp_int(fp, "globalAtomStart", i, mbi1[i].globalAtomStart, mbi2[i].globalAtomStart);
 618         cmp_int(fp, "globalAtomEnd", i, mbi1[i].globalAtomEnd, mbi2[i].globalAtomEnd);
 619         cmp_int(fp, "globalResidueStart", i, mbi1[i].globalResidueStart, mbi2[i].globalResidueStart);
 620         cmp_int(fp, "moleculeIndexStart", i, mbi1[i].moleculeIndexStart, mbi2[i].moleculeIndexStart);
 621     }
 622 }
 623
 624 void compareMtop(FILE *fp, const gmx_mtop_t &mtop1, const gmx_mtop_t &mtop2, real relativeTolerance, real absoluteTolerance)
 625 {
 626     fprintf(fp, "comparing mtop topology\n");
 627     cmp_str(fp, "Name", -1, *mtop1.name, *mtop2.name);
 628     cmp_int(fp, "natoms", -1, mtop1.natoms, mtop2.natoms);
 629     cmp_int(fp, "maxres_renum", -1, mtop1.maxres_renum, mtop2.maxres_renum);
 630     cmp_int(fp, "maxresnr", -1, mtop1.maxresnr, mtop2.maxresnr);
 631     cmp_bool(fp, "bIntermolecularInteractions", -1, mtop1.bIntermolecularInteractions, mtop2.bIntermolecularInteractions);
 632     cmp_bool(fp, "haveMoleculeIndices", -1, mtop1.haveMoleculeIndices, mtop2.haveMoleculeIndices);
 633
 634     compareFfparams(fp, mtop1.ffparams, mtop2.ffparams, relativeTolerance, absoluteTolerance);
 635     compareMoltypes(fp, mtop1.moltype, mtop2.moltype, relativeTolerance, absoluteTolerance);
 636     compareMolblocks(fp, mtop1.molblock, mtop2.molblock);
 637     compareInteractionLists(fp, mtop1.intermolecular_ilist.get(), mtop2.intermolecular_ilist.get());
 638     compareAtomtypes(fp, mtop1.atomtypes, mtop2.atomtypes);
 639     compareAtomGroups(fp, mtop1.groups, mtop2.groups, mtop1.natoms, mtop2.natoms);
 640     compareIntermolecularExclusions(fp, mtop1.intermolecularExclusionGroup, mtop2.intermolecularExclusionGroup);
 641     compareBlockIndices(fp, mtop1.moleculeBlockIndices, mtop2.moleculeBlockIndices);
 642 }
 643
 644 void compareMtopAB(FILE *fp, const gmx_mtop_t &mtop1, real relativeTolerance, real absoluteTolerance)
 645 {
 646     fprintf(fp, "comparing topAB\n");
 647     compareFfparamAB(fp, mtop1.ffparams, relativeTolerance, absoluteTolerance);
 648     compareMoletypeAB(fp, mtop1.moltype, relativeTolerance, absoluteTolerance);
 649 }
 650
 651 void compareAtomGroups(FILE *fp, const SimulationGroups &g0, const SimulationGroups &g1,
 652                        int natoms0, int natoms1)
 653 {
 654     fprintf(fp, "comparing groups\n");
 655
 656     for (auto group : keysOf(g0.groups))
 657     {
 658         std::string buf = gmx::formatString("grps[%d].nr", static_cast<int>(group));
 659         cmp_int(fp, buf.c_str(), -1, g0.groups[group].size(), g1.groups[group].size());
 660         if (g0.groups[group].size() == g1.groups[group].size())
 661         {
 662             for (int j = 0; j < gmx::ssize(g0.groups[group]); j++)
 663             {
 664                 buf = gmx::formatString("grps[%d].name[%d]", static_cast<int>(group), j);
 665                 cmp_str(fp, buf.c_str(), -1,
 666                         *g0.groupNames[g0.groups[group][j]],
 667                         *g1.groupNames[g1.groups[group][j]]);
 668             }
 669         }
 670         cmp_int(fp, "ngrpnr", static_cast<int>(group), g0.numberOfGroupNumbers(group), g1.numberOfGroupNumbers(group));
 671         if (g0.numberOfGroupNumbers(group) == g1.numberOfGroupNumbers(group) && natoms0 == natoms1 &&
 672             (!g0.groupNumbers[group].empty() || !g1.groupNumbers[group].empty()))
 673         {
 674             for (int j = 0; j < natoms0; j++)
 675             {
 676                 cmp_int(fp, c_simulationAtomGroupTypeShortNames[group], j, getGroupType(g0, group, j), getGroupType(g1, group, j));
 677             }
 678         }
 679     }
 680     /* We have compared the names in the groups lists,
 681      * so we can skip the grpname list comparison.
 682      */
 683 }
 684
 685 int getGroupType(const SimulationGroups &group, SimulationAtomGroupType type, int atom)
 686 {
 687     return (group.groupNumbers[type].empty() ? 0 : group.groupNumbers[type][atom]);
 688 }
 689
 690 void copy_moltype(const gmx_moltype_t *src, gmx_moltype_t *dst)
 691 {
 692     dst->name = src->name;
 693     copy_blocka(&src->excls, &dst->excls);
 694     copy_block(&src->cgs, &dst->cgs);
 695     t_atoms *atomsCopy = copy_t_atoms(&src->atoms);
 696     dst->atoms = *atomsCopy;
 697     sfree(atomsCopy);
 698
 699     for (int i = 0; i < F_NRE; ++i)
 700     {
 701         dst->ilist[i] = src->ilist[i];
 702     }
 703 }