src/gromacs/gmxpreprocess/topio.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 by the GROMACS development team.
   7  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   9  * and including many others, as listed in the AUTHORS file in the
  10  * top-level source directory and at http://www.gromacs.org.
  11  *
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  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
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  37  */
  38 #include "gmxpre.h"
  39
  40 #include "topio.h"
  41
  42 #include <cassert>
  43 #include <cctype>
  44 #include <cerrno>
  45 #include <cmath>
  46 #include <cstdio>
  47 #include <cstdlib>
  48 #include <cstring>
  49
  50 #include <algorithm>
  51 #include <memory>
  52
  53 #include <unordered_set>
  54 #include <sys/types.h>
  55
  56 #include "gromacs/fileio/gmxfio.h"
  57 #include "gromacs/fileio/warninp.h"
  58 #include "gromacs/gmxpreprocess/gmxcpp.h"
  59 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  60 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
  61 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
  62 #include "gromacs/gmxpreprocess/grompp_impl.h"
  63 #include "gromacs/gmxpreprocess/readir.h"
  64 #include "gromacs/gmxpreprocess/topdirs.h"
  65 #include "gromacs/gmxpreprocess/toppush.h"
  66 #include "gromacs/gmxpreprocess/topshake.h"
  67 #include "gromacs/gmxpreprocess/toputil.h"
  68 #include "gromacs/gmxpreprocess/vsite_parm.h"
  69 #include "gromacs/math/units.h"
  70 #include "gromacs/math/utilities.h"
  71 #include "gromacs/mdtypes/inputrec.h"
  72 #include "gromacs/mdtypes/md_enums.h"
  73 #include "gromacs/pbcutil/pbc.h"
  74 #include "gromacs/topology/block.h"
  75 #include "gromacs/topology/exclusionblocks.h"
  76 #include "gromacs/topology/ifunc.h"
  77 #include "gromacs/topology/symtab.h"
  78 #include "gromacs/topology/topology.h"
  79 #include "gromacs/utility/cstringutil.h"
  80 #include "gromacs/utility/fatalerror.h"
  81 #include "gromacs/utility/futil.h"
  82 #include "gromacs/utility/gmxassert.h"
  83 #include "gromacs/utility/logger.h"
  84 #include "gromacs/utility/pleasecite.h"
  85 #include "gromacs/utility/smalloc.h"
  86
  87 #define OPENDIR '['  /* starting sign for directive */
  88 #define CLOSEDIR ']' /* ending sign for directive   */
  89
  90 static void gen_pairs(const InteractionsOfType& nbs, InteractionsOfType* pairs, real fudge, int comb)
  91 {
  92     real scaling;
  93     int  ntp = nbs.size();
  94     int  nnn = static_cast<int>(std::sqrt(static_cast<double>(ntp)));
  95     GMX_ASSERT(nnn * nnn == ntp,
  96                "Number of pairs of generated non-bonded parameters should be a perfect square");
  97     int nrfp  = NRFP(F_LJ);
  98     int nrfpA = interaction_function[F_LJ14].nrfpA;
  99     int nrfpB = interaction_function[F_LJ14].nrfpB;
 100
 101     if ((nrfp != nrfpA) || (nrfpA != nrfpB))
 102     {
 103         gmx_incons("Number of force parameters in gen_pairs wrong");
 104     }
 105
 106     fprintf(stderr, "Generating 1-4 interactions: fudge = %g\n", fudge);
 107     pairs->interactionTypes.clear();
 108     int                             i = 0;
 109     std::array<int, 2>              atomNumbers;
 110     std::array<real, MAXFORCEPARAM> forceParam = { NOTSET };
 111     for (const auto& type : nbs.interactionTypes)
 112     {
 113         /* Copy type.atoms */
 114         atomNumbers = { i / nnn, i % nnn };
 115         /* Copy normal and FEP parameters and multiply by fudge factor */
 116         gmx::ArrayRef<const real> existingParam = type.forceParam();
 117         GMX_RELEASE_ASSERT(2 * nrfp <= MAXFORCEPARAM,
 118                            "Can't have more parameters than half of maximum p  arameter number");
 119         for (int j = 0; j < nrfp; j++)
 120         {
 121             /* If we are using sigma/epsilon values, only the epsilon values
 122              * should be scaled, but not sigma.
 123              * The sigma values have even indices 0,2, etc.
 124              */
 125             if ((comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS) && (j % 2 == 0))
 126             {
 127                 scaling = 1.0;
 128             }
 129             else
 130             {
 131                 scaling = fudge;
 132             }
 133
 134             forceParam[j]        = scaling * existingParam[j];
 135             forceParam[nrfp + j] = scaling * existingParam[j];
 136         }
 137         pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
 138         i++;
 139     }
 140 }
 141
 142 double check_mol(const gmx_mtop_t* mtop, warninp* wi)
 143 {
 144     char   buf[256];
 145     int    i, ri, pt;
 146     double q;
 147     real   m, mB;
 148
 149     /* Check mass and charge */
 150     q = 0.0;
 151
 152     for (const gmx_molblock_t& molb : mtop->molblock)
 153     {
 154         const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
 155         for (i = 0; (i < atoms->nr); i++)
 156         {
 157             q += molb.nmol * atoms->atom[i].q;
 158             m  = atoms->atom[i].m;
 159             mB = atoms->atom[i].mB;
 160             pt = atoms->atom[i].ptype;
 161             /* If the particle is an atom or a nucleus it must have a mass,
 162              * else, if it is a shell, a vsite or a bondshell it can have mass zero
 163              */
 164             if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
 165             {
 166                 ri = atoms->atom[i].resind;
 167                 sprintf(buf, "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
 168                         *(atoms->atomname[i]), *(atoms->resinfo[ri].name), atoms->resinfo[ri].nr, m, mB);
 169                 warning_error(wi, buf);
 170             }
 171             else if (((m != 0) || (mB != 0)) && (pt == eptVSite))
 172             {
 173                 ri = atoms->atom[i].resind;
 174                 sprintf(buf,
 175                         "virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state "
 176                         "B)\n"
 177                         "     Check your topology.\n",
 178                         *(atoms->atomname[i]), *(atoms->resinfo[ri].name), atoms->resinfo[ri].nr, m, mB);
 179                 warning_error(wi, buf);
 180                 /* The following statements make LINCS break! */
 181                 /* atoms->atom[i].m=0; */
 182             }
 183         }
 184     }
 185     return q;
 186 }
 187
 188 /*! \brief Returns the rounded charge of a molecule, when close to integer, otherwise returns the original charge.
 189  *
 190  * The results of this routine are only used for checking and for
 191  * printing warning messages. Thus we can assume that charges of molecules
 192  * should be integer. If the user wanted non-integer molecular charge,
 193  * an undesired warning is printed and the user should use grompp -maxwarn 1.
 194  *
 195  * \param qMol     The total, unrounded, charge of the molecule
 196  * \param sumAbsQ  The sum of absolute values of the charges, used for determining the tolerance for the rounding.
 197  */
 198 static double roundedMoleculeCharge(double qMol, double sumAbsQ)
 199 {
 200     /* We use a tolerance of 1e-6 for inaccuracies beyond the 6th decimal
 201      * of the charges for ascii float truncation in the topology files.
 202      * Although the summation here uses double precision, the charges
 203      * are read and stored in single precision when real=float. This can
 204      * lead to rounding errors of half the least significant bit.
 205      * Note that, unfortunately, we can not assume addition of random
 206      * rounding errors. It is not entirely unlikely that many charges
 207      * have a near half-bit rounding error with the same sign.
 208      */
 209     double tolAbs = 1e-6;
 210     double tol    = std::max(tolAbs, 0.5 * GMX_REAL_EPS * sumAbsQ);
 211     double qRound = std::round(qMol);
 212     if (std::abs(qMol - qRound) <= tol)
 213     {
 214         return qRound;
 215     }
 216     else
 217     {
 218         return qMol;
 219     }
 220 }
 221
 222 static void sum_q(const t_atoms* atoms, int numMols, double* qTotA, double* qTotB)
 223 {
 224     /* sum charge */
 225     double qmolA    = 0;
 226     double qmolB    = 0;
 227     double sumAbsQA = 0;
 228     double sumAbsQB = 0;
 229     for (int i = 0; i < atoms->nr; i++)
 230     {
 231         qmolA += atoms->atom[i].q;
 232         qmolB += atoms->atom[i].qB;
 233         sumAbsQA += std::abs(atoms->atom[i].q);
 234         sumAbsQB += std::abs(atoms->atom[i].qB);
 235     }
 236
 237     *qTotA += numMols * roundedMoleculeCharge(qmolA, sumAbsQA);
 238     *qTotB += numMols * roundedMoleculeCharge(qmolB, sumAbsQB);
 239 }
 240
 241 static void get_nbparm(char* nb_str, char* comb_str, int* nb, int* comb, warninp* wi)
 242 {
 243     int  i;
 244     char warn_buf[STRLEN];
 245
 246     *nb = -1;
 247     for (i = 1; (i < eNBF_NR); i++)
 248     {
 249         if (gmx_strcasecmp(nb_str, enbf_names[i]) == 0)
 250         {
 251             *nb = i;
 252         }
 253     }
 254     if (*nb == -1)
 255     {
 256         *nb = strtol(nb_str, nullptr, 10);
 257     }
 258     if ((*nb < 1) || (*nb >= eNBF_NR))
 259     {
 260         sprintf(warn_buf, "Invalid nonbond function selector '%s' using %s", nb_str, enbf_names[1]);
 261         warning_error(wi, warn_buf);
 262         *nb = 1;
 263     }
 264     *comb = -1;
 265     for (i = 1; (i < eCOMB_NR); i++)
 266     {
 267         if (gmx_strcasecmp(comb_str, ecomb_names[i]) == 0)
 268         {
 269             *comb = i;
 270         }
 271     }
 272     if (*comb == -1)
 273     {
 274         *comb = strtol(comb_str, nullptr, 10);
 275     }
 276     if ((*comb < 1) || (*comb >= eCOMB_NR))
 277     {
 278         sprintf(warn_buf, "Invalid combination rule selector '%s' using %s", comb_str, ecomb_names[1]);
 279         warning_error(wi, warn_buf);
 280         *comb = 1;
 281     }
 282 }
 283
 284 static char** cpp_opts(const char* define, const char* include, warninp* wi)
 285 {
 286     int         n, len;
 287     int         ncppopts = 0;
 288     const char* cppadds[2];
 289     char**      cppopts   = nullptr;
 290     const char* option[2] = { "-D", "-I" };
 291     const char* nopt[2]   = { "define", "include" };
 292     const char* ptr;
 293     const char* rptr;
 294     char*       buf;
 295     char        warn_buf[STRLEN];
 296
 297     cppadds[0] = define;
 298     cppadds[1] = include;
 299     for (n = 0; (n < 2); n++)
 300     {
 301         if (cppadds[n])
 302         {
 303             ptr = cppadds[n];
 304             while (*ptr != '\0')
 305             {
 306                 while ((*ptr != '\0') && isspace(*ptr))
 307                 {
 308                     ptr++;
 309                 }
 310                 rptr = ptr;
 311                 while ((*rptr != '\0') && !isspace(*rptr))
 312                 {
 313                     rptr++;
 314                 }
 315                 len = (rptr - ptr);
 316                 if (len > 2)
 317                 {
 318                     snew(buf, (len + 1));
 319                     strncpy(buf, ptr, len);
 320                     if (strstr(ptr, option[n]) != ptr)
 321                     {
 322                         set_warning_line(wi, "mdp file", -1);
 323                         sprintf(warn_buf, "Malformed %s option %s", nopt[n], buf);
 324                         warning(wi, warn_buf);
 325                     }
 326                     else
 327                     {
 328                         srenew(cppopts, ++ncppopts);
 329                         cppopts[ncppopts - 1] = gmx_strdup(buf);
 330                     }
 331                     sfree(buf);
 332                     ptr = rptr;
 333                 }
 334             }
 335         }
 336     }
 337     srenew(cppopts, ++ncppopts);
 338     cppopts[ncppopts - 1] = nullptr;
 339
 340     return cppopts;
 341 }
 342
 343
 344 static void make_atoms_sys(gmx::ArrayRef<const gmx_molblock_t>      molblock,
 345                            gmx::ArrayRef<const MoleculeInformation> molinfo,
 346                            t_atoms*                                 atoms)
 347 {
 348     atoms->nr   = 0;
 349     atoms->atom = nullptr;
 350
 351     for (const gmx_molblock_t& molb : molblock)
 352     {
 353         const t_atoms& mol_atoms = molinfo[molb.type].atoms;
 354
 355         srenew(atoms->atom, atoms->nr + molb.nmol * mol_atoms.nr);
 356
 357         for (int m = 0; m < molb.nmol; m++)
 358         {
 359             for (int a = 0; a < mol_atoms.nr; a++)
 360             {
 361                 atoms->atom[atoms->nr++] = mol_atoms.atom[a];
 362             }
 363         }
 364     }
 365 }
 366
 367
 368 static char** read_topol(const char*                           infile,
 369                          const char*                           outfile,
 370                          const char*                           define,
 371                          const char*                           include,
 372                          t_symtab*                             symtab,
 373                          PreprocessingAtomTypes*               atypes,
 374                          std::vector<MoleculeInformation>*     molinfo,
 375                          std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
 376                          gmx::ArrayRef<InteractionsOfType>     interactions,
 377                          int*                                  combination_rule,
 378                          double*                               reppow,
 379                          t_gromppopts*                         opts,
 380                          real*                                 fudgeQQ,
 381                          std::vector<gmx_molblock_t>*          molblock,
 382                          bool*                                 ffParametrizedWithHBondConstraints,
 383                          bool                                  bFEP,
 384                          bool                                  bZero,
 385                          bool                                  usingFullRangeElectrostatics,
 386                          warninp*                              wi,
 387                          const gmx::MDLogger&                  logger)
 388 {
 389     FILE*                out;
 390     int                  sl, nb_funct;
 391     char *               pline = nullptr, **title = nullptr;
 392     char                 line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
 393     char                 genpairs[32];
 394     char *               dirstr, *dummy2;
 395     int                  nrcopies, nscan, ncombs, ncopy;
 396     double               fLJ, fQQ, fPOW;
 397     MoleculeInformation* mi0 = nullptr;
 398     DirStack*            DS;
 399     Directive            d, newd;
 400     t_nbparam **         nbparam, **pair;
 401     real                 fudgeLJ = -1; /* Multiplication factor to generate 1-4 from LJ */
 402     bool                 bReadDefaults, bReadMolType, bGenPairs, bWarn_copy_A_B;
 403     double               qt = 0, qBt = 0; /* total charge */
 404     int                  dcatt = -1, nmol_couple;
 405     /* File handling variables */
 406     int         status;
 407     bool        done;
 408     gmx_cpp_t   handle;
 409     char*       tmp_line = nullptr;
 410     char        warn_buf[STRLEN];
 411     const char* floating_point_arithmetic_tip =
 412             "Total charge should normally be an integer. See\n"
 413             "http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n"
 414             "for discussion on how close it should be to an integer.\n";
 415     /* We need to open the output file before opening the input file,
 416      * because cpp_open_file can change the current working directory.
 417      */
 418     if (outfile)
 419     {
 420         out = gmx_fio_fopen(outfile, "w");
 421     }
 422     else
 423     {
 424         out = nullptr;
 425     }
 426
 427     /* open input file */
 428     auto cpp_opts_return = cpp_opts(define, include, wi);
 429     status               = cpp_open_file(infile, &handle, cpp_opts_return);
 430     if (status != 0)
 431     {
 432         gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 433     }
 434
 435     /* some local variables */
 436     DS_Init(&DS);                   /* directive stack  */
 437     d       = Directive::d_invalid; /* first thing should be a directive */
 438     nbparam = nullptr;              /* The temporary non-bonded matrix */
 439     pair    = nullptr;              /* The temporary pair interaction matrix */
 440     std::vector<std::vector<gmx::ExclusionBlock>> exclusionBlocks;
 441     nb_funct = F_LJ;
 442
 443     *reppow = 12.0; /* Default value for repulsion power     */
 444
 445     /* Init the number of CMAP torsion angles  and grid spacing */
 446     interactions[F_CMAP].cmakeGridSpacing = 0;
 447     interactions[F_CMAP].cmapAngles       = 0;
 448
 449     bWarn_copy_A_B = bFEP;
 450
 451     PreprocessingBondAtomType bondAtomType;
 452     /* parse the actual file */
 453     bReadDefaults = FALSE;
 454     bGenPairs     = FALSE;
 455     bReadMolType  = FALSE;
 456     nmol_couple   = 0;
 457
 458     do
 459     {
 460         status = cpp_read_line(&handle, STRLEN, line);
 461         done   = (status == eCPP_EOF);
 462         if (!done)
 463         {
 464             if (status != eCPP_OK)
 465             {
 466                 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 467             }
 468             else if (out)
 469             {
 470                 fprintf(out, "%s\n", line);
 471             }
 472
 473             set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
 474
 475             pline = gmx_strdup(line);
 476
 477             /* Strip trailing '\' from pline, if it exists */
 478             sl = strlen(pline);
 479             if ((sl > 0) && (pline[sl - 1] == CONTINUE))
 480             {
 481                 pline[sl - 1] = ' ';
 482             }
 483
 484             /* build one long line from several fragments - necessary for CMAP */
 485             while (continuing(line))
 486             {
 487                 status = cpp_read_line(&handle, STRLEN, line);
 488                 set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
 489
 490                 /* Since we depend on the '\' being present to continue to read, we copy line
 491                  * to a tmp string, strip the '\' from that string, and cat it to pline
 492                  */
 493                 tmp_line = gmx_strdup(line);
 494
 495                 sl = strlen(tmp_line);
 496                 if ((sl > 0) && (tmp_line[sl - 1] == CONTINUE))
 497                 {
 498                     tmp_line[sl - 1] = ' ';
 499                 }
 500
 501                 done = (status == eCPP_EOF);
 502                 if (!done)
 503                 {
 504                     if (status != eCPP_OK)
 505                     {
 506                         gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 507                     }
 508                     else if (out)
 509                     {
 510                         fprintf(out, "%s\n", line);
 511                     }
 512                 }
 513
 514                 srenew(pline, strlen(pline) + strlen(tmp_line) + 1);
 515                 strcat(pline, tmp_line);
 516                 sfree(tmp_line);
 517             }
 518
 519             /* skip trailing and leading spaces and comment text */
 520             strip_comment(pline);
 521             trim(pline);
 522
 523             /* if there is something left... */
 524             if (static_cast<int>(strlen(pline)) > 0)
 525             {
 526                 if (pline[0] == OPENDIR)
 527                 {
 528                     /* A directive on this line: copy the directive
 529                      * without the brackets into dirstr, then
 530                      * skip spaces and tabs on either side of directive
 531                      */
 532                     dirstr = gmx_strdup((pline + 1));
 533                     if ((dummy2 = strchr(dirstr, CLOSEDIR)) != nullptr)
 534                     {
 535                         (*dummy2) = 0;
 536                     }
 537                     trim(dirstr);
 538
 539                     if ((newd = str2dir(dirstr)) == Directive::d_invalid)
 540                     {
 541                         sprintf(errbuf, "Invalid directive %s", dirstr);
 542                         warning_error(wi, errbuf);
 543                     }
 544                     else
 545                     {
 546                         /* Directive found */
 547                         if (DS_Check_Order(DS, newd))
 548                         {
 549                             DS_Push(&DS, newd);
 550                             d = newd;
 551                         }
 552                         else
 553                         {
 554                             /* we should print here which directives should have
 555                                been present, and which actually are */
 556                             gmx_fatal(FARGS, "%s\nInvalid order for directive %s",
 557                                       cpp_error(&handle, eCPP_SYNTAX), dir2str(newd));
 558                             /* d = Directive::d_invalid; */
 559                         }
 560
 561                         if (d == Directive::d_intermolecular_interactions)
 562                         {
 563                             if (*intermolecular_interactions == nullptr)
 564                             {
 565                                 /* We (mis)use the moleculetype processing
 566                                  * to process the intermolecular interactions
 567                                  * by making a "molecule" of the size of the system.
 568                                  */
 569                                 *intermolecular_interactions = std::make_unique<MoleculeInformation>();
 570                                 mi0                          = intermolecular_interactions->get();
 571                                 mi0->initMolInfo();
 572                                 make_atoms_sys(*molblock, *molinfo, &mi0->atoms);
 573                             }
 574                         }
 575                     }
 576                     sfree(dirstr);
 577                 }
 578                 else if (d != Directive::d_invalid)
 579                 {
 580                     /* Not a directive, just a plain string
 581                      * use a gigantic switch to decode,
 582                      * if there is a valid directive!
 583                      */
 584                     switch (d)
 585                     {
 586                         case Directive::d_defaults:
 587                             if (bReadDefaults)
 588                             {
 589                                 gmx_fatal(FARGS, "%s\nFound a second defaults directive.\n",
 590                                           cpp_error(&handle, eCPP_SYNTAX));
 591                             }
 592                             bReadDefaults = TRUE;
 593                             nscan = sscanf(pline, "%s%s%s%lf%lf%lf", nb_str, comb_str, genpairs,
 594                                            &fLJ, &fQQ, &fPOW);
 595                             if (nscan < 2)
 596                             {
 597                                 too_few(wi);
 598                             }
 599                             else
 600                             {
 601                                 bGenPairs = FALSE;
 602                                 fudgeLJ   = 1.0;
 603                                 *fudgeQQ  = 1.0;
 604
 605                                 get_nbparm(nb_str, comb_str, &nb_funct, combination_rule, wi);
 606                                 if (nscan >= 3)
 607                                 {
 608                                     bGenPairs = (gmx::equalCaseInsensitive(genpairs, "Y", 1));
 609                                     if (nb_funct != eNBF_LJ && bGenPairs)
 610                                     {
 611                                         gmx_fatal(FARGS,
 612                                                   "Generating pair parameters is only supported "
 613                                                   "with LJ non-bonded interactions");
 614                                     }
 615                                 }
 616                                 if (nscan >= 4)
 617                                 {
 618                                     fudgeLJ = fLJ;
 619                                 }
 620                                 if (nscan >= 5)
 621                                 {
 622                                     *fudgeQQ = fQQ;
 623                                 }
 624                                 if (nscan >= 6)
 625                                 {
 626                                     *reppow = fPOW;
 627                                 }
 628                             }
 629                             nb_funct = ifunc_index(Directive::d_nonbond_params, nb_funct);
 630
 631                             break;
 632                         case Directive::d_atomtypes:
 633                             push_at(symtab, atypes, &bondAtomType, pline, nb_funct, &nbparam,
 634                                     bGenPairs ? &pair : nullptr, wi);
 635                             break;
 636
 637                         case Directive::d_bondtypes:
 638                             push_bt(d, interactions, 2, nullptr, &bondAtomType, pline, wi);
 639                             break;
 640                         case Directive::d_constrainttypes:
 641                             push_bt(d, interactions, 2, nullptr, &bondAtomType, pline, wi);
 642                             break;
 643                         case Directive::d_pairtypes:
 644                             if (bGenPairs)
 645                             {
 646                                 push_nbt(d, pair, atypes, pline, F_LJ14, wi);
 647                             }
 648                             else
 649                             {
 650                                 push_bt(d, interactions, 2, atypes, nullptr, pline, wi);
 651                             }
 652                             break;
 653                         case Directive::d_angletypes:
 654                             push_bt(d, interactions, 3, nullptr, &bondAtomType, pline, wi);
 655                             break;
 656                         case Directive::d_dihedraltypes:
 657                             /* Special routine that can read both 2 and 4 atom dihedral definitions. */
 658                             push_dihedraltype(d, interactions, &bondAtomType, pline, wi);
 659                             break;
 660
 661                         case Directive::d_nonbond_params:
 662                             push_nbt(d, nbparam, atypes, pline, nb_funct, wi);
 663                             break;
 664
 665                         case Directive::d_implicit_genborn_params:
 666                             // Skip this line, so old topologies with
 667                             // GB parameters can be read.
 668                             break;
 669
 670                         case Directive::d_implicit_surface_params:
 671                             // Skip this line, so that any topologies
 672                             // with surface parameters can be read
 673                             // (even though these were never formally
 674                             // supported).
 675                             break;
 676
 677                         case Directive::d_cmaptypes:
 678                             push_cmaptype(d, interactions, 5, atypes, &bondAtomType, pline, wi);
 679                             break;
 680
 681                         case Directive::d_moleculetype:
 682                         {
 683                             if (!bReadMolType)
 684                             {
 685                                 int ntype;
 686                                 if (opts->couple_moltype != nullptr
 687                                     && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam0 == ecouplamQ
 688                                         || opts->couple_lam1 == ecouplamNONE
 689                                         || opts->couple_lam1 == ecouplamQ))
 690                                 {
 691                                     dcatt = add_atomtype_decoupled(symtab, atypes, &nbparam,
 692                                                                    bGenPairs ? &pair : nullptr);
 693                                 }
 694                                 ntype  = atypes->size();
 695                                 ncombs = (ntype * (ntype + 1)) / 2;
 696                                 generate_nbparams(*combination_rule, nb_funct,
 697                                                   &(interactions[nb_funct]), atypes, wi);
 698                                 ncopy = copy_nbparams(nbparam, nb_funct, &(interactions[nb_funct]), ntype);
 699                                 GMX_LOG(logger.info)
 700                                         .asParagraph()
 701                                         .appendTextFormatted(
 702                                                 "Generated %d of the %d non-bonded parameter "
 703                                                 "combinations",
 704                                                 ncombs - ncopy, ncombs);
 705                                 free_nbparam(nbparam, ntype);
 706                                 if (bGenPairs)
 707                                 {
 708                                     gen_pairs((interactions[nb_funct]), &(interactions[F_LJ14]),
 709                                               fudgeLJ, *combination_rule);
 710                                     ncopy = copy_nbparams(pair, nb_funct, &(interactions[F_LJ14]), ntype);
 711                                     GMX_LOG(logger.info)
 712                                             .asParagraph()
 713                                             .appendTextFormatted(
 714                                                     "Generated %d of the %d 1-4 parameter "
 715                                                     "combinations",
 716                                                     ncombs - ncopy, ncombs);
 717                                     free_nbparam(pair, ntype);
 718                                 }
 719                                 /* Copy GBSA parameters to atomtype array? */
 720
 721                                 bReadMolType = TRUE;
 722                             }
 723
 724                             push_molt(symtab, molinfo, pline, wi);
 725                             exclusionBlocks.emplace_back();
 726                             mi0                    = &molinfo->back();
 727                             mi0->atoms.haveMass    = TRUE;
 728                             mi0->atoms.haveCharge  = TRUE;
 729                             mi0->atoms.haveType    = TRUE;
 730                             mi0->atoms.haveBState  = TRUE;
 731                             mi0->atoms.havePdbInfo = FALSE;
 732                             break;
 733                         }
 734                         case Directive::d_atoms:
 735                             push_atom(symtab, &(mi0->atoms), atypes, pline, wi);
 736                             break;
 737
 738                         case Directive::d_pairs:
 739                             GMX_RELEASE_ASSERT(
 740                                     mi0,
 741                                     "Need to have a valid MoleculeInformation object to work on");
 742                             push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
 743                                       pline, FALSE, bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
 744                             break;
 745                         case Directive::d_pairs_nb:
 746                             GMX_RELEASE_ASSERT(
 747                                     mi0,
 748                                     "Need to have a valid MoleculeInformation object to work on");
 749                             push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
 750                                       pline, FALSE, FALSE, 1.0, bZero, &bWarn_copy_A_B, wi);
 751                             break;
 752
 753                         case Directive::d_vsites2:
 754                         case Directive::d_vsites3:
 755                         case Directive::d_vsites4:
 756                         case Directive::d_bonds:
 757                         case Directive::d_angles:
 758                         case Directive::d_constraints:
 759                         case Directive::d_settles:
 760                         case Directive::d_position_restraints:
 761                         case Directive::d_angle_restraints:
 762                         case Directive::d_angle_restraints_z:
 763                         case Directive::d_distance_restraints:
 764                         case Directive::d_orientation_restraints:
 765                         case Directive::d_dihedral_restraints:
 766                         case Directive::d_dihedrals:
 767                         case Directive::d_polarization:
 768                         case Directive::d_water_polarization:
 769                         case Directive::d_thole_polarization:
 770                             GMX_RELEASE_ASSERT(
 771                                     mi0,
 772                                     "Need to have a valid MoleculeInformation object to work on");
 773                             push_bond(d, interactions, mi0->interactions, &(mi0->atoms), atypes,
 774                                       pline, TRUE, bGenPairs, *fudgeQQ, bZero, &bWarn_copy_A_B, wi);
 775                             break;
 776                         case Directive::d_cmap:
 777                             GMX_RELEASE_ASSERT(
 778                                     mi0,
 779                                     "Need to have a valid MoleculeInformation object to work on");
 780                             push_cmap(d, interactions, mi0->interactions, &(mi0->atoms), atypes, pline, wi);
 781                             break;
 782
 783                         case Directive::d_vsitesn:
 784                             GMX_RELEASE_ASSERT(
 785                                     mi0,
 786                                     "Need to have a valid MoleculeInformation object to work on");
 787                             push_vsitesn(d, mi0->interactions, &(mi0->atoms), pline, wi);
 788                             break;
 789                         case Directive::d_exclusions:
 790                             GMX_ASSERT(!exclusionBlocks.empty(),
 791                                        "exclusionBlocks must always be allocated so exclusions can "
 792                                        "be processed");
 793                             if (exclusionBlocks.back().empty())
 794                             {
 795                                 GMX_RELEASE_ASSERT(mi0,
 796                                                    "Need to have a valid MoleculeInformation "
 797                                                    "object to work on");
 798                                 exclusionBlocks.back().resize(mi0->atoms.nr);
 799                             }
 800                             push_excl(pline, exclusionBlocks.back(), wi);
 801                             break;
 802                         case Directive::d_system:
 803                             trim(pline);
 804                             title = put_symtab(symtab, pline);
 805                             break;
 806                         case Directive::d_molecules:
 807                         {
 808                             int  whichmol;
 809                             bool bCouple;
 810
 811                             push_mol(*molinfo, pline, &whichmol, &nrcopies, wi);
 812                             mi0 = &((*molinfo)[whichmol]);
 813                             molblock->resize(molblock->size() + 1);
 814                             molblock->back().type = whichmol;
 815                             molblock->back().nmol = nrcopies;
 816
 817                             bCouple = (opts->couple_moltype != nullptr
 818                                        && (gmx_strcasecmp("system", opts->couple_moltype) == 0
 819                                            || strcmp(*(mi0->name), opts->couple_moltype) == 0));
 820                             if (bCouple)
 821                             {
 822                                 nmol_couple += nrcopies;
 823                             }
 824
 825                             if (mi0->atoms.nr == 0)
 826                             {
 827                                 gmx_fatal(FARGS, "Molecule type '%s' contains no atoms", *mi0->name);
 828                             }
 829                             GMX_LOG(logger.info)
 830                                     .asParagraph()
 831                                     .appendTextFormatted(
 832                                             "Excluding %d bonded neighbours molecule type '%s'",
 833                                             mi0->nrexcl, *mi0->name);
 834                             sum_q(&mi0->atoms, nrcopies, &qt, &qBt);
 835                             if (!mi0->bProcessed)
 836                             {
 837                                 generate_excl(mi0->nrexcl, mi0->atoms.nr, mi0->interactions, &(mi0->excls));
 838                                 gmx::mergeExclusions(&(mi0->excls), exclusionBlocks[whichmol]);
 839                                 make_shake(mi0->interactions, &mi0->atoms, opts->nshake, logger);
 840
 841                                 if (bCouple)
 842                                 {
 843                                     convert_moltype_couple(mi0, dcatt, *fudgeQQ, opts->couple_lam0,
 844                                                            opts->couple_lam1, opts->bCoupleIntra,
 845                                                            nb_funct, &(interactions[nb_funct]), wi);
 846                                 }
 847                                 stupid_fill_block(&mi0->mols, mi0->atoms.nr, TRUE);
 848                                 mi0->bProcessed = TRUE;
 849                             }
 850                             break;
 851                         }
 852                         default:
 853                             GMX_LOG(logger.warning)
 854                                     .asParagraph()
 855                                     .appendTextFormatted("case: %d", static_cast<int>(d));
 856                             gmx_incons("unknown directive");
 857                     }
 858                 }
 859             }
 860             sfree(pline);
 861             pline = nullptr;
 862         }
 863     } while (!done);
 864
 865     // Check that all strings defined with -D were used when processing topology
 866     std::string unusedDefineWarning = checkAndWarnForUnusedDefines(*handle);
 867     if (!unusedDefineWarning.empty())
 868     {
 869         warning(wi, unusedDefineWarning);
 870     }
 871
 872     sfree(cpp_opts_return);
 873
 874     if (out)
 875     {
 876         gmx_fio_fclose(out);
 877     }
 878
 879     /* List of GROMACS define names for force fields that have been
 880      * parametrized using constraints involving hydrogens only.
 881      *
 882      * We should avoid hardcoded names, but this is hopefully only
 883      * needed temparorily for discouraging use of constraints=all-bonds.
 884      */
 885     const std::array<std::string, 3> ffDefines = { "_FF_AMBER", "_FF_CHARMM", "_FF_OPLSAA" };
 886     *ffParametrizedWithHBondConstraints        = false;
 887     for (const std::string& ffDefine : ffDefines)
 888     {
 889         if (cpp_find_define(&handle, ffDefine))
 890         {
 891             *ffParametrizedWithHBondConstraints = true;
 892         }
 893     }
 894
 895     if (cpp_find_define(&handle, "_FF_GROMOS96") != nullptr)
 896     {
 897         warning(wi,
 898                 "The GROMOS force fields have been parametrized with a physically incorrect "
 899                 "multiple-time-stepping scheme for a twin-range cut-off. When used with "
 900                 "a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), "
 901                 "physical properties, such as the density, might differ from the intended values. "
 902                 "Since there are researchers actively working on validating GROMOS with modern "
 903                 "integrators we have not yet removed the GROMOS force fields, but you should be "
 904                 "aware of these issues and check if molecules in your system are affected before "
 905                 "proceeding. "
 906                 "Further information is available at https://redmine.gromacs.org/issues/2884 , "
 907                 "and a longer explanation of our decision to remove physically incorrect "
 908                 "algorithms "
 909                 "can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 .");
 910     }
 911
 912     cpp_done(handle);
 913
 914     if (opts->couple_moltype)
 915     {
 916         if (nmol_couple == 0)
 917         {
 918             gmx_fatal(FARGS, "Did not find any molecules of type '%s' for coupling", opts->couple_moltype);
 919         }
 920         GMX_LOG(logger.info)
 921                 .asParagraph()
 922                 .appendTextFormatted("Coupling %d copies of molecule type '%s'", nmol_couple,
 923                                      opts->couple_moltype);
 924     }
 925
 926     /* this is not very clean, but fixes core dump on empty system name */
 927     if (!title)
 928     {
 929         title = put_symtab(symtab, "");
 930     }
 931
 932     if (fabs(qt) > 1e-4)
 933     {
 934         sprintf(warn_buf, "System has non-zero total charge: %.6f\n%s\n", qt, floating_point_arithmetic_tip);
 935         warning_note(wi, warn_buf);
 936     }
 937     if (fabs(qBt) > 1e-4 && !gmx_within_tol(qBt, qt, 1e-6))
 938     {
 939         sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt,
 940                 floating_point_arithmetic_tip);
 941         warning_note(wi, warn_buf);
 942     }
 943     if (usingFullRangeElectrostatics && (fabs(qt) > 1e-4 || fabs(qBt) > 1e-4))
 944     {
 945         warning(wi,
 946                 "You are using Ewald electrostatics in a system with net charge. This can lead to "
 947                 "severe artifacts, such as ions moving into regions with low dielectric, due to "
 948                 "the uniform background charge. We suggest to neutralize your system with counter "
 949                 "ions, possibly in combination with a physiological salt concentration.");
 950         please_cite(stdout, "Hub2014a");
 951     }
 952
 953     DS_Done(&DS);
 954
 955     if (*intermolecular_interactions != nullptr)
 956     {
 957         sfree(intermolecular_interactions->get()->atoms.atom);
 958     }
 959
 960     return title;
 961 }
 962
 963 char** do_top(bool                                  bVerbose,
 964               const char*                           topfile,
 965               const char*                           topppfile,
 966               t_gromppopts*                         opts,
 967               bool                                  bZero,
 968               t_symtab*                             symtab,
 969               gmx::ArrayRef<InteractionsOfType>     interactions,
 970               int*                                  combination_rule,
 971               double*                               repulsion_power,
 972               real*                                 fudgeQQ,
 973               PreprocessingAtomTypes*               atypes,
 974               std::vector<MoleculeInformation>*     molinfo,
 975               std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
 976               const t_inputrec*                     ir,
 977               std::vector<gmx_molblock_t>*          molblock,
 978               bool*                                 ffParametrizedWithHBondConstraints,
 979               warninp*                              wi,
 980               const gmx::MDLogger&                  logger)
 981 {
 982     /* Tmpfile might contain a long path */
 983     const char* tmpfile;
 984     char**      title;
 985
 986     if (topppfile)
 987     {
 988         tmpfile = topppfile;
 989     }
 990     else
 991     {
 992         tmpfile = nullptr;
 993     }
 994
 995     if (bVerbose)
 996     {
 997         GMX_LOG(logger.info).asParagraph().appendTextFormatted("processing topology...");
 998     }
 999     title = read_topol(topfile, tmpfile, opts->define, opts->include, symtab, atypes, molinfo,
1000                        intermolecular_interactions, interactions, combination_rule, repulsion_power,
1001                        opts, fudgeQQ, molblock, ffParametrizedWithHBondConstraints,
1002                        ir->efep != efepNO, bZero, EEL_FULL(ir->coulombtype), wi, logger);
1003
1004     if ((*combination_rule != eCOMB_GEOMETRIC) && (ir->vdwtype == evdwUSER))
1005     {
1006         warning(wi,
1007                 "Using sigma/epsilon based combination rules with"
1008                 " user supplied potential function may produce unwanted"
1009                 " results");
1010     }
1011
1012     return title;
1013 }
1014
1015 /*! \brief
1016  * Exclude molecular interactions for QM atoms handled by MiMic.
1017  *
1018  * Update the exclusion lists to include all QM atoms of this molecule,
1019  * replace bonds between QM atoms with CONNBOND and
1020  * set charges of QM atoms to 0.
1021  *
1022  * \param[in,out] molt molecule type with QM atoms
1023  * \param[in] grpnr group informatio
1024  * \param[in,out] ir input record
1025  * \param[in] logger Handle to logging interface.
1026  */
1027 static void generate_qmexcl_moltype(gmx_moltype_t*       molt,
1028                                     const unsigned char* grpnr,
1029                                     t_inputrec*          ir,
1030                                     const gmx::MDLogger& logger)
1031 {
1032     /* This routine expects molt->ilist to be of size F_NRE and ordered. */
1033
1034     /* generates the exclusions between the individual QM atoms, as
1035      * these interactions should be handled by the QM subroutines and
1036      * not by the gromacs routines
1037      */
1038     int   qm_max = 0, qm_nr = 0, link_nr = 0;
1039     int * qm_arr = nullptr, *link_arr = nullptr;
1040     bool* bQMMM;
1041
1042     /* First we search and select the QM atoms in an qm_arr array that
1043      * we use to create the exclusions.
1044      *
1045      * we take the possibility into account that a user has defined more
1046      * than one QM group:
1047      *
1048      * for that we also need to do this an ugly work-about just in case
1049      * the QM group contains the entire system...
1050      */
1051
1052     /* we first search for all the QM atoms and put them in an array
1053      */
1054     for (int j = 0; j < ir->opts.ngQM; j++)
1055     {
1056         for (int i = 0; i < molt->atoms.nr; i++)
1057         {
1058             if (qm_nr >= qm_max)
1059             {
1060                 qm_max += 100;
1061                 srenew(qm_arr, qm_max);
1062             }
1063             if ((grpnr ? grpnr[i] : 0) == j)
1064             {
1065                 qm_arr[qm_nr++]        = i;
1066                 molt->atoms.atom[i].q  = 0.0;
1067                 molt->atoms.atom[i].qB = 0.0;
1068             }
1069         }
1070     }
1071     /* bQMMM[..] is an array containin TRUE/FALSE for atoms that are
1072      * QM/not QM. We first set all elements to false. Afterwards we use
1073      * the qm_arr to change the elements corresponding to the QM atoms
1074      * to TRUE.
1075      */
1076     snew(bQMMM, molt->atoms.nr);
1077     for (int i = 0; i < molt->atoms.nr; i++)
1078     {
1079         bQMMM[i] = FALSE;
1080     }
1081     for (int i = 0; i < qm_nr; i++)
1082     {
1083         bQMMM[qm_arr[i]] = TRUE;
1084     }
1085
1086     /* We remove all bonded interactions (i.e. bonds,
1087      * angles, dihedrals, 1-4's), involving the QM atoms. The way they
1088      * are removed is as follows: if the interaction invloves 2 atoms,
1089      * it is removed if both atoms are QMatoms. If it involves 3 atoms,
1090      * it is removed if at least two of the atoms are QM atoms, if the
1091      * interaction involves 4 atoms, it is removed if there are at least
1092      * 2 QM atoms.  Since this routine is called once before any forces
1093      * are computed, the top->idef.il[N].iatom[] array (see idef.h) can
1094      * be rewritten at this poitn without any problem. 25-9-2002 */
1095
1096     /* first check whether we already have CONNBONDS.
1097      * Note that if we don't, we don't add a param entry and set ftype=0,
1098      * which is ok, since CONNBONDS does not use parameters.
1099      */
1100     int ftype_connbond = 0;
1101     int ind_connbond   = 0;
1102     if (!molt->ilist[F_CONNBONDS].empty())
1103     {
1104         GMX_LOG(logger.info)
1105                 .asParagraph()
1106                 .appendTextFormatted("nr. of CONNBONDS present already: %d",
1107                                      molt->ilist[F_CONNBONDS].size() / 3);
1108         ftype_connbond = molt->ilist[F_CONNBONDS].iatoms[0];
1109         ind_connbond   = molt->ilist[F_CONNBONDS].size();
1110     }
1111     /* now we delete all bonded interactions, except the ones describing
1112      * a chemical bond. These are converted to CONNBONDS
1113      */
1114     for (int ftype = 0; ftype < F_NRE; ftype++)
1115     {
1116         if (!(interaction_function[ftype].flags & IF_BOND) || ftype == F_CONNBONDS)
1117         {
1118             continue;
1119         }
1120         int nratoms = interaction_function[ftype].nratoms;
1121         int j       = 0;
1122         while (j < molt->ilist[ftype].size())
1123         {
1124             bool bexcl;
1125
1126             if (nratoms == 2)
1127             {
1128                 /* Remove an interaction between two atoms when both are
1129                  * in the QM region. Note that we don't have to worry about
1130                  * link atoms here, as they won't have 2-atom interactions.
1131                  */
1132                 int a1 = molt->ilist[ftype].iatoms[1 + j + 0];
1133                 int a2 = molt->ilist[ftype].iatoms[1 + j + 1];
1134                 bexcl  = (bQMMM[a1] && bQMMM[a2]);
1135                 /* A chemical bond between two QM atoms will be copied to
1136                  * the F_CONNBONDS list, for reasons mentioned above.
1137                  */
1138                 if (bexcl && IS_CHEMBOND(ftype))
1139                 {
1140                     InteractionList& ilist = molt->ilist[F_CONNBONDS];
1141                     ilist.iatoms.resize(ind_connbond + 3);
1142                     ilist.iatoms[ind_connbond++] = ftype_connbond;
1143                     ilist.iatoms[ind_connbond++] = a1;
1144                     ilist.iatoms[ind_connbond++] = a2;
1145                 }
1146             }
1147             else
1148             {
1149                 /* MM interactions have to be excluded if they are included
1150                  * in the QM already. Because we use a link atom (H atom)
1151                  * when the QM/MM boundary runs through a chemical bond, this
1152                  * means that as long as one atom is MM, we still exclude,
1153                  * as the interaction is included in the QM via:
1154                  * QMatom1-QMatom2-QMatom-3-Linkatom.
1155                  */
1156                 int numQmAtoms = 0;
1157                 for (int jj = j + 1; jj < j + 1 + nratoms; jj++)
1158                 {
1159                     if (bQMMM[molt->ilist[ftype].iatoms[jj]])
1160                     {
1161                         numQmAtoms++;
1162                     }
1163                 }
1164
1165                 /* MiMiC treats link atoms as quantum atoms - therefore
1166                  * we do not need do additional exclusions here */
1167                 bexcl = numQmAtoms == nratoms;
1168
1169                 if (bexcl && ftype == F_SETTLE)
1170                 {
1171                     gmx_fatal(FARGS,
1172                               "Can not apply QM to molecules with SETTLE, replace the moleculetype "
1173                               "using QM and SETTLE by one without SETTLE");
1174                 }
1175             }
1176             if (bexcl)
1177             {
1178                 /* since the interaction involves QM atoms, these should be
1179                  * removed from the MM ilist
1180                  */
1181                 InteractionList& ilist = molt->ilist[ftype];
1182                 for (int k = j; k < ilist.size() - (nratoms + 1); k++)
1183                 {
1184                     ilist.iatoms[k] = ilist.iatoms[k + (nratoms + 1)];
1185                 }
1186                 ilist.iatoms.resize(ilist.size() - (nratoms + 1));
1187             }
1188             else
1189             {
1190                 j += nratoms + 1; /* the +1 is for the functype */
1191             }
1192         }
1193     }
1194     /* Now, we search for atoms bonded to a QM atom because we also want
1195      * to exclude their nonbonded interactions with the QM atoms. The
1196      * reason for this is that this interaction is accounted for in the
1197      * linkatoms interaction with the QMatoms and would be counted
1198      * twice.  */
1199
1200     /* creating the exclusion block for the QM atoms. Each QM atom has
1201      * as excluded elements all the other QMatoms (and itself).
1202      */
1203     t_blocka qmexcl;
1204     qmexcl.nr  = molt->atoms.nr;
1205     qmexcl.nra = qm_nr * (qm_nr + link_nr) + link_nr * qm_nr;
1206     snew(qmexcl.index, qmexcl.nr + 1);
1207     snew(qmexcl.a, qmexcl.nra);
1208     int j = 0;
1209     for (int i = 0; i < qmexcl.nr; i++)
1210     {
1211         qmexcl.index[i] = j;
1212         if (bQMMM[i])
1213         {
1214             for (int k = 0; k < qm_nr; k++)
1215             {
1216                 qmexcl.a[k + j] = qm_arr[k];
1217             }
1218             for (int k = 0; k < link_nr; k++)
1219             {
1220                 qmexcl.a[qm_nr + k + j] = link_arr[k];
1221             }
1222             j += (qm_nr + link_nr);
1223         }
1224     }
1225     qmexcl.index[qmexcl.nr] = j;
1226
1227     /* and merging with the exclusions already present in sys.
1228      */
1229
1230     std::vector<gmx::ExclusionBlock> qmexcl2(molt->atoms.nr);
1231     gmx::blockaToExclusionBlocks(&qmexcl, qmexcl2);
1232     gmx::mergeExclusions(&(molt->excls), qmexcl2);
1233
1234     /* Finally, we also need to get rid of the pair interactions of the
1235      * classical atom bonded to the boundary QM atoms with the QMatoms,
1236      * as this interaction is already accounted for by the QM, so also
1237      * here we run the risk of double counting! We proceed in a similar
1238      * way as we did above for the other bonded interactions: */
1239     for (int i = F_LJ14; i < F_COUL14; i++)
1240     {
1241         int nratoms = interaction_function[i].nratoms;
1242         int j       = 0;
1243         while (j < molt->ilist[i].size())
1244         {
1245             int  a1    = molt->ilist[i].iatoms[j + 1];
1246             int  a2    = molt->ilist[i].iatoms[j + 2];
1247             bool bexcl = (bQMMM[a1] && bQMMM[a2]);
1248             if (bexcl)
1249             {
1250                 /* since the interaction involves QM atoms, these should be
1251                  * removed from the MM ilist
1252                  */
1253                 InteractionList& ilist = molt->ilist[i];
1254                 for (int k = j; k < ilist.size() - (nratoms + 1); k++)
1255                 {
1256                     ilist.iatoms[k] = ilist.iatoms[k + (nratoms + 1)];
1257                 }
1258                 ilist.iatoms.resize(ilist.size() - (nratoms + 1));
1259             }
1260             else
1261             {
1262                 j += nratoms + 1; /* the +1 is for the functype */
1263             }
1264         }
1265     }
1266
1267     free(qm_arr);
1268     free(bQMMM);
1269     free(link_arr);
1270 } /* generate_qmexcl */
1271
1272 void generate_qmexcl(gmx_mtop_t* sys, t_inputrec* ir, const gmx::MDLogger& logger)
1273 {
1274     /* This routine expects molt->molt[m].ilist to be of size F_NRE and ordered.
1275      */
1276
1277     unsigned char*  grpnr;
1278     int             mol, nat_mol, nr_mol_with_qm_atoms = 0;
1279     gmx_molblock_t* molb;
1280     bool            bQMMM;
1281     int             index_offset = 0;
1282     int             qm_nr        = 0;
1283
1284     grpnr = sys->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].data();
1285
1286     for (size_t mb = 0; mb < sys->molblock.size(); mb++)
1287     {
1288         molb    = &sys->molblock[mb];
1289         nat_mol = sys->moltype[molb->type].atoms.nr;
1290         for (mol = 0; mol < molb->nmol; mol++)
1291         {
1292             bQMMM = FALSE;
1293             for (int i = 0; i < nat_mol; i++)
1294             {
1295                 if ((grpnr ? grpnr[i] : 0) < (ir->opts.ngQM))
1296                 {
1297                     bQMMM = TRUE;
1298                     qm_nr++;
1299                 }
1300             }
1301
1302             if (bQMMM)
1303             {
1304                 nr_mol_with_qm_atoms++;
1305                 if (molb->nmol > 1)
1306                 {
1307                     /* We need to split this molblock */
1308                     if (mol > 0)
1309                     {
1310                         /* Split the molblock at this molecule */
1311                         auto pos = sys->molblock.begin() + mb + 1;
1312                         sys->molblock.insert(pos, sys->molblock[mb]);
1313                         sys->molblock[mb].nmol = mol;
1314                         sys->molblock[mb + 1].nmol -= mol;
1315                         mb++;
1316                         molb = &sys->molblock[mb];
1317                     }
1318                     if (molb->nmol > 1)
1319                     {
1320                         /* Split the molblock after this molecule */
1321                         auto pos = sys->molblock.begin() + mb + 1;
1322                         sys->molblock.insert(pos, sys->molblock[mb]);
1323                         molb                   = &sys->molblock[mb];
1324                         sys->molblock[mb].nmol = 1;
1325                         sys->molblock[mb + 1].nmol -= 1;
1326                     }
1327
1328                     /* Create a copy of a moltype for a molecule
1329                      * containing QM atoms and append it in the end of the list
1330                      */
1331                     std::vector<gmx_moltype_t> temp(sys->moltype.size());
1332                     for (size_t i = 0; i < sys->moltype.size(); ++i)
1333                     {
1334                         copy_moltype(&sys->moltype[i], &temp[i]);
1335                     }
1336                     sys->moltype.resize(sys->moltype.size() + 1);
1337                     for (size_t i = 0; i < temp.size(); ++i)
1338                     {
1339                         copy_moltype(&temp[i], &sys->moltype[i]);
1340                     }
1341                     copy_moltype(&sys->moltype[molb->type], &sys->moltype.back());
1342                     /* Copy the exclusions to a new array, since this is the only
1343                      * thing that needs to be modified for QMMM.
1344                      */
1345                     sys->moltype.back().excls = sys->moltype[molb->type].excls;
1346                     /* Set the molecule type for the QMMM molblock */
1347                     molb->type = sys->moltype.size() - 1;
1348                 }
1349                 generate_qmexcl_moltype(&sys->moltype[molb->type], grpnr, ir, logger);
1350             }
1351             if (grpnr)
1352             {
1353                 grpnr += nat_mol;
1354             }
1355             index_offset += nat_mol;
1356         }
1357     }
1358 }