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) 2018,2019,2020,2021, 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  *
  12  * GROMACS is free software; you can redistribute it and/or
  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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  20  * Lesser General Public License for more details.
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  38 #include "gmxpre.h"
  39
  40 #include "gromacs/utility/enumerationhelpers.h"
  41 #include "gromacs/utility/stringutil.h"
  42 #include "topio.h"
  43
  44 #include <cassert>
  45 #include <cctype>
  46 #include <cerrno>
  47 #include <cmath>
  48 #include <cstdio>
  49 #include <cstdlib>
  50 #include <cstring>
  51
  52 #include <algorithm>
  53 #include <memory>
  54 #include <unordered_set>
  55
  56 #include <sys/types.h>
  57
  58 #include "gromacs/fileio/gmxfio.h"
  59 #include "gromacs/fileio/warninp.h"
  60 #include "gromacs/gmxpreprocess/gmxcpp.h"
  61 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  62 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
  63 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
  64 #include "gromacs/gmxpreprocess/grompp_impl.h"
  65 #include "gromacs/gmxpreprocess/readir.h"
  66 #include "gromacs/gmxpreprocess/topdirs.h"
  67 #include "gromacs/gmxpreprocess/toppush.h"
  68 #include "gromacs/gmxpreprocess/topshake.h"
  69 #include "gromacs/gmxpreprocess/toputil.h"
  70 #include "gromacs/gmxpreprocess/vsite_parm.h"
  71 #include "gromacs/math/units.h"
  72 #include "gromacs/math/utilities.h"
  73 #include "gromacs/mdtypes/inputrec.h"
  74 #include "gromacs/mdtypes/md_enums.h"
  75 #include "gromacs/pbcutil/pbc.h"
  76 #include "gromacs/topology/block.h"
  77 #include "gromacs/topology/exclusionblocks.h"
  78 #include "gromacs/topology/ifunc.h"
  79 #include "gromacs/topology/symtab.h"
  80 #include "gromacs/topology/topology.h"
  81 #include "gromacs/utility/cstringutil.h"
  82 #include "gromacs/utility/fatalerror.h"
  83 #include "gromacs/utility/futil.h"
  84 #include "gromacs/utility/gmxassert.h"
  85 #include "gromacs/utility/logger.h"
  86 #include "gromacs/utility/pleasecite.h"
  87 #include "gromacs/utility/smalloc.h"
  88
  89 #define OPENDIR '['  /* starting sign for directive */
  90 #define CLOSEDIR ']' /* ending sign for directive   */
  91
  92 static void gen_pairs(const InteractionsOfType& nbs, InteractionsOfType* pairs, real fudge, CombinationRule comb)
  93 {
  94     real scaling;
  95     int  ntp = nbs.size();
  96     int  nnn = static_cast<int>(std::sqrt(static_cast<double>(ntp)));
  97     GMX_ASSERT(nnn * nnn == ntp,
  98                "Number of pairs of generated non-bonded parameters should be a perfect square");
  99     int nrfp  = NRFP(F_LJ);
 100     int nrfpA = interaction_function[F_LJ14].nrfpA;
 101     int nrfpB = interaction_function[F_LJ14].nrfpB;
 102
 103     if ((nrfp != nrfpA) || (nrfpA != nrfpB))
 104     {
 105         gmx_incons("Number of force parameters in gen_pairs wrong");
 106     }
 107
 108     fprintf(stderr, "Generating 1-4 interactions: fudge = %g\n", fudge);
 109     pairs->interactionTypes.clear();
 110     int                             i = 0;
 111     std::array<int, 2>              atomNumbers;
 112     std::array<real, MAXFORCEPARAM> forceParam = { NOTSET };
 113     for (const auto& type : nbs.interactionTypes)
 114     {
 115         /* Copy type.atoms */
 116         atomNumbers = { i / nnn, i % nnn };
 117         /* Copy normal and FEP parameters and multiply by fudge factor */
 118         gmx::ArrayRef<const real> existingParam = type.forceParam();
 119         GMX_RELEASE_ASSERT(2 * nrfp <= MAXFORCEPARAM,
 120                            "Can't have more parameters than half of maximum p  arameter number");
 121         for (int j = 0; j < nrfp; j++)
 122         {
 123             /* If we are using sigma/epsilon values, only the epsilon values
 124              * should be scaled, but not sigma.
 125              * The sigma values have even indices 0,2, etc.
 126              */
 127             if ((comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
 128                 && (j % 2 == 0))
 129             {
 130                 scaling = 1.0;
 131             }
 132             else
 133             {
 134                 scaling = fudge;
 135             }
 136
 137             forceParam[j]        = scaling * existingParam[j];
 138             forceParam[nrfp + j] = scaling * existingParam[j];
 139         }
 140         pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
 141         i++;
 142     }
 143 }
 144
 145 double check_mol(const gmx_mtop_t* mtop, warninp* wi)
 146 {
 147     char   buf[256];
 148     int    i, ri, pt;
 149     double q;
 150     real   m, mB;
 151
 152     /* Check mass and charge */
 153     q = 0.0;
 154
 155     for (const gmx_molblock_t& molb : mtop->molblock)
 156     {
 157         const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
 158         for (i = 0; (i < atoms->nr); i++)
 159         {
 160             q += molb.nmol * atoms->atom[i].q;
 161             m  = atoms->atom[i].m;
 162             mB = atoms->atom[i].mB;
 163             pt = atoms->atom[i].ptype;
 164             /* If the particle is an atom or a nucleus it must have a mass,
 165              * else, if it is a shell, a vsite or a bondshell it can have mass zero
 166              */
 167             if (((m <= 0.0) || (mB <= 0.0)) && ((pt == eptAtom) || (pt == eptNucleus)))
 168             {
 169                 ri = atoms->atom[i].resind;
 170                 sprintf(buf,
 171                         "atom %s (Res %s-%d) has mass %g (state A) / %g (state B)\n",
 172                         *(atoms->atomname[i]),
 173                         *(atoms->resinfo[ri].name),
 174                         atoms->resinfo[ri].nr,
 175                         m,
 176                         mB);
 177                 warning_error(wi, buf);
 178             }
 179             else if (((m != 0) || (mB != 0)) && (pt == eptVSite))
 180             {
 181                 ri = atoms->atom[i].resind;
 182                 sprintf(buf,
 183                         "virtual site %s (Res %s-%d) has non-zero mass %g (state A) / %g (state "
 184                         "B)\n"
 185                         "     Check your topology.\n",
 186                         *(atoms->atomname[i]),
 187                         *(atoms->resinfo[ri].name),
 188                         atoms->resinfo[ri].nr,
 189                         m,
 190                         mB);
 191                 warning_error(wi, buf);
 192                 /* The following statements make LINCS break! */
 193                 /* atoms->atom[i].m=0; */
 194             }
 195         }
 196     }
 197     return q;
 198 }
 199
 200 /*! \brief Returns the rounded charge of a molecule, when close to integer, otherwise returns the original charge.
 201  *
 202  * The results of this routine are only used for checking and for
 203  * printing warning messages. Thus we can assume that charges of molecules
 204  * should be integer. If the user wanted non-integer molecular charge,
 205  * an undesired warning is printed and the user should use grompp -maxwarn 1.
 206  *
 207  * \param qMol     The total, unrounded, charge of the molecule
 208  * \param sumAbsQ  The sum of absolute values of the charges, used for determining the tolerance for the rounding.
 209  */
 210 static double roundedMoleculeCharge(double qMol, double sumAbsQ)
 211 {
 212     /* We use a tolerance of 1e-6 for inaccuracies beyond the 6th decimal
 213      * of the charges for ascii float truncation in the topology files.
 214      * Although the summation here uses double precision, the charges
 215      * are read and stored in single precision when real=float. This can
 216      * lead to rounding errors of half the least significant bit.
 217      * Note that, unfortunately, we can not assume addition of random
 218      * rounding errors. It is not entirely unlikely that many charges
 219      * have a near half-bit rounding error with the same sign.
 220      */
 221     double tolAbs = 1e-6;
 222     double tol    = std::max(tolAbs, 0.5 * GMX_REAL_EPS * sumAbsQ);
 223     double qRound = std::round(qMol);
 224     if (std::abs(qMol - qRound) <= tol)
 225     {
 226         return qRound;
 227     }
 228     else
 229     {
 230         return qMol;
 231     }
 232 }
 233
 234 static void sum_q(const t_atoms* atoms, int numMols, double* qTotA, double* qTotB)
 235 {
 236     /* sum charge */
 237     double qmolA    = 0;
 238     double qmolB    = 0;
 239     double sumAbsQA = 0;
 240     double sumAbsQB = 0;
 241     for (int i = 0; i < atoms->nr; i++)
 242     {
 243         qmolA += atoms->atom[i].q;
 244         qmolB += atoms->atom[i].qB;
 245         sumAbsQA += std::abs(atoms->atom[i].q);
 246         sumAbsQB += std::abs(atoms->atom[i].qB);
 247     }
 248
 249     *qTotA += numMols * roundedMoleculeCharge(qmolA, sumAbsQA);
 250     *qTotB += numMols * roundedMoleculeCharge(qmolB, sumAbsQB);
 251 }
 252
 253 static void get_nbparm(char* nb_str, char* comb_str, VanDerWaalsPotential* nb, CombinationRule* comb, warninp* wi)
 254 {
 255     *nb = VanDerWaalsPotential::Count;
 256     for (auto i : gmx::EnumerationArray<VanDerWaalsPotential, bool>::keys())
 257     {
 258         if (gmx_strcasecmp(nb_str, enumValueToString(i)) == 0)
 259         {
 260             *nb = i;
 261         }
 262     }
 263     if (*nb == VanDerWaalsPotential::Count)
 264     {
 265         int integerValue = strtol(nb_str, nullptr, 10);
 266         if ((integerValue < 1) || (integerValue >= static_cast<int>(VanDerWaalsPotential::Count)))
 267         {
 268             std::string message =
 269                     gmx::formatString("Invalid nonbond function selector '%s' using %s",
 270                                       nb_str,
 271                                       enumValueToString(VanDerWaalsPotential::LJ));
 272             warning_error(wi, message);
 273             *nb = VanDerWaalsPotential::LJ;
 274         }
 275         else
 276         {
 277             *nb = static_cast<VanDerWaalsPotential>(integerValue);
 278         }
 279     }
 280     *comb = CombinationRule::Count;
 281     for (auto i : gmx::EnumerationArray<CombinationRule, bool>::keys())
 282     {
 283         if (gmx_strcasecmp(comb_str, enumValueToString(i)) == 0)
 284         {
 285             *comb = i;
 286         }
 287     }
 288     if (*comb == CombinationRule::Count)
 289     {
 290         int integerValue = strtol(comb_str, nullptr, 10);
 291         if ((integerValue < 1) || (integerValue >= static_cast<int>(CombinationRule::Count)))
 292         {
 293             std::string message =
 294                     gmx::formatString("Invalid combination rule selector '%s' using %s",
 295                                       comb_str,
 296                                       enumValueToString(CombinationRule::Geometric));
 297             warning_error(wi, message);
 298             *comb = CombinationRule::Geometric;
 299         }
 300         else
 301         {
 302             *comb = static_cast<CombinationRule>(integerValue);
 303         }
 304     }
 305 }
 306
 307 static char** cpp_opts(const char* define, const char* include, warninp* wi)
 308 {
 309     int         n, len;
 310     int         ncppopts = 0;
 311     const char* cppadds[2];
 312     char**      cppopts   = nullptr;
 313     const char* option[2] = { "-D", "-I" };
 314     const char* nopt[2]   = { "define", "include" };
 315     const char* ptr;
 316     const char* rptr;
 317     char*       buf;
 318     char        warn_buf[STRLEN];
 319
 320     cppadds[0] = define;
 321     cppadds[1] = include;
 322     for (n = 0; (n < 2); n++)
 323     {
 324         if (cppadds[n])
 325         {
 326             ptr = cppadds[n];
 327             while (*ptr != '\0')
 328             {
 329                 while ((*ptr != '\0') && isspace(*ptr))
 330                 {
 331                     ptr++;
 332                 }
 333                 rptr = ptr;
 334                 while ((*rptr != '\0') && !isspace(*rptr))
 335                 {
 336                     rptr++;
 337                 }
 338                 len = (rptr - ptr);
 339                 if (len > 2)
 340                 {
 341                     snew(buf, (len + 1));
 342                     strncpy(buf, ptr, len);
 343                     if (strstr(ptr, option[n]) != ptr)
 344                     {
 345                         set_warning_line(wi, "mdp file", -1);
 346                         sprintf(warn_buf, "Malformed %s option %s", nopt[n], buf);
 347                         warning(wi, warn_buf);
 348                     }
 349                     else
 350                     {
 351                         srenew(cppopts, ++ncppopts);
 352                         cppopts[ncppopts - 1] = gmx_strdup(buf);
 353                     }
 354                     sfree(buf);
 355                     ptr = rptr;
 356                 }
 357             }
 358         }
 359     }
 360     srenew(cppopts, ++ncppopts);
 361     cppopts[ncppopts - 1] = nullptr;
 362
 363     return cppopts;
 364 }
 365
 366
 367 static void make_atoms_sys(gmx::ArrayRef<const gmx_molblock_t>      molblock,
 368                            gmx::ArrayRef<const MoleculeInformation> molinfo,
 369                            t_atoms*                                 atoms)
 370 {
 371     atoms->nr   = 0;
 372     atoms->atom = nullptr;
 373
 374     for (const gmx_molblock_t& molb : molblock)
 375     {
 376         const t_atoms& mol_atoms = molinfo[molb.type].atoms;
 377
 378         srenew(atoms->atom, atoms->nr + molb.nmol * mol_atoms.nr);
 379
 380         for (int m = 0; m < molb.nmol; m++)
 381         {
 382             for (int a = 0; a < mol_atoms.nr; a++)
 383             {
 384                 atoms->atom[atoms->nr++] = mol_atoms.atom[a];
 385             }
 386         }
 387     }
 388 }
 389
 390
 391 static char** read_topol(const char*                           infile,
 392                          const char*                           outfile,
 393                          const char*                           define,
 394                          const char*                           include,
 395                          t_symtab*                             symtab,
 396                          PreprocessingAtomTypes*               atypes,
 397                          std::vector<MoleculeInformation>*     molinfo,
 398                          std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
 399                          gmx::ArrayRef<InteractionsOfType>     interactions,
 400                          CombinationRule*                      combination_rule,
 401                          double*                               reppow,
 402                          t_gromppopts*                         opts,
 403                          real*                                 fudgeQQ,
 404                          std::vector<gmx_molblock_t>*          molblock,
 405                          bool*                                 ffParametrizedWithHBondConstraints,
 406                          bool                                  bFEP,
 407                          bool                                  bZero,
 408                          bool                                  usingFullRangeElectrostatics,
 409                          warninp*                              wi,
 410                          const gmx::MDLogger&                  logger)
 411 {
 412     FILE*                out;
 413     int                  sl;
 414     char *               pline = nullptr, **title = nullptr;
 415     char                 line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
 416     char                 genpairs[32];
 417     char *               dirstr, *dummy2;
 418     int                  nrcopies, nscan, ncombs, ncopy;
 419     double               fLJ, fQQ, fPOW;
 420     MoleculeInformation* mi0 = nullptr;
 421     DirStack*            DS;
 422     Directive            d, newd;
 423     t_nbparam **         nbparam, **pair;
 424     real                 fudgeLJ = -1; /* Multiplication factor to generate 1-4 from LJ */
 425     bool                 bReadDefaults, bReadMolType, bGenPairs, bWarn_copy_A_B;
 426     double               qt = 0, qBt = 0; /* total charge */
 427     int                  dcatt = -1, nmol_couple;
 428     /* File handling variables */
 429     int         status;
 430     bool        done;
 431     gmx_cpp_t   handle;
 432     char*       tmp_line = nullptr;
 433     char        warn_buf[STRLEN];
 434     const char* floating_point_arithmetic_tip =
 435             "Total charge should normally be an integer. See\n"
 436             "http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n"
 437             "for discussion on how close it should be to an integer.\n";
 438     /* We need to open the output file before opening the input file,
 439      * because cpp_open_file can change the current working directory.
 440      */
 441     if (outfile)
 442     {
 443         out = gmx_fio_fopen(outfile, "w");
 444     }
 445     else
 446     {
 447         out = nullptr;
 448     }
 449
 450     /* open input file */
 451     auto cpp_opts_return = cpp_opts(define, include, wi);
 452     status               = cpp_open_file(infile, &handle, cpp_opts_return);
 453     if (status != 0)
 454     {
 455         gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 456     }
 457
 458     /* some local variables */
 459     DS_Init(&DS);                   /* directive stack  */
 460     d       = Directive::d_invalid; /* first thing should be a directive */
 461     nbparam = nullptr;              /* The temporary non-bonded matrix */
 462     pair    = nullptr;              /* The temporary pair interaction matrix */
 463     std::vector<std::vector<gmx::ExclusionBlock>> exclusionBlocks;
 464     VanDerWaalsPotential                          nb_funct = VanDerWaalsPotential::LJ;
 465
 466     *reppow = 12.0; /* Default value for repulsion power     */
 467
 468     /* Init the number of CMAP torsion angles  and grid spacing */
 469     interactions[F_CMAP].cmakeGridSpacing = 0;
 470     interactions[F_CMAP].cmapAngles       = 0;
 471
 472     bWarn_copy_A_B = bFEP;
 473
 474     PreprocessingBondAtomType bondAtomType;
 475     /* parse the actual file */
 476     bReadDefaults = FALSE;
 477     bGenPairs     = FALSE;
 478     bReadMolType  = FALSE;
 479     nmol_couple   = 0;
 480
 481     do
 482     {
 483         status = cpp_read_line(&handle, STRLEN, line);
 484         done   = (status == eCPP_EOF);
 485         if (!done)
 486         {
 487             if (status != eCPP_OK)
 488             {
 489                 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 490             }
 491             else if (out)
 492             {
 493                 fprintf(out, "%s\n", line);
 494             }
 495
 496             set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
 497
 498             pline = gmx_strdup(line);
 499
 500             /* Strip trailing '\' from pline, if it exists */
 501             sl = strlen(pline);
 502             if ((sl > 0) && (pline[sl - 1] == CONTINUE))
 503             {
 504                 pline[sl - 1] = ' ';
 505             }
 506
 507             /* build one long line from several fragments - necessary for CMAP */
 508             while (continuing(line))
 509             {
 510                 status = cpp_read_line(&handle, STRLEN, line);
 511                 set_warning_line(wi, cpp_cur_file(&handle), cpp_cur_linenr(&handle));
 512
 513                 /* Since we depend on the '\' being present to continue to read, we copy line
 514                  * to a tmp string, strip the '\' from that string, and cat it to pline
 515                  */
 516                 tmp_line = gmx_strdup(line);
 517
 518                 sl = strlen(tmp_line);
 519                 if ((sl > 0) && (tmp_line[sl - 1] == CONTINUE))
 520                 {
 521                     tmp_line[sl - 1] = ' ';
 522                 }
 523
 524                 done = (status == eCPP_EOF);
 525                 if (!done)
 526                 {
 527                     if (status != eCPP_OK)
 528                     {
 529                         gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 530                     }
 531                     else if (out)
 532                     {
 533                         fprintf(out, "%s\n", line);
 534                     }
 535                 }
 536
 537                 srenew(pline, strlen(pline) + strlen(tmp_line) + 1);
 538                 strcat(pline, tmp_line);
 539                 sfree(tmp_line);
 540             }
 541
 542             /* skip trailing and leading spaces and comment text */
 543             strip_comment(pline);
 544             trim(pline);
 545
 546             /* if there is something left... */
 547             if (static_cast<int>(strlen(pline)) > 0)
 548             {
 549                 if (pline[0] == OPENDIR)
 550                 {
 551                     /* A directive on this line: copy the directive
 552                      * without the brackets into dirstr, then
 553                      * skip spaces and tabs on either side of directive
 554                      */
 555                     dirstr = gmx_strdup((pline + 1));
 556                     if ((dummy2 = strchr(dirstr, CLOSEDIR)) != nullptr)
 557                     {
 558                         (*dummy2) = 0;
 559                     }
 560                     trim(dirstr);
 561
 562                     if ((newd = str2dir(dirstr)) == Directive::d_invalid)
 563                     {
 564                         sprintf(errbuf, "Invalid directive %s", dirstr);
 565                         warning_error(wi, errbuf);
 566                     }
 567                     else
 568                     {
 569                         /* Directive found */
 570                         if (DS_Check_Order(DS, newd))
 571                         {
 572                             DS_Push(&DS, newd);
 573                             d = newd;
 574                         }
 575                         else
 576                         {
 577                             /* we should print here which directives should have
 578                                been present, and which actually are */
 579                             gmx_fatal(FARGS,
 580                                       "%s\nInvalid order for directive %s",
 581                                       cpp_error(&handle, eCPP_SYNTAX),
 582                                       dir2str(newd));
 583                             /* d = Directive::d_invalid; */
 584                         }
 585
 586                         if (d == Directive::d_intermolecular_interactions)
 587                         {
 588                             if (*intermolecular_interactions == nullptr)
 589                             {
 590                                 /* We (mis)use the moleculetype processing
 591                                  * to process the intermolecular interactions
 592                                  * by making a "molecule" of the size of the system.
 593                                  */
 594                                 *intermolecular_interactions = std::make_unique<MoleculeInformation>();
 595                                 mi0                          = intermolecular_interactions->get();
 596                                 mi0->initMolInfo();
 597                                 make_atoms_sys(*molblock, *molinfo, &mi0->atoms);
 598                             }
 599                         }
 600                     }
 601                     sfree(dirstr);
 602                 }
 603                 else if (d != Directive::d_invalid)
 604                 {
 605                     /* Not a directive, just a plain string
 606                      * use a gigantic switch to decode,
 607                      * if there is a valid directive!
 608                      */
 609                     switch (d)
 610                     {
 611                         case Directive::d_defaults:
 612                             if (bReadDefaults)
 613                             {
 614                                 gmx_fatal(FARGS,
 615                                           "%s\nFound a second defaults directive.\n",
 616                                           cpp_error(&handle, eCPP_SYNTAX));
 617                             }
 618                             bReadDefaults = TRUE;
 619                             nscan         = sscanf(
 620                                     pline, "%s%s%s%lf%lf%lf", nb_str, comb_str, genpairs, &fLJ, &fQQ, &fPOW);
 621                             if (nscan < 2)
 622                             {
 623                                 too_few(wi);
 624                             }
 625                             else
 626                             {
 627                                 bGenPairs = FALSE;
 628                                 fudgeLJ   = 1.0;
 629                                 *fudgeQQ  = 1.0;
 630
 631                                 get_nbparm(nb_str, comb_str, &nb_funct, combination_rule, wi);
 632                                 if (nscan >= 3)
 633                                 {
 634                                     bGenPairs = (gmx::equalCaseInsensitive(genpairs, "Y", 1));
 635                                     if (nb_funct != VanDerWaalsPotential::LJ && bGenPairs)
 636                                     {
 637                                         gmx_fatal(FARGS,
 638                                                   "Generating pair parameters is only supported "
 639                                                   "with LJ non-bonded interactions");
 640                                     }
 641                                 }
 642                                 if (nscan >= 4)
 643                                 {
 644                                     fudgeLJ = fLJ;
 645                                 }
 646                                 if (nscan >= 5)
 647                                 {
 648                                     *fudgeQQ = fQQ;
 649                                 }
 650                                 if (nscan >= 6)
 651                                 {
 652                                     *reppow = fPOW;
 653                                 }
 654                             }
 655                             nb_funct = static_cast<VanDerWaalsPotential>(ifunc_index(
 656                                     Directive::d_nonbond_params, static_cast<int>(nb_funct)));
 657
 658                             break;
 659                         case Directive::d_atomtypes:
 660                             push_at(symtab,
 661                                     atypes,
 662                                     &bondAtomType,
 663                                     pline,
 664                                     static_cast<int>(nb_funct),
 665                                     &nbparam,
 666                                     bGenPairs ? &pair : nullptr,
 667                                     wi);
 668                             break;
 669
 670                         case Directive::d_bondtypes: // Intended to fall through
 671                         case Directive::d_constrainttypes:
 672                             push_bt(d, interactions, 2, nullptr, &bondAtomType, pline, wi);
 673                             break;
 674                         case Directive::d_pairtypes:
 675                             if (bGenPairs)
 676                             {
 677                                 push_nbt(d, pair, atypes, pline, F_LJ14, wi);
 678                             }
 679                             else
 680                             {
 681                                 push_bt(d, interactions, 2, atypes, nullptr, pline, wi);
 682                             }
 683                             break;
 684                         case Directive::d_angletypes:
 685                             push_bt(d, interactions, 3, nullptr, &bondAtomType, pline, wi);
 686                             break;
 687                         case Directive::d_dihedraltypes:
 688                             /* Special routine that can read both 2 and 4 atom dihedral definitions. */
 689                             push_dihedraltype(d, interactions, &bondAtomType, pline, wi);
 690                             break;
 691
 692                         case Directive::d_nonbond_params:
 693                             push_nbt(d, nbparam, atypes, pline, static_cast<int>(nb_funct), wi);
 694                             break;
 695
 696                         case Directive::d_implicit_genborn_params: // NOLINT bugprone-branch-clone
 697                             // Skip this line, so old topologies with
 698                             // GB parameters can be read.
 699                             break;
 700
 701                         case Directive::d_implicit_surface_params:
 702                             // Skip this line, so that any topologies
 703                             // with surface parameters can be read
 704                             // (even though these were never formally
 705                             // supported).
 706                             break;
 707
 708                         case Directive::d_cmaptypes:
 709                             push_cmaptype(d, interactions, 5, atypes, &bondAtomType, pline, wi);
 710                             break;
 711
 712                         case Directive::d_moleculetype:
 713                         {
 714                             if (!bReadMolType)
 715                             {
 716                                 int ntype;
 717                                 if (opts->couple_moltype != nullptr
 718                                     && (opts->couple_lam0 == ecouplamNONE || opts->couple_lam0 == ecouplamQ
 719                                         || opts->couple_lam1 == ecouplamNONE
 720                                         || opts->couple_lam1 == ecouplamQ))
 721                                 {
 722                                     dcatt = add_atomtype_decoupled(
 723                                             symtab, atypes, &nbparam, bGenPairs ? &pair : nullptr);
 724                                 }
 725                                 ntype  = atypes->size();
 726                                 ncombs = (ntype * (ntype + 1)) / 2;
 727                                 generate_nbparams(*combination_rule,
 728                                                   static_cast<int>(nb_funct),
 729                                                   &(interactions[static_cast<int>(nb_funct)]),
 730                                                   atypes,
 731                                                   wi);
 732                                 ncopy = copy_nbparams(nbparam,
 733                                                       static_cast<int>(nb_funct),
 734                                                       &(interactions[static_cast<int>(nb_funct)]),
 735                                                       ntype);
 736                                 GMX_LOG(logger.info)
 737                                         .asParagraph()
 738                                         .appendTextFormatted(
 739                                                 "Generated %d of the %d non-bonded parameter "
 740                                                 "combinations",
 741                                                 ncombs - ncopy,
 742                                                 ncombs);
 743                                 free_nbparam(nbparam, ntype);
 744                                 if (bGenPairs)
 745                                 {
 746                                     gen_pairs((interactions[static_cast<int>(nb_funct)]),
 747                                               &(interactions[F_LJ14]),
 748                                               fudgeLJ,
 749                                               *combination_rule);
 750                                     ncopy = copy_nbparams(
 751                                             pair, static_cast<int>(nb_funct), &(interactions[F_LJ14]), ntype);
 752                                     GMX_LOG(logger.info)
 753                                             .asParagraph()
 754                                             .appendTextFormatted(
 755                                                     "Generated %d of the %d 1-4 parameter "
 756                                                     "combinations",
 757                                                     ncombs - ncopy,
 758                                                     ncombs);
 759                                     free_nbparam(pair, ntype);
 760                                 }
 761                                 /* Copy GBSA parameters to atomtype array? */
 762
 763                                 bReadMolType = TRUE;
 764                             }
 765
 766                             push_molt(symtab, molinfo, pline, wi);
 767                             exclusionBlocks.emplace_back();
 768                             mi0                    = &molinfo->back();
 769                             mi0->atoms.haveMass    = TRUE;
 770                             mi0->atoms.haveCharge  = TRUE;
 771                             mi0->atoms.haveType    = TRUE;
 772                             mi0->atoms.haveBState  = TRUE;
 773                             mi0->atoms.havePdbInfo = FALSE;
 774                             break;
 775                         }
 776                         case Directive::d_atoms:
 777                             push_atom(symtab, &(mi0->atoms), atypes, pline, wi);
 778                             break;
 779
 780                         case Directive::d_pairs:
 781                             GMX_RELEASE_ASSERT(
 782                                     mi0,
 783                                     "Need to have a valid MoleculeInformation object to work on");
 784                             push_bond(d,
 785                                       interactions,
 786                                       mi0->interactions,
 787                                       &(mi0->atoms),
 788                                       atypes,
 789                                       pline,
 790                                       FALSE,
 791                                       bGenPairs,
 792                                       *fudgeQQ,
 793                                       bZero,
 794                                       &bWarn_copy_A_B,
 795                                       wi);
 796                             break;
 797                         case Directive::d_pairs_nb:
 798                             GMX_RELEASE_ASSERT(
 799                                     mi0,
 800                                     "Need to have a valid MoleculeInformation object to work on");
 801                             push_bond(d,
 802                                       interactions,
 803                                       mi0->interactions,
 804                                       &(mi0->atoms),
 805                                       atypes,
 806                                       pline,
 807                                       FALSE,
 808                                       FALSE,
 809                                       1.0,
 810                                       bZero,
 811                                       &bWarn_copy_A_B,
 812                                       wi);
 813                             break;
 814
 815                         case Directive::d_vsites1:
 816                         case Directive::d_vsites2:
 817                         case Directive::d_vsites3:
 818                         case Directive::d_vsites4:
 819                         case Directive::d_bonds:
 820                         case Directive::d_angles:
 821                         case Directive::d_constraints:
 822                         case Directive::d_settles:
 823                         case Directive::d_position_restraints:
 824                         case Directive::d_angle_restraints:
 825                         case Directive::d_angle_restraints_z:
 826                         case Directive::d_distance_restraints:
 827                         case Directive::d_orientation_restraints:
 828                         case Directive::d_dihedral_restraints:
 829                         case Directive::d_dihedrals:
 830                         case Directive::d_polarization:
 831                         case Directive::d_water_polarization:
 832                         case Directive::d_thole_polarization:
 833                             GMX_RELEASE_ASSERT(
 834                                     mi0,
 835                                     "Need to have a valid MoleculeInformation object to work on");
 836                             push_bond(d,
 837                                       interactions,
 838                                       mi0->interactions,
 839                                       &(mi0->atoms),
 840                                       atypes,
 841                                       pline,
 842                                       TRUE,
 843                                       bGenPairs,
 844                                       *fudgeQQ,
 845                                       bZero,
 846                                       &bWarn_copy_A_B,
 847                                       wi);
 848                             break;
 849                         case Directive::d_cmap:
 850                             GMX_RELEASE_ASSERT(
 851                                     mi0,
 852                                     "Need to have a valid MoleculeInformation object to work on");
 853                             push_cmap(d, interactions, mi0->interactions, &(mi0->atoms), atypes, pline, wi);
 854                             break;
 855
 856                         case Directive::d_vsitesn:
 857                             GMX_RELEASE_ASSERT(
 858                                     mi0,
 859                                     "Need to have a valid MoleculeInformation object to work on");
 860                             push_vsitesn(d, mi0->interactions, &(mi0->atoms), pline, wi);
 861                             break;
 862                         case Directive::d_exclusions:
 863                             GMX_ASSERT(!exclusionBlocks.empty(),
 864                                        "exclusionBlocks must always be allocated so exclusions can "
 865                                        "be processed");
 866                             if (exclusionBlocks.back().empty())
 867                             {
 868                                 GMX_RELEASE_ASSERT(mi0,
 869                                                    "Need to have a valid MoleculeInformation "
 870                                                    "object to work on");
 871                                 exclusionBlocks.back().resize(mi0->atoms.nr);
 872                             }
 873                             push_excl(pline, exclusionBlocks.back(), wi);
 874                             break;
 875                         case Directive::d_system:
 876                             trim(pline);
 877                             title = put_symtab(symtab, pline);
 878                             break;
 879                         case Directive::d_molecules:
 880                         {
 881                             int  whichmol;
 882                             bool bCouple;
 883
 884                             push_mol(*molinfo, pline, &whichmol, &nrcopies, wi);
 885                             mi0 = &((*molinfo)[whichmol]);
 886                             molblock->resize(molblock->size() + 1);
 887                             molblock->back().type = whichmol;
 888                             molblock->back().nmol = nrcopies;
 889
 890                             bCouple = (opts->couple_moltype != nullptr
 891                                        && (gmx_strcasecmp("system", opts->couple_moltype) == 0
 892                                            || strcmp(*(mi0->name), opts->couple_moltype) == 0));
 893                             if (bCouple)
 894                             {
 895                                 nmol_couple += nrcopies;
 896                             }
 897
 898                             if (mi0->atoms.nr == 0)
 899                             {
 900                                 gmx_fatal(FARGS, "Molecule type '%s' contains no atoms", *mi0->name);
 901                             }
 902                             GMX_LOG(logger.info)
 903                                     .asParagraph()
 904                                     .appendTextFormatted(
 905                                             "Excluding %d bonded neighbours molecule type '%s'",
 906                                             mi0->nrexcl,
 907                                             *mi0->name);
 908                             sum_q(&mi0->atoms, nrcopies, &qt, &qBt);
 909                             if (!mi0->bProcessed)
 910                             {
 911                                 generate_excl(mi0->nrexcl, mi0->atoms.nr, mi0->interactions, &(mi0->excls));
 912                                 gmx::mergeExclusions(&(mi0->excls), exclusionBlocks[whichmol]);
 913                                 make_shake(mi0->interactions, &mi0->atoms, opts->nshake, logger);
 914
 915                                 if (bCouple)
 916                                 {
 917                                     convert_moltype_couple(mi0,
 918                                                            dcatt,
 919                                                            *fudgeQQ,
 920                                                            opts->couple_lam0,
 921                                                            opts->couple_lam1,
 922                                                            opts->bCoupleIntra,
 923                                                            static_cast<int>(nb_funct),
 924                                                            &(interactions[static_cast<int>(nb_funct)]),
 925                                                            wi);
 926                                 }
 927                                 stupid_fill_block(&mi0->mols, mi0->atoms.nr, TRUE);
 928                                 mi0->bProcessed = TRUE;
 929                             }
 930                             break;
 931                         }
 932                         default:
 933                             GMX_LOG(logger.warning)
 934                                     .asParagraph()
 935                                     .appendTextFormatted("case: %d", static_cast<int>(d));
 936                             gmx_incons("unknown directive");
 937                     }
 938                 }
 939             }
 940             sfree(pline);
 941             pline = nullptr;
 942         }
 943     } while (!done);
 944
 945     // Check that all strings defined with -D were used when processing topology
 946     std::string unusedDefineWarning = checkAndWarnForUnusedDefines(*handle);
 947     if (!unusedDefineWarning.empty())
 948     {
 949         warning(wi, unusedDefineWarning);
 950     }
 951
 952     sfree(cpp_opts_return);
 953
 954     if (out)
 955     {
 956         gmx_fio_fclose(out);
 957     }
 958
 959     /* List of GROMACS define names for force fields that have been
 960      * parametrized using constraints involving hydrogens only.
 961      *
 962      * We should avoid hardcoded names, but this is hopefully only
 963      * needed temparorily for discouraging use of constraints=all-bonds.
 964      */
 965     const std::array<std::string, 3> ffDefines = { "_FF_AMBER", "_FF_CHARMM", "_FF_OPLSAA" };
 966     *ffParametrizedWithHBondConstraints        = false;
 967     for (const std::string& ffDefine : ffDefines)
 968     {
 969         if (cpp_find_define(&handle, ffDefine))
 970         {
 971             *ffParametrizedWithHBondConstraints = true;
 972         }
 973     }
 974
 975     if (cpp_find_define(&handle, "_FF_GROMOS96") != nullptr)
 976     {
 977         warning(wi,
 978                 "The GROMOS force fields have been parametrized with a physically incorrect "
 979                 "multiple-time-stepping scheme for a twin-range cut-off. When used with "
 980                 "a single-range cut-off (or a correct Trotter multiple-time-stepping scheme), "
 981                 "physical properties, such as the density, might differ from the intended values. "
 982                 "Since there are researchers actively working on validating GROMOS with modern "
 983                 "integrators we have not yet removed the GROMOS force fields, but you should be "
 984                 "aware of these issues and check if molecules in your system are affected before "
 985                 "proceeding. "
 986                 "Further information is available at https://redmine.gromacs.org/issues/2884 , "
 987                 "and a longer explanation of our decision to remove physically incorrect "
 988                 "algorithms "
 989                 "can be found at https://doi.org/10.26434/chemrxiv.11474583.v1 .");
 990     }
 991     // TODO: Update URL for Issue #2884 in conjunction with updating grompp.warn in regressiontests.
 992
 993     cpp_done(handle);
 994
 995     if (opts->couple_moltype)
 996     {
 997         if (nmol_couple == 0)
 998         {
 999             gmx_fatal(FARGS, "Did not find any molecules of type '%s' for coupling", opts->couple_moltype);
1000         }
1001         GMX_LOG(logger.info)
1002                 .asParagraph()
1003                 .appendTextFormatted(
1004                         "Coupling %d copies of molecule type '%s'", nmol_couple, opts->couple_moltype);
1005     }
1006
1007     /* this is not very clean, but fixes core dump on empty system name */
1008     if (!title)
1009     {
1010         title = put_symtab(symtab, "");
1011     }
1012
1013     if (fabs(qt) > 1e-4)
1014     {
1015         sprintf(warn_buf, "System has non-zero total charge: %.6f\n%s\n", qt, floating_point_arithmetic_tip);
1016         warning_note(wi, warn_buf);
1017     }
1018     if (fabs(qBt) > 1e-4 && !gmx_within_tol(qBt, qt, 1e-6))
1019     {
1020         sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt, floating_point_arithmetic_tip);
1021         warning_note(wi, warn_buf);
1022     }
1023     if (usingFullRangeElectrostatics && (fabs(qt) > 1e-4 || fabs(qBt) > 1e-4))
1024     {
1025         warning(wi,
1026                 "You are using Ewald electrostatics in a system with net charge. This can lead to "
1027                 "severe artifacts, such as ions moving into regions with low dielectric, due to "
1028                 "the uniform background charge. We suggest to neutralize your system with counter "
1029                 "ions, possibly in combination with a physiological salt concentration.");
1030         please_cite(stdout, "Hub2014a");
1031     }
1032
1033     DS_Done(&DS);
1034
1035     if (*intermolecular_interactions != nullptr)
1036     {
1037         sfree(intermolecular_interactions->get()->atoms.atom);
1038     }
1039
1040     return title;
1041 }
1042
1043 char** do_top(bool                                  bVerbose,
1044               const char*                           topfile,
1045               const char*                           topppfile,
1046               t_gromppopts*                         opts,
1047               bool                                  bZero,
1048               t_symtab*                             symtab,
1049               gmx::ArrayRef<InteractionsOfType>     interactions,
1050               CombinationRule*                      combination_rule,
1051               double*                               repulsion_power,
1052               real*                                 fudgeQQ,
1053               PreprocessingAtomTypes*               atypes,
1054               std::vector<MoleculeInformation>*     molinfo,
1055               std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
1056               const t_inputrec*                     ir,
1057               std::vector<gmx_molblock_t>*          molblock,
1058               bool*                                 ffParametrizedWithHBondConstraints,
1059               warninp*                              wi,
1060               const gmx::MDLogger&                  logger)
1061 {
1062     /* Tmpfile might contain a long path */
1063     const char* tmpfile;
1064     char**      title;
1065
1066     if (topppfile)
1067     {
1068         tmpfile = topppfile;
1069     }
1070     else
1071     {
1072         tmpfile = nullptr;
1073     }
1074
1075     if (bVerbose)
1076     {
1077         GMX_LOG(logger.info).asParagraph().appendTextFormatted("processing topology...");
1078     }
1079     title = read_topol(topfile,
1080                        tmpfile,
1081                        opts->define,
1082                        opts->include,
1083                        symtab,
1084                        atypes,
1085                        molinfo,
1086                        intermolecular_interactions,
1087                        interactions,
1088                        combination_rule,
1089                        repulsion_power,
1090                        opts,
1091                        fudgeQQ,
1092                        molblock,
1093                        ffParametrizedWithHBondConstraints,
1094                        ir->efep != FreeEnergyPerturbationType::No,
1095                        bZero,
1096                        EEL_FULL(ir->coulombtype),
1097                        wi,
1098                        logger);
1099
1100     if ((*combination_rule != CombinationRule::Geometric) && (ir->vdwtype == VanDerWaalsType::User))
1101     {
1102         warning(wi,
1103                 "Using sigma/epsilon based combination rules with"
1104                 " user supplied potential function may produce unwanted"
1105                 " results");
1106     }
1107
1108     return title;
1109 }
1110
1111 /*! \brief
1112  * Exclude molecular interactions for QM atoms handled by MiMic.
1113  *
1114  * Update the exclusion lists to include all QM atoms of this molecule,
1115  * replace bonds between QM atoms with CONNBOND and
1116  * set charges of QM atoms to 0.
1117  *
1118  * \param[in,out] molt molecule type with QM atoms
1119  * \param[in] grpnr group informatio
1120  * \param[in,out] ir input record
1121  * \param[in] logger Handle to logging interface.
1122  */
1123 static void generate_qmexcl_moltype(gmx_moltype_t*       molt,
1124                                     const unsigned char* grpnr,
1125                                     t_inputrec*          ir,
1126                                     const gmx::MDLogger& logger)
1127 {
1128     /* This routine expects molt->ilist to be of size F_NRE and ordered. */
1129
1130     /* generates the exclusions between the individual QM atoms, as
1131      * these interactions should be handled by the QM subroutines and
1132      * not by the gromacs routines
1133      */
1134     int   qm_max = 0, qm_nr = 0, link_nr = 0;
1135     int * qm_arr = nullptr, *link_arr = nullptr;
1136     bool* bQMMM;
1137
1138     /* First we search and select the QM atoms in an qm_arr array that
1139      * we use to create the exclusions.
1140      *
1141      * we take the possibility into account that a user has defined more
1142      * than one QM group:
1143      *
1144      * for that we also need to do this an ugly work-about just in case
1145      * the QM group contains the entire system...
1146      */
1147
1148     /* we first search for all the QM atoms and put them in an array
1149      */
1150     for (int j = 0; j < ir->opts.ngQM; j++)
1151     {
1152         for (int i = 0; i < molt->atoms.nr; i++)
1153         {
1154             if (qm_nr >= qm_max)
1155             {
1156                 qm_max += 100;
1157                 srenew(qm_arr, qm_max);
1158             }
1159             if ((grpnr ? grpnr[i] : 0) == j)
1160             {
1161                 qm_arr[qm_nr++]        = i;
1162                 molt->atoms.atom[i].q  = 0.0;
1163                 molt->atoms.atom[i].qB = 0.0;
1164             }
1165         }
1166     }
1167     /* bQMMM[..] is an array containin TRUE/FALSE for atoms that are
1168      * QM/not QM. We first set all elements to false. Afterwards we use
1169      * the qm_arr to change the elements corresponding to the QM atoms
1170      * to TRUE.
1171      */
1172     snew(bQMMM, molt->atoms.nr);
1173     for (int i = 0; i < molt->atoms.nr; i++)
1174     {
1175         bQMMM[i] = FALSE;
1176     }
1177     for (int i = 0; i < qm_nr; i++)
1178     {
1179         bQMMM[qm_arr[i]] = TRUE;
1180     }
1181
1182     /* We remove all bonded interactions (i.e. bonds,
1183      * angles, dihedrals, 1-4's), involving the QM atoms. The way they
1184      * are removed is as follows: if the interaction invloves 2 atoms,
1185      * it is removed if both atoms are QMatoms. If it involves 3 atoms,
1186      * it is removed if at least two of the atoms are QM atoms, if the
1187      * interaction involves 4 atoms, it is removed if there are at least
1188      * 2 QM atoms.  Since this routine is called once before any forces
1189      * are computed, the top->idef.il[N].iatom[] array (see idef.h) can
1190      * be rewritten at this poitn without any problem. 25-9-2002 */
1191
1192     /* first check whether we already have CONNBONDS.
1193      * Note that if we don't, we don't add a param entry and set ftype=0,
1194      * which is ok, since CONNBONDS does not use parameters.
1195      */
1196     int ftype_connbond = 0;
1197     int ind_connbond   = 0;
1198     if (!molt->ilist[F_CONNBONDS].empty())
1199     {
1200         GMX_LOG(logger.info)
1201                 .asParagraph()
1202                 .appendTextFormatted("nr. of CONNBONDS present already: %d",
1203                                      molt->ilist[F_CONNBONDS].size() / 3);
1204         ftype_connbond = molt->ilist[F_CONNBONDS].iatoms[0];
1205         ind_connbond   = molt->ilist[F_CONNBONDS].size();
1206     }
1207     /* now we delete all bonded interactions, except the ones describing
1208      * a chemical bond. These are converted to CONNBONDS
1209      */
1210     for (int ftype = 0; ftype < F_NRE; ftype++)
1211     {
1212         if (!(interaction_function[ftype].flags & IF_BOND) || ftype == F_CONNBONDS)
1213         {
1214             continue;
1215         }
1216         int nratoms = interaction_function[ftype].nratoms;
1217         int j       = 0;
1218         while (j < molt->ilist[ftype].size())
1219         {
1220             bool bexcl;
1221
1222             if (nratoms == 2)
1223             {
1224                 /* Remove an interaction between two atoms when both are
1225                  * in the QM region. Note that we don't have to worry about
1226                  * link atoms here, as they won't have 2-atom interactions.
1227                  */
1228                 int a1 = molt->ilist[ftype].iatoms[1 + j + 0];
1229                 int a2 = molt->ilist[ftype].iatoms[1 + j + 1];
1230                 bexcl  = (bQMMM[a1] && bQMMM[a2]);
1231                 /* A chemical bond between two QM atoms will be copied to
1232                  * the F_CONNBONDS list, for reasons mentioned above.
1233                  */
1234                 if (bexcl && IS_CHEMBOND(ftype))
1235                 {
1236                     InteractionList& ilist = molt->ilist[F_CONNBONDS];
1237                     ilist.iatoms.resize(ind_connbond + 3);
1238                     ilist.iatoms[ind_connbond++] = ftype_connbond;
1239                     ilist.iatoms[ind_connbond++] = a1;
1240                     ilist.iatoms[ind_connbond++] = a2;
1241                 }
1242             }
1243             else
1244             {
1245                 /* MM interactions have to be excluded if they are included
1246                  * in the QM already. Because we use a link atom (H atom)
1247                  * when the QM/MM boundary runs through a chemical bond, this
1248                  * means that as long as one atom is MM, we still exclude,
1249                  * as the interaction is included in the QM via:
1250                  * QMatom1-QMatom2-QMatom-3-Linkatom.
1251                  */
1252                 int numQmAtoms = 0;
1253                 for (int jj = j + 1; jj < j + 1 + nratoms; jj++)
1254                 {
1255                     if (bQMMM[molt->ilist[ftype].iatoms[jj]])
1256                     {
1257                         numQmAtoms++;
1258                     }
1259                 }
1260
1261                 /* MiMiC treats link atoms as quantum atoms - therefore
1262                  * we do not need do additional exclusions here */
1263                 bexcl = numQmAtoms == nratoms;
1264
1265                 if (bexcl && ftype == F_SETTLE)
1266                 {
1267                     gmx_fatal(FARGS,
1268                               "Can not apply QM to molecules with SETTLE, replace the moleculetype "
1269                               "using QM and SETTLE by one without SETTLE");
1270                 }
1271             }
1272             if (bexcl)
1273             {
1274                 /* since the interaction involves QM atoms, these should be
1275                  * removed from the MM ilist
1276                  */
1277                 InteractionList& ilist = molt->ilist[ftype];
1278                 for (int k = j; k < ilist.size() - (nratoms + 1); k++)
1279                 {
1280                     ilist.iatoms[k] = ilist.iatoms[k + (nratoms + 1)];
1281                 }
1282                 ilist.iatoms.resize(ilist.size() - (nratoms + 1));
1283             }
1284             else
1285             {
1286                 j += nratoms + 1; /* the +1 is for the functype */
1287             }
1288         }
1289     }
1290     /* Now, we search for atoms bonded to a QM atom because we also want
1291      * to exclude their nonbonded interactions with the QM atoms. The
1292      * reason for this is that this interaction is accounted for in the
1293      * linkatoms interaction with the QMatoms and would be counted
1294      * twice.  */
1295
1296     /* creating the exclusion block for the QM atoms. Each QM atom has
1297      * as excluded elements all the other QMatoms (and itself).
1298      */
1299     t_blocka qmexcl;
1300     qmexcl.nr  = molt->atoms.nr;
1301     qmexcl.nra = qm_nr * (qm_nr + link_nr) + link_nr * qm_nr;
1302     snew(qmexcl.index, qmexcl.nr + 1);
1303     snew(qmexcl.a, qmexcl.nra);
1304     int j = 0;
1305     for (int i = 0; i < qmexcl.nr; i++)
1306     {
1307         qmexcl.index[i] = j;
1308         if (bQMMM[i])
1309         {
1310             for (int k = 0; k < qm_nr; k++)
1311             {
1312                 qmexcl.a[k + j] = qm_arr[k];
1313             }
1314             for (int k = 0; k < link_nr; k++)
1315             {
1316                 qmexcl.a[qm_nr + k + j] = link_arr[k];
1317             }
1318             j += (qm_nr + link_nr);
1319         }
1320     }
1321     qmexcl.index[qmexcl.nr] = j;
1322
1323     /* and merging with the exclusions already present in sys.
1324      */
1325
1326     std::vector<gmx::ExclusionBlock> qmexcl2(molt->atoms.nr);
1327     gmx::blockaToExclusionBlocks(&qmexcl, qmexcl2);
1328     gmx::mergeExclusions(&(molt->excls), qmexcl2);
1329
1330     /* Finally, we also need to get rid of the pair interactions of the
1331      * classical atom bonded to the boundary QM atoms with the QMatoms,
1332      * as this interaction is already accounted for by the QM, so also
1333      * here we run the risk of double counting! We proceed in a similar
1334      * way as we did above for the other bonded interactions: */
1335     for (int i = F_LJ14; i < F_COUL14; i++)
1336     {
1337         int nratoms = interaction_function[i].nratoms;
1338         int j       = 0;
1339         while (j < molt->ilist[i].size())
1340         {
1341             int  a1    = molt->ilist[i].iatoms[j + 1];
1342             int  a2    = molt->ilist[i].iatoms[j + 2];
1343             bool bexcl = (bQMMM[a1] && bQMMM[a2]);
1344             if (bexcl)
1345             {
1346                 /* since the interaction involves QM atoms, these should be
1347                  * removed from the MM ilist
1348                  */
1349                 InteractionList& ilist = molt->ilist[i];
1350                 for (int k = j; k < ilist.size() - (nratoms + 1); k++)
1351                 {
1352                     ilist.iatoms[k] = ilist.iatoms[k + (nratoms + 1)];
1353                 }
1354                 ilist.iatoms.resize(ilist.size() - (nratoms + 1));
1355             }
1356             else
1357             {
1358                 j += nratoms + 1; /* the +1 is for the functype */
1359             }
1360         }
1361     }
1362
1363     free(qm_arr);
1364     free(bQMMM);
1365     free(link_arr);
1366 } /* generate_qmexcl */
1367
1368 void generate_qmexcl(gmx_mtop_t* sys, t_inputrec* ir, const gmx::MDLogger& logger)
1369 {
1370     /* This routine expects molt->molt[m].ilist to be of size F_NRE and ordered.
1371      */
1372
1373     unsigned char*  grpnr;
1374     int             mol, nat_mol, nr_mol_with_qm_atoms = 0;
1375     gmx_molblock_t* molb;
1376     bool            bQMMM;
1377     int             index_offset = 0;
1378     int             qm_nr        = 0;
1379
1380     grpnr = sys->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].data();
1381
1382     for (size_t mb = 0; mb < sys->molblock.size(); mb++)
1383     {
1384         molb    = &sys->molblock[mb];
1385         nat_mol = sys->moltype[molb->type].atoms.nr;
1386         for (mol = 0; mol < molb->nmol; mol++)
1387         {
1388             bQMMM = FALSE;
1389             for (int i = 0; i < nat_mol; i++)
1390             {
1391                 if ((grpnr ? grpnr[i] : 0) < (ir->opts.ngQM))
1392                 {
1393                     bQMMM = TRUE;
1394                     qm_nr++;
1395                 }
1396             }
1397
1398             if (bQMMM)
1399             {
1400                 nr_mol_with_qm_atoms++;
1401                 if (molb->nmol > 1)
1402                 {
1403                     /* We need to split this molblock */
1404                     if (mol > 0)
1405                     {
1406                         /* Split the molblock at this molecule */
1407                         auto pos = sys->molblock.begin() + mb + 1;
1408                         sys->molblock.insert(pos, sys->molblock[mb]);
1409                         sys->molblock[mb].nmol = mol;
1410                         sys->molblock[mb + 1].nmol -= mol;
1411                         mb++;
1412                         molb = &sys->molblock[mb];
1413                     }
1414                     if (molb->nmol > 1)
1415                     {
1416                         /* Split the molblock after this molecule */
1417                         auto pos = sys->molblock.begin() + mb + 1;
1418                         sys->molblock.insert(pos, sys->molblock[mb]);
1419                         molb                   = &sys->molblock[mb];
1420                         sys->molblock[mb].nmol = 1;
1421                         sys->molblock[mb + 1].nmol -= 1;
1422                     }
1423
1424                     /* Create a copy of a moltype for a molecule
1425                      * containing QM atoms and append it in the end of the list
1426                      */
1427                     std::vector<gmx_moltype_t> temp(sys->moltype.size());
1428                     for (size_t i = 0; i < sys->moltype.size(); ++i)
1429                     {
1430                         copy_moltype(&sys->moltype[i], &temp[i]);
1431                     }
1432                     sys->moltype.resize(sys->moltype.size() + 1);
1433                     for (size_t i = 0; i < temp.size(); ++i)
1434                     {
1435                         copy_moltype(&temp[i], &sys->moltype[i]);
1436                     }
1437                     copy_moltype(&sys->moltype[molb->type], &sys->moltype.back());
1438                     /* Copy the exclusions to a new array, since this is the only
1439                      * thing that needs to be modified for QMMM.
1440                      */
1441                     sys->moltype.back().excls = sys->moltype[molb->type].excls;
1442                     /* Set the molecule type for the QMMM molblock */
1443                     molb->type = sys->moltype.size() - 1;
1444                 }
1445                 generate_qmexcl_moltype(&sys->moltype[molb->type], grpnr, ir, logger);
1446             }
1447             if (grpnr)
1448             {
1449                 grpnr += nat_mol;
1450             }
1451             index_offset += nat_mol;
1452         }
1453     }
1454 }