src/gromacs/gmxpreprocess/convparm.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  *
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  38 /* This file is completely threadsafe - keep it that way! */
  39 #include "gmxpre.h"
  40
  41 #include "convparm.h"
  42
  43 #include <cassert>
  44 #include <cmath>
  45 #include <cstring>
  46
  47 #include <memory>
  48
  49 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  50 #include "gromacs/gmxpreprocess/grompp_impl.h"
  51 #include "gromacs/gmxpreprocess/topio.h"
  52 #include "gromacs/gmxpreprocess/toputil.h"
  53 #include "gromacs/math/functions.h"
  54 #include "gromacs/math/units.h"
  55 #include "gromacs/math/utilities.h"
  56 #include "gromacs/math/vec.h"
  57 #include "gromacs/mdtypes/md_enums.h"
  58 #include "gromacs/topology/ifunc.h"
  59 #include "gromacs/topology/topology.h"
  60 #include "gromacs/utility/fatalerror.h"
  61 #include "gromacs/utility/smalloc.h"
  62
  63 static int round_check(real r, int limit, int ftype, const char* name)
  64 {
  65     const int i = gmx::roundToInt(r);
  66
  67     if (r - i > 0.01 || r - i < -0.01)
  68     {
  69         gmx_fatal(FARGS,
  70                   "A non-integer value (%f) was supplied for '%s' in %s",
  71                   r,
  72                   name,
  73                   interaction_function[ftype].longname);
  74     }
  75
  76     if (i < limit)
  77     {
  78         gmx_fatal(FARGS,
  79                   "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
  80                   name,
  81                   interaction_function[ftype].longname,
  82                   i,
  83                   limit);
  84     }
  85
  86     return i;
  87 }
  88
  89 static void set_ljparams(CombinationRule comb, double reppow, double v, double w, real* c6, real* c12)
  90 {
  91     if (comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
  92     {
  93         if (v >= 0)
  94         {
  95             *c6  = 4 * w * gmx::power6(v);
  96             *c12 = 4 * w * std::pow(v, reppow);
  97         }
  98         else
  99         {
 100             /* Interpret negative sigma as c6=0 and c12 with -sigma */
 101             *c6  = 0;
 102             *c12 = 4 * w * std::pow(-v, reppow);
 103         }
 104     }
 105     else
 106     {
 107         *c6  = v;
 108         *c12 = w;
 109     }
 110 }
 111
 112 /* A return value of 0 means parameters were assigned successfully,
 113  * returning -1 means this is an all-zero interaction that should not be added.
 114  */
 115 static int assign_param(t_functype                ftype,
 116                         t_iparams*                newparam,
 117                         gmx::ArrayRef<const real> old,
 118                         CombinationRule           comb,
 119                         double                    reppow)
 120 {
 121     bool all_param_zero = true;
 122
 123     /* Set to zero */
 124     for (int j = 0; (j < MAXFORCEPARAM); j++)
 125     {
 126         newparam->generic.buf[j] = 0.0;
 127         /* If all parameters are zero we might not add some interaction types (selected below).
 128          * We cannot apply this to ALL interactions, since many have valid reasons for having
 129          * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
 130          * we use it for angles and torsions that are typically generated automatically.
 131          */
 132         all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
 133     }
 134
 135     if (all_param_zero)
 136     {
 137         if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
 138             || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
 139         {
 140             return -1;
 141         }
 142     }
 143
 144     switch (ftype)
 145     {
 146         case F_G96ANGLES:
 147             /* Post processing of input data: store cosine iso angle itself */
 148             newparam->harmonic.rA  = cos(old[0] * gmx::c_deg2Rad);
 149             newparam->harmonic.krA = old[1];
 150             newparam->harmonic.rB  = cos(old[2] * gmx::c_deg2Rad);
 151             newparam->harmonic.krB = old[3];
 152             break;
 153         case F_G96BONDS:
 154             /* Post processing of input data: store square of length itself */
 155             newparam->harmonic.rA  = gmx::square(old[0]);
 156             newparam->harmonic.krA = old[1];
 157             newparam->harmonic.rB  = gmx::square(old[2]);
 158             newparam->harmonic.krB = old[3];
 159             break;
 160         case F_FENEBONDS:
 161             newparam->fene.bm = old[0];
 162             newparam->fene.kb = old[1];
 163             break;
 164         case F_RESTRBONDS:
 165             newparam->restraint.lowA = old[0];
 166             newparam->restraint.up1A = old[1];
 167             newparam->restraint.up2A = old[2];
 168             newparam->restraint.kA   = old[3];
 169             newparam->restraint.lowB = old[4];
 170             newparam->restraint.up1B = old[5];
 171             newparam->restraint.up2B = old[6];
 172             newparam->restraint.kB   = old[7];
 173             break;
 174         case F_TABBONDS:
 175         case F_TABBONDSNC:
 176         case F_TABANGLES:
 177         case F_TABDIHS:
 178             newparam->tab.table = round_check(old[0], 0, ftype, "table index");
 179             newparam->tab.kA    = old[1];
 180             newparam->tab.kB    = old[3];
 181             break;
 182         case F_CROSS_BOND_BONDS:
 183             newparam->cross_bb.r1e = old[0];
 184             newparam->cross_bb.r2e = old[1];
 185             newparam->cross_bb.krr = old[2];
 186             break;
 187         case F_CROSS_BOND_ANGLES:
 188             newparam->cross_ba.r1e = old[0];
 189             newparam->cross_ba.r2e = old[1];
 190             newparam->cross_ba.r3e = old[2];
 191             newparam->cross_ba.krt = old[3];
 192             break;
 193         case F_UREY_BRADLEY:
 194             newparam->u_b.thetaA  = old[0];
 195             newparam->u_b.kthetaA = old[1];
 196             newparam->u_b.r13A    = old[2];
 197             newparam->u_b.kUBA    = old[3];
 198             newparam->u_b.thetaB  = old[4];
 199             newparam->u_b.kthetaB = old[5];
 200             newparam->u_b.r13B    = old[6];
 201             newparam->u_b.kUBB    = old[7];
 202             break;
 203         case F_QUARTIC_ANGLES:
 204             newparam->qangle.theta = old[0];
 205             for (int i = 0; i < 5; i++)
 206             {
 207                 newparam->qangle.c[i] = old[i + 1];
 208             }
 209             break;
 210         case F_LINEAR_ANGLES:
 211             newparam->linangle.aA    = old[0];
 212             newparam->linangle.klinA = old[1];
 213             newparam->linangle.aB    = old[2];
 214             newparam->linangle.klinB = old[3];
 215             break;
 216         case F_BONDS:
 217         case F_ANGLES:
 218         case F_HARMONIC:
 219         case F_IDIHS:
 220             newparam->harmonic.rA  = old[0];
 221             newparam->harmonic.krA = old[1];
 222             newparam->harmonic.rB  = old[2];
 223             newparam->harmonic.krB = old[3];
 224             break;
 225         case F_RESTRANGLES:
 226             newparam->harmonic.rA  = old[0];
 227             newparam->harmonic.krA = old[1];
 228             break;
 229         case F_MORSE:
 230             newparam->morse.b0A   = old[0];
 231             newparam->morse.cbA   = old[1];
 232             newparam->morse.betaA = old[2];
 233             newparam->morse.b0B   = old[3];
 234             newparam->morse.cbB   = old[4];
 235             newparam->morse.betaB = old[5];
 236             break;
 237         case F_CUBICBONDS:
 238             newparam->cubic.b0   = old[0];
 239             newparam->cubic.kb   = old[1];
 240             newparam->cubic.kcub = old[2];
 241             break;
 242         case F_CONNBONDS: break;
 243         case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
 244         case F_ANHARM_POL:
 245             newparam->anharm_polarize.alpha = old[0];
 246             newparam->anharm_polarize.drcut = old[1];
 247             newparam->anharm_polarize.khyp  = old[2];
 248             break;
 249         case F_WATER_POL:
 250             newparam->wpol.al_x = old[0];
 251             newparam->wpol.al_y = old[1];
 252             newparam->wpol.al_z = old[2];
 253             newparam->wpol.rOH  = old[3];
 254             newparam->wpol.rHH  = old[4];
 255             newparam->wpol.rOD  = old[5];
 256             break;
 257         case F_THOLE_POL:
 258             newparam->thole.a      = old[0];
 259             newparam->thole.alpha1 = old[1];
 260             newparam->thole.alpha2 = old[2];
 261             break;
 262         case F_BHAM:
 263             newparam->bham.a = old[0];
 264             newparam->bham.b = old[1];
 265             newparam->bham.c = old[2];
 266             break;
 267         case F_LJ14:
 268             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
 269             set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
 270             break;
 271         case F_LJC14_Q:
 272             newparam->ljc14.fqq = old[0];
 273             newparam->ljc14.qi  = old[1];
 274             newparam->ljc14.qj  = old[2];
 275             set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
 276             break;
 277         case F_LJC_PAIRS_NB:
 278             newparam->ljcnb.qi = old[0];
 279             newparam->ljcnb.qj = old[1];
 280             set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
 281             break;
 282         case F_LJ:
 283             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
 284             break;
 285         case F_PDIHS:
 286         case F_PIDIHS:
 287         case F_ANGRES:
 288         case F_ANGRESZ:
 289             newparam->pdihs.phiA = old[0];
 290             newparam->pdihs.cpA  = old[1];
 291
 292             /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
 293              * so I have changed the lower limit to -99 /EL
 294              */
 295             newparam->pdihs.phiB = old[3];
 296             newparam->pdihs.cpB  = old[4];
 297             /* If both force constants are zero there is no interaction. Return -1 to signal
 298              * this entry should NOT be added.
 299              */
 300             if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
 301             {
 302                 return -1;
 303             }
 304
 305             newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
 306
 307             break;
 308         case F_RESTRDIHS:
 309             newparam->pdihs.phiA = old[0];
 310             newparam->pdihs.cpA  = old[1];
 311             break;
 312         case F_POSRES:
 313             newparam->posres.fcA[XX]   = old[0];
 314             newparam->posres.fcA[YY]   = old[1];
 315             newparam->posres.fcA[ZZ]   = old[2];
 316             newparam->posres.fcB[XX]   = old[3];
 317             newparam->posres.fcB[YY]   = old[4];
 318             newparam->posres.fcB[ZZ]   = old[5];
 319             newparam->posres.pos0A[XX] = old[6];
 320             newparam->posres.pos0A[YY] = old[7];
 321             newparam->posres.pos0A[ZZ] = old[8];
 322             newparam->posres.pos0B[XX] = old[9];
 323             newparam->posres.pos0B[YY] = old[10];
 324             newparam->posres.pos0B[ZZ] = old[11];
 325             break;
 326         case F_FBPOSRES:
 327             newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
 328             if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
 329             {
 330                 gmx_fatal(FARGS,
 331                           "Invalid geometry for flat-bottomed position restraint.\n"
 332                           "Expected number between 1 and %d. Found %d\n",
 333                           efbposresNR - 1,
 334                           newparam->fbposres.geom);
 335             }
 336             newparam->fbposres.r        = old[1];
 337             newparam->fbposres.k        = old[2];
 338             newparam->fbposres.pos0[XX] = old[3];
 339             newparam->fbposres.pos0[YY] = old[4];
 340             newparam->fbposres.pos0[ZZ] = old[5];
 341             break;
 342         case F_DISRES:
 343             newparam->disres.label = round_check(old[0], 0, ftype, "label");
 344             newparam->disres.type  = round_check(old[1], 1, ftype, "type'");
 345             newparam->disres.low   = old[2];
 346             newparam->disres.up1   = old[3];
 347             newparam->disres.up2   = old[4];
 348             newparam->disres.kfac  = old[5];
 349             break;
 350         case F_ORIRES:
 351             newparam->orires.ex    = round_check(old[0], 1, ftype, "experiment") - 1;
 352             newparam->orires.label = round_check(old[1], 1, ftype, "label");
 353             newparam->orires.power = round_check(old[2], 0, ftype, "power");
 354             newparam->orires.c     = old[3];
 355             newparam->orires.obs   = old[4];
 356             newparam->orires.kfac  = old[5];
 357             break;
 358         case F_DIHRES:
 359             newparam->dihres.phiA  = old[0];
 360             newparam->dihres.dphiA = old[1];
 361             newparam->dihres.kfacA = old[2];
 362             newparam->dihres.phiB  = old[3];
 363             newparam->dihres.dphiB = old[4];
 364             newparam->dihres.kfacB = old[5];
 365             break;
 366         case F_RBDIHS:
 367             for (int i = 0; (i < NR_RBDIHS); i++)
 368             {
 369                 newparam->rbdihs.rbcA[i] = old[i];
 370                 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
 371             }
 372             break;
 373         case F_CBTDIHS:
 374             for (int i = 0; (i < NR_CBTDIHS); i++)
 375             {
 376                 newparam->cbtdihs.cbtcA[i] = old[i];
 377             }
 378             break;
 379         case F_FOURDIHS:
 380             /* Read the dihedral parameters to temporary arrays,
 381              * and convert them to the computationally faster
 382              * Ryckaert-Bellemans form.
 383              */
 384             /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
 385             newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
 386             newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
 387             newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
 388             newparam->rbdihs.rbcA[3] = -2.0 * old[2];
 389             newparam->rbdihs.rbcA[4] = -4.0 * old[3];
 390             newparam->rbdihs.rbcA[5] = 0.0;
 391
 392             newparam->rbdihs.rbcB[0] =
 393                     old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
 394             newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
 395             newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
 396             newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
 397             newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
 398             newparam->rbdihs.rbcB[5] = 0.0;
 399             break;
 400         case F_CONSTR:
 401         case F_CONSTRNC:
 402             newparam->constr.dA = old[0];
 403             newparam->constr.dB = old[1];
 404             break;
 405         case F_SETTLE:
 406             newparam->settle.doh = old[0];
 407             newparam->settle.dhh = old[1];
 408             break;
 409         case F_VSITE1:
 410         case F_VSITE2:
 411         case F_VSITE2FD:
 412         case F_VSITE3:
 413         case F_VSITE3FD:
 414         case F_VSITE3OUT:
 415         case F_VSITE4FD:
 416         case F_VSITE4FDN:
 417             newparam->vsite.a = old[0];
 418             newparam->vsite.b = old[1];
 419             newparam->vsite.c = old[2];
 420             newparam->vsite.d = old[3];
 421             newparam->vsite.e = old[4];
 422             newparam->vsite.f = old[5];
 423             break;
 424         case F_VSITE3FAD:
 425             newparam->vsite.a = old[1] * cos(gmx::c_deg2Rad * old[0]);
 426             newparam->vsite.b = old[1] * sin(gmx::c_deg2Rad * old[0]);
 427             newparam->vsite.c = old[2];
 428             newparam->vsite.d = old[3];
 429             newparam->vsite.e = old[4];
 430             newparam->vsite.f = old[5];
 431             break;
 432         case F_VSITEN:
 433             newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
 434             newparam->vsiten.a = old[1];
 435             break;
 436         case F_CMAP:
 437             newparam->cmap.cmapA = static_cast<int>(old[0]);
 438             newparam->cmap.cmapB = static_cast<int>(old[1]);
 439             break;
 440         case F_GB12_NOLONGERUSED:
 441         case F_GB13_NOLONGERUSED:
 442         case F_GB14_NOLONGERUSED: break;
 443         default:
 444             gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
 445     }
 446     return 0;
 447 }
 448
 449 static int enter_params(gmx_ffparams_t*           ffparams,
 450                         t_functype                ftype,
 451                         gmx::ArrayRef<const real> forceparams,
 452                         CombinationRule           comb,
 453                         real                      reppow,
 454                         int                       start,
 455                         bool                      bAppend)
 456 {
 457     t_iparams newparam;
 458     int       rc;
 459
 460     if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
 461     {
 462         /* -1 means this interaction is all-zero and should not be added */
 463         return rc;
 464     }
 465
 466     if (!bAppend)
 467     {
 468         if (ftype != F_DISRES)
 469         {
 470             for (int type = start; type < ffparams->numTypes(); type++)
 471             {
 472                 // Note that the first condition is always met by starting the loop at start
 473                 if (ffparams->functype[type] == ftype
 474                     && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 475                 {
 476                     return type;
 477                 }
 478             }
 479         }
 480         else
 481         {
 482             // Distance restraints should have unique labels and pairs with the same label
 483             // should be consecutive, so we here we only need to check the last type in the list.
 484             // This changes the complexity from quadratic to linear in the number of restraints.
 485             const int type = ffparams->numTypes() - 1;
 486             if (type >= 0 && ffparams->functype[type] == ftype
 487                 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 488             {
 489                 return type;
 490             }
 491         }
 492     }
 493
 494     const int type = ffparams->numTypes();
 495
 496     ffparams->iparams.push_back(newparam);
 497     ffparams->functype.push_back(ftype);
 498
 499     GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
 500
 501     return type;
 502 }
 503
 504 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
 505 {
 506     ilist->iatoms.push_back(type);
 507     for (const auto& atom : a)
 508     {
 509         ilist->iatoms.push_back(atom);
 510     }
 511 }
 512
 513 static void enter_function(const InteractionsOfType* p,
 514                            t_functype                ftype,
 515                            CombinationRule           comb,
 516                            real                      reppow,
 517                            gmx_ffparams_t*           ffparams,
 518                            InteractionList*          il,
 519                            bool                      bNB,
 520                            bool                      bAppend)
 521 {
 522     int start = ffparams->numTypes();
 523
 524     for (const auto& parm : p->interactionTypes)
 525     {
 526         int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
 527         /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
 528         if (!bNB && type >= 0)
 529         {
 530             GMX_RELEASE_ASSERT(il, "Need valid interaction list");
 531             GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
 532                                "Need to have correct number of atoms for the parameter");
 533             append_interaction(il, type, parm.atoms());
 534         }
 535     }
 536 }
 537
 538 void convertInteractionsOfType(int                                      atnr,
 539                                gmx::ArrayRef<const InteractionsOfType>  nbtypes,
 540                                gmx::ArrayRef<const MoleculeInformation> mi,
 541                                const MoleculeInformation*               intermolecular_interactions,
 542                                CombinationRule                          comb,
 543                                double                                   reppow,
 544                                real                                     fudgeQQ,
 545                                gmx_mtop_t*                              mtop)
 546 {
 547     int             i;
 548     unsigned long   flags;
 549     gmx_ffparams_t* ffp;
 550     gmx_moltype_t*  molt;
 551
 552     ffp       = &mtop->ffparams;
 553     ffp->atnr = atnr;
 554     ffp->functype.clear();
 555     ffp->iparams.clear();
 556     ffp->reppow = reppow;
 557
 558     enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
 559     enter_function(
 560             &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);
 561
 562     for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 563     {
 564         molt = &mtop->moltype[mt];
 565         for (i = 0; (i < F_NRE); i++)
 566         {
 567             molt->ilist[i].iatoms.clear();
 568
 569             gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
 570
 571             flags = interaction_function[i].flags;
 572             if ((i != F_LJ) && (i != F_BHAM)
 573                 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
 574             {
 575                 enter_function(&(interactions[i]),
 576                                static_cast<t_functype>(i),
 577                                comb,
 578                                reppow,
 579                                ffp,
 580                                &molt->ilist[i],
 581                                FALSE,
 582                                (i == F_POSRES || i == F_FBPOSRES));
 583             }
 584         }
 585     }
 586
 587     mtop->bIntermolecularInteractions = FALSE;
 588     if (intermolecular_interactions != nullptr)
 589     {
 590         /* Process the intermolecular interaction list */
 591         mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
 592
 593         for (i = 0; (i < F_NRE); i++)
 594         {
 595             (*mtop->intermolecular_ilist)[i].iatoms.clear();
 596
 597             gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
 598
 599             if (!interactions[i].interactionTypes.empty())
 600             {
 601                 flags = interaction_function[i].flags;
 602                 /* For intermolecular interactions we (currently)
 603                  * only support potentials.
 604                  * Constraints and virtual sites would be possible,
 605                  * but require a lot of extra (bug-prone) code.
 606                  */
 607                 if (!(flags & IF_BOND))
 608                 {
 609                     gmx_fatal(FARGS,
 610                               "The intermolecular_interaction section may only contain bonded "
 611                               "potentials");
 612                 }
 613                 else if (NRAL(i) == 1) /* e.g. position restraints */
 614                 {
 615                     gmx_fatal(FARGS,
 616                               "Single atom interactions don't make sense in the "
 617                               "intermolecular_interaction section, you can put them in the "
 618                               "moleculetype section");
 619                 }
 620                 else if (flags & IF_CHEMBOND)
 621                 {
 622                     gmx_fatal(FARGS,
 623                               "The intermolecular_interaction can not contain chemically bonding "
 624                               "interactions");
 625                 }
 626                 else
 627                 {
 628                     enter_function(&(interactions[i]),
 629                                    static_cast<t_functype>(i),
 630                                    comb,
 631                                    reppow,
 632                                    ffp,
 633                                    &(*mtop->intermolecular_ilist)[i],
 634                                    FALSE,
 635                                    FALSE);
 636
 637                     mtop->bIntermolecularInteractions = TRUE;
 638                 }
 639             }
 640         }
 641
 642         if (!mtop->bIntermolecularInteractions)
 643         {
 644             mtop->intermolecular_ilist.reset(nullptr);
 645         }
 646     }
 647
 648     ffp->fudgeQQ = fudgeQQ;
 649 }