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, 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
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  11  *
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  14  * as published by the Free Software Foundation; either version 2.1
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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, "A non-integer value (%f) was supplied for '%s' in %s", r, name,
  70                   interaction_function[ftype].longname);
  71     }
  72
  73     if (i < limit)
  74     {
  75         gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d", name,
  76                   interaction_function[ftype].longname, i, limit);
  77     }
  78
  79     return i;
  80 }
  81
  82 static void set_ljparams(int comb, double reppow, double v, double w, real* c6, real* c12)
  83 {
  84     if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
  85     {
  86         if (v >= 0)
  87         {
  88             *c6  = 4 * w * gmx::power6(v);
  89             *c12 = 4 * w * std::pow(v, reppow);
  90         }
  91         else
  92         {
  93             /* Interpret negative sigma as c6=0 and c12 with -sigma */
  94             *c6  = 0;
  95             *c12 = 4 * w * std::pow(-v, reppow);
  96         }
  97     }
  98     else
  99     {
 100         *c6  = v;
 101         *c12 = w;
 102     }
 103 }
 104
 105 /* A return value of 0 means parameters were assigned successfully,
 106  * returning -1 means this is an all-zero interaction that should not be added.
 107  */
 108 static int assign_param(t_functype ftype, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
 109 {
 110     bool all_param_zero = true;
 111
 112     /* Set to zero */
 113     for (int j = 0; (j < MAXFORCEPARAM); j++)
 114     {
 115         newparam->generic.buf[j] = 0.0;
 116         /* If all parameters are zero we might not add some interaction types (selected below).
 117          * We cannot apply this to ALL interactions, since many have valid reasons for having
 118          * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
 119          * we use it for angles and torsions that are typically generated automatically.
 120          */
 121         all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
 122     }
 123
 124     if (all_param_zero)
 125     {
 126         if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
 127             || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
 128         {
 129             return -1;
 130         }
 131     }
 132
 133     switch (ftype)
 134     {
 135         case F_G96ANGLES:
 136             /* Post processing of input data: store cosine iso angle itself */
 137             newparam->harmonic.rA  = cos(old[0] * DEG2RAD);
 138             newparam->harmonic.krA = old[1];
 139             newparam->harmonic.rB  = cos(old[2] * DEG2RAD);
 140             newparam->harmonic.krB = old[3];
 141             break;
 142         case F_G96BONDS:
 143             /* Post processing of input data: store square of length itself */
 144             newparam->harmonic.rA  = gmx::square(old[0]);
 145             newparam->harmonic.krA = old[1];
 146             newparam->harmonic.rB  = gmx::square(old[2]);
 147             newparam->harmonic.krB = old[3];
 148             break;
 149         case F_FENEBONDS:
 150             newparam->fene.bm = old[0];
 151             newparam->fene.kb = old[1];
 152             break;
 153         case F_RESTRBONDS:
 154             newparam->restraint.lowA = old[0];
 155             newparam->restraint.up1A = old[1];
 156             newparam->restraint.up2A = old[2];
 157             newparam->restraint.kA   = old[3];
 158             newparam->restraint.lowB = old[4];
 159             newparam->restraint.up1B = old[5];
 160             newparam->restraint.up2B = old[6];
 161             newparam->restraint.kB   = old[7];
 162             break;
 163         case F_TABBONDS:
 164         case F_TABBONDSNC:
 165         case F_TABANGLES:
 166         case F_TABDIHS:
 167             newparam->tab.table = round_check(old[0], 0, ftype, "table index");
 168             newparam->tab.kA    = old[1];
 169             newparam->tab.kB    = old[3];
 170             break;
 171         case F_CROSS_BOND_BONDS:
 172             newparam->cross_bb.r1e = old[0];
 173             newparam->cross_bb.r2e = old[1];
 174             newparam->cross_bb.krr = old[2];
 175             break;
 176         case F_CROSS_BOND_ANGLES:
 177             newparam->cross_ba.r1e = old[0];
 178             newparam->cross_ba.r2e = old[1];
 179             newparam->cross_ba.r3e = old[2];
 180             newparam->cross_ba.krt = old[3];
 181             break;
 182         case F_UREY_BRADLEY:
 183             newparam->u_b.thetaA  = old[0];
 184             newparam->u_b.kthetaA = old[1];
 185             newparam->u_b.r13A    = old[2];
 186             newparam->u_b.kUBA    = old[3];
 187             newparam->u_b.thetaB  = old[4];
 188             newparam->u_b.kthetaB = old[5];
 189             newparam->u_b.r13B    = old[6];
 190             newparam->u_b.kUBB    = old[7];
 191             break;
 192         case F_QUARTIC_ANGLES:
 193             newparam->qangle.theta = old[0];
 194             for (int i = 0; i < 5; i++)
 195             {
 196                 newparam->qangle.c[i] = old[i + 1];
 197             }
 198             break;
 199         case F_LINEAR_ANGLES:
 200             newparam->linangle.aA    = old[0];
 201             newparam->linangle.klinA = old[1];
 202             newparam->linangle.aB    = old[2];
 203             newparam->linangle.klinB = old[3];
 204             break;
 205         case F_BONDS:
 206         case F_ANGLES:
 207         case F_HARMONIC:
 208         case F_IDIHS:
 209             newparam->harmonic.rA  = old[0];
 210             newparam->harmonic.krA = old[1];
 211             newparam->harmonic.rB  = old[2];
 212             newparam->harmonic.krB = old[3];
 213             break;
 214         case F_RESTRANGLES:
 215             newparam->harmonic.rA  = old[0];
 216             newparam->harmonic.krA = old[1];
 217             break;
 218         case F_MORSE:
 219             newparam->morse.b0A   = old[0];
 220             newparam->morse.cbA   = old[1];
 221             newparam->morse.betaA = old[2];
 222             newparam->morse.b0B   = old[3];
 223             newparam->morse.cbB   = old[4];
 224             newparam->morse.betaB = old[5];
 225             break;
 226         case F_CUBICBONDS:
 227             newparam->cubic.b0   = old[0];
 228             newparam->cubic.kb   = old[1];
 229             newparam->cubic.kcub = old[2];
 230             break;
 231         case F_CONNBONDS: break;
 232         case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
 233         case F_ANHARM_POL:
 234             newparam->anharm_polarize.alpha = old[0];
 235             newparam->anharm_polarize.drcut = old[1];
 236             newparam->anharm_polarize.khyp  = old[2];
 237             break;
 238         case F_WATER_POL:
 239             newparam->wpol.al_x = old[0];
 240             newparam->wpol.al_y = old[1];
 241             newparam->wpol.al_z = old[2];
 242             newparam->wpol.rOH  = old[3];
 243             newparam->wpol.rHH  = old[4];
 244             newparam->wpol.rOD  = old[5];
 245             break;
 246         case F_THOLE_POL:
 247             newparam->thole.a      = old[0];
 248             newparam->thole.alpha1 = old[1];
 249             newparam->thole.alpha2 = old[2];
 250             if ((old[1] > 0) && (old[2] > 0))
 251             {
 252                 newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
 253             }
 254             else
 255             {
 256                 newparam->thole.rfac = 1;
 257             }
 258             break;
 259         case F_BHAM:
 260             newparam->bham.a = old[0];
 261             newparam->bham.b = old[1];
 262             newparam->bham.c = old[2];
 263             break;
 264         case F_LJ14:
 265             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
 266             set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
 267             break;
 268         case F_LJC14_Q:
 269             newparam->ljc14.fqq = old[0];
 270             newparam->ljc14.qi  = old[1];
 271             newparam->ljc14.qj  = old[2];
 272             set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
 273             break;
 274         case F_LJC_PAIRS_NB:
 275             newparam->ljcnb.qi = old[0];
 276             newparam->ljcnb.qj = old[1];
 277             set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
 278             break;
 279         case F_LJ:
 280             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
 281             break;
 282         case F_PDIHS:
 283         case F_PIDIHS:
 284         case F_ANGRES:
 285         case F_ANGRESZ:
 286             newparam->pdihs.phiA = old[0];
 287             newparam->pdihs.cpA  = old[1];
 288
 289             /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
 290              * so I have changed the lower limit to -99 /EL
 291              */
 292             newparam->pdihs.phiB = old[3];
 293             newparam->pdihs.cpB  = old[4];
 294             /* If both force constants are zero there is no interaction. Return -1 to signal
 295              * this entry should NOT be added.
 296              */
 297             if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
 298             {
 299                 return -1;
 300             }
 301
 302             newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
 303
 304             break;
 305         case F_RESTRDIHS:
 306             newparam->pdihs.phiA = old[0];
 307             newparam->pdihs.cpA  = old[1];
 308             break;
 309         case F_POSRES:
 310             newparam->posres.fcA[XX]   = old[0];
 311             newparam->posres.fcA[YY]   = old[1];
 312             newparam->posres.fcA[ZZ]   = old[2];
 313             newparam->posres.fcB[XX]   = old[3];
 314             newparam->posres.fcB[YY]   = old[4];
 315             newparam->posres.fcB[ZZ]   = old[5];
 316             newparam->posres.pos0A[XX] = old[6];
 317             newparam->posres.pos0A[YY] = old[7];
 318             newparam->posres.pos0A[ZZ] = old[8];
 319             newparam->posres.pos0B[XX] = old[9];
 320             newparam->posres.pos0B[YY] = old[10];
 321             newparam->posres.pos0B[ZZ] = old[11];
 322             break;
 323         case F_FBPOSRES:
 324             newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
 325             if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
 326             {
 327                 gmx_fatal(FARGS,
 328                           "Invalid geometry for flat-bottomed position restraint.\n"
 329                           "Expected number between 1 and %d. Found %d\n",
 330                           efbposresNR - 1, newparam->fbposres.geom);
 331             }
 332             newparam->fbposres.r        = old[1];
 333             newparam->fbposres.k        = old[2];
 334             newparam->fbposres.pos0[XX] = old[3];
 335             newparam->fbposres.pos0[YY] = old[4];
 336             newparam->fbposres.pos0[ZZ] = old[5];
 337             break;
 338         case F_DISRES:
 339             newparam->disres.label = round_check(old[0], 0, ftype, "label");
 340             newparam->disres.type  = round_check(old[1], 1, ftype, "type'");
 341             newparam->disres.low   = old[2];
 342             newparam->disres.up1   = old[3];
 343             newparam->disres.up2   = old[4];
 344             newparam->disres.kfac  = old[5];
 345             break;
 346         case F_ORIRES:
 347             newparam->orires.ex    = round_check(old[0], 1, ftype, "experiment") - 1;
 348             newparam->orires.label = round_check(old[1], 1, ftype, "label");
 349             newparam->orires.power = round_check(old[2], 0, ftype, "power");
 350             newparam->orires.c     = old[3];
 351             newparam->orires.obs   = old[4];
 352             newparam->orires.kfac  = old[5];
 353             break;
 354         case F_DIHRES:
 355             newparam->dihres.phiA  = old[0];
 356             newparam->dihres.dphiA = old[1];
 357             newparam->dihres.kfacA = old[2];
 358             newparam->dihres.phiB  = old[3];
 359             newparam->dihres.dphiB = old[4];
 360             newparam->dihres.kfacB = old[5];
 361             break;
 362         case F_RBDIHS:
 363             for (int i = 0; (i < NR_RBDIHS); i++)
 364             {
 365                 newparam->rbdihs.rbcA[i] = old[i];
 366                 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
 367             }
 368             break;
 369         case F_CBTDIHS:
 370             for (int i = 0; (i < NR_CBTDIHS); i++)
 371             {
 372                 newparam->cbtdihs.cbtcA[i] = old[i];
 373             }
 374             break;
 375         case F_FOURDIHS:
 376             /* Read the dihedral parameters to temporary arrays,
 377              * and convert them to the computationally faster
 378              * Ryckaert-Bellemans form.
 379              */
 380             /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
 381             newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
 382             newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
 383             newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
 384             newparam->rbdihs.rbcA[3] = -2.0 * old[2];
 385             newparam->rbdihs.rbcA[4] = -4.0 * old[3];
 386             newparam->rbdihs.rbcA[5] = 0.0;
 387
 388             newparam->rbdihs.rbcB[0] =
 389                     old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
 390             newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
 391             newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
 392             newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
 393             newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
 394             newparam->rbdihs.rbcB[5] = 0.0;
 395             break;
 396         case F_CONSTR:
 397         case F_CONSTRNC:
 398             newparam->constr.dA = old[0];
 399             newparam->constr.dB = old[1];
 400             break;
 401         case F_SETTLE:
 402             newparam->settle.doh = old[0];
 403             newparam->settle.dhh = old[1];
 404             break;
 405         case F_VSITE1:
 406         case F_VSITE2:
 407         case F_VSITE2FD:
 408         case F_VSITE3:
 409         case F_VSITE3FD:
 410         case F_VSITE3OUT:
 411         case F_VSITE4FD:
 412         case F_VSITE4FDN:
 413             newparam->vsite.a = old[0];
 414             newparam->vsite.b = old[1];
 415             newparam->vsite.c = old[2];
 416             newparam->vsite.d = old[3];
 417             newparam->vsite.e = old[4];
 418             newparam->vsite.f = old[5];
 419             break;
 420         case F_VSITE3FAD:
 421             newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
 422             newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
 423             newparam->vsite.c = old[2];
 424             newparam->vsite.d = old[3];
 425             newparam->vsite.e = old[4];
 426             newparam->vsite.f = old[5];
 427             break;
 428         case F_VSITEN:
 429             newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
 430             newparam->vsiten.a = old[1];
 431             break;
 432         case F_CMAP:
 433             newparam->cmap.cmapA = static_cast<int>(old[0]);
 434             newparam->cmap.cmapB = static_cast<int>(old[1]);
 435             break;
 436         case F_GB12_NOLONGERUSED:
 437         case F_GB13_NOLONGERUSED:
 438         case F_GB14_NOLONGERUSED: break;
 439         default:
 440             gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
 441     }
 442     return 0;
 443 }
 444
 445 static int enter_params(gmx_ffparams_t*           ffparams,
 446                         t_functype                ftype,
 447                         gmx::ArrayRef<const real> forceparams,
 448                         int                       comb,
 449                         real                      reppow,
 450                         int                       start,
 451                         bool                      bAppend)
 452 {
 453     t_iparams newparam;
 454     int       rc;
 455
 456     if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
 457     {
 458         /* -1 means this interaction is all-zero and should not be added */
 459         return rc;
 460     }
 461
 462     if (!bAppend)
 463     {
 464         if (ftype != F_DISRES)
 465         {
 466             for (int type = start; type < ffparams->numTypes(); type++)
 467             {
 468                 // Note that the first condition is always met by starting the loop at start
 469                 if (ffparams->functype[type] == ftype
 470                     && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 471                 {
 472                     return type;
 473                 }
 474             }
 475         }
 476         else
 477         {
 478             // Distance restraints should have unique labels and pairs with the same label
 479             // should be consecutive, so we here we only need to check the last type in the list.
 480             // This changes the complexity from quadratic to linear in the number of restraints.
 481             const int type = ffparams->numTypes() - 1;
 482             if (type >= 0 && ffparams->functype[type] == ftype
 483                 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 484             {
 485                 return type;
 486             }
 487         }
 488     }
 489
 490     const int type = ffparams->numTypes();
 491
 492     ffparams->iparams.push_back(newparam);
 493     ffparams->functype.push_back(ftype);
 494
 495     GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
 496
 497     return type;
 498 }
 499
 500 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
 501 {
 502     ilist->iatoms.push_back(type);
 503     for (const auto& atom : a)
 504     {
 505         ilist->iatoms.push_back(atom);
 506     }
 507 }
 508
 509 static void enter_function(const InteractionsOfType* p,
 510                            t_functype                ftype,
 511                            int                       comb,
 512                            real                      reppow,
 513                            gmx_ffparams_t*           ffparams,
 514                            InteractionList*          il,
 515                            bool                      bNB,
 516                            bool                      bAppend)
 517 {
 518     int start = ffparams->numTypes();
 519
 520     for (auto& parm : p->interactionTypes)
 521     {
 522         int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
 523         /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
 524         if (!bNB && type >= 0)
 525         {
 526             GMX_RELEASE_ASSERT(il, "Need valid interaction list");
 527             GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
 528                                "Need to have correct number of atoms for the parameter");
 529             append_interaction(il, type, parm.atoms());
 530         }
 531     }
 532 }
 533
 534 void convertInteractionsOfType(int                                      atnr,
 535                                gmx::ArrayRef<const InteractionsOfType>  nbtypes,
 536                                gmx::ArrayRef<const MoleculeInformation> mi,
 537                                const MoleculeInformation*               intermolecular_interactions,
 538                                int                                      comb,
 539                                double                                   reppow,
 540                                real                                     fudgeQQ,
 541                                gmx_mtop_t*                              mtop)
 542 {
 543     int             i;
 544     unsigned long   flags;
 545     gmx_ffparams_t* ffp;
 546     gmx_moltype_t*  molt;
 547
 548     ffp       = &mtop->ffparams;
 549     ffp->atnr = atnr;
 550     ffp->functype.clear();
 551     ffp->iparams.clear();
 552     ffp->reppow = reppow;
 553
 554     enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
 555     enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
 556                    TRUE, TRUE);
 557
 558     for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 559     {
 560         molt = &mtop->moltype[mt];
 561         for (i = 0; (i < F_NRE); i++)
 562         {
 563             molt->ilist[i].iatoms.clear();
 564
 565             gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
 566
 567             flags = interaction_function[i].flags;
 568             if ((i != F_LJ) && (i != F_BHAM)
 569                 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
 570             {
 571                 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow, ffp,
 572                                &molt->ilist[i], FALSE, (i == F_POSRES || i == F_FBPOSRES));
 573             }
 574         }
 575     }
 576
 577     mtop->bIntermolecularInteractions = FALSE;
 578     if (intermolecular_interactions != nullptr)
 579     {
 580         /* Process the intermolecular interaction list */
 581         mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
 582
 583         for (i = 0; (i < F_NRE); i++)
 584         {
 585             (*mtop->intermolecular_ilist)[i].iatoms.clear();
 586
 587             gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
 588
 589             if (!interactions[i].interactionTypes.empty())
 590             {
 591                 flags = interaction_function[i].flags;
 592                 /* For intermolecular interactions we (currently)
 593                  * only support potentials.
 594                  * Constraints and virtual sites would be possible,
 595                  * but require a lot of extra (bug-prone) code.
 596                  */
 597                 if (!(flags & IF_BOND))
 598                 {
 599                     gmx_fatal(FARGS,
 600                               "The intermolecular_interaction section may only contain bonded "
 601                               "potentials");
 602                 }
 603                 else if (NRAL(i) == 1) /* e.g. position restraints */
 604                 {
 605                     gmx_fatal(FARGS,
 606                               "Single atom interactions don't make sense in the "
 607                               "intermolecular_interaction section, you can put them in the "
 608                               "moleculetype section");
 609                 }
 610                 else if (flags & IF_CHEMBOND)
 611                 {
 612                     gmx_fatal(FARGS,
 613                               "The intermolecular_interaction can not contain chemically bonding "
 614                               "interactions");
 615                 }
 616                 else
 617                 {
 618                     enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
 619                                    ffp, &(*mtop->intermolecular_ilist)[i], FALSE, FALSE);
 620
 621                     mtop->bIntermolecularInteractions = TRUE;
 622                 }
 623             }
 624         }
 625
 626         if (!mtop->bIntermolecularInteractions)
 627         {
 628             mtop->intermolecular_ilist.reset(nullptr);
 629         }
 630     }
 631
 632     ffp->fudgeQQ = fudgeQQ;
 633 }