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) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
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  13  * as published by the Free Software Foundation; either version 2.1
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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "convparm.h"
  41
  42 #include <cassert>
  43 #include <cmath>
  44 #include <cstring>
  45
  46 #include <memory>
  47
  48 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  49 #include "gromacs/gmxpreprocess/grompp_impl.h"
  50 #include "gromacs/gmxpreprocess/topio.h"
  51 #include "gromacs/gmxpreprocess/toputil.h"
  52 #include "gromacs/math/functions.h"
  53 #include "gromacs/math/units.h"
  54 #include "gromacs/math/utilities.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/mdtypes/md_enums.h"
  57 #include "gromacs/topology/ifunc.h"
  58 #include "gromacs/topology/topology.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 static int round_check(real r, int limit, int ftype, const char* name)
  63 {
  64     const int i = gmx::roundToInt(r);
  65
  66     if (r - i > 0.01 || r - i < -0.01)
  67     {
  68         gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s", r, name,
  69                   interaction_function[ftype].longname);
  70     }
  71
  72     if (i < limit)
  73     {
  74         gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d", name,
  75                   interaction_function[ftype].longname, i, limit);
  76     }
  77
  78     return i;
  79 }
  80
  81 static void set_ljparams(int comb, double reppow, double v, double w, real* c6, real* c12)
  82 {
  83     if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
  84     {
  85         if (v >= 0)
  86         {
  87             *c6  = 4 * w * gmx::power6(v);
  88             *c12 = 4 * w * std::pow(v, reppow);
  89         }
  90         else
  91         {
  92             /* Interpret negative sigma as c6=0 and c12 with -sigma */
  93             *c6  = 0;
  94             *c12 = 4 * w * std::pow(-v, reppow);
  95         }
  96     }
  97     else
  98     {
  99         *c6  = v;
 100         *c12 = w;
 101     }
 102 }
 103
 104 /* A return value of 0 means parameters were assigned successfully,
 105  * returning -1 means this is an all-zero interaction that should not be added.
 106  */
 107 static int assign_param(t_functype ftype, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
 108 {
 109     bool all_param_zero = true;
 110
 111     /* Set to zero */
 112     for (int j = 0; (j < MAXFORCEPARAM); j++)
 113     {
 114         newparam->generic.buf[j] = 0.0;
 115         /* If all parameters are zero we might not add some interaction types (selected below).
 116          * We cannot apply this to ALL interactions, since many have valid reasons for having
 117          * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
 118          * we use it for angles and torsions that are typically generated automatically.
 119          */
 120         all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
 121     }
 122
 123     if (all_param_zero)
 124     {
 125         if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
 126             || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
 127         {
 128             return -1;
 129         }
 130     }
 131
 132     switch (ftype)
 133     {
 134         case F_G96ANGLES:
 135             /* Post processing of input data: store cosine iso angle itself */
 136             newparam->harmonic.rA  = cos(old[0] * DEG2RAD);
 137             newparam->harmonic.krA = old[1];
 138             newparam->harmonic.rB  = cos(old[2] * DEG2RAD);
 139             newparam->harmonic.krB = old[3];
 140             break;
 141         case F_G96BONDS:
 142             /* Post processing of input data: store square of length itself */
 143             newparam->harmonic.rA  = gmx::square(old[0]);
 144             newparam->harmonic.krA = old[1];
 145             newparam->harmonic.rB  = gmx::square(old[2]);
 146             newparam->harmonic.krB = old[3];
 147             break;
 148         case F_FENEBONDS:
 149             newparam->fene.bm = old[0];
 150             newparam->fene.kb = old[1];
 151             break;
 152         case F_RESTRBONDS:
 153             newparam->restraint.lowA = old[0];
 154             newparam->restraint.up1A = old[1];
 155             newparam->restraint.up2A = old[2];
 156             newparam->restraint.kA   = old[3];
 157             newparam->restraint.lowB = old[4];
 158             newparam->restraint.up1B = old[5];
 159             newparam->restraint.up2B = old[6];
 160             newparam->restraint.kB   = old[7];
 161             break;
 162         case F_TABBONDS:
 163         case F_TABBONDSNC:
 164         case F_TABANGLES:
 165         case F_TABDIHS:
 166             newparam->tab.table = round_check(old[0], 0, ftype, "table index");
 167             newparam->tab.kA    = old[1];
 168             newparam->tab.kB    = old[3];
 169             break;
 170         case F_CROSS_BOND_BONDS:
 171             newparam->cross_bb.r1e = old[0];
 172             newparam->cross_bb.r2e = old[1];
 173             newparam->cross_bb.krr = old[2];
 174             break;
 175         case F_CROSS_BOND_ANGLES:
 176             newparam->cross_ba.r1e = old[0];
 177             newparam->cross_ba.r2e = old[1];
 178             newparam->cross_ba.r3e = old[2];
 179             newparam->cross_ba.krt = old[3];
 180             break;
 181         case F_UREY_BRADLEY:
 182             newparam->u_b.thetaA  = old[0];
 183             newparam->u_b.kthetaA = old[1];
 184             newparam->u_b.r13A    = old[2];
 185             newparam->u_b.kUBA    = old[3];
 186             newparam->u_b.thetaB  = old[4];
 187             newparam->u_b.kthetaB = old[5];
 188             newparam->u_b.r13B    = old[6];
 189             newparam->u_b.kUBB    = old[7];
 190             break;
 191         case F_QUARTIC_ANGLES:
 192             newparam->qangle.theta = old[0];
 193             for (int i = 0; i < 5; i++)
 194             {
 195                 newparam->qangle.c[i] = old[i + 1];
 196             }
 197             break;
 198         case F_LINEAR_ANGLES:
 199             newparam->linangle.aA    = old[0];
 200             newparam->linangle.klinA = old[1];
 201             newparam->linangle.aB    = old[2];
 202             newparam->linangle.klinB = old[3];
 203             break;
 204         case F_BONDS:
 205         case F_ANGLES:
 206         case F_HARMONIC:
 207         case F_IDIHS:
 208             newparam->harmonic.rA  = old[0];
 209             newparam->harmonic.krA = old[1];
 210             newparam->harmonic.rB  = old[2];
 211             newparam->harmonic.krB = old[3];
 212             break;
 213         case F_RESTRANGLES:
 214             newparam->harmonic.rA  = old[0];
 215             newparam->harmonic.krA = old[1];
 216             break;
 217         case F_MORSE:
 218             newparam->morse.b0A   = old[0];
 219             newparam->morse.cbA   = old[1];
 220             newparam->morse.betaA = old[2];
 221             newparam->morse.b0B   = old[3];
 222             newparam->morse.cbB   = old[4];
 223             newparam->morse.betaB = old[5];
 224             break;
 225         case F_CUBICBONDS:
 226             newparam->cubic.b0   = old[0];
 227             newparam->cubic.kb   = old[1];
 228             newparam->cubic.kcub = old[2];
 229             break;
 230         case F_CONNBONDS: break;
 231         case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
 232         case F_ANHARM_POL:
 233             newparam->anharm_polarize.alpha = old[0];
 234             newparam->anharm_polarize.drcut = old[1];
 235             newparam->anharm_polarize.khyp  = old[2];
 236             break;
 237         case F_WATER_POL:
 238             newparam->wpol.al_x = old[0];
 239             newparam->wpol.al_y = old[1];
 240             newparam->wpol.al_z = old[2];
 241             newparam->wpol.rOH  = old[3];
 242             newparam->wpol.rHH  = old[4];
 243             newparam->wpol.rOD  = old[5];
 244             break;
 245         case F_THOLE_POL:
 246             newparam->thole.a      = old[0];
 247             newparam->thole.alpha1 = old[1];
 248             newparam->thole.alpha2 = old[2];
 249             if ((old[1] > 0) && (old[2] > 0))
 250             {
 251                 newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
 252             }
 253             else
 254             {
 255                 newparam->thole.rfac = 1;
 256             }
 257             break;
 258         case F_BHAM:
 259             newparam->bham.a = old[0];
 260             newparam->bham.b = old[1];
 261             newparam->bham.c = old[2];
 262             break;
 263         case F_LJ14:
 264             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
 265             set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
 266             break;
 267         case F_LJC14_Q:
 268             newparam->ljc14.fqq = old[0];
 269             newparam->ljc14.qi  = old[1];
 270             newparam->ljc14.qj  = old[2];
 271             set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
 272             break;
 273         case F_LJC_PAIRS_NB:
 274             newparam->ljcnb.qi = old[0];
 275             newparam->ljcnb.qj = old[1];
 276             set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
 277             break;
 278         case F_LJ:
 279             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
 280             break;
 281         case F_PDIHS:
 282         case F_PIDIHS:
 283         case F_ANGRES:
 284         case F_ANGRESZ:
 285             newparam->pdihs.phiA = old[0];
 286             newparam->pdihs.cpA  = old[1];
 287
 288             /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
 289              * so I have changed the lower limit to -99 /EL
 290              */
 291             newparam->pdihs.phiB = old[3];
 292             newparam->pdihs.cpB  = old[4];
 293             /* If both force constants are zero there is no interaction. Return -1 to signal
 294              * this entry should NOT be added.
 295              */
 296             if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
 297             {
 298                 return -1;
 299             }
 300
 301             newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
 302
 303             break;
 304         case F_RESTRDIHS:
 305             newparam->pdihs.phiA = old[0];
 306             newparam->pdihs.cpA  = old[1];
 307             break;
 308         case F_POSRES:
 309             newparam->posres.fcA[XX]   = old[0];
 310             newparam->posres.fcA[YY]   = old[1];
 311             newparam->posres.fcA[ZZ]   = old[2];
 312             newparam->posres.fcB[XX]   = old[3];
 313             newparam->posres.fcB[YY]   = old[4];
 314             newparam->posres.fcB[ZZ]   = old[5];
 315             newparam->posres.pos0A[XX] = old[6];
 316             newparam->posres.pos0A[YY] = old[7];
 317             newparam->posres.pos0A[ZZ] = old[8];
 318             newparam->posres.pos0B[XX] = old[9];
 319             newparam->posres.pos0B[YY] = old[10];
 320             newparam->posres.pos0B[ZZ] = old[11];
 321             break;
 322         case F_FBPOSRES:
 323             newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
 324             if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
 325             {
 326                 gmx_fatal(FARGS,
 327                           "Invalid geometry for flat-bottomed position restraint.\n"
 328                           "Expected number between 1 and %d. Found %d\n",
 329                           efbposresNR - 1, newparam->fbposres.geom);
 330             }
 331             newparam->fbposres.r        = old[1];
 332             newparam->fbposres.k        = old[2];
 333             newparam->fbposres.pos0[XX] = old[3];
 334             newparam->fbposres.pos0[YY] = old[4];
 335             newparam->fbposres.pos0[ZZ] = old[5];
 336             break;
 337         case F_DISRES:
 338             newparam->disres.label = round_check(old[0], 0, ftype, "label");
 339             newparam->disres.type  = round_check(old[1], 1, ftype, "type'");
 340             newparam->disres.low   = old[2];
 341             newparam->disres.up1   = old[3];
 342             newparam->disres.up2   = old[4];
 343             newparam->disres.kfac  = old[5];
 344             break;
 345         case F_ORIRES:
 346             newparam->orires.ex    = round_check(old[0], 1, ftype, "experiment") - 1;
 347             newparam->orires.label = round_check(old[1], 1, ftype, "label");
 348             newparam->orires.power = round_check(old[2], 0, ftype, "power");
 349             newparam->orires.c     = old[3];
 350             newparam->orires.obs   = old[4];
 351             newparam->orires.kfac  = old[5];
 352             break;
 353         case F_DIHRES:
 354             newparam->dihres.phiA  = old[0];
 355             newparam->dihres.dphiA = old[1];
 356             newparam->dihres.kfacA = old[2];
 357             newparam->dihres.phiB  = old[3];
 358             newparam->dihres.dphiB = old[4];
 359             newparam->dihres.kfacB = old[5];
 360             break;
 361         case F_RBDIHS:
 362             for (int i = 0; (i < NR_RBDIHS); i++)
 363             {
 364                 newparam->rbdihs.rbcA[i] = old[i];
 365                 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
 366             }
 367             break;
 368         case F_CBTDIHS:
 369             for (int i = 0; (i < NR_CBTDIHS); i++)
 370             {
 371                 newparam->cbtdihs.cbtcA[i] = old[i];
 372             }
 373             break;
 374         case F_FOURDIHS:
 375             /* Read the dihedral parameters to temporary arrays,
 376              * and convert them to the computationally faster
 377              * Ryckaert-Bellemans form.
 378              */
 379             /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
 380             newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
 381             newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
 382             newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
 383             newparam->rbdihs.rbcA[3] = -2.0 * old[2];
 384             newparam->rbdihs.rbcA[4] = -4.0 * old[3];
 385             newparam->rbdihs.rbcA[5] = 0.0;
 386
 387             newparam->rbdihs.rbcB[0] =
 388                     old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
 389             newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
 390             newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
 391             newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
 392             newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
 393             newparam->rbdihs.rbcB[5] = 0.0;
 394             break;
 395         case F_CONSTR:
 396         case F_CONSTRNC:
 397             newparam->constr.dA = old[0];
 398             newparam->constr.dB = old[1];
 399             break;
 400         case F_SETTLE:
 401             newparam->settle.doh = old[0];
 402             newparam->settle.dhh = old[1];
 403             break;
 404         case F_VSITE2:
 405         case F_VSITE2FD:
 406         case F_VSITE3:
 407         case F_VSITE3FD:
 408         case F_VSITE3OUT:
 409         case F_VSITE4FD:
 410         case F_VSITE4FDN:
 411             newparam->vsite.a = old[0];
 412             newparam->vsite.b = old[1];
 413             newparam->vsite.c = old[2];
 414             newparam->vsite.d = old[3];
 415             newparam->vsite.e = old[4];
 416             newparam->vsite.f = old[5];
 417             break;
 418         case F_VSITE3FAD:
 419             newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
 420             newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
 421             newparam->vsite.c = old[2];
 422             newparam->vsite.d = old[3];
 423             newparam->vsite.e = old[4];
 424             newparam->vsite.f = old[5];
 425             break;
 426         case F_VSITEN:
 427             newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
 428             newparam->vsiten.a = old[1];
 429             break;
 430         case F_CMAP:
 431             newparam->cmap.cmapA = static_cast<int>(old[0]);
 432             newparam->cmap.cmapB = static_cast<int>(old[1]);
 433             break;
 434         case F_GB12_NOLONGERUSED:
 435         case F_GB13_NOLONGERUSED:
 436         case F_GB14_NOLONGERUSED: break;
 437         default:
 438             gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
 439     }
 440     return 0;
 441 }
 442
 443 static int enter_params(gmx_ffparams_t*           ffparams,
 444                         t_functype                ftype,
 445                         gmx::ArrayRef<const real> forceparams,
 446                         int                       comb,
 447                         real                      reppow,
 448                         int                       start,
 449                         bool                      bAppend)
 450 {
 451     t_iparams newparam;
 452     int       type;
 453     int       rc;
 454
 455     if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
 456     {
 457         /* -1 means this interaction is all-zero and should not be added */
 458         return rc;
 459     }
 460
 461     if (!bAppend)
 462     {
 463         for (type = start; (type < ffparams->numTypes()); type++)
 464         {
 465             if (ffparams->functype[type] == ftype)
 466             {
 467                 if (memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 468                 {
 469                     return type;
 470                 }
 471             }
 472         }
 473     }
 474     else
 475     {
 476         type = ffparams->numTypes();
 477     }
 478
 479     ffparams->iparams.push_back(newparam);
 480     ffparams->functype.push_back(ftype);
 481
 482     GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
 483
 484     return type;
 485 }
 486
 487 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
 488 {
 489     ilist->iatoms.push_back(type);
 490     for (const auto& atom : a)
 491     {
 492         ilist->iatoms.push_back(atom);
 493     }
 494 }
 495
 496 static void enter_function(const InteractionsOfType* p,
 497                            t_functype                ftype,
 498                            int                       comb,
 499                            real                      reppow,
 500                            gmx_ffparams_t*           ffparams,
 501                            InteractionList*          il,
 502                            bool                      bNB,
 503                            bool                      bAppend)
 504 {
 505     int start = ffparams->numTypes();
 506
 507     for (auto& parm : p->interactionTypes)
 508     {
 509         int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
 510         /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
 511         if (!bNB && type >= 0)
 512         {
 513             GMX_RELEASE_ASSERT(il, "Need valid interaction list");
 514             GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
 515                                "Need to have correct number of atoms for the parameter");
 516             append_interaction(il, type, parm.atoms());
 517         }
 518     }
 519 }
 520
 521 void convertInteractionsOfType(int                                      atnr,
 522                                gmx::ArrayRef<const InteractionsOfType>  nbtypes,
 523                                gmx::ArrayRef<const MoleculeInformation> mi,
 524                                const MoleculeInformation*               intermolecular_interactions,
 525                                int                                      comb,
 526                                double                                   reppow,
 527                                real                                     fudgeQQ,
 528                                gmx_mtop_t*                              mtop)
 529 {
 530     int             i;
 531     unsigned long   flags;
 532     gmx_ffparams_t* ffp;
 533     gmx_moltype_t*  molt;
 534
 535     ffp       = &mtop->ffparams;
 536     ffp->atnr = atnr;
 537     ffp->functype.clear();
 538     ffp->iparams.clear();
 539     ffp->reppow = reppow;
 540
 541     enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
 542     enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
 543                    TRUE, TRUE);
 544
 545     for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 546     {
 547         molt = &mtop->moltype[mt];
 548         for (i = 0; (i < F_NRE); i++)
 549         {
 550             molt->ilist[i].iatoms.clear();
 551
 552             gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
 553
 554             flags = interaction_function[i].flags;
 555             if ((i != F_LJ) && (i != F_BHAM)
 556                 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
 557             {
 558                 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow, ffp,
 559                                &molt->ilist[i], FALSE, (i == F_POSRES || i == F_FBPOSRES));
 560             }
 561         }
 562     }
 563
 564     mtop->bIntermolecularInteractions = FALSE;
 565     if (intermolecular_interactions != nullptr)
 566     {
 567         /* Process the intermolecular interaction list */
 568         mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
 569
 570         for (i = 0; (i < F_NRE); i++)
 571         {
 572             (*mtop->intermolecular_ilist)[i].iatoms.clear();
 573
 574             gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
 575
 576             if (!interactions[i].interactionTypes.empty())
 577             {
 578                 flags = interaction_function[i].flags;
 579                 /* For intermolecular interactions we (currently)
 580                  * only support potentials.
 581                  * Constraints and virtual sites would be possible,
 582                  * but require a lot of extra (bug-prone) code.
 583                  */
 584                 if (!(flags & IF_BOND))
 585                 {
 586                     gmx_fatal(FARGS,
 587                               "The intermolecular_interaction section may only contain bonded "
 588                               "potentials");
 589                 }
 590                 else if (NRAL(i) == 1) /* e.g. position restraints */
 591                 {
 592                     gmx_fatal(FARGS,
 593                               "Single atom interactions don't make sense in the "
 594                               "intermolecular_interaction section, you can put them in the "
 595                               "moleculetype section");
 596                 }
 597                 else if (flags & IF_CHEMBOND)
 598                 {
 599                     gmx_fatal(FARGS,
 600                               "The intermolecular_interaction can not contain chemically bonding "
 601                               "interactions");
 602                 }
 603                 else
 604                 {
 605                     enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
 606                                    ffp, &(*mtop->intermolecular_ilist)[i], FALSE, FALSE);
 607
 608                     mtop->bIntermolecularInteractions = TRUE;
 609                 }
 610             }
 611         }
 612
 613         if (!mtop->bIntermolecularInteractions)
 614         {
 615             mtop->intermolecular_ilist.reset(nullptr);
 616         }
 617     }
 618
 619     ffp->fudgeQQ = fudgeQQ;
 620 }