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  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  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",
  69                   r, name, 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",
  75                   name, 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,
  82                          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
 109 assign_param(t_functype ftype, t_iparams *newparam,
 110              gmx::ArrayRef<const real> old, int comb, double reppow)
 111 {
 112     bool     all_param_zero = true;
 113
 114     /* Set to zero */
 115     for (int j = 0; (j < MAXFORCEPARAM); j++)
 116     {
 117         newparam->generic.buf[j] = 0.0;
 118         /* If all parameters are zero we might not add some interaction types (selected below).
 119          * We cannot apply this to ALL interactions, since many have valid reasons for having
 120          * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
 121          * we use it for angles and torsions that are typically generated automatically.
 122          */
 123         all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
 124     }
 125
 126     if (all_param_zero)
 127     {
 128         if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS ||
 129             ftype == F_PDIHS || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
 130         {
 131             return -1;
 132         }
 133     }
 134
 135     switch (ftype)
 136     {
 137         case F_G96ANGLES:
 138             /* Post processing of input data: store cosine iso angle itself */
 139             newparam->harmonic.rA  = cos(old[0]*DEG2RAD);
 140             newparam->harmonic.krA = old[1];
 141             newparam->harmonic.rB  = cos(old[2]*DEG2RAD);
 142             newparam->harmonic.krB = old[3];
 143             break;
 144         case F_G96BONDS:
 145             /* Post processing of input data: store square of length itself */
 146             newparam->harmonic.rA  = gmx::square(old[0]);
 147             newparam->harmonic.krA = old[1];
 148             newparam->harmonic.rB  = gmx::square(old[2]);
 149             newparam->harmonic.krB = old[3];
 150             break;
 151         case F_FENEBONDS:
 152             newparam->fene.bm = old[0];
 153             newparam->fene.kb = old[1];
 154             break;
 155         case F_RESTRBONDS:
 156             newparam->restraint.lowA = old[0];
 157             newparam->restraint.up1A = old[1];
 158             newparam->restraint.up2A = old[2];
 159             newparam->restraint.kA   = old[3];
 160             newparam->restraint.lowB = old[4];
 161             newparam->restraint.up1B = old[5];
 162             newparam->restraint.up2B = old[6];
 163             newparam->restraint.kB   = old[7];
 164             break;
 165         case F_TABBONDS:
 166         case F_TABBONDSNC:
 167         case F_TABANGLES:
 168         case F_TABDIHS:
 169             newparam->tab.table = round_check(old[0], 0, ftype, "table index");
 170             newparam->tab.kA    = old[1];
 171             newparam->tab.kB    = old[3];
 172             break;
 173         case F_CROSS_BOND_BONDS:
 174             newparam->cross_bb.r1e = old[0];
 175             newparam->cross_bb.r2e = old[1];
 176             newparam->cross_bb.krr = old[2];
 177             break;
 178         case F_CROSS_BOND_ANGLES:
 179             newparam->cross_ba.r1e = old[0];
 180             newparam->cross_ba.r2e = old[1];
 181             newparam->cross_ba.r3e = old[2];
 182             newparam->cross_ba.krt = old[3];
 183             break;
 184         case F_UREY_BRADLEY:
 185             newparam->u_b.thetaA  = old[0];
 186             newparam->u_b.kthetaA = old[1];
 187             newparam->u_b.r13A    = old[2];
 188             newparam->u_b.kUBA    = old[3];
 189             newparam->u_b.thetaB  = old[4];
 190             newparam->u_b.kthetaB = old[5];
 191             newparam->u_b.r13B    = old[6];
 192             newparam->u_b.kUBB    = old[7];
 193             break;
 194         case F_QUARTIC_ANGLES:
 195             newparam->qangle.theta = old[0];
 196             for (int i = 0; i < 5; i++)
 197             {
 198                 newparam->qangle.c[i] = old[i+1];
 199             }
 200             break;
 201         case F_LINEAR_ANGLES:
 202             newparam->linangle.aA    = old[0];
 203             newparam->linangle.klinA = old[1];
 204             newparam->linangle.aB    = old[2];
 205             newparam->linangle.klinB = old[3];
 206             break;
 207         case F_BONDS:
 208         case F_ANGLES:
 209         case F_HARMONIC:
 210         case F_IDIHS:
 211             newparam->harmonic.rA  = old[0];
 212             newparam->harmonic.krA = old[1];
 213             newparam->harmonic.rB  = old[2];
 214             newparam->harmonic.krB = old[3];
 215             break;
 216         case F_RESTRANGLES:
 217             newparam->harmonic.rA  = old[0];
 218             newparam->harmonic.krA = old[1];
 219             break;
 220         case F_MORSE:
 221             newparam->morse.b0A    = old[0];
 222             newparam->morse.cbA    = old[1];
 223             newparam->morse.betaA  = old[2];
 224             newparam->morse.b0B    = old[3];
 225             newparam->morse.cbB    = old[4];
 226             newparam->morse.betaB  = old[5];
 227             break;
 228         case F_CUBICBONDS:
 229             newparam->cubic.b0    = old[0];
 230             newparam->cubic.kb    = old[1];
 231             newparam->cubic.kcub  = old[2];
 232             break;
 233         case F_CONNBONDS:
 234             break;
 235         case F_POLARIZATION:
 236             newparam->polarize.alpha = old[0];
 237             break;
 238         case F_ANHARM_POL:
 239             newparam->anharm_polarize.alpha = old[0];
 240             newparam->anharm_polarize.drcut = old[1];
 241             newparam->anharm_polarize.khyp  = old[2];
 242             break;
 243         case F_WATER_POL:
 244             newparam->wpol.al_x   = old[0];
 245             newparam->wpol.al_y   = old[1];
 246             newparam->wpol.al_z   = old[2];
 247             newparam->wpol.rOH    = old[3];
 248             newparam->wpol.rHH    = old[4];
 249             newparam->wpol.rOD    = old[5];
 250             break;
 251         case F_THOLE_POL:
 252             newparam->thole.a      = old[0];
 253             newparam->thole.alpha1 = old[1];
 254             newparam->thole.alpha2 = old[2];
 255             if ((old[1] > 0) && (old[2] > 0))
 256             {
 257                 newparam->thole.rfac = old[0]*gmx::invsixthroot(old[1]*old[2]);
 258             }
 259             else
 260             {
 261                 newparam->thole.rfac = 1;
 262             }
 263             break;
 264         case F_BHAM:
 265             newparam->bham.a = old[0];
 266             newparam->bham.b = old[1];
 267             newparam->bham.c = old[2];
 268             break;
 269         case F_LJ14:
 270             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
 271             set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
 272             break;
 273         case F_LJC14_Q:
 274             newparam->ljc14.fqq = old[0];
 275             newparam->ljc14.qi  = old[1];
 276             newparam->ljc14.qj  = old[2];
 277             set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
 278             break;
 279         case F_LJC_PAIRS_NB:
 280             newparam->ljcnb.qi = old[0];
 281             newparam->ljcnb.qj = old[1];
 282             set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
 283             break;
 284         case F_LJ:
 285             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
 286             break;
 287         case F_PDIHS:
 288         case F_PIDIHS:
 289         case F_ANGRES:
 290         case F_ANGRESZ:
 291             newparam->pdihs.phiA = old[0];
 292             newparam->pdihs.cpA  = old[1];
 293
 294             /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
 295              * so I have changed the lower limit to -99 /EL
 296              */
 297             newparam->pdihs.phiB = old[3];
 298             newparam->pdihs.cpB  = old[4];
 299             /* If both force constants are zero there is no interaction. Return -1 to signal
 300              * this entry should NOT be added.
 301              */
 302             if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
 303             {
 304                 return -1;
 305             }
 306
 307             newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
 308
 309             break;
 310         case F_RESTRDIHS:
 311             newparam->pdihs.phiA = old[0];
 312             newparam->pdihs.cpA  = old[1];
 313             break;
 314         case F_POSRES:
 315             newparam->posres.fcA[XX]   = old[0];
 316             newparam->posres.fcA[YY]   = old[1];
 317             newparam->posres.fcA[ZZ]   = old[2];
 318             newparam->posres.fcB[XX]   = old[3];
 319             newparam->posres.fcB[YY]   = old[4];
 320             newparam->posres.fcB[ZZ]   = old[5];
 321             newparam->posres.pos0A[XX] = old[6];
 322             newparam->posres.pos0A[YY] = old[7];
 323             newparam->posres.pos0A[ZZ] = old[8];
 324             newparam->posres.pos0B[XX] = old[9];
 325             newparam->posres.pos0B[YY] = old[10];
 326             newparam->posres.pos0B[ZZ] = old[11];
 327             break;
 328         case F_FBPOSRES:
 329             newparam->fbposres.geom     = round_check(old[0], 0, ftype, "geometry");
 330             if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
 331             {
 332                 gmx_fatal(FARGS, "Invalid geometry for flat-bottomed position restraint.\n"
 333                           "Expected number between 1 and %d. Found %d\n", 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] = old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
 393             newparam->rbdihs.rbcB[1] = 0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
 394             newparam->rbdihs.rbcB[2] = 4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
 395             newparam->rbdihs.rbcB[3] = -2.0*old[NR_FOURDIHS+2];
 396             newparam->rbdihs.rbcB[4] = -4.0*old[NR_FOURDIHS+3];
 397             newparam->rbdihs.rbcB[5] = 0.0;
 398             break;
 399         case F_CONSTR:
 400         case F_CONSTRNC:
 401             newparam->constr.dA = old[0];
 402             newparam->constr.dB = old[1];
 403             break;
 404         case F_SETTLE:
 405             newparam->settle.doh = old[0];
 406             newparam->settle.dhh = old[1];
 407             break;
 408         case F_VSITE2:
 409         case F_VSITE3:
 410         case F_VSITE3FD:
 411         case F_VSITE3OUT:
 412         case F_VSITE4FD:
 413         case F_VSITE4FDN:
 414             newparam->vsite.a = old[0];
 415             newparam->vsite.b = old[1];
 416             newparam->vsite.c = old[2];
 417             newparam->vsite.d = old[3];
 418             newparam->vsite.e = old[4];
 419             newparam->vsite.f = old[5];
 420             break;
 421         case F_VSITE3FAD:
 422             newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
 423             newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
 424             newparam->vsite.c = old[2];
 425             newparam->vsite.d = old[3];
 426             newparam->vsite.e = old[4];
 427             newparam->vsite.f = old[5];
 428             break;
 429         case F_VSITEN:
 430             newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
 431             newparam->vsiten.a = old[1];
 432             break;
 433         case F_CMAP:
 434             newparam->cmap.cmapA = static_cast<int>(old[0]);
 435             newparam->cmap.cmapB = static_cast<int>(old[1]);
 436             break;
 437         case F_GB12_NOLONGERUSED:
 438         case F_GB13_NOLONGERUSED:
 439         case F_GB14_NOLONGERUSED:
 440             break;
 441         default:
 442             gmx_fatal(FARGS, "unknown function type %d in %s line %d",
 443                       ftype, __FILE__, __LINE__);
 444     }
 445     return 0;
 446 }
 447
 448 static int enter_params(gmx_ffparams_t *ffparams, t_functype ftype,
 449                         gmx::ArrayRef<const real> forceparams, int comb, real reppow,
 450                         int start, bool bAppend)
 451 {
 452     t_iparams newparam;
 453     int       type;
 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         for (type = start; (type < ffparams->numTypes()); type++)
 465         {
 466             if (ffparams->functype[type] == ftype)
 467             {
 468                 if (memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 469                 {
 470                     return type;
 471                 }
 472             }
 473         }
 474     }
 475     else
 476     {
 477         type = ffparams->numTypes();
 478     }
 479
 480     ffparams->iparams.push_back(newparam);
 481     ffparams->functype.push_back(ftype);
 482
 483     GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(),
 484                "sizes should match");
 485
 486     return type;
 487 }
 488
 489 static void append_interaction(InteractionList *ilist,
 490                                int type, gmx::ArrayRef<const int> a)
 491 {
 492     ilist->iatoms.push_back(type);
 493     for (const auto &atom : a)
 494     {
 495         ilist->iatoms.push_back(atom);
 496     }
 497 }
 498
 499 static void enter_function(const InteractionsOfType *p, t_functype ftype, int comb, real reppow,
 500                            gmx_ffparams_t *ffparams, InteractionList *il,
 501                            bool bNB, bool bAppend)
 502 {
 503     int start = ffparams->numTypes();
 504
 505     for (auto &parm : p->interactionTypes)
 506     {
 507         int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
 508         /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
 509         if (!bNB && type >= 0)
 510         {
 511             GMX_RELEASE_ASSERT(il, "Need valid interaction list");
 512             GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype), "Need to have correct number of atoms for the parameter");
 513             append_interaction(il, type, parm.atoms());
 514         }
 515     }
 516 }
 517
 518 void convertInteractionsOfType(int atnr, gmx::ArrayRef<const InteractionsOfType> nbtypes,
 519                                gmx::ArrayRef<const MoleculeInformation> mi,
 520                                const MoleculeInformation *intermolecular_interactions,
 521                                int comb, double reppow, real fudgeQQ,
 522                                gmx_mtop_t *mtop)
 523 {
 524     int             i;
 525     unsigned long   flags;
 526     gmx_ffparams_t *ffp;
 527     gmx_moltype_t  *molt;
 528
 529     ffp           = &mtop->ffparams;
 530     ffp->atnr     = atnr;
 531     ffp->functype.clear();
 532     ffp->iparams.clear();
 533     ffp->reppow   = reppow;
 534
 535     enter_function(&(nbtypes[F_LJ]),  static_cast<t_functype>(F_LJ),    comb, reppow, ffp, nullptr,
 536                    TRUE, TRUE);
 537     enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM),  comb, reppow, ffp, nullptr,
 538                    TRUE, TRUE);
 539
 540     for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 541     {
 542         molt = &mtop->moltype[mt];
 543         for (i = 0; (i < F_NRE); i++)
 544         {
 545             molt->ilist[i].iatoms.clear();
 546
 547             gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
 548
 549             flags = interaction_function[i].flags;
 550             if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
 551                                                  (flags & IF_VSITE) ||
 552                                                  (flags & IF_CONSTRAINT)))
 553             {
 554                 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
 555                                ffp, &molt->ilist[i],
 556                                FALSE, (i == F_POSRES  || i == F_FBPOSRES));
 557             }
 558         }
 559     }
 560
 561     mtop->bIntermolecularInteractions = FALSE;
 562     if (intermolecular_interactions != nullptr)
 563     {
 564         /* Process the intermolecular interaction list */
 565         mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
 566
 567         for (i = 0; (i < F_NRE); i++)
 568         {
 569             (*mtop->intermolecular_ilist)[i].iatoms.clear();
 570
 571             gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
 572
 573             if (!interactions[i].interactionTypes.empty())
 574             {
 575                 flags = interaction_function[i].flags;
 576                 /* For intermolecular interactions we (currently)
 577                  * only support potentials.
 578                  * Constraints and virtual sites would be possible,
 579                  * but require a lot of extra (bug-prone) code.
 580                  */
 581                 if (!(flags & IF_BOND))
 582                 {
 583                     gmx_fatal(FARGS, "The intermolecular_interaction section may only contain bonded potentials");
 584                 }
 585                 else if (NRAL(i) == 1) /* e.g. position restraints */
 586                 {
 587                     gmx_fatal(FARGS, "Single atom interactions don't make sense in the intermolecular_interaction section, you can put them in the moleculetype section");
 588                 }
 589                 else if (flags & IF_CHEMBOND)
 590                 {
 591                     gmx_fatal(FARGS, "The intermolecular_interaction can not contain chemically bonding interactions");
 592                 }
 593                 else
 594                 {
 595                     enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
 596                                    ffp, &(*mtop->intermolecular_ilist)[i],
 597                                    FALSE, FALSE);
 598
 599                     mtop->bIntermolecularInteractions = TRUE;
 600                 }
 601             }
 602         }
 603
 604         if (!mtop->bIntermolecularInteractions)
 605         {
 606             mtop->intermolecular_ilist.reset(nullptr);
 607         }
 608     }
 609
 610     ffp->fudgeQQ = fudgeQQ;
 611 }