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
  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(int comb, double reppow, double v, double w, real* c6, real* c12)
  90 {
  91     if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
  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, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
 116 {
 117     bool all_param_zero = true;
 118
 119     /* Set to zero */
 120     for (int j = 0; (j < MAXFORCEPARAM); j++)
 121     {
 122         newparam->generic.buf[j] = 0.0;
 123         /* If all parameters are zero we might not add some interaction types (selected below).
 124          * We cannot apply this to ALL interactions, since many have valid reasons for having
 125          * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
 126          * we use it for angles and torsions that are typically generated automatically.
 127          */
 128         all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
 129     }
 130
 131     if (all_param_zero)
 132     {
 133         if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
 134             || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
 135         {
 136             return -1;
 137         }
 138     }
 139
 140     switch (ftype)
 141     {
 142         case F_G96ANGLES:
 143             /* Post processing of input data: store cosine iso angle itself */
 144             newparam->harmonic.rA  = cos(old[0] * DEG2RAD);
 145             newparam->harmonic.krA = old[1];
 146             newparam->harmonic.rB  = cos(old[2] * DEG2RAD);
 147             newparam->harmonic.krB = old[3];
 148             break;
 149         case F_G96BONDS:
 150             /* Post processing of input data: store square of length itself */
 151             newparam->harmonic.rA  = gmx::square(old[0]);
 152             newparam->harmonic.krA = old[1];
 153             newparam->harmonic.rB  = gmx::square(old[2]);
 154             newparam->harmonic.krB = old[3];
 155             break;
 156         case F_FENEBONDS:
 157             newparam->fene.bm = old[0];
 158             newparam->fene.kb = old[1];
 159             break;
 160         case F_RESTRBONDS:
 161             newparam->restraint.lowA = old[0];
 162             newparam->restraint.up1A = old[1];
 163             newparam->restraint.up2A = old[2];
 164             newparam->restraint.kA   = old[3];
 165             newparam->restraint.lowB = old[4];
 166             newparam->restraint.up1B = old[5];
 167             newparam->restraint.up2B = old[6];
 168             newparam->restraint.kB   = old[7];
 169             break;
 170         case F_TABBONDS:
 171         case F_TABBONDSNC:
 172         case F_TABANGLES:
 173         case F_TABDIHS:
 174             newparam->tab.table = round_check(old[0], 0, ftype, "table index");
 175             newparam->tab.kA    = old[1];
 176             newparam->tab.kB    = old[3];
 177             break;
 178         case F_CROSS_BOND_BONDS:
 179             newparam->cross_bb.r1e = old[0];
 180             newparam->cross_bb.r2e = old[1];
 181             newparam->cross_bb.krr = old[2];
 182             break;
 183         case F_CROSS_BOND_ANGLES:
 184             newparam->cross_ba.r1e = old[0];
 185             newparam->cross_ba.r2e = old[1];
 186             newparam->cross_ba.r3e = old[2];
 187             newparam->cross_ba.krt = old[3];
 188             break;
 189         case F_UREY_BRADLEY:
 190             newparam->u_b.thetaA  = old[0];
 191             newparam->u_b.kthetaA = old[1];
 192             newparam->u_b.r13A    = old[2];
 193             newparam->u_b.kUBA    = old[3];
 194             newparam->u_b.thetaB  = old[4];
 195             newparam->u_b.kthetaB = old[5];
 196             newparam->u_b.r13B    = old[6];
 197             newparam->u_b.kUBB    = old[7];
 198             break;
 199         case F_QUARTIC_ANGLES:
 200             newparam->qangle.theta = old[0];
 201             for (int i = 0; i < 5; i++)
 202             {
 203                 newparam->qangle.c[i] = old[i + 1];
 204             }
 205             break;
 206         case F_LINEAR_ANGLES:
 207             newparam->linangle.aA    = old[0];
 208             newparam->linangle.klinA = old[1];
 209             newparam->linangle.aB    = old[2];
 210             newparam->linangle.klinB = old[3];
 211             break;
 212         case F_BONDS:
 213         case F_ANGLES:
 214         case F_HARMONIC:
 215         case F_IDIHS:
 216             newparam->harmonic.rA  = old[0];
 217             newparam->harmonic.krA = old[1];
 218             newparam->harmonic.rB  = old[2];
 219             newparam->harmonic.krB = old[3];
 220             break;
 221         case F_RESTRANGLES:
 222             newparam->harmonic.rA  = old[0];
 223             newparam->harmonic.krA = old[1];
 224             break;
 225         case F_MORSE:
 226             newparam->morse.b0A   = old[0];
 227             newparam->morse.cbA   = old[1];
 228             newparam->morse.betaA = old[2];
 229             newparam->morse.b0B   = old[3];
 230             newparam->morse.cbB   = old[4];
 231             newparam->morse.betaB = old[5];
 232             break;
 233         case F_CUBICBONDS:
 234             newparam->cubic.b0   = old[0];
 235             newparam->cubic.kb   = old[1];
 236             newparam->cubic.kcub = old[2];
 237             break;
 238         case F_CONNBONDS: break;
 239         case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
 240         case F_ANHARM_POL:
 241             newparam->anharm_polarize.alpha = old[0];
 242             newparam->anharm_polarize.drcut = old[1];
 243             newparam->anharm_polarize.khyp  = old[2];
 244             break;
 245         case F_WATER_POL:
 246             newparam->wpol.al_x = old[0];
 247             newparam->wpol.al_y = old[1];
 248             newparam->wpol.al_z = old[2];
 249             newparam->wpol.rOH  = old[3];
 250             newparam->wpol.rHH  = old[4];
 251             newparam->wpol.rOD  = old[5];
 252             break;
 253         case F_THOLE_POL:
 254             newparam->thole.a      = old[0];
 255             newparam->thole.alpha1 = old[1];
 256             newparam->thole.alpha2 = old[2];
 257             if ((old[1] > 0) && (old[2] > 0))
 258             {
 259                 newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
 260             }
 261             else
 262             {
 263                 newparam->thole.rfac = 1;
 264             }
 265             break;
 266         case F_BHAM:
 267             newparam->bham.a = old[0];
 268             newparam->bham.b = old[1];
 269             newparam->bham.c = old[2];
 270             break;
 271         case F_LJ14:
 272             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
 273             set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
 274             break;
 275         case F_LJC14_Q:
 276             newparam->ljc14.fqq = old[0];
 277             newparam->ljc14.qi  = old[1];
 278             newparam->ljc14.qj  = old[2];
 279             set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
 280             break;
 281         case F_LJC_PAIRS_NB:
 282             newparam->ljcnb.qi = old[0];
 283             newparam->ljcnb.qj = old[1];
 284             set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
 285             break;
 286         case F_LJ:
 287             set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
 288             break;
 289         case F_PDIHS:
 290         case F_PIDIHS:
 291         case F_ANGRES:
 292         case F_ANGRESZ:
 293             newparam->pdihs.phiA = old[0];
 294             newparam->pdihs.cpA  = old[1];
 295
 296             /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
 297              * so I have changed the lower limit to -99 /EL
 298              */
 299             newparam->pdihs.phiB = old[3];
 300             newparam->pdihs.cpB  = old[4];
 301             /* If both force constants are zero there is no interaction. Return -1 to signal
 302              * this entry should NOT be added.
 303              */
 304             if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
 305             {
 306                 return -1;
 307             }
 308
 309             newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
 310
 311             break;
 312         case F_RESTRDIHS:
 313             newparam->pdihs.phiA = old[0];
 314             newparam->pdihs.cpA  = old[1];
 315             break;
 316         case F_POSRES:
 317             newparam->posres.fcA[XX]   = old[0];
 318             newparam->posres.fcA[YY]   = old[1];
 319             newparam->posres.fcA[ZZ]   = old[2];
 320             newparam->posres.fcB[XX]   = old[3];
 321             newparam->posres.fcB[YY]   = old[4];
 322             newparam->posres.fcB[ZZ]   = old[5];
 323             newparam->posres.pos0A[XX] = old[6];
 324             newparam->posres.pos0A[YY] = old[7];
 325             newparam->posres.pos0A[ZZ] = old[8];
 326             newparam->posres.pos0B[XX] = old[9];
 327             newparam->posres.pos0B[YY] = old[10];
 328             newparam->posres.pos0B[ZZ] = old[11];
 329             break;
 330         case F_FBPOSRES:
 331             newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
 332             if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
 333             {
 334                 gmx_fatal(FARGS,
 335                           "Invalid geometry for flat-bottomed position restraint.\n"
 336                           "Expected number between 1 and %d. Found %d\n",
 337                           efbposresNR - 1,
 338                           newparam->fbposres.geom);
 339             }
 340             newparam->fbposres.r        = old[1];
 341             newparam->fbposres.k        = old[2];
 342             newparam->fbposres.pos0[XX] = old[3];
 343             newparam->fbposres.pos0[YY] = old[4];
 344             newparam->fbposres.pos0[ZZ] = old[5];
 345             break;
 346         case F_DISRES:
 347             newparam->disres.label = round_check(old[0], 0, ftype, "label");
 348             newparam->disres.type  = round_check(old[1], 1, ftype, "type'");
 349             newparam->disres.low   = old[2];
 350             newparam->disres.up1   = old[3];
 351             newparam->disres.up2   = old[4];
 352             newparam->disres.kfac  = old[5];
 353             break;
 354         case F_ORIRES:
 355             newparam->orires.ex    = round_check(old[0], 1, ftype, "experiment") - 1;
 356             newparam->orires.label = round_check(old[1], 1, ftype, "label");
 357             newparam->orires.power = round_check(old[2], 0, ftype, "power");
 358             newparam->orires.c     = old[3];
 359             newparam->orires.obs   = old[4];
 360             newparam->orires.kfac  = old[5];
 361             break;
 362         case F_DIHRES:
 363             newparam->dihres.phiA  = old[0];
 364             newparam->dihres.dphiA = old[1];
 365             newparam->dihres.kfacA = old[2];
 366             newparam->dihres.phiB  = old[3];
 367             newparam->dihres.dphiB = old[4];
 368             newparam->dihres.kfacB = old[5];
 369             break;
 370         case F_RBDIHS:
 371             for (int i = 0; (i < NR_RBDIHS); i++)
 372             {
 373                 newparam->rbdihs.rbcA[i] = old[i];
 374                 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
 375             }
 376             break;
 377         case F_CBTDIHS:
 378             for (int i = 0; (i < NR_CBTDIHS); i++)
 379             {
 380                 newparam->cbtdihs.cbtcA[i] = old[i];
 381             }
 382             break;
 383         case F_FOURDIHS:
 384             /* Read the dihedral parameters to temporary arrays,
 385              * and convert them to the computationally faster
 386              * Ryckaert-Bellemans form.
 387              */
 388             /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
 389             newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
 390             newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
 391             newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
 392             newparam->rbdihs.rbcA[3] = -2.0 * old[2];
 393             newparam->rbdihs.rbcA[4] = -4.0 * old[3];
 394             newparam->rbdihs.rbcA[5] = 0.0;
 395
 396             newparam->rbdihs.rbcB[0] =
 397                     old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
 398             newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
 399             newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
 400             newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
 401             newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
 402             newparam->rbdihs.rbcB[5] = 0.0;
 403             break;
 404         case F_CONSTR:
 405         case F_CONSTRNC:
 406             newparam->constr.dA = old[0];
 407             newparam->constr.dB = old[1];
 408             break;
 409         case F_SETTLE:
 410             newparam->settle.doh = old[0];
 411             newparam->settle.dhh = old[1];
 412             break;
 413         case F_VSITE1:
 414         case F_VSITE2:
 415         case F_VSITE2FD:
 416         case F_VSITE3:
 417         case F_VSITE3FD:
 418         case F_VSITE3OUT:
 419         case F_VSITE4FD:
 420         case F_VSITE4FDN:
 421             newparam->vsite.a = old[0];
 422             newparam->vsite.b = old[1];
 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_VSITE3FAD:
 429             newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
 430             newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
 431             newparam->vsite.c = old[2];
 432             newparam->vsite.d = old[3];
 433             newparam->vsite.e = old[4];
 434             newparam->vsite.f = old[5];
 435             break;
 436         case F_VSITEN:
 437             newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
 438             newparam->vsiten.a = old[1];
 439             break;
 440         case F_CMAP:
 441             newparam->cmap.cmapA = static_cast<int>(old[0]);
 442             newparam->cmap.cmapB = static_cast<int>(old[1]);
 443             break;
 444         case F_GB12_NOLONGERUSED:
 445         case F_GB13_NOLONGERUSED:
 446         case F_GB14_NOLONGERUSED: break;
 447         default:
 448             gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
 449     }
 450     return 0;
 451 }
 452
 453 static int enter_params(gmx_ffparams_t*           ffparams,
 454                         t_functype                ftype,
 455                         gmx::ArrayRef<const real> forceparams,
 456                         int                       comb,
 457                         real                      reppow,
 458                         int                       start,
 459                         bool                      bAppend)
 460 {
 461     t_iparams newparam;
 462     int       rc;
 463
 464     if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
 465     {
 466         /* -1 means this interaction is all-zero and should not be added */
 467         return rc;
 468     }
 469
 470     if (!bAppend)
 471     {
 472         if (ftype != F_DISRES)
 473         {
 474             for (int type = start; type < ffparams->numTypes(); type++)
 475             {
 476                 // Note that the first condition is always met by starting the loop at start
 477                 if (ffparams->functype[type] == ftype
 478                     && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 479                 {
 480                     return type;
 481                 }
 482             }
 483         }
 484         else
 485         {
 486             // Distance restraints should have unique labels and pairs with the same label
 487             // should be consecutive, so we here we only need to check the last type in the list.
 488             // This changes the complexity from quadratic to linear in the number of restraints.
 489             const int type = ffparams->numTypes() - 1;
 490             if (type >= 0 && ffparams->functype[type] == ftype
 491                 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
 492             {
 493                 return type;
 494             }
 495         }
 496     }
 497
 498     const int type = ffparams->numTypes();
 499
 500     ffparams->iparams.push_back(newparam);
 501     ffparams->functype.push_back(ftype);
 502
 503     GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
 504
 505     return type;
 506 }
 507
 508 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
 509 {
 510     ilist->iatoms.push_back(type);
 511     for (const auto& atom : a)
 512     {
 513         ilist->iatoms.push_back(atom);
 514     }
 515 }
 516
 517 static void enter_function(const InteractionsOfType* p,
 518                            t_functype                ftype,
 519                            int                       comb,
 520                            real                      reppow,
 521                            gmx_ffparams_t*           ffparams,
 522                            InteractionList*          il,
 523                            bool                      bNB,
 524                            bool                      bAppend)
 525 {
 526     int start = ffparams->numTypes();
 527
 528     for (auto& parm : p->interactionTypes)
 529     {
 530         int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
 531         /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
 532         if (!bNB && type >= 0)
 533         {
 534             GMX_RELEASE_ASSERT(il, "Need valid interaction list");
 535             GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
 536                                "Need to have correct number of atoms for the parameter");
 537             append_interaction(il, type, parm.atoms());
 538         }
 539     }
 540 }
 541
 542 void convertInteractionsOfType(int                                      atnr,
 543                                gmx::ArrayRef<const InteractionsOfType>  nbtypes,
 544                                gmx::ArrayRef<const MoleculeInformation> mi,
 545                                const MoleculeInformation*               intermolecular_interactions,
 546                                int                                      comb,
 547                                double                                   reppow,
 548                                real                                     fudgeQQ,
 549                                gmx_mtop_t*                              mtop)
 550 {
 551     int             i;
 552     unsigned long   flags;
 553     gmx_ffparams_t* ffp;
 554     gmx_moltype_t*  molt;
 555
 556     ffp       = &mtop->ffparams;
 557     ffp->atnr = atnr;
 558     ffp->functype.clear();
 559     ffp->iparams.clear();
 560     ffp->reppow = reppow;
 561
 562     enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
 563     enter_function(
 564             &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);
 565
 566     for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
 567     {
 568         molt = &mtop->moltype[mt];
 569         for (i = 0; (i < F_NRE); i++)
 570         {
 571             molt->ilist[i].iatoms.clear();
 572
 573             gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
 574
 575             flags = interaction_function[i].flags;
 576             if ((i != F_LJ) && (i != F_BHAM)
 577                 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
 578             {
 579                 enter_function(&(interactions[i]),
 580                                static_cast<t_functype>(i),
 581                                comb,
 582                                reppow,
 583                                ffp,
 584                                &molt->ilist[i],
 585                                FALSE,
 586                                (i == F_POSRES || i == F_FBPOSRES));
 587             }
 588         }
 589     }
 590
 591     mtop->bIntermolecularInteractions = FALSE;
 592     if (intermolecular_interactions != nullptr)
 593     {
 594         /* Process the intermolecular interaction list */
 595         mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
 596
 597         for (i = 0; (i < F_NRE); i++)
 598         {
 599             (*mtop->intermolecular_ilist)[i].iatoms.clear();
 600
 601             gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
 602
 603             if (!interactions[i].interactionTypes.empty())
 604             {
 605                 flags = interaction_function[i].flags;
 606                 /* For intermolecular interactions we (currently)
 607                  * only support potentials.
 608                  * Constraints and virtual sites would be possible,
 609                  * but require a lot of extra (bug-prone) code.
 610                  */
 611                 if (!(flags & IF_BOND))
 612                 {
 613                     gmx_fatal(FARGS,
 614                               "The intermolecular_interaction section may only contain bonded "
 615                               "potentials");
 616                 }
 617                 else if (NRAL(i) == 1) /* e.g. position restraints */
 618                 {
 619                     gmx_fatal(FARGS,
 620                               "Single atom interactions don't make sense in the "
 621                               "intermolecular_interaction section, you can put them in the "
 622                               "moleculetype section");
 623                 }
 624                 else if (flags & IF_CHEMBOND)
 625                 {
 626                     gmx_fatal(FARGS,
 627                               "The intermolecular_interaction can not contain chemically bonding "
 628                               "interactions");
 629                 }
 630                 else
 631                 {
 632                     enter_function(&(interactions[i]),
 633                                    static_cast<t_functype>(i),
 634                                    comb,
 635                                    reppow,
 636                                    ffp,
 637                                    &(*mtop->intermolecular_ilist)[i],
 638                                    FALSE,
 639                                    FALSE);
 640
 641                     mtop->bIntermolecularInteractions = TRUE;
 642                 }
 643             }
 644         }
 645
 646         if (!mtop->bIntermolecularInteractions)
 647         {
 648             mtop->intermolecular_ilist.reset(nullptr);
 649         }
 650     }
 651
 652     ffp->fudgeQQ = fudgeQQ;
 653 }