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38 /* This file is completely threadsafe - keep it that way! */
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"
63 static int round_check(real r, int limit, int ftype, const char* name)
65 const int i = gmx::roundToInt(r);
67 if (r - i > 0.01 || r - i < -0.01)
69 gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s", r, name,
70 interaction_function[ftype].longname);
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);
82 static void set_ljparams(int comb, double reppow, double v, double w, real* c6, real* c12)
84 if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
88 *c6 = 4 * w * gmx::power6(v);
89 *c12 = 4 * w * std::pow(v, reppow);
93 /* Interpret negative sigma as c6=0 and c12 with -sigma */
95 *c12 = 4 * w * std::pow(-v, reppow);
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.
108 static int assign_param(t_functype ftype, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
110 bool all_param_zero = true;
113 for (int j = 0; (j < MAXFORCEPARAM); j++)
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.
121 all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
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)
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];
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];
150 newparam->fene.bm = old[0];
151 newparam->fene.kb = old[1];
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];
167 newparam->tab.table = round_check(old[0], 0, ftype, "table index");
168 newparam->tab.kA = old[1];
169 newparam->tab.kB = old[3];
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];
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];
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];
192 case F_QUARTIC_ANGLES:
193 newparam->qangle.theta = old[0];
194 for (int i = 0; i < 5; i++)
196 newparam->qangle.c[i] = old[i + 1];
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];
209 newparam->harmonic.rA = old[0];
210 newparam->harmonic.krA = old[1];
211 newparam->harmonic.rB = old[2];
212 newparam->harmonic.krB = old[3];
215 newparam->harmonic.rA = old[0];
216 newparam->harmonic.krA = old[1];
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];
227 newparam->cubic.b0 = old[0];
228 newparam->cubic.kb = old[1];
229 newparam->cubic.kcub = old[2];
231 case F_CONNBONDS: break;
232 case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
234 newparam->anharm_polarize.alpha = old[0];
235 newparam->anharm_polarize.drcut = old[1];
236 newparam->anharm_polarize.khyp = old[2];
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];
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))
252 newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
256 newparam->thole.rfac = 1;
260 newparam->bham.a = old[0];
261 newparam->bham.b = old[1];
262 newparam->bham.c = old[2];
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);
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);
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);
280 set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
286 newparam->pdihs.phiA = old[0];
287 newparam->pdihs.cpA = old[1];
289 /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
290 * so I have changed the lower limit to -99 /EL
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.
297 if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
302 newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
306 newparam->pdihs.phiA = old[0];
307 newparam->pdihs.cpA = old[1];
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];
324 newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
325 if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
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);
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];
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];
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];
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];
363 for (int i = 0; (i < NR_RBDIHS); i++)
365 newparam->rbdihs.rbcA[i] = old[i];
366 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
370 for (int i = 0; (i < NR_CBTDIHS); i++)
372 newparam->cbtdihs.cbtcA[i] = old[i];
376 /* Read the dihedral parameters to temporary arrays,
377 * and convert them to the computationally faster
378 * Ryckaert-Bellemans form.
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;
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;
398 newparam->constr.dA = old[0];
399 newparam->constr.dB = old[1];
402 newparam->settle.doh = old[0];
403 newparam->settle.dhh = old[1];
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];
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];
429 newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
430 newparam->vsiten.a = old[1];
433 newparam->cmap.cmapA = static_cast<int>(old[0]);
434 newparam->cmap.cmapB = static_cast<int>(old[1]);
436 case F_GB12_NOLONGERUSED:
437 case F_GB13_NOLONGERUSED:
438 case F_GB14_NOLONGERUSED: break;
440 gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
445 static int enter_params(gmx_ffparams_t* ffparams,
447 gmx::ArrayRef<const real> forceparams,
457 if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
459 /* -1 means this interaction is all-zero and should not be added */
465 for (type = start; (type < ffparams->numTypes()); type++)
467 if (ffparams->functype[type] == ftype)
469 if (memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
478 type = ffparams->numTypes();
481 ffparams->iparams.push_back(newparam);
482 ffparams->functype.push_back(ftype);
484 GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
489 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
491 ilist->iatoms.push_back(type);
492 for (const auto& atom : a)
494 ilist->iatoms.push_back(atom);
498 static void enter_function(const InteractionsOfType* p,
502 gmx_ffparams_t* ffparams,
507 int start = ffparams->numTypes();
509 for (auto& parm : p->interactionTypes)
511 int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
512 /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
513 if (!bNB && type >= 0)
515 GMX_RELEASE_ASSERT(il, "Need valid interaction list");
516 GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
517 "Need to have correct number of atoms for the parameter");
518 append_interaction(il, type, parm.atoms());
523 void convertInteractionsOfType(int atnr,
524 gmx::ArrayRef<const InteractionsOfType> nbtypes,
525 gmx::ArrayRef<const MoleculeInformation> mi,
526 const MoleculeInformation* intermolecular_interactions,
537 ffp = &mtop->ffparams;
539 ffp->functype.clear();
540 ffp->iparams.clear();
541 ffp->reppow = reppow;
543 enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
544 enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
547 for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
549 molt = &mtop->moltype[mt];
550 for (i = 0; (i < F_NRE); i++)
552 molt->ilist[i].iatoms.clear();
554 gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
556 flags = interaction_function[i].flags;
557 if ((i != F_LJ) && (i != F_BHAM)
558 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
560 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow, ffp,
561 &molt->ilist[i], FALSE, (i == F_POSRES || i == F_FBPOSRES));
566 mtop->bIntermolecularInteractions = FALSE;
567 if (intermolecular_interactions != nullptr)
569 /* Process the intermolecular interaction list */
570 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
572 for (i = 0; (i < F_NRE); i++)
574 (*mtop->intermolecular_ilist)[i].iatoms.clear();
576 gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
578 if (!interactions[i].interactionTypes.empty())
580 flags = interaction_function[i].flags;
581 /* For intermolecular interactions we (currently)
582 * only support potentials.
583 * Constraints and virtual sites would be possible,
584 * but require a lot of extra (bug-prone) code.
586 if (!(flags & IF_BOND))
589 "The intermolecular_interaction section may only contain bonded "
592 else if (NRAL(i) == 1) /* e.g. position restraints */
595 "Single atom interactions don't make sense in the "
596 "intermolecular_interaction section, you can put them in the "
597 "moleculetype section");
599 else if (flags & IF_CHEMBOND)
602 "The intermolecular_interaction can not contain chemically bonding "
607 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
608 ffp, &(*mtop->intermolecular_ilist)[i], FALSE, FALSE);
610 mtop->bIntermolecularInteractions = TRUE;
615 if (!mtop->bIntermolecularInteractions)
617 mtop->intermolecular_ilist.reset(nullptr);
621 ffp->fudgeQQ = fudgeQQ;