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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)
70 "A non-integer value (%f) was supplied for '%s' in %s",
73 interaction_function[ftype].longname);
79 "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
81 interaction_function[ftype].longname,
89 static void set_ljparams(CombinationRule comb, double reppow, double v, double w, real* c6, real* c12)
91 if (comb == CombinationRule::Arithmetic || comb == CombinationRule::GeomSigEps)
95 *c6 = 4 * w * gmx::power6(v);
96 *c12 = 4 * w * std::pow(v, reppow);
100 /* Interpret negative sigma as c6=0 and c12 with -sigma */
102 *c12 = 4 * w * std::pow(-v, reppow);
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.
115 static int assign_param(t_functype ftype,
117 gmx::ArrayRef<const real> old,
118 CombinationRule comb,
121 bool all_param_zero = true;
124 for (int j = 0; (j < MAXFORCEPARAM); j++)
126 newparam->generic.buf[j] = 0.0;
127 /* If all parameters are zero we might not add some interaction types (selected below).
128 * We cannot apply this to ALL interactions, since many have valid reasons for having
129 * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
130 * we use it for angles and torsions that are typically generated automatically.
132 all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
137 if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS || ftype == F_PDIHS
138 || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
147 /* Post processing of input data: store cosine iso angle itself */
148 newparam->harmonic.rA = cos(old[0] * gmx::c_deg2Rad);
149 newparam->harmonic.krA = old[1];
150 newparam->harmonic.rB = cos(old[2] * gmx::c_deg2Rad);
151 newparam->harmonic.krB = old[3];
154 /* Post processing of input data: store square of length itself */
155 newparam->harmonic.rA = gmx::square(old[0]);
156 newparam->harmonic.krA = old[1];
157 newparam->harmonic.rB = gmx::square(old[2]);
158 newparam->harmonic.krB = old[3];
161 newparam->fene.bm = old[0];
162 newparam->fene.kb = old[1];
165 newparam->restraint.lowA = old[0];
166 newparam->restraint.up1A = old[1];
167 newparam->restraint.up2A = old[2];
168 newparam->restraint.kA = old[3];
169 newparam->restraint.lowB = old[4];
170 newparam->restraint.up1B = old[5];
171 newparam->restraint.up2B = old[6];
172 newparam->restraint.kB = old[7];
178 newparam->tab.table = round_check(old[0], 0, ftype, "table index");
179 newparam->tab.kA = old[1];
180 newparam->tab.kB = old[3];
182 case F_CROSS_BOND_BONDS:
183 newparam->cross_bb.r1e = old[0];
184 newparam->cross_bb.r2e = old[1];
185 newparam->cross_bb.krr = old[2];
187 case F_CROSS_BOND_ANGLES:
188 newparam->cross_ba.r1e = old[0];
189 newparam->cross_ba.r2e = old[1];
190 newparam->cross_ba.r3e = old[2];
191 newparam->cross_ba.krt = old[3];
194 newparam->u_b.thetaA = old[0];
195 newparam->u_b.kthetaA = old[1];
196 newparam->u_b.r13A = old[2];
197 newparam->u_b.kUBA = old[3];
198 newparam->u_b.thetaB = old[4];
199 newparam->u_b.kthetaB = old[5];
200 newparam->u_b.r13B = old[6];
201 newparam->u_b.kUBB = old[7];
203 case F_QUARTIC_ANGLES:
204 newparam->qangle.theta = old[0];
205 for (int i = 0; i < 5; i++)
207 newparam->qangle.c[i] = old[i + 1];
210 case F_LINEAR_ANGLES:
211 newparam->linangle.aA = old[0];
212 newparam->linangle.klinA = old[1];
213 newparam->linangle.aB = old[2];
214 newparam->linangle.klinB = old[3];
220 newparam->harmonic.rA = old[0];
221 newparam->harmonic.krA = old[1];
222 newparam->harmonic.rB = old[2];
223 newparam->harmonic.krB = old[3];
226 newparam->harmonic.rA = old[0];
227 newparam->harmonic.krA = old[1];
230 newparam->morse.b0A = old[0];
231 newparam->morse.cbA = old[1];
232 newparam->morse.betaA = old[2];
233 newparam->morse.b0B = old[3];
234 newparam->morse.cbB = old[4];
235 newparam->morse.betaB = old[5];
238 newparam->cubic.b0 = old[0];
239 newparam->cubic.kb = old[1];
240 newparam->cubic.kcub = old[2];
242 case F_CONNBONDS: break;
243 case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
245 newparam->anharm_polarize.alpha = old[0];
246 newparam->anharm_polarize.drcut = old[1];
247 newparam->anharm_polarize.khyp = old[2];
250 newparam->wpol.al_x = old[0];
251 newparam->wpol.al_y = old[1];
252 newparam->wpol.al_z = old[2];
253 newparam->wpol.rOH = old[3];
254 newparam->wpol.rHH = old[4];
255 newparam->wpol.rOD = old[5];
258 newparam->thole.a = old[0];
259 newparam->thole.alpha1 = old[1];
260 newparam->thole.alpha2 = old[2];
261 if ((old[1] > 0) && (old[2] > 0))
263 newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
267 newparam->thole.rfac = 1;
271 newparam->bham.a = old[0];
272 newparam->bham.b = old[1];
273 newparam->bham.c = old[2];
276 set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
277 set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
280 newparam->ljc14.fqq = old[0];
281 newparam->ljc14.qi = old[1];
282 newparam->ljc14.qj = old[2];
283 set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
286 newparam->ljcnb.qi = old[0];
287 newparam->ljcnb.qj = old[1];
288 set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
291 set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
297 newparam->pdihs.phiA = old[0];
298 newparam->pdihs.cpA = old[1];
300 /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
301 * so I have changed the lower limit to -99 /EL
303 newparam->pdihs.phiB = old[3];
304 newparam->pdihs.cpB = old[4];
305 /* If both force constants are zero there is no interaction. Return -1 to signal
306 * this entry should NOT be added.
308 if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
313 newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
317 newparam->pdihs.phiA = old[0];
318 newparam->pdihs.cpA = old[1];
321 newparam->posres.fcA[XX] = old[0];
322 newparam->posres.fcA[YY] = old[1];
323 newparam->posres.fcA[ZZ] = old[2];
324 newparam->posres.fcB[XX] = old[3];
325 newparam->posres.fcB[YY] = old[4];
326 newparam->posres.fcB[ZZ] = old[5];
327 newparam->posres.pos0A[XX] = old[6];
328 newparam->posres.pos0A[YY] = old[7];
329 newparam->posres.pos0A[ZZ] = old[8];
330 newparam->posres.pos0B[XX] = old[9];
331 newparam->posres.pos0B[YY] = old[10];
332 newparam->posres.pos0B[ZZ] = old[11];
335 newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
336 if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
339 "Invalid geometry for flat-bottomed position restraint.\n"
340 "Expected number between 1 and %d. Found %d\n",
342 newparam->fbposres.geom);
344 newparam->fbposres.r = old[1];
345 newparam->fbposres.k = old[2];
346 newparam->fbposres.pos0[XX] = old[3];
347 newparam->fbposres.pos0[YY] = old[4];
348 newparam->fbposres.pos0[ZZ] = old[5];
351 newparam->disres.label = round_check(old[0], 0, ftype, "label");
352 newparam->disres.type = round_check(old[1], 1, ftype, "type'");
353 newparam->disres.low = old[2];
354 newparam->disres.up1 = old[3];
355 newparam->disres.up2 = old[4];
356 newparam->disres.kfac = old[5];
359 newparam->orires.ex = round_check(old[0], 1, ftype, "experiment") - 1;
360 newparam->orires.label = round_check(old[1], 1, ftype, "label");
361 newparam->orires.power = round_check(old[2], 0, ftype, "power");
362 newparam->orires.c = old[3];
363 newparam->orires.obs = old[4];
364 newparam->orires.kfac = old[5];
367 newparam->dihres.phiA = old[0];
368 newparam->dihres.dphiA = old[1];
369 newparam->dihres.kfacA = old[2];
370 newparam->dihres.phiB = old[3];
371 newparam->dihres.dphiB = old[4];
372 newparam->dihres.kfacB = old[5];
375 for (int i = 0; (i < NR_RBDIHS); i++)
377 newparam->rbdihs.rbcA[i] = old[i];
378 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
382 for (int i = 0; (i < NR_CBTDIHS); i++)
384 newparam->cbtdihs.cbtcA[i] = old[i];
388 /* Read the dihedral parameters to temporary arrays,
389 * and convert them to the computationally faster
390 * Ryckaert-Bellemans form.
392 /* Use conversion formula for OPLS to Ryckaert-Bellemans: */
393 newparam->rbdihs.rbcA[0] = old[1] + 0.5 * (old[0] + old[2]);
394 newparam->rbdihs.rbcA[1] = 0.5 * (3.0 * old[2] - old[0]);
395 newparam->rbdihs.rbcA[2] = 4.0 * old[3] - old[1];
396 newparam->rbdihs.rbcA[3] = -2.0 * old[2];
397 newparam->rbdihs.rbcA[4] = -4.0 * old[3];
398 newparam->rbdihs.rbcA[5] = 0.0;
400 newparam->rbdihs.rbcB[0] =
401 old[NR_FOURDIHS + 1] + 0.5 * (old[NR_FOURDIHS + 0] + old[NR_FOURDIHS + 2]);
402 newparam->rbdihs.rbcB[1] = 0.5 * (3.0 * old[NR_FOURDIHS + 2] - old[NR_FOURDIHS + 0]);
403 newparam->rbdihs.rbcB[2] = 4.0 * old[NR_FOURDIHS + 3] - old[NR_FOURDIHS + 1];
404 newparam->rbdihs.rbcB[3] = -2.0 * old[NR_FOURDIHS + 2];
405 newparam->rbdihs.rbcB[4] = -4.0 * old[NR_FOURDIHS + 3];
406 newparam->rbdihs.rbcB[5] = 0.0;
410 newparam->constr.dA = old[0];
411 newparam->constr.dB = old[1];
414 newparam->settle.doh = old[0];
415 newparam->settle.dhh = old[1];
425 newparam->vsite.a = old[0];
426 newparam->vsite.b = old[1];
427 newparam->vsite.c = old[2];
428 newparam->vsite.d = old[3];
429 newparam->vsite.e = old[4];
430 newparam->vsite.f = old[5];
433 newparam->vsite.a = old[1] * cos(gmx::c_deg2Rad * old[0]);
434 newparam->vsite.b = old[1] * sin(gmx::c_deg2Rad * old[0]);
435 newparam->vsite.c = old[2];
436 newparam->vsite.d = old[3];
437 newparam->vsite.e = old[4];
438 newparam->vsite.f = old[5];
441 newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
442 newparam->vsiten.a = old[1];
445 newparam->cmap.cmapA = static_cast<int>(old[0]);
446 newparam->cmap.cmapB = static_cast<int>(old[1]);
448 case F_GB12_NOLONGERUSED:
449 case F_GB13_NOLONGERUSED:
450 case F_GB14_NOLONGERUSED: break;
452 gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
457 static int enter_params(gmx_ffparams_t* ffparams,
459 gmx::ArrayRef<const real> forceparams,
460 CombinationRule comb,
468 if ((rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
470 /* -1 means this interaction is all-zero and should not be added */
476 if (ftype != F_DISRES)
478 for (int type = start; type < ffparams->numTypes(); type++)
480 // Note that the first condition is always met by starting the loop at start
481 if (ffparams->functype[type] == ftype
482 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
490 // Distance restraints should have unique labels and pairs with the same label
491 // should be consecutive, so we here we only need to check the last type in the list.
492 // This changes the complexity from quadratic to linear in the number of restraints.
493 const int type = ffparams->numTypes() - 1;
494 if (type >= 0 && ffparams->functype[type] == ftype
495 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
502 const int type = ffparams->numTypes();
504 ffparams->iparams.push_back(newparam);
505 ffparams->functype.push_back(ftype);
507 GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
512 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
514 ilist->iatoms.push_back(type);
515 for (const auto& atom : a)
517 ilist->iatoms.push_back(atom);
521 static void enter_function(const InteractionsOfType* p,
523 CombinationRule comb,
525 gmx_ffparams_t* ffparams,
530 int start = ffparams->numTypes();
532 for (const auto& parm : p->interactionTypes)
534 int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
535 /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
536 if (!bNB && type >= 0)
538 GMX_RELEASE_ASSERT(il, "Need valid interaction list");
539 GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
540 "Need to have correct number of atoms for the parameter");
541 append_interaction(il, type, parm.atoms());
546 void convertInteractionsOfType(int atnr,
547 gmx::ArrayRef<const InteractionsOfType> nbtypes,
548 gmx::ArrayRef<const MoleculeInformation> mi,
549 const MoleculeInformation* intermolecular_interactions,
550 CombinationRule comb,
560 ffp = &mtop->ffparams;
562 ffp->functype.clear();
563 ffp->iparams.clear();
564 ffp->reppow = reppow;
566 enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
568 &(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr, TRUE, TRUE);
570 for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
572 molt = &mtop->moltype[mt];
573 for (i = 0; (i < F_NRE); i++)
575 molt->ilist[i].iatoms.clear();
577 gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
579 flags = interaction_function[i].flags;
580 if ((i != F_LJ) && (i != F_BHAM)
581 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
583 enter_function(&(interactions[i]),
584 static_cast<t_functype>(i),
590 (i == F_POSRES || i == F_FBPOSRES));
595 mtop->bIntermolecularInteractions = FALSE;
596 if (intermolecular_interactions != nullptr)
598 /* Process the intermolecular interaction list */
599 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
601 for (i = 0; (i < F_NRE); i++)
603 (*mtop->intermolecular_ilist)[i].iatoms.clear();
605 gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
607 if (!interactions[i].interactionTypes.empty())
609 flags = interaction_function[i].flags;
610 /* For intermolecular interactions we (currently)
611 * only support potentials.
612 * Constraints and virtual sites would be possible,
613 * but require a lot of extra (bug-prone) code.
615 if (!(flags & IF_BOND))
618 "The intermolecular_interaction section may only contain bonded "
621 else if (NRAL(i) == 1) /* e.g. position restraints */
624 "Single atom interactions don't make sense in the "
625 "intermolecular_interaction section, you can put them in the "
626 "moleculetype section");
628 else if (flags & IF_CHEMBOND)
631 "The intermolecular_interaction can not contain chemically bonding "
636 enter_function(&(interactions[i]),
637 static_cast<t_functype>(i),
641 &(*mtop->intermolecular_ilist)[i],
645 mtop->bIntermolecularInteractions = TRUE;
650 if (!mtop->bIntermolecularInteractions)
652 mtop->intermolecular_ilist.reset(nullptr);
656 ffp->fudgeQQ = fudgeQQ;