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[gromacs.git] / src / gromacs / gmxpreprocess / convparm.cpp
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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.
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8 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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37 */
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, "A non-integer value (%f) was supplied for '%s' in %s", r, name,
70 interaction_function[ftype].longname);
71 }
72
73 if (i < limit)
74 {
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);
77 }
78
79 return i;
80 }
81
82 static void set_ljparams(int comb, double reppow, double v, double w, 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 assign_param(t_functype ftype, t_iparams* newparam, gmx::ArrayRef<const real> old, int comb, double reppow)
109 {
110 bool all_param_zero = true;
111
112 /* Set to zero */
113 for (int j = 0; (j < MAXFORCEPARAM); j++)
114 {
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.
120 */
121 all_param_zero = all_param_zero && fabs(old[j]) < GMX_REAL_MIN;
122 }
123
124 if (all_param_zero)
125 {
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)
128 {
129 return -1;
130 }
131 }
132
133 switch (ftype)
134 {
135 case F_G96ANGLES:
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];
141 break;
142 case F_G96BONDS:
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];
148 break;
149 case F_FENEBONDS:
150 newparam->fene.bm = old[0];
151 newparam->fene.kb = old[1];
152 break;
153 case F_RESTRBONDS:
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];
162 break;
163 case F_TABBONDS:
164 case F_TABBONDSNC:
165 case F_TABANGLES:
166 case F_TABDIHS:
167 newparam->tab.table = round_check(old[0], 0, ftype, "table index");
168 newparam->tab.kA = old[1];
169 newparam->tab.kB = old[3];
170 break;
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];
175 break;
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];
181 break;
182 case F_UREY_BRADLEY:
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];
191 break;
192 case F_QUARTIC_ANGLES:
193 newparam->qangle.theta = old[0];
194 for (int i = 0; i < 5; i++)
195 {
196 newparam->qangle.c[i] = old[i + 1];
197 }
198 break;
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];
204 break;
205 case F_BONDS:
206 case F_ANGLES:
207 case F_HARMONIC:
208 case F_IDIHS:
209 newparam->harmonic.rA = old[0];
210 newparam->harmonic.krA = old[1];
211 newparam->harmonic.rB = old[2];
212 newparam->harmonic.krB = old[3];
213 break;
214 case F_RESTRANGLES:
215 newparam->harmonic.rA = old[0];
216 newparam->harmonic.krA = old[1];
217 break;
218 case F_MORSE:
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];
225 break;
226 case F_CUBICBONDS:
227 newparam->cubic.b0 = old[0];
228 newparam->cubic.kb = old[1];
229 newparam->cubic.kcub = old[2];
230 break;
231 case F_CONNBONDS: break;
232 case F_POLARIZATION: newparam->polarize.alpha = old[0]; break;
233 case F_ANHARM_POL:
234 newparam->anharm_polarize.alpha = old[0];
235 newparam->anharm_polarize.drcut = old[1];
236 newparam->anharm_polarize.khyp = old[2];
237 break;
238 case F_WATER_POL:
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];
245 break;
246 case F_THOLE_POL:
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))
251 {
252 newparam->thole.rfac = old[0] * gmx::invsixthroot(old[1] * old[2]);
253 }
254 else
255 {
256 newparam->thole.rfac = 1;
257 }
258 break;
259 case F_BHAM:
260 newparam->bham.a = old[0];
261 newparam->bham.b = old[1];
262 newparam->bham.c = old[2];
263 break;
264 case F_LJ14:
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);
267 break;
268 case F_LJC14_Q:
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);
273 break;
274 case F_LJC_PAIRS_NB:
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);
278 break;
279 case F_LJ:
280 set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
281 break;
282 case F_PDIHS:
283 case F_PIDIHS:
284 case F_ANGRES:
285 case F_ANGRESZ:
286 newparam->pdihs.phiA = old[0];
287 newparam->pdihs.cpA = old[1];
288
289 /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
290 * so I have changed the lower limit to -99 /EL
291 */
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.
296 */
297 if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
298 {
299 return -1;
300 }
301
302 newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
303
304 break;
305 case F_RESTRDIHS:
306 newparam->pdihs.phiA = old[0];
307 newparam->pdihs.cpA = old[1];
308 break;
309 case F_POSRES:
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];
322 break;
323 case F_FBPOSRES:
324 newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
325 if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
326 {
327 gmx_fatal(FARGS,
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);
331 }
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];
337 break;
338 case F_DISRES:
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];
345 break;
346 case F_ORIRES:
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];
353 break;
354 case F_DIHRES:
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];
361 break;
362 case F_RBDIHS:
363 for (int i = 0; (i < NR_RBDIHS); i++)
364 {
365 newparam->rbdihs.rbcA[i] = old[i];
366 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS + i];
367 }
368 break;
369 case F_CBTDIHS:
370 for (int i = 0; (i < NR_CBTDIHS); i++)
371 {
372 newparam->cbtdihs.cbtcA[i] = old[i];
373 }
374 break;
375 case F_FOURDIHS:
376 /* Read the dihedral parameters to temporary arrays,
377 * and convert them to the computationally faster
378 * Ryckaert-Bellemans form.
379 */
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;
387
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;
395 break;
396 case F_CONSTR:
397 case F_CONSTRNC:
398 newparam->constr.dA = old[0];
399 newparam->constr.dB = old[1];
400 break;
401 case F_SETTLE:
402 newparam->settle.doh = old[0];
403 newparam->settle.dhh = old[1];
404 break;
405 case F_VSITE1:
406 case F_VSITE2:
407 case F_VSITE2FD:
408 case F_VSITE3:
409 case F_VSITE3FD:
410 case F_VSITE3OUT:
411 case F_VSITE4FD:
412 case F_VSITE4FDN:
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];
419 break;
420 case F_VSITE3FAD:
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];
427 break;
428 case F_VSITEN:
429 newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
430 newparam->vsiten.a = old[1];
431 break;
432 case F_CMAP:
433 newparam->cmap.cmapA = static_cast<int>(old[0]);
434 newparam->cmap.cmapB = static_cast<int>(old[1]);
435 break;
436 case F_GB12_NOLONGERUSED:
437 case F_GB13_NOLONGERUSED:
438 case F_GB14_NOLONGERUSED: break;
439 default:
440 gmx_fatal(FARGS, "unknown function type %d in %s line %d", ftype, __FILE__, __LINE__);
441 }
442 return 0;
443 }
444
445 static int enter_params(gmx_ffparams_t* ffparams,
446 t_functype ftype,
447 gmx::ArrayRef<const real> forceparams,
448 int comb,
449 real reppow,
450 int start,
451 bool bAppend)
452 {
453 t_iparams newparam;
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 if (ftype != F_DISRES)
465 {
466 for (int type = start; type < ffparams->numTypes(); type++)
467 {
468 // Note that the first condition is always met by starting the loop at start
469 if (ffparams->functype[type] == ftype
470 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
471 {
472 return type;
473 }
474 }
475 }
476 else
477 {
478 // Distance restraints should have unique labels and pairs with the same label
479 // should be consecutive, so we here we only need to check the last type in the list.
480 // This changes the complexity from quadratic to linear in the number of restraints.
481 const int type = ffparams->numTypes() - 1;
482 if (type >= 0 && ffparams->functype[type] == ftype
483 && memcmp(&newparam, &ffparams->iparams[type], static_cast<size_t>(sizeof(newparam))) == 0)
484 {
485 return type;
486 }
487 }
488 }
489
490 const int type = ffparams->numTypes();
491
492 ffparams->iparams.push_back(newparam);
493 ffparams->functype.push_back(ftype);
494
495 GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match");
496
497 return type;
498 }
499
500 static void append_interaction(InteractionList* ilist, int type, gmx::ArrayRef<const int> a)
501 {
502 ilist->iatoms.push_back(type);
503 for (const auto& atom : a)
504 {
505 ilist->iatoms.push_back(atom);
506 }
507 }
508
509 static void enter_function(const InteractionsOfType* p,
510 t_functype ftype,
511 int comb,
512 real reppow,
513 gmx_ffparams_t* ffparams,
514 InteractionList* il,
515 bool bNB,
516 bool bAppend)
517 {
518 int start = ffparams->numTypes();
519
520 for (auto& parm : p->interactionTypes)
521 {
522 int type = enter_params(ffparams, ftype, parm.forceParam(), comb, reppow, start, bAppend);
523 /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
524 if (!bNB && type >= 0)
525 {
526 GMX_RELEASE_ASSERT(il, "Need valid interaction list");
527 GMX_RELEASE_ASSERT(parm.atoms().ssize() == NRAL(ftype),
528 "Need to have correct number of atoms for the parameter");
529 append_interaction(il, type, parm.atoms());
530 }
531 }
532 }
533
534 void convertInteractionsOfType(int atnr,
535 gmx::ArrayRef<const InteractionsOfType> nbtypes,
536 gmx::ArrayRef<const MoleculeInformation> mi,
537 const MoleculeInformation* intermolecular_interactions,
538 int comb,
539 double reppow,
540 real fudgeQQ,
541 gmx_mtop_t* mtop)
542 {
543 int i;
544 unsigned long flags;
545 gmx_ffparams_t* ffp;
546 gmx_moltype_t* molt;
547
548 ffp = &mtop->ffparams;
549 ffp->atnr = atnr;
550 ffp->functype.clear();
551 ffp->iparams.clear();
552 ffp->reppow = reppow;
553
554 enter_function(&(nbtypes[F_LJ]), static_cast<t_functype>(F_LJ), comb, reppow, ffp, nullptr, TRUE, TRUE);
555 enter_function(&(nbtypes[F_BHAM]), static_cast<t_functype>(F_BHAM), comb, reppow, ffp, nullptr,
556 TRUE, TRUE);
557
558 for (size_t mt = 0; mt < mtop->moltype.size(); mt++)
559 {
560 molt = &mtop->moltype[mt];
561 for (i = 0; (i < F_NRE); i++)
562 {
563 molt->ilist[i].iatoms.clear();
564
565 gmx::ArrayRef<const InteractionsOfType> interactions = mi[mt].interactions;
566
567 flags = interaction_function[i].flags;
568 if ((i != F_LJ) && (i != F_BHAM)
569 && ((flags & IF_BOND) || (flags & IF_VSITE) || (flags & IF_CONSTRAINT)))
570 {
571 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow, ffp,
572 &molt->ilist[i], FALSE, (i == F_POSRES || i == F_FBPOSRES));
573 }
574 }
575 }
576
577 mtop->bIntermolecularInteractions = FALSE;
578 if (intermolecular_interactions != nullptr)
579 {
580 /* Process the intermolecular interaction list */
581 mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
582
583 for (i = 0; (i < F_NRE); i++)
584 {
585 (*mtop->intermolecular_ilist)[i].iatoms.clear();
586
587 gmx::ArrayRef<const InteractionsOfType> interactions = intermolecular_interactions->interactions;
588
589 if (!interactions[i].interactionTypes.empty())
590 {
591 flags = interaction_function[i].flags;
592 /* For intermolecular interactions we (currently)
593 * only support potentials.
594 * Constraints and virtual sites would be possible,
595 * but require a lot of extra (bug-prone) code.
596 */
597 if (!(flags & IF_BOND))
598 {
599 gmx_fatal(FARGS,
600 "The intermolecular_interaction section may only contain bonded "
601 "potentials");
602 }
603 else if (NRAL(i) == 1) /* e.g. position restraints */
604 {
605 gmx_fatal(FARGS,
606 "Single atom interactions don't make sense in the "
607 "intermolecular_interaction section, you can put them in the "
608 "moleculetype section");
609 }
610 else if (flags & IF_CHEMBOND)
611 {
612 gmx_fatal(FARGS,
613 "The intermolecular_interaction can not contain chemically bonding "
614 "interactions");
615 }
616 else
617 {
618 enter_function(&(interactions[i]), static_cast<t_functype>(i), comb, reppow,
619 ffp, &(*mtop->intermolecular_ilist)[i], FALSE, FALSE);
620
621 mtop->bIntermolecularInteractions = TRUE;
622 }
623 }
624 }
625
626 if (!mtop->bIntermolecularInteractions)
627 {
628 mtop->intermolecular_ilist.reset(nullptr);
629 }
630 }
631
632 ffp->fudgeQQ = fudgeQQ;
633 }
The ultimate molecular dynamics simulation package