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37 /* This file is completely threadsafe - keep it that way! */
43 #include "gromacs/math/units.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/legacyheaders/typedefs.h"
47 #include "gromacs/utility/fatalerror.h"
51 #include "gromacs/legacyheaders/names.h"
52 #include "gpp_atomtype.h"
53 #include "gromacs/math/utilities.h"
55 static int round_check(real r, int limit, int ftype, const char *name)
68 if (r-i > 0.01 || r-i < -0.01)
70 gmx_fatal(FARGS, "A non-integer value (%f) was supplied for '%s' in %s",
71 r, name, interaction_function[ftype].longname);
76 gmx_fatal(FARGS, "Value of '%s' in %s is %d, which is smaller than the minimum of %d",
77 name, interaction_function[ftype].longname, i, limit);
83 static void set_ljparams(int comb, double reppow, real v, real w,
86 if (comb == eCOMB_ARITHMETIC || comb == eCOMB_GEOM_SIG_EPS)
90 *c6 = 4*w*pow(v, 6.0);
91 *c12 = 4*w*pow(v, reppow);
95 /* Interpret negative sigma as c6=0 and c12 with -sigma */
97 *c12 = 4*w*pow(-v, reppow);
107 /* A return value of 0 means parameters were assigned successfully,
108 * returning -1 means this is an all-zero interaction that should not be added.
111 assign_param(t_functype ftype, t_iparams *newparam,
112 real old[MAXFORCEPARAM], int comb, double reppow)
116 gmx_bool all_param_zero = TRUE;
119 for (j = 0; (j < MAXFORCEPARAM); j++)
121 newparam->generic.buf[j] = 0.0;
122 /* If all parameters are zero we might not add some interaction types (selected below).
123 * We cannot apply this to ALL interactions, since many have valid reasons for having
124 * zero parameters (e.g. an index to a Cmap interaction, or LJ parameters), but
125 * we use it for angles and torsions that are typically generated automatically.
127 all_param_zero = (all_param_zero == TRUE) && fabs(old[j]) < GMX_REAL_MIN;
130 if (all_param_zero == TRUE)
132 if (IS_ANGLE(ftype) || IS_RESTRAINT_TYPE(ftype) || ftype == F_IDIHS ||
133 ftype == F_PDIHS || ftype == F_PIDIHS || ftype == F_RBDIHS || ftype == F_FOURDIHS)
142 /* Post processing of input data: store cosine iso angle itself */
143 newparam->harmonic.rA = cos(old[0]*DEG2RAD);
144 newparam->harmonic.krA = old[1];
145 newparam->harmonic.rB = cos(old[2]*DEG2RAD);
146 newparam->harmonic.krB = old[3];
149 /* Post processing of input data: store square of length itself */
150 newparam->harmonic.rA = sqr(old[0]);
151 newparam->harmonic.krA = old[1];
152 newparam->harmonic.rB = sqr(old[2]);
153 newparam->harmonic.krB = old[3];
156 newparam->fene.bm = old[0];
157 newparam->fene.kb = old[1];
160 newparam->restraint.lowA = old[0];
161 newparam->restraint.up1A = old[1];
162 newparam->restraint.up2A = old[2];
163 newparam->restraint.kA = old[3];
164 newparam->restraint.lowB = old[4];
165 newparam->restraint.up1B = old[5];
166 newparam->restraint.up2B = old[6];
167 newparam->restraint.kB = old[7];
173 newparam->tab.table = round_check(old[0], 0, ftype, "table index");
174 newparam->tab.kA = old[1];
175 newparam->tab.kB = old[3];
177 case F_CROSS_BOND_BONDS:
178 newparam->cross_bb.r1e = old[0];
179 newparam->cross_bb.r2e = old[1];
180 newparam->cross_bb.krr = old[2];
182 case F_CROSS_BOND_ANGLES:
183 newparam->cross_ba.r1e = old[0];
184 newparam->cross_ba.r2e = old[1];
185 newparam->cross_ba.r3e = old[2];
186 newparam->cross_ba.krt = old[3];
189 newparam->u_b.thetaA = old[0];
190 newparam->u_b.kthetaA = old[1];
191 newparam->u_b.r13A = old[2];
192 newparam->u_b.kUBA = old[3];
193 newparam->u_b.thetaB = old[4];
194 newparam->u_b.kthetaB = old[5];
195 newparam->u_b.r13B = old[6];
196 newparam->u_b.kUBB = old[7];
198 case F_QUARTIC_ANGLES:
199 newparam->qangle.theta = old[0];
200 for (i = 0; i < 5; i++)
202 newparam->qangle.c[i] = old[i+1];
205 case F_LINEAR_ANGLES:
206 newparam->linangle.aA = old[0];
207 newparam->linangle.klinA = old[1];
208 newparam->linangle.aB = old[2];
209 newparam->linangle.klinB = old[3];
215 newparam->harmonic.rA = old[0];
216 newparam->harmonic.krA = old[1];
217 newparam->harmonic.rB = old[2];
218 newparam->harmonic.krB = old[3];
221 newparam->harmonic.rA = old[0];
222 newparam->harmonic.krA = old[1];
225 newparam->morse.b0A = old[0];
226 newparam->morse.cbA = old[1];
227 newparam->morse.betaA = old[2];
228 newparam->morse.b0B = old[3];
229 newparam->morse.cbB = old[4];
230 newparam->morse.betaB = old[5];
233 newparam->cubic.b0 = old[0];
234 newparam->cubic.kb = old[1];
235 newparam->cubic.kcub = old[2];
240 newparam->polarize.alpha = old[0];
243 newparam->anharm_polarize.alpha = old[0];
244 newparam->anharm_polarize.drcut = old[1];
245 newparam->anharm_polarize.khyp = old[2];
248 newparam->wpol.al_x = old[0];
249 newparam->wpol.al_y = old[1];
250 newparam->wpol.al_z = old[2];
251 newparam->wpol.rOH = old[3];
252 newparam->wpol.rHH = old[4];
253 newparam->wpol.rOD = old[5];
256 newparam->thole.a = old[0];
257 newparam->thole.alpha1 = old[1];
258 newparam->thole.alpha2 = old[2];
259 if ((old[1] > 0) && (old[2] > 0))
261 newparam->thole.rfac = old[0]*pow(old[1]*old[2], -1.0/6.0);
265 newparam->thole.rfac = 1;
269 newparam->bham.a = old[0];
270 newparam->bham.b = old[1];
271 newparam->bham.c = old[2];
274 set_ljparams(comb, reppow, old[0], old[1], &newparam->lj14.c6A, &newparam->lj14.c12A);
275 set_ljparams(comb, reppow, old[2], old[3], &newparam->lj14.c6B, &newparam->lj14.c12B);
278 newparam->ljc14.fqq = old[0];
279 newparam->ljc14.qi = old[1];
280 newparam->ljc14.qj = old[2];
281 set_ljparams(comb, reppow, old[3], old[4], &newparam->ljc14.c6, &newparam->ljc14.c12);
284 newparam->ljcnb.qi = old[0];
285 newparam->ljcnb.qj = old[1];
286 set_ljparams(comb, reppow, old[2], old[3], &newparam->ljcnb.c6, &newparam->ljcnb.c12);
289 set_ljparams(comb, reppow, old[0], old[1], &newparam->lj.c6, &newparam->lj.c12);
295 newparam->pdihs.phiA = old[0];
296 newparam->pdihs.cpA = old[1];
298 /* Change 20100720: Amber occasionally uses negative multiplicities (mathematically OK),
299 * so I have changed the lower limit to -99 /EL
301 newparam->pdihs.phiB = old[3];
302 newparam->pdihs.cpB = old[4];
303 /* If both force constants are zero there is no interaction. Return -1 to signal
304 * this entry should NOT be added.
306 if (fabs(newparam->pdihs.cpA) < GMX_REAL_MIN && fabs(newparam->pdihs.cpB) < GMX_REAL_MIN)
311 newparam->pdihs.mult = round_check(old[2], -99, ftype, "multiplicity");
315 newparam->pdihs.phiA = old[0];
316 newparam->pdihs.cpA = old[1];
319 newparam->posres.fcA[XX] = old[0];
320 newparam->posres.fcA[YY] = old[1];
321 newparam->posres.fcA[ZZ] = old[2];
322 newparam->posres.fcB[XX] = old[3];
323 newparam->posres.fcB[YY] = old[4];
324 newparam->posres.fcB[ZZ] = old[5];
325 newparam->posres.pos0A[XX] = old[6];
326 newparam->posres.pos0A[YY] = old[7];
327 newparam->posres.pos0A[ZZ] = old[8];
328 newparam->posres.pos0B[XX] = old[9];
329 newparam->posres.pos0B[YY] = old[10];
330 newparam->posres.pos0B[ZZ] = old[11];
333 newparam->fbposres.geom = round_check(old[0], 0, ftype, "geometry");
334 if (!(newparam->fbposres.geom > efbposresZERO && newparam->fbposres.geom < efbposresNR))
336 gmx_fatal(FARGS, "Invalid geometry for flat-bottomed position restraint.\n"
337 "Expected number between 1 and %d. Found %d\n", efbposresNR-1,
338 newparam->fbposres.geom);
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];
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];
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];
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];
371 for (i = 0; (i < NR_RBDIHS); i++)
373 newparam->rbdihs.rbcA[i] = old[i];
374 newparam->rbdihs.rbcB[i] = old[NR_RBDIHS+i];
378 for (i = 0; (i < NR_CBTDIHS); i++)
380 newparam->cbtdihs.cbtcA[i] = old[i];
384 /* Read the dihedral parameters to temporary arrays,
385 * and convert them to the computationally faster
386 * Ryckaert-Bellemans form.
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;
396 newparam->rbdihs.rbcB[0] = old[NR_FOURDIHS+1]+0.5*(old[NR_FOURDIHS+0]+old[NR_FOURDIHS+2]);
397 newparam->rbdihs.rbcB[1] = 0.5*(3.0*old[NR_FOURDIHS+2]-old[NR_FOURDIHS+0]);
398 newparam->rbdihs.rbcB[2] = 4.0*old[NR_FOURDIHS+3]-old[NR_FOURDIHS+1];
399 newparam->rbdihs.rbcB[3] = -2.0*old[NR_FOURDIHS+2];
400 newparam->rbdihs.rbcB[4] = -4.0*old[NR_FOURDIHS+3];
401 newparam->rbdihs.rbcB[5] = 0.0;
405 newparam->constr.dA = old[0];
406 newparam->constr.dB = old[1];
409 newparam->settle.doh = old[0];
410 newparam->settle.dhh = old[1];
418 newparam->vsite.a = old[0];
419 newparam->vsite.b = old[1];
420 newparam->vsite.c = old[2];
421 newparam->vsite.d = old[3];
422 newparam->vsite.e = old[4];
423 newparam->vsite.f = old[5];
426 newparam->vsite.a = old[1] * cos(DEG2RAD * old[0]);
427 newparam->vsite.b = old[1] * sin(DEG2RAD * old[0]);
428 newparam->vsite.c = old[2];
429 newparam->vsite.d = old[3];
430 newparam->vsite.e = old[4];
431 newparam->vsite.f = old[5];
434 newparam->vsiten.n = round_check(old[0], 1, ftype, "number of atoms");
435 newparam->vsiten.a = old[1];
438 newparam->cmap.cmapA = old[0];
439 newparam->cmap.cmapB = old[1];
444 newparam->gb.sar = old[0];
445 newparam->gb.st = old[1];
446 newparam->gb.pi = old[2];
447 newparam->gb.gbr = old[3];
448 newparam->gb.bmlt = old[4];
451 gmx_fatal(FARGS, "unknown function type %d in %s line %d",
452 ftype, __FILE__, __LINE__);
457 static int enter_params(gmx_ffparams_t *ffparams, t_functype ftype,
458 real forceparams[MAXFORCEPARAM], int comb, real reppow,
459 int start, gmx_bool bAppend)
465 if ( (rc = assign_param(ftype, &newparam, forceparams, comb, reppow)) < 0)
467 /* -1 means this interaction is all-zero and should not be added */
473 for (type = start; (type < ffparams->ntypes); type++)
475 if (ffparams->functype[type] == ftype)
479 /* Occasionally, the way the 1-3 reference distance is
480 * computed can lead to non-binary-identical results, but I
482 if ((gmx_within_tol(newparam.gb.sar, ffparams->iparams[type].gb.sar, 1e-6)) &&
483 (gmx_within_tol(newparam.gb.st, ffparams->iparams[type].gb.st, 1e-6)) &&
484 (gmx_within_tol(newparam.gb.pi, ffparams->iparams[type].gb.pi, 1e-6)) &&
485 (gmx_within_tol(newparam.gb.gbr, ffparams->iparams[type].gb.gbr, 1e-6)) &&
486 (gmx_within_tol(newparam.gb.bmlt, ffparams->iparams[type].gb.bmlt, 1e-6)))
493 if (memcmp(&newparam, &ffparams->iparams[type], (size_t)sizeof(newparam)) == 0)
503 type = ffparams->ntypes;
507 fprintf(debug, "copying newparam to ffparams->iparams[%d] (ntypes=%d)\n",
508 type, ffparams->ntypes);
510 memcpy(&ffparams->iparams[type], &newparam, (size_t)sizeof(newparam));
513 ffparams->functype[type] = ftype;
518 static void append_interaction(t_ilist *ilist,
519 int type, int nral, atom_id a[MAXATOMLIST])
526 ilist->iatoms[where1++] = type;
527 for (i = 0; (i < nral); i++)
529 ilist->iatoms[where1++] = a[i];
533 static void enter_function(t_params *p, t_functype ftype, int comb, real reppow,
534 gmx_ffparams_t *ffparams, t_ilist *il,
536 gmx_bool bNB, gmx_bool bAppend)
538 int k, type, nr, nral, delta, start;
540 start = ffparams->ntypes;
543 for (k = 0; k < nr; k++)
545 if (*maxtypes <= ffparams->ntypes)
548 srenew(ffparams->functype, *maxtypes);
549 srenew(ffparams->iparams, *maxtypes);
552 fprintf(debug, "%s, line %d: srenewed idef->functype and idef->iparams to %d\n",
553 __FILE__, __LINE__, *maxtypes);
556 type = enter_params(ffparams, ftype, p->param[k].c, comb, reppow, start, bAppend);
557 /* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
558 if (!bNB && type >= 0)
562 srenew(il->iatoms, il->nr+delta);
563 append_interaction(il, type, nral, p->param[k].a);
568 void convert_params(int atnr, t_params nbtypes[],
569 t_molinfo *mi, int comb, double reppow, real fudgeQQ,
572 int i, j, maxtypes, mt;
580 ffp = &mtop->ffparams;
583 ffp->functype = NULL;
585 ffp->reppow = reppow;
587 enter_function(&(nbtypes[F_LJ]), (t_functype)F_LJ, comb, reppow, ffp, NULL,
588 &maxtypes, TRUE, TRUE);
589 enter_function(&(nbtypes[F_BHAM]), (t_functype)F_BHAM, comb, reppow, ffp, NULL,
590 &maxtypes, TRUE, TRUE);
592 for (mt = 0; mt < mtop->nmoltype; mt++)
594 molt = &mtop->moltype[mt];
595 for (i = 0; (i < F_NRE); i++)
597 molt->ilist[i].nr = 0;
598 molt->ilist[i].iatoms = NULL;
600 plist = mi[mt].plist;
602 flags = interaction_function[i].flags;
603 if ((i != F_LJ) && (i != F_BHAM) && ((flags & IF_BOND) ||
604 (flags & IF_VSITE) ||
605 (flags & IF_CONSTRAINT)))
607 enter_function(&(plist[i]), (t_functype)i, comb, reppow,
608 ffp, &molt->ilist[i],
609 &maxtypes, FALSE, (i == F_POSRES || i == F_FBPOSRES));
615 fprintf(debug, "%s, line %d: There are %d functypes in idef\n",
616 __FILE__, __LINE__, ffp->ntypes);
619 ffp->fudgeQQ = fudgeQQ;