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44 #include "gromacs/utility/smalloc.h"
52 #include "gmx_fatal.h"
54 #include "gpp_atomtype.h"
56 typedef struct gpp_atomtype {
57 int nr; /* The number of atomtypes */
58 t_atom *atom; /* Array of atoms */
59 char ***atomname; /* Names of the atomtypes */
60 t_param *nb; /* Nonbonded force default params */
61 int *bondatomtype; /* The bond_atomtype for each atomtype */
62 real *radius; /* Radius for GBSA stuff */
63 real *vol; /* Effective volume for GBSA */
64 real *surftens; /* Surface tension with water, for GBSA */
65 real *gb_radius; /* Radius for Still model */
66 real *S_hct; /* Overlap factor for HCT model */
67 int *atomnumber; /* Atomic number, used for QM/MM */
70 int get_atomtype_type(const char *str, gpp_atomtype_t ga)
74 /* Atom types are always case sensitive */
75 for (i = 0; (i < ga->nr); i++)
77 if (strcmp(str, *(ga->atomname[i])) == 0)
86 int get_atomtype_ntypes(gpp_atomtype_t ga)
91 char *get_atomtype_name(int nt, gpp_atomtype_t ga)
93 if ((nt < 0) || (nt >= ga->nr))
98 return *(ga->atomname[nt]);
101 real get_atomtype_massA(int nt, gpp_atomtype_t ga)
103 if ((nt < 0) || (nt >= ga->nr))
108 return ga->atom[nt].m;
111 real get_atomtype_massB(int nt, gpp_atomtype_t ga)
113 if ((nt < 0) || (nt >= ga->nr))
118 return ga->atom[nt].mB;
121 real get_atomtype_qA(int nt, gpp_atomtype_t ga)
123 if ((nt < 0) || (nt >= ga->nr))
128 return ga->atom[nt].q;
131 real get_atomtype_qB(int nt, gpp_atomtype_t ga)
133 if ((nt < 0) || (nt >= ga->nr))
138 return ga->atom[nt].qB;
141 int get_atomtype_ptype(int nt, gpp_atomtype_t ga)
143 if ((nt < 0) || (nt >= ga->nr))
148 return ga->atom[nt].ptype;
151 int get_atomtype_batype(int nt, gpp_atomtype_t ga)
153 if ((nt < 0) || (nt >= ga->nr))
158 return ga->bondatomtype[nt];
161 int get_atomtype_atomnumber(int nt, gpp_atomtype_t ga)
163 if ((nt < 0) || (nt >= ga->nr))
168 return ga->atomnumber[nt];
171 real get_atomtype_radius(int nt, gpp_atomtype_t ga)
173 if ((nt < 0) || (nt >= ga->nr))
178 return ga->radius[nt];
181 real get_atomtype_vol(int nt, gpp_atomtype_t ga)
183 if ((nt < 0) || (nt >= ga->nr))
191 real get_atomtype_surftens(int nt, gpp_atomtype_t ga)
193 if ((nt < 0) || (nt >= ga->nr))
198 return ga->surftens[nt];
201 real get_atomtype_gb_radius(int nt, gpp_atomtype_t ga)
203 if ((nt < 0) || (nt >= ga->nr))
208 return ga->gb_radius[nt];
211 real get_atomtype_S_hct(int nt, gpp_atomtype_t ga)
213 if ((nt < 0) || (nt >= ga->nr))
218 return ga->S_hct[nt];
221 real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t ga)
223 if ((nt < 0) || (nt >= ga->nr))
227 if ((param < 0) || (param >= MAXFORCEPARAM))
231 return ga->nb[nt].c[param];
234 gpp_atomtype_t init_atomtype(void)
244 ga->bondatomtype = NULL;
248 ga->atomnumber = NULL;
249 ga->gb_radius = NULL;
256 set_atomtype_gbparam(gpp_atomtype_t ga, int i,
257 real radius, real vol, real surftens,
258 real gb_radius, real S_hct)
260 if ( (i < 0) || (i >= ga->nr))
265 ga->radius[i] = radius;
267 ga->surftens[i] = surftens;
268 ga->gb_radius[i] = gb_radius;
269 ga->S_hct[i] = S_hct;
275 int set_atomtype(int nt, gpp_atomtype_t ga, t_symtab *tab,
276 t_atom *a, const char *name, t_param *nb,
278 real radius, real vol, real surftens, int atomnumber,
279 real gb_radius, real S_hct)
281 if ((nt < 0) || (nt >= ga->nr))
287 ga->atomname[nt] = put_symtab(tab, name);
289 ga->bondatomtype[nt] = bondatomtype;
290 ga->radius[nt] = radius;
292 ga->surftens[nt] = surftens;
293 ga->atomnumber[nt] = atomnumber;
294 ga->gb_radius[nt] = gb_radius;
295 ga->S_hct[nt] = S_hct;
300 int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
301 t_atom *a, const char *name, t_param *nb,
303 real radius, real vol, real surftens, real atomnumber,
304 real gb_radius, real S_hct)
308 for (i = 0; (i < ga->nr); i++)
310 if (strcmp(*ga->atomname[i], name) == 0)
314 fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
322 srenew(ga->atom, ga->nr);
323 srenew(ga->atomname, ga->nr);
324 srenew(ga->nb, ga->nr);
325 srenew(ga->bondatomtype, ga->nr);
326 srenew(ga->radius, ga->nr);
327 srenew(ga->vol, ga->nr);
328 srenew(ga->surftens, ga->nr);
329 srenew(ga->atomnumber, ga->nr);
330 srenew(ga->gb_radius, ga->nr);
331 srenew(ga->S_hct, ga->nr);
333 return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
334 vol, surftens, atomnumber, gb_radius, S_hct);
342 void print_at (FILE * out, gpp_atomtype_t ga)
345 t_atom *atom = ga->atom;
346 t_param *nb = ga->nb;
348 fprintf (out, "[ %s ]\n", dir2str(d_atomtypes));
349 fprintf (out, "; %6s %8s %8s %8s %12s %12s\n",
350 "type", "mass", "charge", "particle", "c6", "c12");
351 for (i = 0; (i < ga->nr); i++)
353 fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n",
354 *(ga->atomname[i]), atom[i].m, atom[i].q, "A",
361 void done_atomtype(gpp_atomtype_t ga)
366 sfree(ga->bondatomtype);
369 sfree(ga->gb_radius);
372 sfree(ga->atomnumber);
378 static int search_atomtypes(gpp_atomtype_t ga, int *n, int typelist[],
380 t_param param[], int ftype)
382 int i, nn, nrfp, j, k, ntype, tli;
383 gmx_bool bFound = FALSE;
387 ntype = get_atomtype_ntypes(ga);
389 for (i = 0; (i < nn); i++)
391 if (typelist[i] == thistype)
393 /* This type number has already been added */
397 /* Otherwise, check if the parameters are identical to any previously added type */
400 for (j = 0; j < ntype && bFound; j++)
402 /* Check nonbonded parameters */
403 for (k = 0; k < nrfp && bFound; k++)
405 bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
408 /* Check radius, volume, surftens */
411 (get_atomtype_radius(tli, ga) == get_atomtype_radius(thistype, ga)) &&
412 (get_atomtype_vol(tli, ga) == get_atomtype_vol(thistype, ga)) &&
413 (get_atomtype_surftens(tli, ga) == get_atomtype_surftens(thistype, ga)) &&
414 (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga)) &&
415 (get_atomtype_gb_radius(tli, ga) == get_atomtype_gb_radius(thistype, ga)) &&
416 (get_atomtype_S_hct(tli, ga) == get_atomtype_S_hct(thistype, ga));
428 fprintf(debug, "Renumbering atomtype %d to %d\n", thistype, nn);
432 gmx_fatal(FARGS, "Atomtype horror n = %d, %s, %d", nn, __FILE__, __LINE__);
434 typelist[nn] = thistype;
442 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
444 gpp_atomtype_t ga, gmx_bool bVerbose)
446 int i, j, k, l, molt, mi, mj, nat, nrfp, ftype, ntype;
456 char ***new_atomname;
458 ntype = get_atomtype_ntypes(ga);
459 snew(typelist, ntype);
463 fprintf(stderr, "renumbering atomtypes...\n");
466 /* Since the bonded interactions have been assigned now,
467 * we want to reduce the number of atom types by merging
468 * ones with identical nonbonded interactions, in addition
469 * to removing unused ones.
471 * With Generalized-Born electrostatics, or implicit solvent
472 * we also check that the atomtype radius, effective_volume
473 * and surface tension match.
475 * With QM/MM we also check that the atom numbers match
478 /* Get nonbonded interaction type */
479 if (plist[F_LJ].nr > 0)
488 /* Renumber atomtypes by first making a list of which ones are actually used.
489 * We provide the list of nonbonded parameters so search_atomtypes
490 * can determine if two types should be merged.
493 for (molt = 0; molt < mtop->nmoltype; molt++)
495 atoms = &mtop->moltype[molt].atoms;
496 for (i = 0; (i < atoms->nr); i++)
498 atoms->atom[i].type =
499 search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
500 plist[ftype].param, ftype);
501 atoms->atom[i].typeB =
502 search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
503 plist[ftype].param, ftype);
507 for (i = 0; i < 2; i++)
509 if (wall_atomtype[i] >= 0)
511 wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
512 plist[ftype].param, ftype);
516 snew(new_radius, nat);
518 snew(new_surftens, nat);
519 snew(new_atomnumber, nat);
520 snew(new_gb_radius, nat);
521 snew(new_S_hct, nat);
522 snew(new_atomname, nat);
524 /* We now have a list of unique atomtypes in typelist */
528 pr_ivec(debug, 0, "typelist", typelist, nat, TRUE);
533 snew(nbsnew, plist[ftype].nr);
537 for (i = k = 0; (i < nat); i++)
540 for (j = 0; (j < nat); j++, k++)
543 for (l = 0; (l < nrfp); l++)
545 nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
548 new_radius[i] = get_atomtype_radius(mi, ga);
549 new_vol[i] = get_atomtype_vol(mi, ga);
550 new_surftens[i] = get_atomtype_surftens(mi, ga);
551 new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
552 new_gb_radius[i] = get_atomtype_gb_radius(mi, ga);
553 new_S_hct[i] = get_atomtype_S_hct(mi, ga);
554 new_atomname[i] = ga->atomname[mi];
557 for (i = 0; (i < nat*nat); i++)
559 for (l = 0; (l < nrfp); l++)
561 plist[ftype].param[i].c[l] = nbsnew[i].c[l];
565 mtop->ffparams.atnr = nat;
570 sfree(ga->atomnumber);
571 sfree(ga->gb_radius);
573 /* Dangling atomname pointers ? */
576 ga->radius = new_radius;
578 ga->surftens = new_surftens;
579 ga->atomnumber = new_atomnumber;
580 ga->gb_radius = new_gb_radius;
581 ga->S_hct = new_S_hct;
582 ga->atomname = new_atomname;
590 void copy_atomtype_atomtypes(gpp_atomtype_t ga, t_atomtypes *atomtypes)
594 /* Copy the atomtype data to the topology atomtype list */
595 ntype = get_atomtype_ntypes(ga);
596 atomtypes->nr = ntype;
597 snew(atomtypes->radius, ntype);
598 snew(atomtypes->vol, ntype);
599 snew(atomtypes->surftens, ntype);
600 snew(atomtypes->atomnumber, ntype);
601 snew(atomtypes->gb_radius, ntype);
602 snew(atomtypes->S_hct, ntype);
604 for (i = 0; i < ntype; i++)
606 atomtypes->radius[i] = ga->radius[i];
607 atomtypes->vol[i] = ga->vol[i];
608 atomtypes->surftens[i] = ga->surftens[i];
609 atomtypes->atomnumber[i] = ga->atomnumber[i];
610 atomtypes->gb_radius[i] = ga->gb_radius[i];
611 atomtypes->S_hct[i] = ga->S_hct[i];