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39 #include "gpp_atomtype.h"
45 #include "gromacs/gmxpreprocess/topdirs.h"
46 #include "gromacs/gmxpreprocess/toputil.h"
47 #include "gromacs/legacyheaders/txtdump.h"
48 #include "gromacs/topology/symtab.h"
49 #include "gromacs/utility/fatalerror.h"
50 #include "gromacs/utility/smalloc.h"
52 typedef struct gpp_atomtype {
53 int nr; /* The number of atomtypes */
54 t_atom *atom; /* Array of atoms */
55 char ***atomname; /* Names of the atomtypes */
56 t_param *nb; /* Nonbonded force default params */
57 int *bondatomtype; /* The bond_atomtype for each atomtype */
58 real *radius; /* Radius for GBSA stuff */
59 real *vol; /* Effective volume for GBSA */
60 real *surftens; /* Surface tension with water, for GBSA */
61 real *gb_radius; /* Radius for Still model */
62 real *S_hct; /* Overlap factor for HCT model */
63 int *atomnumber; /* Atomic number, used for QM/MM */
66 int get_atomtype_type(const char *str, gpp_atomtype_t ga)
70 /* Atom types are always case sensitive */
71 for (i = 0; (i < ga->nr); i++)
73 if (strcmp(str, *(ga->atomname[i])) == 0)
82 int get_atomtype_ntypes(gpp_atomtype_t ga)
87 char *get_atomtype_name(int nt, gpp_atomtype_t ga)
89 if ((nt < 0) || (nt >= ga->nr))
94 return *(ga->atomname[nt]);
97 real get_atomtype_massA(int nt, gpp_atomtype_t ga)
99 if ((nt < 0) || (nt >= ga->nr))
104 return ga->atom[nt].m;
107 real get_atomtype_massB(int nt, gpp_atomtype_t ga)
109 if ((nt < 0) || (nt >= ga->nr))
114 return ga->atom[nt].mB;
117 real get_atomtype_qA(int nt, gpp_atomtype_t ga)
119 if ((nt < 0) || (nt >= ga->nr))
124 return ga->atom[nt].q;
127 real get_atomtype_qB(int nt, gpp_atomtype_t ga)
129 if ((nt < 0) || (nt >= ga->nr))
134 return ga->atom[nt].qB;
137 int get_atomtype_ptype(int nt, gpp_atomtype_t ga)
139 if ((nt < 0) || (nt >= ga->nr))
144 return ga->atom[nt].ptype;
147 int get_atomtype_batype(int nt, gpp_atomtype_t ga)
149 if ((nt < 0) || (nt >= ga->nr))
154 return ga->bondatomtype[nt];
157 int get_atomtype_atomnumber(int nt, gpp_atomtype_t ga)
159 if ((nt < 0) || (nt >= ga->nr))
164 return ga->atomnumber[nt];
167 real get_atomtype_radius(int nt, gpp_atomtype_t ga)
169 if ((nt < 0) || (nt >= ga->nr))
174 return ga->radius[nt];
177 real get_atomtype_vol(int nt, gpp_atomtype_t ga)
179 if ((nt < 0) || (nt >= ga->nr))
187 real get_atomtype_surftens(int nt, gpp_atomtype_t ga)
189 if ((nt < 0) || (nt >= ga->nr))
194 return ga->surftens[nt];
197 real get_atomtype_gb_radius(int nt, gpp_atomtype_t ga)
199 if ((nt < 0) || (nt >= ga->nr))
204 return ga->gb_radius[nt];
207 real get_atomtype_S_hct(int nt, gpp_atomtype_t ga)
209 if ((nt < 0) || (nt >= ga->nr))
214 return ga->S_hct[nt];
217 real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t ga)
219 if ((nt < 0) || (nt >= ga->nr))
223 if ((param < 0) || (param >= MAXFORCEPARAM))
227 return ga->nb[nt].c[param];
230 gpp_atomtype_t init_atomtype(void)
240 ga->bondatomtype = NULL;
244 ga->atomnumber = NULL;
245 ga->gb_radius = NULL;
252 set_atomtype_gbparam(gpp_atomtype_t ga, int i,
253 real radius, real vol, real surftens,
254 real gb_radius, real S_hct)
256 if ( (i < 0) || (i >= ga->nr))
261 ga->radius[i] = radius;
263 ga->surftens[i] = surftens;
264 ga->gb_radius[i] = gb_radius;
265 ga->S_hct[i] = S_hct;
271 int set_atomtype(int nt, gpp_atomtype_t ga, t_symtab *tab,
272 t_atom *a, const char *name, t_param *nb,
274 real radius, real vol, real surftens, int atomnumber,
275 real gb_radius, real S_hct)
277 if ((nt < 0) || (nt >= ga->nr))
283 ga->atomname[nt] = put_symtab(tab, name);
285 ga->bondatomtype[nt] = bondatomtype;
286 ga->radius[nt] = radius;
288 ga->surftens[nt] = surftens;
289 ga->atomnumber[nt] = atomnumber;
290 ga->gb_radius[nt] = gb_radius;
291 ga->S_hct[nt] = S_hct;
296 int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
297 t_atom *a, const char *name, t_param *nb,
299 real radius, real vol, real surftens, int atomnumber,
300 real gb_radius, real S_hct)
304 for (i = 0; (i < ga->nr); i++)
306 if (strcmp(*ga->atomname[i], name) == 0)
310 fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
318 srenew(ga->atom, ga->nr);
319 srenew(ga->atomname, ga->nr);
320 srenew(ga->nb, ga->nr);
321 srenew(ga->bondatomtype, ga->nr);
322 srenew(ga->radius, ga->nr);
323 srenew(ga->vol, ga->nr);
324 srenew(ga->surftens, ga->nr);
325 srenew(ga->atomnumber, ga->nr);
326 srenew(ga->gb_radius, ga->nr);
327 srenew(ga->S_hct, ga->nr);
329 return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
330 vol, surftens, atomnumber, gb_radius, S_hct);
338 void print_at (FILE * out, gpp_atomtype_t ga)
341 t_atom *atom = ga->atom;
342 t_param *nb = ga->nb;
344 fprintf (out, "[ %s ]\n", dir2str(d_atomtypes));
345 fprintf (out, "; %6s %8s %8s %8s %12s %12s\n",
346 "type", "mass", "charge", "particle", "c6", "c12");
347 for (i = 0; (i < ga->nr); i++)
349 fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n",
350 *(ga->atomname[i]), atom[i].m, atom[i].q, "A",
357 void done_atomtype(gpp_atomtype_t ga)
362 sfree(ga->bondatomtype);
365 sfree(ga->gb_radius);
368 sfree(ga->atomnumber);
373 static int search_atomtypes(gpp_atomtype_t ga, int *n, int typelist[],
375 t_param param[], int ftype)
377 int i, nn, nrfp, j, k, ntype, tli;
378 gmx_bool bFound = FALSE;
382 ntype = get_atomtype_ntypes(ga);
384 for (i = 0; (i < nn); i++)
386 if (typelist[i] == thistype)
388 /* This type number has already been added */
392 /* Otherwise, check if the parameters are identical to any previously added type */
395 for (j = 0; j < ntype && bFound; j++)
397 /* Check nonbonded parameters */
398 for (k = 0; k < nrfp && bFound; k++)
400 bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
403 /* Check radius, volume, surftens */
406 (get_atomtype_radius(tli, ga) == get_atomtype_radius(thistype, ga)) &&
407 (get_atomtype_vol(tli, ga) == get_atomtype_vol(thistype, ga)) &&
408 (get_atomtype_surftens(tli, ga) == get_atomtype_surftens(thistype, ga)) &&
409 (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga)) &&
410 (get_atomtype_gb_radius(tli, ga) == get_atomtype_gb_radius(thistype, ga)) &&
411 (get_atomtype_S_hct(tli, ga) == get_atomtype_S_hct(thistype, ga));
423 fprintf(debug, "Renumbering atomtype %d to %d\n", thistype, nn);
427 gmx_fatal(FARGS, "Atomtype horror n = %d, %s, %d", nn, __FILE__, __LINE__);
429 typelist[nn] = thistype;
437 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
439 gpp_atomtype_t ga, gmx_bool bVerbose)
441 int i, j, k, l, molt, mi, mj, nat, nrfp, ftype, ntype;
451 char ***new_atomname;
453 ntype = get_atomtype_ntypes(ga);
454 snew(typelist, ntype);
458 fprintf(stderr, "renumbering atomtypes...\n");
461 /* Since the bonded interactions have been assigned now,
462 * we want to reduce the number of atom types by merging
463 * ones with identical nonbonded interactions, in addition
464 * to removing unused ones.
466 * With Generalized-Born electrostatics, or implicit solvent
467 * we also check that the atomtype radius, effective_volume
468 * and surface tension match.
470 * With QM/MM we also check that the atom numbers match
473 /* Get nonbonded interaction type */
474 if (plist[F_LJ].nr > 0)
483 /* Renumber atomtypes by first making a list of which ones are actually used.
484 * We provide the list of nonbonded parameters so search_atomtypes
485 * can determine if two types should be merged.
488 for (molt = 0; molt < mtop->nmoltype; molt++)
490 atoms = &mtop->moltype[molt].atoms;
491 for (i = 0; (i < atoms->nr); i++)
493 atoms->atom[i].type =
494 search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
495 plist[ftype].param, ftype);
496 atoms->atom[i].typeB =
497 search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
498 plist[ftype].param, ftype);
502 for (i = 0; i < 2; i++)
504 if (wall_atomtype[i] >= 0)
506 wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
507 plist[ftype].param, ftype);
511 snew(new_radius, nat);
513 snew(new_surftens, nat);
514 snew(new_atomnumber, nat);
515 snew(new_gb_radius, nat);
516 snew(new_S_hct, nat);
517 snew(new_atomname, nat);
519 /* We now have a list of unique atomtypes in typelist */
523 pr_ivec(debug, 0, "typelist", typelist, nat, TRUE);
528 snew(nbsnew, plist[ftype].nr);
532 for (i = k = 0; (i < nat); i++)
535 for (j = 0; (j < nat); j++, k++)
538 for (l = 0; (l < nrfp); l++)
540 nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
543 new_radius[i] = get_atomtype_radius(mi, ga);
544 new_vol[i] = get_atomtype_vol(mi, ga);
545 new_surftens[i] = get_atomtype_surftens(mi, ga);
546 new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
547 new_gb_radius[i] = get_atomtype_gb_radius(mi, ga);
548 new_S_hct[i] = get_atomtype_S_hct(mi, ga);
549 new_atomname[i] = ga->atomname[mi];
552 for (i = 0; (i < nat*nat); i++)
554 for (l = 0; (l < nrfp); l++)
556 plist[ftype].param[i].c[l] = nbsnew[i].c[l];
560 mtop->ffparams.atnr = nat;
565 sfree(ga->atomnumber);
566 sfree(ga->gb_radius);
568 /* Dangling atomname pointers ? */
571 ga->radius = new_radius;
573 ga->surftens = new_surftens;
574 ga->atomnumber = new_atomnumber;
575 ga->gb_radius = new_gb_radius;
576 ga->S_hct = new_S_hct;
577 ga->atomname = new_atomname;
585 void copy_atomtype_atomtypes(gpp_atomtype_t ga, t_atomtypes *atomtypes)
589 /* Copy the atomtype data to the topology atomtype list */
590 ntype = get_atomtype_ntypes(ga);
591 atomtypes->nr = ntype;
592 snew(atomtypes->radius, ntype);
593 snew(atomtypes->vol, ntype);
594 snew(atomtypes->surftens, ntype);
595 snew(atomtypes->atomnumber, ntype);
596 snew(atomtypes->gb_radius, ntype);
597 snew(atomtypes->S_hct, ntype);
599 for (i = 0; i < ntype; i++)
601 atomtypes->radius[i] = ga->radius[i];
602 atomtypes->vol[i] = ga->vol[i];
603 atomtypes->surftens[i] = ga->surftens[i];
604 atomtypes->atomnumber[i] = ga->atomnumber[i];
605 atomtypes->gb_radius[i] = ga->gb_radius[i];
606 atomtypes->S_hct[i] = ga->S_hct[i];