2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2011, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
51 #include "gmx_fatal.h"
53 #include "gpp_atomtype.h"
55 typedef struct gpp_atomtype {
56 int nr; /* The number of atomtypes */
57 t_atom *atom; /* Array of atoms */
58 char ***atomname; /* Names of the atomtypes */
59 t_param *nb; /* Nonbonded force default params */
60 int *bondatomtype; /* The bond_atomtype for each atomtype */
61 real *radius; /* Radius for GBSA stuff */
62 real *vol; /* Effective volume for GBSA */
63 real *surftens; /* Surface tension with water, for GBSA */
64 real *gb_radius; /* Radius for Still model */
65 real *S_hct; /* Overlap factor for HCT model */
66 int *atomnumber; /* Atomic number, used for QM/MM */
69 int get_atomtype_type(const char *str, gpp_atomtype_t ga)
73 /* Atom types are always case sensitive */
74 for (i = 0; (i < ga->nr); i++)
76 if (strcmp(str, *(ga->atomname[i])) == 0)
85 int get_atomtype_ntypes(gpp_atomtype_t ga)
90 char *get_atomtype_name(int nt, gpp_atomtype_t ga)
92 if ((nt < 0) || (nt >= ga->nr))
97 return *(ga->atomname[nt]);
100 real get_atomtype_massA(int nt, gpp_atomtype_t ga)
102 if ((nt < 0) || (nt >= ga->nr))
107 return ga->atom[nt].m;
110 real get_atomtype_massB(int nt, gpp_atomtype_t ga)
112 if ((nt < 0) || (nt >= ga->nr))
117 return ga->atom[nt].mB;
120 real get_atomtype_qA(int nt, gpp_atomtype_t ga)
122 if ((nt < 0) || (nt >= ga->nr))
127 return ga->atom[nt].q;
130 real get_atomtype_qB(int nt, gpp_atomtype_t ga)
132 if ((nt < 0) || (nt >= ga->nr))
137 return ga->atom[nt].qB;
140 int get_atomtype_ptype(int nt, gpp_atomtype_t ga)
142 if ((nt < 0) || (nt >= ga->nr))
147 return ga->atom[nt].ptype;
150 int get_atomtype_batype(int nt, gpp_atomtype_t ga)
152 if ((nt < 0) || (nt >= ga->nr))
157 return ga->bondatomtype[nt];
160 int get_atomtype_atomnumber(int nt, gpp_atomtype_t ga)
162 if ((nt < 0) || (nt >= ga->nr))
167 return ga->atomnumber[nt];
170 real get_atomtype_radius(int nt, gpp_atomtype_t ga)
172 if ((nt < 0) || (nt >= ga->nr))
177 return ga->radius[nt];
180 real get_atomtype_vol(int nt, gpp_atomtype_t ga)
182 if ((nt < 0) || (nt >= ga->nr))
190 real get_atomtype_surftens(int nt, gpp_atomtype_t ga)
192 if ((nt < 0) || (nt >= ga->nr))
197 return ga->surftens[nt];
200 real get_atomtype_gb_radius(int nt, gpp_atomtype_t ga)
202 if ((nt < 0) || (nt >= ga->nr))
207 return ga->gb_radius[nt];
210 real get_atomtype_S_hct(int nt, gpp_atomtype_t ga)
212 if ((nt < 0) || (nt >= ga->nr))
217 return ga->S_hct[nt];
220 real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t ga)
222 if ((nt < 0) || (nt >= ga->nr))
226 if ((param < 0) || (param >= MAXFORCEPARAM))
230 return ga->nb[nt].c[param];
233 gpp_atomtype_t init_atomtype(void)
243 ga->bondatomtype = NULL;
247 ga->atomnumber = NULL;
248 ga->gb_radius = NULL;
255 set_atomtype_gbparam(gpp_atomtype_t ga, int i,
256 real radius, real vol, real surftens,
257 real gb_radius, real S_hct)
259 if ( (i < 0) || (i >= ga->nr))
264 ga->radius[i] = radius;
266 ga->surftens[i] = surftens;
267 ga->gb_radius[i] = gb_radius;
268 ga->S_hct[i] = S_hct;
274 int set_atomtype(int nt, gpp_atomtype_t ga, t_symtab *tab,
275 t_atom *a, const char *name, t_param *nb,
277 real radius, real vol, real surftens, int atomnumber,
278 real gb_radius, real S_hct)
280 if ((nt < 0) || (nt >= ga->nr))
286 ga->atomname[nt] = put_symtab(tab, name);
288 ga->bondatomtype[nt] = bondatomtype;
289 ga->radius[nt] = radius;
291 ga->surftens[nt] = surftens;
292 ga->atomnumber[nt] = atomnumber;
293 ga->gb_radius[nt] = gb_radius;
294 ga->S_hct[nt] = S_hct;
299 int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
300 t_atom *a, const char *name, t_param *nb,
302 real radius, real vol, real surftens, real atomnumber,
303 real gb_radius, real S_hct)
307 for (i = 0; (i < ga->nr); i++)
309 if (strcmp(*ga->atomname[i], name) == 0)
313 fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
321 srenew(ga->atom, ga->nr);
322 srenew(ga->atomname, ga->nr);
323 srenew(ga->nb, ga->nr);
324 srenew(ga->bondatomtype, ga->nr);
325 srenew(ga->radius, ga->nr);
326 srenew(ga->vol, ga->nr);
327 srenew(ga->surftens, ga->nr);
328 srenew(ga->atomnumber, ga->nr);
329 srenew(ga->gb_radius, ga->nr);
330 srenew(ga->S_hct, ga->nr);
332 return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
333 vol, surftens, atomnumber, gb_radius, S_hct);
341 void print_at (FILE * out, gpp_atomtype_t ga)
344 t_atom *atom = ga->atom;
345 t_param *nb = ga->nb;
347 fprintf (out, "[ %s ]\n", dir2str(d_atomtypes));
348 fprintf (out, "; %6s %8s %8s %8s %12s %12s\n",
349 "type", "mass", "charge", "particle", "c6", "c12");
350 for (i = 0; (i < ga->nr); i++)
352 fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n",
353 *(ga->atomname[i]), atom[i].m, atom[i].q, "A",
360 void done_atomtype(gpp_atomtype_t ga)
365 sfree(ga->bondatomtype);
368 sfree(ga->gb_radius);
371 sfree(ga->atomnumber);
377 static int search_atomtypes(gpp_atomtype_t ga, int *n, int typelist[],
379 t_param param[], int ftype)
381 int i, nn, nrfp, j, k, ntype, tli;
382 gmx_bool bFound = FALSE;
386 ntype = get_atomtype_ntypes(ga);
388 for (i = 0; (i < nn); i++)
390 if (typelist[i] == thistype)
392 /* This type number has already been added */
396 /* Otherwise, check if the parameters are identical to any previously added type */
399 for (j = 0; j < ntype && bFound; j++)
401 /* Check nonbonded parameters */
402 for (k = 0; k < nrfp && bFound; k++)
404 bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
407 /* Check radius, volume, surftens */
410 (get_atomtype_radius(tli, ga) == get_atomtype_radius(thistype, ga)) &&
411 (get_atomtype_vol(tli, ga) == get_atomtype_vol(thistype, ga)) &&
412 (get_atomtype_surftens(tli, ga) == get_atomtype_surftens(thistype, ga)) &&
413 (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga)) &&
414 (get_atomtype_gb_radius(tli, ga) == get_atomtype_gb_radius(thistype, ga)) &&
415 (get_atomtype_S_hct(tli, ga) == get_atomtype_S_hct(thistype, ga));
427 fprintf(debug, "Renumbering atomtype %d to %d\n", thistype, nn);
431 gmx_fatal(FARGS, "Atomtype horror n = %d, %s, %d", nn, __FILE__, __LINE__);
433 typelist[nn] = thistype;
441 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
443 gpp_atomtype_t ga, gmx_bool bVerbose)
445 int i, j, k, l, molt, mi, mj, nat, nrfp, ftype, ntype;
455 char ***new_atomname;
457 ntype = get_atomtype_ntypes(ga);
458 snew(typelist, ntype);
462 fprintf(stderr, "renumbering atomtypes...\n");
465 /* Since the bonded interactions have been assigned now,
466 * we want to reduce the number of atom types by merging
467 * ones with identical nonbonded interactions, in addition
468 * to removing unused ones.
470 * With Generalized-Born electrostatics, or implicit solvent
471 * we also check that the atomtype radius, effective_volume
472 * and surface tension match.
474 * With QM/MM we also check that the atom numbers match
477 /* Get nonbonded interaction type */
478 if (plist[F_LJ].nr > 0)
487 /* Renumber atomtypes by first making a list of which ones are actually used.
488 * We provide the list of nonbonded parameters so search_atomtypes
489 * can determine if two types should be merged.
492 for (molt = 0; molt < mtop->nmoltype; molt++)
494 atoms = &mtop->moltype[molt].atoms;
495 for (i = 0; (i < atoms->nr); i++)
497 atoms->atom[i].type =
498 search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
499 plist[ftype].param, ftype);
500 atoms->atom[i].typeB =
501 search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
502 plist[ftype].param, ftype);
506 for (i = 0; i < 2; i++)
508 if (wall_atomtype[i] >= 0)
510 wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
511 plist[ftype].param, ftype);
515 snew(new_radius, nat);
517 snew(new_surftens, nat);
518 snew(new_atomnumber, nat);
519 snew(new_gb_radius, nat);
520 snew(new_S_hct, nat);
521 snew(new_atomname, nat);
523 /* We now have a list of unique atomtypes in typelist */
527 pr_ivec(debug, 0, "typelist", typelist, nat, TRUE);
532 snew(nbsnew, plist[ftype].nr);
536 for (i = k = 0; (i < nat); i++)
539 for (j = 0; (j < nat); j++, k++)
542 for (l = 0; (l < nrfp); l++)
544 nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
547 new_radius[i] = get_atomtype_radius(mi, ga);
548 new_vol[i] = get_atomtype_vol(mi, ga);
549 new_surftens[i] = get_atomtype_surftens(mi, ga);
550 new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
551 new_gb_radius[i] = get_atomtype_gb_radius(mi, ga);
552 new_S_hct[i] = get_atomtype_S_hct(mi, ga);
553 new_atomname[i] = ga->atomname[mi];
556 for (i = 0; (i < nat*nat); i++)
558 for (l = 0; (l < nrfp); l++)
560 plist[ftype].param[i].c[l] = nbsnew[i].c[l];
564 mtop->ffparams.atnr = nat;
569 sfree(ga->atomnumber);
570 sfree(ga->gb_radius);
572 /* Dangling atomname pointers ? */
575 ga->radius = new_radius;
577 ga->surftens = new_surftens;
578 ga->atomnumber = new_atomnumber;
579 ga->gb_radius = new_gb_radius;
580 ga->S_hct = new_S_hct;
581 ga->atomname = new_atomname;
589 void copy_atomtype_atomtypes(gpp_atomtype_t ga, t_atomtypes *atomtypes)
593 /* Copy the atomtype data to the topology atomtype list */
594 ntype = get_atomtype_ntypes(ga);
595 atomtypes->nr = ntype;
596 snew(atomtypes->radius, ntype);
597 snew(atomtypes->vol, ntype);
598 snew(atomtypes->surftens, ntype);
599 snew(atomtypes->atomnumber, ntype);
600 snew(atomtypes->gb_radius, ntype);
601 snew(atomtypes->S_hct, ntype);
603 for (i = 0; i < ntype; i++)
605 atomtypes->radius[i] = ga->radius[i];
606 atomtypes->vol[i] = ga->vol[i];
607 atomtypes->surftens[i] = ga->surftens[i];
608 atomtypes->atomnumber[i] = ga->atomnumber[i];
609 atomtypes->gb_radius[i] = ga->gb_radius[i];
610 atomtypes->S_hct[i] = ga->S_hct[i];