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39 #include "gpp_atomtype.h"
45 #include "gromacs/gmxpreprocess/grompp_impl.h"
46 #include "gromacs/gmxpreprocess/notset.h"
47 #include "gromacs/gmxpreprocess/topdirs.h"
48 #include "gromacs/gmxpreprocess/toputil.h"
49 #include "gromacs/math/vecdump.h"
50 #include "gromacs/topology/ifunc.h"
51 #include "gromacs/topology/symtab.h"
52 #include "gromacs/topology/topology.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/smalloc.h"
58 int nr; /* The number of atomtypes */
59 t_atom *atom; /* Array of atoms */
60 char ***atomname; /* Names of the atomtypes */
61 t_param *nb; /* Nonbonded force default params */
62 int *bondatomtype; /* The bond_atomtype for each atomtype */
63 int *atomnumber; /* Atomic number, used for QM/MM */
66 int get_atomtype_type(const char *str, gpp_atomtype *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 *ga)
87 char *get_atomtype_name(int nt, gpp_atomtype *ga)
89 if ((nt < 0) || (nt >= ga->nr))
94 return *(ga->atomname[nt]);
97 real get_atomtype_massA(int nt, gpp_atomtype *ga)
99 if ((nt < 0) || (nt >= ga->nr))
104 return ga->atom[nt].m;
107 real get_atomtype_massB(int nt, gpp_atomtype *ga)
109 if ((nt < 0) || (nt >= ga->nr))
114 return ga->atom[nt].mB;
117 real get_atomtype_qA(int nt, gpp_atomtype *ga)
119 if ((nt < 0) || (nt >= ga->nr))
124 return ga->atom[nt].q;
127 real get_atomtype_qB(int nt, gpp_atomtype *ga)
129 if ((nt < 0) || (nt >= ga->nr))
134 return ga->atom[nt].qB;
137 int get_atomtype_ptype(int nt, gpp_atomtype *ga)
139 if ((nt < 0) || (nt >= ga->nr))
144 return ga->atom[nt].ptype;
147 int get_atomtype_batype(int nt, const gpp_atomtype* ga)
149 if ((nt < 0) || (nt >= ga->nr))
154 return ga->bondatomtype[nt];
157 int get_atomtype_atomnumber(int nt, gpp_atomtype *ga)
159 if ((nt < 0) || (nt >= ga->nr))
164 return ga->atomnumber[nt];
167 real get_atomtype_nbparam(int nt, int param, gpp_atomtype *ga)
169 if ((nt < 0) || (nt >= ga->nr))
173 if ((param < 0) || (param >= MAXFORCEPARAM))
177 return ga->nb[nt].c[param];
180 gpp_atomtype *init_atomtype()
188 ga->atomname = nullptr;
190 ga->bondatomtype = nullptr;
191 ga->atomnumber = nullptr;
196 int set_atomtype(int nt, gpp_atomtype *ga, t_symtab *tab,
197 t_atom *a, const char *name, t_param *nb,
198 int bondatomtype, int atomnumber)
200 if ((nt < 0) || (nt >= ga->nr))
206 ga->atomname[nt] = put_symtab(tab, name);
208 ga->bondatomtype[nt] = bondatomtype;
209 ga->atomnumber[nt] = atomnumber;
214 int add_atomtype(gpp_atomtype *ga, t_symtab *tab,
215 t_atom *a, const char *name, t_param *nb,
216 int bondatomtype, int atomnumber)
220 for (i = 0; (i < ga->nr); i++)
222 if (strcmp(*ga->atomname[i], name) == 0)
230 srenew(ga->atom, ga->nr);
231 srenew(ga->atomname, ga->nr);
232 srenew(ga->nb, ga->nr);
233 srenew(ga->bondatomtype, ga->nr);
234 srenew(ga->atomnumber, ga->nr);
236 return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, atomnumber);
244 void print_at (FILE * out, gpp_atomtype *ga)
247 t_atom *atom = ga->atom;
248 t_param *nb = ga->nb;
250 fprintf (out, "[ %s ]\n", dir2str(Directive::d_atomtypes));
251 fprintf (out, "; %6s %8s %8s %8s %12s %12s\n",
252 "type", "mass", "charge", "particle", "c6", "c12");
253 for (i = 0; (i < ga->nr); i++)
255 fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n",
256 *(ga->atomname[i]), atom[i].m, atom[i].q, "A",
257 nb[i].c0(), nb[i].c1());
263 void done_atomtype(gpp_atomtype *ga)
268 sfree(ga->bondatomtype);
269 sfree(ga->atomnumber);
274 static int search_atomtypes(gpp_atomtype *ga, int *n, int typelist[],
276 t_param param[], int ftype)
278 int i, nn, nrfp, j, k, ntype, tli;
283 ntype = get_atomtype_ntypes(ga);
285 for (i = 0; (i < nn); i++)
287 if (typelist[i] == thistype)
289 /* This type number has already been added */
293 /* Otherwise, check if the parameters are identical to any previously added type */
296 for (j = 0; j < ntype && bFound; j++)
298 /* Check nonbonded parameters */
299 for (k = 0; k < nrfp && bFound; k++)
301 bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
304 /* Check atomnumber */
307 (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga));
319 gmx_fatal(FARGS, "Atomtype horror n = %d, %s, %d", nn, __FILE__, __LINE__);
321 typelist[nn] = thistype;
329 void renum_atype(t_params plist[], gmx_mtop_t *mtop,
331 gpp_atomtype *ga, bool bVerbose)
333 int i, j, k, l, mi, mj, nat, nrfp, ftype, ntype;
338 char ***new_atomname;
340 ntype = get_atomtype_ntypes(ga);
341 snew(typelist, ntype);
345 fprintf(stderr, "renumbering atomtypes...\n");
348 /* Since the bonded interactions have been assigned now,
349 * we want to reduce the number of atom types by merging
350 * ones with identical nonbonded interactions, in addition
351 * to removing unused ones.
353 * With QM/MM we also check that the atom numbers match
356 /* Get nonbonded interaction type */
357 if (plist[F_LJ].nr > 0)
366 /* Renumber atomtypes by first making a list of which ones are actually used.
367 * We provide the list of nonbonded parameters so search_atomtypes
368 * can determine if two types should be merged.
371 for (gmx_moltype_t &moltype : mtop->moltype)
373 atoms = &moltype.atoms;
374 for (i = 0; (i < atoms->nr); i++)
376 atoms->atom[i].type =
377 search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
378 plist[ftype].param, ftype);
379 atoms->atom[i].typeB =
380 search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
381 plist[ftype].param, ftype);
385 for (i = 0; i < 2; i++)
387 if (wall_atomtype[i] >= 0)
389 wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
390 plist[ftype].param, ftype);
394 snew(new_atomnumber, nat);
395 snew(new_atomname, nat);
396 /* We now have a list of unique atomtypes in typelist */
400 snew(nbsnew, plist[ftype].nr);
404 for (i = k = 0; (i < nat); i++)
407 for (j = 0; (j < nat); j++, k++)
410 for (l = 0; (l < nrfp); l++)
412 nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
415 new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
416 new_atomname[i] = ga->atomname[mi];
419 for (i = 0; (i < nat*nat); i++)
421 for (l = 0; (l < nrfp); l++)
423 plist[ftype].param[i].c[l] = nbsnew[i].c[l];
427 mtop->ffparams.atnr = nat;
429 sfree(ga->atomnumber);
430 /* Dangling atomname pointers ? */
433 ga->atomnumber = new_atomnumber;
434 ga->atomname = new_atomname;
442 void copy_atomtype_atomtypes(gpp_atomtype *ga, t_atomtypes *atomtypes)
446 /* Copy the atomtype data to the topology atomtype list */
447 ntype = get_atomtype_ntypes(ga);
448 atomtypes->nr = ntype;
449 snew(atomtypes->atomnumber, ntype);
451 for (i = 0; i < ntype; i++)
453 atomtypes->atomnumber[i] = ga->atomnumber[i];