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37 /* This file is completely threadsafe - keep it that way! */
42 #include "gromacs/math/utilities.h"
43 #include "gromacs/legacyheaders/macros.h"
44 #include "gromacs/utility/cstringutil.h"
45 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/fileio/confio.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/legacyheaders/txtdump.h"
49 #include "gromacs/legacyheaders/readinp.h"
50 #include "gromacs/legacyheaders/names.h"
53 #include "gpp_nextnb.h"
54 #include "gpp_atomtype.h"
55 #include "fflibutil.h"
59 #include "gromacs/utility/fatalerror.h"
61 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
65 char libfilename[128];
66 char format[128], f1[128];
67 char buf[1024], elem[16], type[16], nbbuf[16], **newbuf;
68 int i, nb, nnnm, line = 1;
70 t_nm2type *nm2t = NULL;
75 gmx_fatal(FARGS, "Can not find %s in library directory", fn);
82 /* Read a line from the file */
83 bCont = (fgets2(buf, 1023, fp) != NULL);
89 if (sscanf(buf, "%s%s%lf%lf%d", elem, type, &qq, &mm, &nb) == 5)
91 /* If we can read the first four, there probably is more */
93 snew(nm2t[nnnm].blen, nb);
97 strcpy(format, "%*s%*s%*s%*s%*s");
98 for (i = 0; (i < nb); i++)
100 /* Complicated format statement */
103 if (sscanf(buf, f1, nbbuf, &(nm2t[nnnm].blen[i])) != 2)
105 gmx_fatal(FARGS, "Error on line %d of %s", line, libfilename);
107 newbuf[i] = gmx_strdup(nbbuf);
108 strcat(format, "%*s%*s");
115 nm2t[nnnm].elem = gmx_strdup(elem);
116 nm2t[nnnm].type = gmx_strdup(type);
119 nm2t[nnnm].nbonds = nb;
120 nm2t[nnnm].bond = newbuf;
133 t_nm2type *rd_nm2type(const char *ffdir, int *nnm)
139 nff = fflib_search_file_end(ffdir, ".n2t", FALSE, &ff);
142 for (f = 0; f < nff; f++)
144 rd_nm2type_file(ff[f], nnm, &nm);
152 void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[])
156 fprintf(fp, "; nm2type database\n");
157 for (i = 0; (i < nnm); i++)
159 fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d",
160 nm2t[i].elem, nm2t[i].type,
161 nm2t[i].q, nm2t[i].m, nm2t[i].nbonds);
162 for (j = 0; (j < nm2t[i].nbonds); j++)
164 fprintf(fp, " %-5s %6.4f", nm2t[i].bond[j], nm2t[i].blen[j]);
171 ematchNone, ematchWild, ematchElem, ematchExact, ematchNR
174 static int match_str(const char *atom, const char *template_string)
176 if (!atom || !template_string)
180 else if (gmx_strcasecmp(atom, template_string) == 0)
184 else if (atom[0] == template_string[0])
188 else if (strcmp(template_string, "*") == 0)
198 int nm2type(int nnm, t_nm2type nm2t[], struct t_symtab *tab, t_atoms *atoms,
199 gpp_atomtype_t atype, int *nbonds, t_params *bonds)
203 int i, j, k, m, n, nresolved, nb, maxbond, ai, aj, best, im, nqual[2][ematchNR];
204 int *bbb, *n_mask, *m_mask, **match, **quality;
205 char *aname_i, *aname_m, *aname_n, *type;
211 for (i = 0; (i < atoms->nr); i++)
213 maxbond = max(maxbond, nbonds[i]);
217 fprintf(debug, "Max number of bonds per atom is %d\n", maxbond);
220 snew(n_mask, maxbond);
221 snew(m_mask, maxbond);
222 snew(match, maxbond);
223 for (i = 0; (i < maxbond); i++)
225 snew(match[i], maxbond);
229 for (i = 0; (i < atoms->nr); i++)
231 aname_i = *atoms->atomname[i];
233 for (j = 0; (j < bonds->nr); j++)
235 ai = bonds->param[j].AI;
236 aj = bonds->param[j].AJ;
248 gmx_fatal(FARGS, "Counting number of bonds nb = %d, nbonds[%d] = %d",
253 fprintf(debug, "%4s has bonds to", aname_i);
254 for (j = 0; (j < nb); j++)
256 fprintf(debug, " %4s", *atoms->atomname[bbb[j]]);
258 fprintf(debug, "\n");
261 for (k = 0; (k < ematchNR); k++)
266 /* First check for names */
267 for (k = 0; (k < nnm); k++)
269 if (nm2t[k].nbonds == nb)
271 im = match_str(*atoms->atomname[i], nm2t[k].elem);
274 for (j = 0; (j < ematchNR); j++)
279 /* Fill a matrix with matching quality */
280 for (m = 0; (m < nb); m++)
282 aname_m = *atoms->atomname[bbb[m]];
283 for (n = 0; (n < nb); n++)
285 aname_n = nm2t[k].bond[n];
286 match[m][n] = match_str(aname_m, aname_n);
289 /* Now pick the best matches */
290 for (m = 0; (m < nb); m++)
295 for (j = ematchNR-1; (j > 0); j--)
297 for (m = 0; (m < nb); m++)
299 for (n = 0; (n < nb); n++)
301 if ((n_mask[n] == 0) &&
312 if ((nqual[cur][ematchExact]+
313 nqual[cur][ematchElem]+
314 nqual[cur][ematchWild]) == nb)
316 if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
318 ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
319 (nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
321 ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
322 (nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
323 (nqual[cur][ematchWild] > nqual[prev][ematchWild])))
339 type = nm2t[best].type;
341 if ((k = get_atomtype_type(type, atype)) == NOTSET)
343 atoms->atom[i].qB = alpha;
344 atoms->atom[i].m = atoms->atom[i].mB = mm;
345 k = add_atomtype(atype, tab, &(atoms->atom[i]), type, param,
346 atoms->atom[i].type, 0, 0, 0, atomnr, 0, 0);
348 atoms->atom[i].type = k;
349 atoms->atom[i].typeB = k;
350 atoms->atom[i].q = qq;
351 atoms->atom[i].qB = qq;
352 atoms->atom[i].m = mm;
353 atoms->atom[i].mB = mm;
358 fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
359 *atoms->atomname[i], i+1, nb);