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42 #include "gromacs/legacyheaders/macros.h"
45 #include "gpp_atomtype.h"
47 #include "gromacs/topology/block.h"
48 #include "gromacs/topology/symtab.h"
49 #include "gromacs/utility/fatalerror.h"
50 #include "gromacs/utility/smalloc.h"
54 void set_p_string(t_param *p, const char *s)
58 if (strlen(s) < sizeof(p->s)-1)
60 strncpy(p->s, s, sizeof(p->s));
64 gmx_fatal(FARGS, "Increase MAXSLEN in include/grompp-impl.h to at least %d,"
65 " or shorten your definition of bonds like %s to at most %d",
66 strlen(s)+1, s, MAXSLEN-1);
75 void pr_alloc (int extra, t_params *pr)
79 /* get new space for arrays */
82 gmx_fatal(FARGS, "Trying to make array smaller.\n");
88 if ((pr->nr == 0) && (pr->param != NULL))
90 fprintf(stderr, "Warning: dangling pointer at %lx\n",
91 (unsigned long)pr->param);
94 if (pr->nr+extra > pr->maxnr)
96 pr->maxnr = max(1.2*pr->maxnr, pr->maxnr + extra);
97 srenew(pr->param, pr->maxnr);
98 for (i = pr->nr; (i < pr->maxnr); i++)
100 for (j = 0; (j < MAXATOMLIST); j++)
102 pr->param[i].a[j] = 0;
104 for (j = 0; (j < MAXFORCEPARAM); j++)
106 pr->param[i].c[j] = 0;
108 set_p_string(&(pr->param[i]), "");
113 void init_plist(t_params plist[])
117 for (i = 0; (i < F_NRE); i++)
121 plist[i].param = NULL;
125 plist[i].cmap = NULL;
126 plist[i].grid_spacing = 0;
129 plist[i].cmap_types = NULL;
133 void cp_param(t_param *dest, t_param *src)
137 for (j = 0; (j < MAXATOMLIST); j++)
139 dest->a[j] = src->a[j];
141 for (j = 0; (j < MAXFORCEPARAM); j++)
143 dest->c[j] = src->c[j];
145 strncpy(dest->s, src->s, sizeof(dest->s));
148 void add_param_to_list(t_params *list, t_param *b)
152 /* allocate one position extra */
155 /* fill the arrays */
156 for (j = 0; (j < MAXFORCEPARAM); j++)
158 list->param[list->nr].c[j] = b->c[j];
160 for (j = 0; (j < MAXATOMLIST); j++)
162 list->param[list->nr].a[j] = b->a[j];
164 memset(list->param[list->nr].s, 0, sizeof(list->param[list->nr].s));
170 void init_molinfo(t_molinfo *mol)
173 mol->excl_set = FALSE;
174 mol->bProcessed = FALSE;
175 init_plist(mol->plist);
176 init_block(&mol->cgs);
177 init_block(&mol->mols);
178 init_blocka(&mol->excls);
179 init_atom(&mol->atoms);
184 void done_bt (t_params *pl)
189 void done_mi(t_molinfo *mi)
193 done_atom (&(mi->atoms));
194 done_block(&(mi->cgs));
195 done_block(&(mi->mols));
196 for (i = 0; (i < F_NRE); i++)
198 done_bt(&(mi->plist[i]));
202 /* PRINTING STRUCTURES */
204 void print_bt(FILE *out, directive d, gpp_atomtype_t at,
205 int ftype, int fsubtype, t_params plist[],
208 /* This dihp is a DIRTY patch because the dih-types do not use
209 * all four atoms to determine the type.
211 const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
213 int i, j, f, nral, nrfp;
214 gmx_bool bDih = FALSE, bSwapParity;
216 bt = &(plist[ftype]);
244 case F_CROSS_BOND_ANGLES:
247 case F_CROSS_BOND_BONDS:
297 fprintf(out, "[ %s ]\n", dir2str(d));
301 fprintf (out, "%3s %4s", "ai", "aj");
302 for (j = 2; (j < nral); j++)
304 fprintf (out, " %3c%c", 'a', 'i'+j);
309 for (j = 0; (j < 2); j++)
311 fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
315 fprintf (out, " funct");
316 for (j = 0; (j < nrfp); j++)
318 fprintf (out, " %12c%1d", 'c', j);
322 /* print bondtypes */
323 for (i = 0; (i < bt->nr); i++)
325 bSwapParity = (bt->param[i].C0 == NOTSET) && (bt->param[i].C1 == -1);
328 for (j = 0; (j < nral); j++)
330 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
335 for (j = 0; (j < 2); j++)
337 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
340 fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
342 if (bt->param[i].s[0])
344 fprintf(out, " %s", bt->param[i].s);
348 for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET)); j++)
350 fprintf (out, "%13.6e ", bt->param[i].c[j]);
360 void print_blocka(FILE *out, const char *szName,
361 const char *szIndex, const char *szA,
366 fprintf (out, "; %s\n", szName);
367 fprintf (out, "; %4s %s\n", szIndex, szA);
368 for (i = 0; (i < block->nr); i++)
370 for (i = 0; (i < block->nr); i++)
372 fprintf (out, "%6d", i+1);
373 for (j = block->index[i]; (j < ((int)block->index[i+1])); j++)
375 fprintf (out, "%5d", block->a[j]+1);
383 void print_excl(FILE *out, int natoms, t_excls excls[])
390 for (i = 0; i < natoms && !have_excl; i++)
392 have_excl = (excls[i].nr > 0);
397 fprintf (out, "[ %s ]\n", dir2str(d_exclusions));
398 fprintf (out, "; %4s %s\n", "i", "excluded from i");
399 for (i = 0; i < natoms; i++)
403 fprintf (out, "%6d ", i+1);
404 for (j = 0; j < excls[i].nr; j++)
406 fprintf (out, " %5d", excls[i].e[j]+1);
416 static double get_residue_charge(const t_atoms *atoms, int at)
421 ri = atoms->atom[at].resind;
423 while (at < atoms->nr && atoms->atom[at].resind == ri)
425 q += atoms->atom[at].q;
432 void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
433 gmx_bool bRTPresname)
441 as = dir2str(d_atoms);
442 fprintf(out, "[ %s ]\n", as);
443 fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
444 "nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
450 fprintf(debug, "This molecule has %d atoms and %d residues\n",
456 /* if the information is present... */
457 for (i = 0; (i < at->nr); i++)
459 ri = at->atom[i].resind;
460 if ((i == 0 || ri != at->atom[i-1].resind) &&
461 at->resinfo[ri].rtp != NULL)
463 qres = get_residue_charge(at, i);
464 fprintf(out, "; residue %3d %-3s rtp %-4s q ",
466 *at->resinfo[ri].name,
467 *at->resinfo[ri].rtp);
468 if (fabs(qres) < 0.001)
470 fprintf(out, " %s", "0.0");
474 fprintf(out, "%+3.1f", qres);
478 tpA = at->atom[i].type;
479 if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
481 gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
484 fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
489 *(at->resinfo[at->atom[i].resind].rtp) :
490 *(at->resinfo[at->atom[i].resind].name),
491 *(at->atomname[i]), cgnr[i],
492 at->atom[i].q, at->atom[i].m);
493 if (PERTURBED(at->atom[i]))
495 tpB = at->atom[i].typeB;
496 if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
498 gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
500 fprintf(out, " %6s %10g %10g",
501 tpnmB, at->atom[i].qB, at->atom[i].mB);
503 qtot += (double)at->atom[i].q;
504 if (fabs(qtot) < 4*GMX_REAL_EPS)
508 fprintf(out, " ; qtot %.4g\n", qtot);
515 void print_bondeds(FILE *out, int natoms, directive d,
516 int ftype, int fsubtype, t_params plist[])
519 gpp_atomtype_t atype;
524 atype = init_atomtype();
528 for (i = 0; (i < natoms); i++)
531 sprintf(buf, "%4d", (i+1));
532 add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
534 print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
539 done_atomtype(atype);