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) 2012,2014,2015, 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.
47 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
48 #include "gromacs/gmxpreprocess/topdirs.h"
49 #include "gromacs/legacyheaders/macros.h"
50 #include "gromacs/topology/block.h"
51 #include "gromacs/topology/symtab.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/utility/gmxassert.h"
54 #include "gromacs/utility/smalloc.h"
58 void set_p_string(t_param *p, const char *s)
62 if (strlen(s) < sizeof(p->s)-1)
64 strncpy(p->s, s, sizeof(p->s));
68 gmx_fatal(FARGS, "Increase MAXSLEN in the grompp code to at least %d,"
69 " or shorten your definition of bonds like %s to at most %d",
70 strlen(s)+1, s, MAXSLEN-1);
79 void pr_alloc (int extra, t_params *pr)
83 /* get new space for arrays */
86 gmx_fatal(FARGS, "Trying to make array smaller.\n");
92 GMX_ASSERT(pr->nr != 0 || pr->param == NULL, "Invalid t_params object");
93 if (pr->nr+extra > pr->maxnr)
95 pr->maxnr = std::max(static_cast<int>(1.2*pr->maxnr), pr->maxnr + extra);
96 srenew(pr->param, pr->maxnr);
97 for (i = pr->nr; (i < pr->maxnr); i++)
99 for (j = 0; (j < MAXATOMLIST); j++)
101 pr->param[i].a[j] = 0;
103 for (j = 0; (j < MAXFORCEPARAM); j++)
105 pr->param[i].c[j] = 0;
107 set_p_string(&(pr->param[i]), "");
112 void init_plist(t_params plist[])
116 for (i = 0; (i < F_NRE); i++)
120 plist[i].param = NULL;
124 plist[i].cmap = NULL;
125 plist[i].grid_spacing = 0;
128 plist[i].cmap_types = NULL;
132 void cp_param(t_param *dest, t_param *src)
136 for (j = 0; (j < MAXATOMLIST); j++)
138 dest->a[j] = src->a[j];
140 for (j = 0; (j < MAXFORCEPARAM); j++)
142 dest->c[j] = src->c[j];
144 strncpy(dest->s, src->s, sizeof(dest->s));
147 void add_param_to_list(t_params *list, t_param *b)
151 /* allocate one position extra */
154 /* fill the arrays */
155 for (j = 0; (j < MAXFORCEPARAM); j++)
157 list->param[list->nr].c[j] = b->c[j];
159 for (j = 0; (j < MAXATOMLIST); j++)
161 list->param[list->nr].a[j] = b->a[j];
163 memset(list->param[list->nr].s, 0, sizeof(list->param[list->nr].s));
169 void init_molinfo(t_molinfo *mol)
172 mol->excl_set = FALSE;
173 mol->bProcessed = FALSE;
174 init_plist(mol->plist);
175 init_block(&mol->cgs);
176 init_block(&mol->mols);
177 init_blocka(&mol->excls);
178 init_atom(&mol->atoms);
183 void done_bt (t_params *pl)
188 void done_mi(t_molinfo *mi)
192 done_atom (&(mi->atoms));
193 done_block(&(mi->cgs));
194 done_block(&(mi->mols));
195 for (i = 0; (i < F_NRE); i++)
197 done_bt(&(mi->plist[i]));
201 /* PRINTING STRUCTURES */
203 void print_bt(FILE *out, directive d, gpp_atomtype_t at,
204 int ftype, int fsubtype, t_params plist[],
207 /* This dihp is a DIRTY patch because the dih-types do not use
208 * all four atoms to determine the type.
210 const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
212 int i, j, f, nral, nrfp;
213 gmx_bool bDih = FALSE, bSwapParity;
215 bt = &(plist[ftype]);
243 case F_CROSS_BOND_ANGLES:
246 case F_CROSS_BOND_BONDS:
296 fprintf(out, "[ %s ]\n", dir2str(d));
300 fprintf (out, "%3s %4s", "ai", "aj");
301 for (j = 2; (j < nral); j++)
303 fprintf (out, " %3c%c", 'a', 'i'+j);
308 for (j = 0; (j < 2); j++)
310 fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
314 fprintf (out, " funct");
315 for (j = 0; (j < nrfp); j++)
317 fprintf (out, " %12c%1d", 'c', j);
321 /* print bondtypes */
322 for (i = 0; (i < bt->nr); i++)
324 bSwapParity = (bt->param[i].C0 == NOTSET) && (bt->param[i].C1 == -1);
327 for (j = 0; (j < nral); j++)
329 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
334 for (j = 0; (j < 2); j++)
336 fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
339 fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
341 if (bt->param[i].s[0])
343 fprintf(out, " %s", bt->param[i].s);
347 for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET)); j++)
349 fprintf (out, "%13.6e ", bt->param[i].c[j]);
359 void print_blocka(FILE *out, const char *szName,
360 const char *szIndex, const char *szA,
365 fprintf (out, "; %s\n", szName);
366 fprintf (out, "; %4s %s\n", szIndex, szA);
367 for (i = 0; (i < block->nr); i++)
369 for (i = 0; (i < block->nr); i++)
371 fprintf (out, "%6d", i+1);
372 for (j = block->index[i]; (j < ((int)block->index[i+1])); j++)
374 fprintf (out, "%5d", block->a[j]+1);
382 void print_excl(FILE *out, int natoms, t_excls excls[])
389 for (i = 0; i < natoms && !have_excl; i++)
391 have_excl = (excls[i].nr > 0);
396 fprintf (out, "[ %s ]\n", dir2str(d_exclusions));
397 fprintf (out, "; %4s %s\n", "i", "excluded from i");
398 for (i = 0; i < natoms; i++)
402 fprintf (out, "%6d ", i+1);
403 for (j = 0; j < excls[i].nr; j++)
405 fprintf (out, " %5d", excls[i].e[j]+1);
415 static double get_residue_charge(const t_atoms *atoms, int at)
420 ri = atoms->atom[at].resind;
422 while (at < atoms->nr && atoms->atom[at].resind == ri)
424 q += atoms->atom[at].q;
431 void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
432 gmx_bool bRTPresname)
440 as = dir2str(d_atoms);
441 fprintf(out, "[ %s ]\n", as);
442 fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
443 "nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
449 fprintf(debug, "This molecule has %d atoms and %d residues\n",
455 /* if the information is present... */
456 for (i = 0; (i < at->nr); i++)
458 ri = at->atom[i].resind;
459 if ((i == 0 || ri != at->atom[i-1].resind) &&
460 at->resinfo[ri].rtp != NULL)
462 qres = get_residue_charge(at, i);
463 fprintf(out, "; residue %3d %-3s rtp %-4s q ",
465 *at->resinfo[ri].name,
466 *at->resinfo[ri].rtp);
467 if (fabs(qres) < 0.001)
469 fprintf(out, " %s", "0.0");
473 fprintf(out, "%+3.1f", qres);
477 tpA = at->atom[i].type;
478 if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
480 gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
483 /* This is true by construction, but static analysers don't know */
484 GMX_ASSERT(!bRTPresname || at->resinfo[at->atom[i].resind].rtp, "-rtpres did not have residue name available");
485 fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
490 *(at->resinfo[at->atom[i].resind].rtp) :
491 *(at->resinfo[at->atom[i].resind].name),
492 *(at->atomname[i]), cgnr[i],
493 at->atom[i].q, at->atom[i].m);
494 if (PERTURBED(at->atom[i]))
496 tpB = at->atom[i].typeB;
497 if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
499 gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
501 fprintf(out, " %6s %10g %10g",
502 tpnmB, at->atom[i].qB, at->atom[i].mB);
504 qtot += (double)at->atom[i].q;
505 if (fabs(qtot) < 4*GMX_REAL_EPS)
509 fprintf(out, " ; qtot %.4g\n", qtot);
516 void print_bondeds(FILE *out, int natoms, directive d,
517 int ftype, int fsubtype, t_params plist[])
520 gpp_atomtype_t atype;
525 atype = init_atomtype();
529 for (i = 0; (i < natoms); i++)
532 sprintf(buf, "%4d", (i+1));
533 add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
535 print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
540 done_atomtype(atype);