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) 2013,2014, 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.
37 #include "gromacs/topology/topology.h"
39 #include "gromacs/topology/symtab.h"
40 #include "gromacs/utility/smalloc.h"
42 static void init_groups(gmx_groups_t *groups)
45 groups->grpname = NULL;
46 for (int g = 0; g < egcNR; g++)
48 groups->grps[g].nm_ind = NULL;
49 groups->ngrpnr[g] = 0;
50 groups->grpnr[g] = NULL;
55 void init_mtop(gmx_mtop_t *mtop)
61 mtop->molblock = NULL;
62 mtop->maxres_renum = 0;
64 init_groups(&mtop->groups);
65 init_block(&mtop->mols);
66 open_symtab(&mtop->symtab);
69 void init_top(t_topology *top)
72 init_atom(&(top->atoms));
73 init_atomtypes(&(top->atomtypes));
74 init_block(&top->cgs);
75 init_block(&top->mols);
76 init_blocka(&top->excls);
77 open_symtab(&top->symtab);
81 void done_moltype(gmx_moltype_t *molt)
83 done_atom(&molt->atoms);
84 done_block(&molt->cgs);
85 done_blocka(&molt->excls);
87 for (int f = 0; f < F_NRE; f++)
89 sfree(molt->ilist[f].iatoms);
90 molt->ilist[f].nalloc = 0;
94 void done_molblock(gmx_molblock_t *molb)
96 if (molb->nposres_xA > 0)
99 sfree(molb->posres_xA);
101 if (molb->nposres_xB > 0)
103 molb->nposres_xB = 0;
104 sfree(molb->posres_xB);
108 void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab)
112 done_symtab(&mtop->symtab);
115 sfree(mtop->ffparams.functype);
116 sfree(mtop->ffparams.iparams);
118 for (int i = 0; i < mtop->nmoltype; i++)
120 done_moltype(&mtop->moltype[i]);
122 sfree(mtop->moltype);
123 for (int i = 0; i < mtop->nmolblock; i++)
125 done_molblock(&mtop->molblock[i]);
127 sfree(mtop->molblock);
128 done_block(&mtop->mols);
131 void done_top(t_topology *top)
133 sfree(top->idef.functype);
134 sfree(top->idef.iparams);
135 for (int f = 0; f < F_NRE; ++f)
137 sfree(top->idef.il[f].iatoms);
138 top->idef.il[f].iatoms = NULL;
139 top->idef.il[f].nalloc = 0;
142 done_atom(&(top->atoms));
145 done_atomtypes(&(top->atomtypes));
147 done_symtab(&(top->symtab));
148 done_block(&(top->cgs));
149 done_block(&(top->mols));
150 done_blocka(&(top->excls));