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.
40 #include "gromacs/topology/block.h"
42 #include "gromacs/utility/smalloc.h"
44 void init_block(t_block *block)
47 block->nalloc_index = 1;
48 snew(block->index, block->nalloc_index);
52 void init_blocka(t_blocka *block)
56 block->nalloc_index = 1;
57 snew(block->index, block->nalloc_index);
63 t_blocka *new_blocka(void)
68 snew(block->index, 1);
73 void done_block(t_block *block)
77 block->nalloc_index = 0;
80 void done_blocka(t_blocka *block)
88 block->nalloc_index = 0;
92 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup)
96 grp->nalloc_index = 2;
97 snew(grp->index, grp->nalloc_index);
99 grp->index[1] = natom;
104 grp->nalloc_index = natom+1;
105 snew(grp->index, grp->nalloc_index);
106 snew(grp->index, natom+1);
107 for (int i = 0; i <= natom; ++i)
115 void stupid_fill_blocka(t_blocka *grp, int natom)
117 grp->nalloc_a = natom;
118 snew(grp->a, grp->nalloc_a);
119 for (int i = 0; i < natom; ++i)
125 grp->nalloc_index = natom + 1;
126 snew(grp->index, grp->nalloc_index);
127 for (int i = 0; i <= natom; ++i)
134 void copy_blocka(const t_blocka *src, t_blocka *dest)
137 /* Workaround for inconsistent handling of nalloc_index in
138 * other parts of the code. Often nalloc_index and nalloc_a
141 dest->nalloc_index = std::max(src->nalloc_index, dest->nr + 1);
142 snew(dest->index, dest->nalloc_index);
143 for (int i = 0; i < dest->nr+1; ++i)
145 dest->index[i] = src->index[i];
147 dest->nra = src->nra;
149 dest->nalloc_a = std::max(src->nalloc_a, dest->nra);
150 snew(dest->a, dest->nalloc_a);
151 for (int i = 0; i < dest->nra; ++i)
153 dest->a[i] = src->a[i];