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) 2010,2014,2015,2016,2017,2018,2019, 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 #ifndef GMX_TOPOLOGY_INDEX_H
38 #define GMX_TOPOLOGY_INDEX_H
42 #include "gromacs/utility/arrayref.h"
43 #include "gromacs/utility/basedefinitions.h"
48 void check_index(const char* gname, int n, int index[], const char* traj, int natoms);
49 /* Checks if any index is smaller than zero or larger than natoms,
50 * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
51 * and traj (if traj=NULL, "the trajectory" is used).
54 struct t_blocka* init_index(const char* gfile, char*** grpname);
55 /* Lower level routine than the next */
57 void rd_index(const char* statfile, int ngrps, int isize[], int* index[], char* grpnames[]);
58 /* Assume the group file is generated, so the
59 * format need not be user-friendly. The format is:
60 * nr of groups, total nr of atoms
61 * for each group: name nr of element, elements.
63 * The function opens a file, reads ngrps groups, asks the
64 * user for group numbers, and puts the resulting sizes in
65 * isize, the int s in index and the names of
66 * the groups in grpnames.
68 * It is also assumed, that when ngrps groups are requested
69 * memory has been allocated for ngrps index arrays, and that
70 * the dimension of the isize and grpnames arrays are ngrps.
73 void get_index(const t_atoms* atoms, const char* fnm, int ngrps, int isize[], int* index[], char* grpnames[]);
74 /* Does the same as rd_index, but if the fnm pointer is NULL it
75 * will not read from fnm, but it will make default index groups
76 * for the atoms in *atoms.
83 struct t_blocka* clust;
87 t_cluster_ndx* cluster_index(FILE* fplog, const char* ndx);
90 void write_index(const char* outf, struct t_blocka* b, char** gnames, gmx_bool bDuplicate, int natoms);
91 /* Writes index blocks to outf (writes an indexfile) */
94 * Add a new group with \p name to \p b.
96 * \param[in] b Block struct to add group to.
97 * \param[in] gnames Names of groups.
98 * \param[in] a Group to add to Block.
99 * \param[in] name Group name.
101 void add_grp(struct t_blocka* b, char*** gnames, gmx::ArrayRef<const int> a, const std::string& name);
102 /* Ads group a with name name to block b and namelist gnames */
104 void analyse(const t_atoms* atoms, struct t_blocka* gb, char*** gn, gmx_bool bASK, gmx_bool bVerb);
105 /* Makes index groups gb with names gn for atoms in atoms.
106 * bASK=FALSE gives default groups.
109 /*! \brief Look up a group in a list.
111 * \param[inout] s The string to look up
112 * \param[in] ngrps The number of groups
113 * \param[in] grpname The names of the groups
114 * \return the group number or -1 if not found.
116 int find_group(const char* s, int ngrps, char** grpname);