src/gromacs/topology/index.h

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   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, 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.
  10  *
  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.
  15  *
  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.
  20  *
  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.
  25  *
  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.
  33  *
  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.
  36  */
  37 #ifndef GMX_TOPOLOGY_INDEX_H
  38 #define GMX_TOPOLOGY_INDEX_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/utility/basedefinitions.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 struct t_atoms;
  49 struct t_blocka;
  50
  51 void check_index(char *gname, int n, int index[],
  52                  char *traj, int natoms);
  53 /* Checks if any index is smaller than zero or larger than natoms,
  54  * if so a fatal_error is given with the gname (if gname=NULL, "Index" is used)
  55  * and traj (if traj=NULL, "the trajectory" is used).
  56  */
  57
  58 struct t_blocka *init_index(const char *gfile, char ***grpname);
  59 /* Lower level routine than the next */
  60
  61 void rd_index(const char *statfile, int ngrps, int isize[],
  62               int *index[], char *grpnames[]);
  63 /* Assume the group file is generated, so the
  64  * format need not be user-friendly. The format is:
  65  * nr of groups, total nr of atoms
  66  * for each group: name nr of element, elements.
  67  *
  68  * The function opens a file, reads ngrps groups, asks the
  69  * user for group numbers, and puts the resulting sizes in
  70  * isize, the int s in index and the names of
  71  * the groups in grpnames.
  72  *
  73  * It is also assumed, that when ngrps groups are requested
  74  * memory has been allocated for ngrps index arrays, and that
  75  * the dimension of the isize and grpnames arrays are ngrps.
  76  */
  77
  78 void rd_index_nrs(char *statfile, int ngrps, int isize[],
  79                   int *index[], char *grpnames[], int grpnr[]);
  80 /* the same but also reads the number of the selected group*/
  81
  82 void get_index(const t_atoms *atoms, const char *fnm, int ngrps,
  83                int isize[], int *index[], char *grpnames[]);
  84 /* Does the same as rd_index, but if the fnm pointer is NULL it
  85  * will not read from fnm, but it will make default index groups
  86  * for the atoms in *atoms.
  87  */
  88
  89 typedef struct {
  90     int               maxframe;
  91     char            **grpname;
  92     struct t_blocka  *clust;
  93     int              *inv_clust;
  94 } t_cluster_ndx;
  95
  96 t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx);
  97
  98
  99 void write_index(const char *outf, struct t_blocka *b, char **gnames, gmx_bool bDuplicate, int natoms);
 100 /* Writes index blocks to outf (writes an indexfile) */
 101
 102 void add_grp(struct t_blocka *b, char ***gnames, int nra, int a[], const char *name);
 103 /* Ads group a with name name to block b and namelist gnames */
 104
 105 void analyse(const t_atoms *atoms, struct t_blocka *gb, char ***gn,
 106              gmx_bool bASK, gmx_bool bVerb);
 107 /* Makes index groups gb with names gn for atoms in atoms.
 108  * bASK=FALSE gives default groups.
 109  */
 110
 111 /*! \brief Look up a group in a list.
 112  *
 113  * \param[inout] s    The string to look up
 114  * \param[in] ngrps   The number of groups
 115  * \param[in] grpname The names of the groups
 116  * \return the group number or -1 if not found.
 117  */
 118 int find_group(const char *s, int ngrps, char **grpname);
 119
 120
 121 #ifdef __cplusplus
 122 }
 123 #endif
 124
 125 #endif