src/gromacs/topology/block.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, 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_BLOCK_H
  38 #define GMX_TOPOLOGY_BLOCK_H
  39
  40 #include <stdio.h>
  41
  42 #include "gromacs/utility/basedefinitions.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48 /* the block structure points into an array (usually of ints).
  49    It is a list of starting indices for objects of consecutive ids, such
  50    as molecules.
  51    For example, if this block denotes molecules, then the first molecule
  52    ranges from index[0] to index[1]-1 in the atom list.
  53
  54    This makes the mapping from atoms to molecules O(Nmolecules) instead
  55    of O(Natoms) in size.  */
  56 typedef struct t_block
  57 {
  58     int      nr;           /* The number of blocks          */
  59     int     *index;        /* Array of indices (dim: nr+1)  */
  60     int      nalloc_index; /* The allocation size for index */
  61 } t_block;
  62
  63 typedef struct t_blocka
  64 {
  65     int      nr;    /* The number of blocks              */
  66     int     *index; /* Array of indices in a (dim: nr+1) */
  67     int      nra;   /* The number of atoms               */
  68     int     *a;     /* Array of atom numbers in each group  */
  69     /* (dim: nra)                           */
  70     /* Block i (0<=i<nr) runs from          */
  71     /* index[i] to index[i+1]-1. There will */
  72     /* allways be an extra entry in index   */
  73     /* to terminate the table               */
  74     int nalloc_index;           /* The allocation size for index        */
  75     int nalloc_a;               /* The allocation size for a            */
  76 } t_blocka;
  77
  78 void init_block(t_block *block);
  79 void init_blocka(t_blocka *block);
  80 t_blocka *new_blocka(void);
  81 /* allocate new block */
  82
  83 void done_block(t_block *block);
  84 void done_blocka(t_blocka *block);
  85
  86 void copy_blocka(const t_blocka *src, t_blocka *dest);
  87
  88 void stupid_fill_block(t_block *grp, int natom, gmx_bool bOneIndexGroup);
  89 /* Fill a block structure with numbers identical to the index
  90  * (0, 1, 2, .. natom-1)
  91  * If bOneIndexGroup, then all atoms are  lumped in one index group,
  92  * otherwise there is one atom per index entry
  93  */
  94
  95 void stupid_fill_blocka(t_blocka *grp, int natom);
  96 /* Fill a block structure with numbers identical to the index
  97  * (0, 1, 2, .. natom-1)
  98  * There is one atom per index entry
  99  */
 100
 101 void pr_block(FILE *fp, int indent, const char *title, const t_block *block, gmx_bool bShowNumbers);
 102 void pr_blocka(FILE *fp, int indent, const char *title, const t_blocka *block, gmx_bool bShowNumbers);
 103
 104 #ifdef __cplusplus
 105 }
 106 #endif
 107
 108 #endif