src/gmxlib/trajana/position.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  10  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  11  * Copyright (c) 2001-2009, The GROMACS development team,
  12  * check out http://www.gromacs.org for more information.
  13
  14  * This program is free software; you can redistribute it and/or
  15  * modify it under the terms of the GNU General Public License
  16  * as published by the Free Software Foundation; either version 2
  17  * of the License, or (at your option) any later version.
  18  *
  19  * If you want to redistribute modifications, please consider that
  20  * scientific software is very special. Version control is crucial -
  21  * bugs must be traceable. We will be happy to consider code for
  22  * inclusion in the official distribution, but derived work must not
  23  * be called official GROMACS. Details are found in the README & COPYING
  24  * files - if they are missing, get the official version at www.gromacs.org.
  25  *
  26  * To help us fund GROMACS development, we humbly ask that you cite
  27  * the papers on the package - you can find them in the top README file.
  28  *
  29  * For more info, check our website at http://www.gromacs.org
  30  */
  31 /*! \internal \file
  32  * \brief Implementation of functions in position.h.
  33  */
  34 #ifdef HAVE_CONFIG_H
  35 #include <config.h>
  36 #endif
  37
  38 #include <string.h>
  39
  40 #include <smalloc.h>
  41 #include <typedefs.h>
  42 #include <vec.h>
  43
  44 #include <indexutil.h>
  45 #include <position.h>
  46
  47 /*!
  48  * \param[out] pos      Output structure.
  49  *
  50  * Any contents of \p pos are discarded without freeing.
  51  */
  52 void
  53 gmx_ana_pos_clear(gmx_ana_pos_t *pos)
  54 {
  55     pos->nr = 0;
  56     pos->x  = NULL;
  57     gmx_ana_indexmap_clear(&pos->m);
  58     pos->g  = NULL;
  59 }
  60
  61 /*!
  62  * \param[in,out] pos   Position data structure.
  63  * \param[in]     n     Maximum number of positions.
  64  * \param[in]     isize Maximum number of atoms.
  65  *
  66  * Ensures that enough memory is allocated in \p pos to calculate \p n
  67  * positions from \p isize atoms.
  68  */
  69 void
  70 gmx_ana_pos_reserve(gmx_ana_pos_t *pos, int n, int isize)
  71 {
  72     if (pos->nr < n)
  73     {
  74         pos->nr = n;
  75         srenew(pos->x, n);
  76     }
  77     if (isize > 0)
  78     {
  79         gmx_ana_indexmap_reserve(&pos->m, n, isize);
  80     }
  81 }
  82
  83 /*!
  84  * \param[out]    pos  Position data structure to initialize.
  85  * \param[in]     x    Position vector to use.
  86  */
  87 void
  88 gmx_ana_pos_init_const(gmx_ana_pos_t *pos, rvec x)
  89 {
  90     gmx_ana_pos_clear(pos);
  91     pos->nr = 1;
  92     snew(pos->x, 1);
  93     copy_rvec(x, pos->x[0]);
  94     gmx_ana_indexmap_init(&pos->m, NULL, NULL, INDEX_UNKNOWN);
  95     pos->g  = NULL;
  96 }
  97
  98 /*!
  99  * \param[in,out] pos   Position data structure.
 100  *
 101  * Frees any memory allocated within \p pos.
 102  * The pointer \p pos itself is not freed.
 103  *
 104  * \see gmx_ana_pos_free()
 105  */
 106 void
 107 gmx_ana_pos_deinit(gmx_ana_pos_t *pos)
 108 {
 109     pos->nr = 0;
 110     sfree(pos->x); pos->x = NULL;
 111     gmx_ana_indexmap_deinit(&pos->m);
 112 }
 113
 114 /*!
 115  * \param[in,out] pos   Position data structure.
 116  *
 117  * Frees any memory allocated for \p pos.
 118  * The pointer \p pos is also freed, and is invalid after the call.
 119  *
 120  * \see gmx_ana_pos_deinit()
 121  */
 122 void
 123 gmx_ana_pos_free(gmx_ana_pos_t *pos)
 124 {
 125     gmx_ana_pos_deinit(pos);
 126     sfree(pos);
 127 }
 128
 129 /*!
 130  * \param[in,out] dest   Destination positions.
 131  * \param[in]     src    Source positions.
 132  * \param[in]     bFirst If TRUE, memory is allocated for \p dest and a full
 133  *   copy is made; otherwise, only variable parts are copied, and no memory
 134  *   is allocated.
 135  *
 136  * \p dest should have been initialized somehow (calloc() is enough).
 137  */
 138 void
 139 gmx_ana_pos_copy(gmx_ana_pos_t *dest, gmx_ana_pos_t *src, bool bFirst)
 140 {
 141     if (bFirst)
 142     {
 143         gmx_ana_pos_reserve(dest, src->nr, 0);
 144     }
 145     dest->nr = src->nr;
 146     memcpy(dest->x, src->x, dest->nr*sizeof(*dest->x));
 147     gmx_ana_indexmap_copy(&dest->m, &src->m, bFirst);
 148     dest->g = src->g;
 149 }