include/enxio.h

   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  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Gromacs Runs On Most of All Computer Systems
  34  */
  35
  36 #ifndef _enxio_h
  37 #define _enxio_h
  38
  39 #include "sysstuff.h"
  40 #include "typedefs.h"
  41 #include "pbc.h"
  42 #include "gmxfio.h"
  43
  44 #ifdef __cplusplus
  45 extern "C" {
  46 #endif
  47
  48   /**************************************************************
  49    * These are the base datatypes + functions for reading and
  50    * writing energy files (.edr). They are either called directly
  51    * (as in the processing tools), or indirectly through mdebin.c
  52    * during mdrun.
  53    *
  54    * The routines in the corresponding c-file enxio.c
  55    * are based on the lower level routines in gmxfio.c.
  56    * The file pointer returned from open_enx
  57    * can also be used with the routines in gmxfio.h
  58    *
  59    **************************************************************/
  60
  61   typedef struct {
  62     char *name;
  63     char *unit;
  64   } gmx_enxnm_t;
  65
  66   /*
  67    * Index for the IDs of additional blocks in the energy file.
  68    * Blocks can be added without sacrificing backward and forward
  69    * compatibility of the energy files.
  70    *
  71    * For backward compatibility, the order of these should not be changed.
  72    */
  73   enum {
  74     enxOR,     /* Time and ensemble averaged data for orientation restraints */
  75     enxORI,    /* Instantaneous data for orientation restraints              */
  76     enxORT,    /* Order tensor(s) for orientation restraints                 */
  77     enxDISRE,  /* Distance restraint blocks                                  */
  78
  79     enxDHCOLL, /* Data about the free energy blocks in this frame.           */
  80     enxDHHIST, /* BAR histogram                                              */
  81     enxDH,     /* BAR raw delta H data                                       */
  82
  83     enxNR      /* Total number of extra blocks in the current code,
  84                 * note that the enxio code can read files written by
  85                 * future code which contain more blocks.
  86                 */
  87   };
  88
  89   /* names for the above enum */
  90   extern const char *enx_block_id_name[];
  91
  92
  93   /* the subblocks that are contained in energy file blocks. Each of these
  94      has a number of values of a single data type in a .edr file. */
  95   typedef struct
  96   {
  97       int nr;               /* number of items in subblock */
  98       xdr_datatype type;    /* the block type */
  99
 100       /* the values: pointers for each type */
 101       float*             fval;
 102       double*            dval;
 103       int*               ival;
 104       gmx_large_int_t*   lval;
 105       unsigned char*     cval;
 106       char**             sval;
 107
 108       /* the allocated sizes, defined separately.
 109          (nonzero sizes can be free()d later): */
 110       int fval_alloc;
 111       int dval_alloc;
 112       int ival_alloc;
 113       int lval_alloc;
 114       int cval_alloc;
 115       int sval_alloc;
 116   } t_enxsubblock;
 117
 118
 119   /* the energy file blocks. Each block contains a number of sub-blocks
 120      of a single type that contain the actual data. */
 121   typedef struct t_enxblock{
 122       int id;               /* block id, from the enx enums above */
 123       int nsub;             /* number of subblocks */
 124       t_enxsubblock *sub;   /* the subblocks */
 125       int nsub_alloc;       /* number of allocated subblocks */
 126   } t_enxblock;
 127
 128
 129   /* The frames that are read/written */
 130   typedef struct {
 131     double   t;             /* Timestamp of this frame                       */
 132     gmx_large_int_t step;   /* MD step                                       */
 133     gmx_large_int_t nsteps; /* The number of steps between frames            */
 134     double   dt;            /* The MD time step                              */
 135     int      nsum;          /* The number of terms for the sums in ener      */
 136     int      nre;           /* Number of energies                            */
 137     int      e_size;        /* Size (in bytes) of energies                   */
 138     int      e_alloc;       /* Allocated size (in elements) of ener          */
 139     t_energy *ener;         /* The energies                                  */
 140     int      nblock;        /* Number of following energy blocks             */
 141     t_enxblock *block;      /* The blocks                                    */
 142     int      nblock_alloc;  /* The number of blocks allocated                */
 143   } t_enxframe;
 144
 145   /* file handle */
 146   typedef struct ener_file *ener_file_t;
 147
 148   /*
 149    * An energy file is read like this:
 150    *
 151    * ener_file_t fp;
 152    * t_enxframe *fr;
 153    *
 154    * fp = open_enx(...);
 155    * do_enxnms(fp,...);
 156    * snew(fr,1);
 157    * while (do_enx(fp,fr)) {
 158    * ...
 159    * }
 160    * free_enxframe(fr);
 161    * sfree(fr);
 162    */
 163   /* New energy reading and writing interface */
 164
 165
 166   /* initialize a pre-allocated frame */
 167   void init_enxframe(t_enxframe *ef);
 168   /* delete a frame's memory (except the ef itself) */
 169   void free_enxframe(t_enxframe *ef);
 170
 171
 172   ener_file_t open_enx(const char *fn,const char *mode);
 173
 174   t_fileio *enx_file_pointer(const ener_file_t ef);
 175
 176   void close_enx(ener_file_t ef);
 177
 178   void do_enxnms(ener_file_t ef,int *nre,gmx_enxnm_t **enms);
 179
 180   void free_enxnms(int n,gmx_enxnm_t *nms);
 181   /* Frees nms and all strings in it */
 182
 183   gmx_bool do_enx(ener_file_t ef,t_enxframe *fr);
 184   /* Reads enx_frames, memory in fr is (re)allocated if necessary */
 185
 186   void get_enx_state(const char *fn, real t,
 187                             gmx_groups_t *groups, t_inputrec *ir,
 188                             t_state *state);
 189   /*
 190    * Reads state variables from enx file fn at time t.
 191    * atoms and ir are required for determining which things must be read.
 192    * Currently pcoupl and tcoupl state are read from enx.
 193    */
 194
 195
 196   /* block funtions */
 197
 198   /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
 199   void add_blocks_enxframe(t_enxframe *ef, int n);
 200
 201   /* find a block by id number; if prev!=NULL, it searches from
 202      that block's next block.
 203      Returns NULL if no block is found with the given id. */
 204   t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev);
 205
 206
 207    /* allocate n subblocks to a block (if neccesary). Don't touch existing
 208       subbblocks. */
 209   void add_subblocks_enxblock(t_enxblock *eb, int n);
 210
 211
 212
 213 #ifdef __cplusplus
 214 }
 215 #endif
 216
 217 #endif  /* _enerio_h */