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) 2013, 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.
38 #ifndef GMX_FILEIO_ENXIO_H
39 #define GMX_FILEIO_ENXIO_H
41 #include "../legacyheaders/sysstuff.h"
42 #include "../legacyheaders/typedefs.h"
43 #include "../legacyheaders/pbc.h"
50 /**************************************************************
51 * These are the base datatypes + functions for reading and
52 * writing energy files (.edr). They are either called directly
53 * (as in the processing tools), or indirectly through mdebin.c
56 * The routines in the corresponding c-file enxio.c
57 * are based on the lower level routines in gmxfio.c.
58 * The file pointer returned from open_enx
59 * can also be used with the routines in gmxfio.h
61 **************************************************************/
69 * Index for the IDs of additional blocks in the energy file.
70 * Blocks can be added without sacrificing backward and forward
71 * compatibility of the energy files.
73 * For backward compatibility, the order of these should not be changed.
76 enxOR, /* Time and ensemble averaged data for orientation restraints */
77 enxORI, /* Instantaneous data for orientation restraints */
78 enxORT, /* Order tensor(s) for orientation restraints */
79 enxDISRE, /* Distance restraint blocks */
81 enxDHCOLL, /* Data about the free energy blocks in this frame. */
82 enxDHHIST, /* BAR histogram */
83 enxDH, /* BAR raw delta H data */
85 enxNR /* Total number of extra blocks in the current code,
86 * note that the enxio code can read files written by
87 * future code which contain more blocks.
91 /* names for the above enum */
92 extern const char *enx_block_id_name[];
95 /* the subblocks that are contained in energy file blocks. Each of these
96 has a number of values of a single data type in a .edr file. */
99 int nr; /* number of items in subblock */
100 xdr_datatype type; /* the block type */
102 /* the values: pointers for each type */
106 gmx_large_int_t* lval;
110 /* the allocated sizes, defined separately.
111 (nonzero sizes can be free()d later): */
121 /* the energy file blocks. Each block contains a number of sub-blocks
122 of a single type that contain the actual data. */
123 typedef struct t_enxblock{
124 int id; /* block id, from the enx enums above */
125 int nsub; /* number of subblocks */
126 t_enxsubblock *sub; /* the subblocks */
127 int nsub_alloc; /* number of allocated subblocks */
131 /* The frames that are read/written */
133 double t; /* Timestamp of this frame */
134 gmx_large_int_t step; /* MD step */
135 gmx_large_int_t nsteps; /* The number of steps between frames */
136 double dt; /* The MD time step */
137 int nsum; /* The number of terms for the sums in ener */
138 int nre; /* Number of energies */
139 int e_size; /* Size (in bytes) of energies */
140 int e_alloc; /* Allocated size (in elements) of ener */
141 t_energy *ener; /* The energies */
142 int nblock; /* Number of following energy blocks */
143 t_enxblock *block; /* The blocks */
144 int nblock_alloc; /* The number of blocks allocated */
148 typedef struct ener_file *ener_file_t;
151 * An energy file is read like this:
156 * fp = open_enx(...);
159 * while (do_enx(fp,fr)) {
165 /* New energy reading and writing interface */
168 /* initialize a pre-allocated frame */
169 void init_enxframe(t_enxframe *ef);
170 /* delete a frame's memory (except the ef itself) */
171 void free_enxframe(t_enxframe *ef);
174 ener_file_t open_enx(const char *fn, const char *mode);
176 t_fileio *enx_file_pointer(const ener_file_t ef);
178 void close_enx(ener_file_t ef);
180 void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms);
182 void free_enxnms(int n, gmx_enxnm_t *nms);
183 /* Frees nms and all strings in it */
185 gmx_bool do_enx(ener_file_t ef, t_enxframe *fr);
186 /* Reads enx_frames, memory in fr is (re)allocated if necessary */
188 void get_enx_state(const char *fn, real t,
189 gmx_groups_t *groups, t_inputrec *ir,
192 * Reads state variables from enx file fn at time t.
193 * atoms and ir are required for determining which things must be read.
194 * Currently pcoupl and tcoupl state are read from enx.
200 /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
201 void add_blocks_enxframe(t_enxframe *ef, int n);
203 /* find a block by id number; if prev!=NULL, it searches from
204 that block's next block.
205 Returns NULL if no block is found with the given id. */
206 t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev);
209 /* allocate n subblocks to a block (if neccesary). Don't touch existing
211 void add_subblocks_enxblock(t_enxblock *eb, int n);
219 #endif /* GMX_FILEIO_ENERIO_H */