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37 #ifndef GMX_FILEIO_ENXIO_H
38 #define GMX_FILEIO_ENXIO_H
40 #include "gromacs/fileio/xdr_datatype.h"
41 #include "gromacs/mdtypes/state.h"
42 #include "gromacs/trajectory/energy.h"
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
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
59 **************************************************************/
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.
71 * For backward compatibility, the order of these should not be changed.
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 */
79 enxDHCOLL
, /* Data about the free energy blocks in this frame. */
80 enxDHHIST
, /* BAR histogram */
81 enxDH
, /* BAR raw delta H data */
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.
89 /* names for the above enum */
90 extern const char *enx_block_id_name
[];
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. */
97 int nr
; /* number of items in subblock */
98 xdr_datatype type
; /* the block type */
100 /* the values: pointers for each type */
108 /* the allocated sizes, defined separately.
109 (nonzero sizes can be free()d later): */
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 */
129 /* The frames that are read/written */
131 double t
; /* Timestamp of this frame */
132 gmx_int64_t step
; /* MD step */
133 gmx_int64_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 */
146 typedef struct ener_file
*ener_file_t
;
149 * An energy file is read like this:
154 * fp = open_enx(...);
157 * while (do_enx(fp,fr)) {
163 /* New energy reading and writing interface */
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
);
172 ener_file_t
open_enx(const char *fn
, const char *mode
);
174 struct t_fileio
*enx_file_pointer(const ener_file_t ef
);
176 /* Free the contents of ef */
177 void close_enx(ener_file_t ef
);
179 /* Free the contents of ef, and ef itself */
180 void done_ener_file(ener_file_t ef
);
182 void do_enxnms(ener_file_t ef
, int *nre
, gmx_enxnm_t
**enms
);
184 void free_enxnms(int n
, gmx_enxnm_t
*nms
);
185 /* Frees nms and all strings in it */
187 gmx_bool
do_enx(ener_file_t ef
, t_enxframe
*fr
);
188 /* Reads enx_frames, memory in fr is (re)allocated if necessary */
190 void get_enx_state(const char *fn
, real t
,
191 const gmx_groups_t
*groups
, t_inputrec
*ir
,
194 * Reads state variables from enx file fn at time t.
195 * atoms and ir are required for determining which things must be read.
196 * Currently pcoupl and tcoupl state are read from enx.
202 /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
203 void add_blocks_enxframe(t_enxframe
*ef
, int n
);
205 /* find a block by id number; if prev!=NULL, it searches from
206 that block's next block.
207 Returns NULL if no block is found with the given id. */
208 t_enxblock
*find_block_id_enxframe(t_enxframe
*ef
, int id
, t_enxblock
*prev
);
211 /* allocate n subblocks to a block (if neccesary). Don't touch existing
213 void add_subblocks_enxblock(t_enxblock
*eb
, int n
);
215 void comp_enx(const char *fn1
, const char *fn2
, real ftol
, real abstol
,
216 const char *lastener
);
217 /* Compare two binary energy files */