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37 #ifndef GMX_FILEIO_ENXIO_H
38 #define GMX_FILEIO_ENXIO_H
40 #include "../legacyheaders/typedefs.h"
41 #include "../legacyheaders/pbc.h"
43 #include "xdr_datatype.h"
49 /**************************************************************
50 * These are the base datatypes + functions for reading and
51 * writing energy files (.edr). They are either called directly
52 * (as in the processing tools), or indirectly through mdebin.c
55 * The routines in the corresponding c-file enxio.c
56 * are based on the lower level routines in gmxfio.c.
57 * The file pointer returned from open_enx
58 * can also be used with the routines in gmxfio.h
60 **************************************************************/
68 * Index for the IDs of additional blocks in the energy file.
69 * Blocks can be added without sacrificing backward and forward
70 * compatibility of the energy files.
72 * For backward compatibility, the order of these should not be changed.
75 enxOR, /* Time and ensemble averaged data for orientation restraints */
76 enxORI, /* Instantaneous data for orientation restraints */
77 enxORT, /* Order tensor(s) for orientation restraints */
78 enxDISRE, /* Distance restraint blocks */
80 enxDHCOLL, /* Data about the free energy blocks in this frame. */
81 enxDHHIST, /* BAR histogram */
82 enxDH, /* BAR raw delta H data */
84 enxNR /* Total number of extra blocks in the current code,
85 * note that the enxio code can read files written by
86 * future code which contain more blocks.
90 /* names for the above enum */
91 extern const char *enx_block_id_name[];
94 /* the subblocks that are contained in energy file blocks. Each of these
95 has a number of values of a single data type in a .edr file. */
98 int nr; /* number of items in subblock */
99 xdr_datatype type; /* the block type */
101 /* the values: pointers for each type */
109 /* the allocated sizes, defined separately.
110 (nonzero sizes can be free()d later): */
120 /* the energy file blocks. Each block contains a number of sub-blocks
121 of a single type that contain the actual data. */
122 typedef struct t_enxblock{
123 int id; /* block id, from the enx enums above */
124 int nsub; /* number of subblocks */
125 t_enxsubblock *sub; /* the subblocks */
126 int nsub_alloc; /* number of allocated subblocks */
130 /* The frames that are read/written */
132 double t; /* Timestamp of this frame */
133 gmx_int64_t step; /* MD step */
134 gmx_int64_t nsteps; /* The number of steps between frames */
135 double dt; /* The MD time step */
136 int nsum; /* The number of terms for the sums in ener */
137 int nre; /* Number of energies */
138 int e_size; /* Size (in bytes) of energies */
139 int e_alloc; /* Allocated size (in elements) of ener */
140 t_energy *ener; /* The energies */
141 int nblock; /* Number of following energy blocks */
142 t_enxblock *block; /* The blocks */
143 int nblock_alloc; /* The number of blocks allocated */
147 typedef struct ener_file *ener_file_t;
150 * An energy file is read like this:
155 * fp = open_enx(...);
158 * while (do_enx(fp,fr)) {
164 /* New energy reading and writing interface */
167 /* initialize a pre-allocated frame */
168 void init_enxframe(t_enxframe *ef);
169 /* delete a frame's memory (except the ef itself) */
170 void free_enxframe(t_enxframe *ef);
173 ener_file_t open_enx(const char *fn, const char *mode);
175 t_fileio *enx_file_pointer(const ener_file_t ef);
177 void close_enx(ener_file_t ef);
179 void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms);
181 void free_enxnms(int n, gmx_enxnm_t *nms);
182 /* Frees nms and all strings in it */
184 gmx_bool do_enx(ener_file_t ef, t_enxframe *fr);
185 /* Reads enx_frames, memory in fr is (re)allocated if necessary */
187 void get_enx_state(const char *fn, real t,
188 gmx_groups_t *groups, t_inputrec *ir,
191 * Reads state variables from enx file fn at time t.
192 * atoms and ir are required for determining which things must be read.
193 * Currently pcoupl and tcoupl state are read from enx.
199 /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
200 void add_blocks_enxframe(t_enxframe *ef, int n);
202 /* find a block by id number; if prev!=NULL, it searches from
203 that block's next block.
204 Returns NULL if no block is found with the given id. */
205 t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev);
208 /* allocate n subblocks to a block (if neccesary). Don't touch existing
210 void add_subblocks_enxblock(t_enxblock *eb, int n);