/usr/include/gromacs/fileio/enxio.h is in libgromacs-dev 2018.1-1.
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* This file is part of the GROMACS molecular simulation package.
*
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* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
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#ifndef GMX_FILEIO_ENXIO_H
#define GMX_FILEIO_ENXIO_H
#include "gromacs/fileio/xdr_datatype.h"
#include "gromacs/trajectory/energy.h"
#include "gromacs/utility/basedefinitions.h"
struct gmx_groups_t;
struct t_fileio;
struct t_inputrec;
class t_state;
/**************************************************************
* These are the base datatypes + functions for reading and
* writing energy files (.edr). They are either called directly
* (as in the processing tools), or indirectly through mdebin.c
* during mdrun.
*
* The routines in the corresponding c-file enxio.c
* are based on the lower level routines in gmxfio.c.
* The file pointer returned from open_enx
* can also be used with the routines in gmxfio.h
*
**************************************************************/
typedef struct {
char *name;
char *unit;
} gmx_enxnm_t;
/*
* Index for the IDs of additional blocks in the energy file.
* Blocks can be added without sacrificing backward and forward
* compatibility of the energy files.
*
* For backward compatibility, the order of these should not be changed.
*/
enum {
enxOR, /* Time and ensemble averaged data for orientation restraints */
enxORI, /* Instantaneous data for orientation restraints */
enxORT, /* Order tensor(s) for orientation restraints */
enxDISRE, /* Distance restraint blocks */
enxDHCOLL, /* Data about the free energy blocks in this frame. */
enxDHHIST, /* BAR histogram */
enxDH, /* BAR raw delta H data */
enxAWH, /* AWH data */
enxNR /* Total number of extra blocks in the current code,
* note that the enxio code can read files written by
* future code which contain more blocks.
*/
};
/* names for the above enum */
extern const char *enx_block_id_name[];
/* the subblocks that are contained in energy file blocks. Each of these
has a number of values of a single data type in a .edr file. */
struct t_enxsubblock
{
int nr; /* number of items in subblock */
xdr_datatype type; /* the block type */
/* the values: pointers for each type */
float* fval;
double* dval;
int* ival;
gmx_int64_t* lval;
unsigned char* cval;
char** sval;
/* the allocated sizes, defined separately.
(nonzero sizes can be free()d later): */
int fval_alloc;
int dval_alloc;
int ival_alloc;
int lval_alloc;
int cval_alloc;
int sval_alloc;
};
/* the energy file blocks. Each block contains a number of sub-blocks
of a single type that contain the actual data. */
typedef struct t_enxblock{
int id; /* block id, from the enx enums above */
int nsub; /* number of subblocks */
t_enxsubblock *sub; /* the subblocks */
int nsub_alloc; /* number of allocated subblocks */
} t_enxblock;
/* The frames that are read/written */
struct t_enxframe {
double t; /* Timestamp of this frame */
gmx_int64_t step; /* MD step */
gmx_int64_t nsteps; /* The number of steps between frames */
double dt; /* The MD time step */
int nsum; /* The number of terms for the sums in ener */
int nre; /* Number of energies */
int e_size; /* Size (in bytes) of energies */
int e_alloc; /* Allocated size (in elements) of ener */
t_energy *ener; /* The energies */
int nblock; /* Number of following energy blocks */
t_enxblock *block; /* The blocks */
int nblock_alloc; /* The number of blocks allocated */
};
/* file handle */
typedef struct ener_file *ener_file_t;
/*
* An energy file is read like this:
*
* ener_file_t fp;
* t_enxframe *fr;
*
* fp = open_enx(...);
* do_enxnms(fp,...);
* snew(fr,1);
* while (do_enx(fp,fr)) {
* ...
* }
* free_enxframe(fr);
* sfree(fr);
*/
/* New energy reading and writing interface */
/* initialize a pre-allocated frame */
void init_enxframe(t_enxframe *ef);
/* delete a frame's memory (except the ef itself) */
void free_enxframe(t_enxframe *ef);
ener_file_t open_enx(const char *fn, const char *mode);
struct t_fileio *enx_file_pointer(const ener_file_t ef);
/* Free the contents of ef */
void close_enx(ener_file_t ef);
/* Free the contents of ef, and ef itself */
void done_ener_file(ener_file_t ef);
void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms);
void free_enxnms(int n, gmx_enxnm_t *nms);
/* Frees nms and all strings in it */
gmx_bool do_enx(ener_file_t ef, t_enxframe *fr);
/* Reads enx_frames, memory in fr is (re)allocated if necessary */
void get_enx_state(const char *fn, real t,
const gmx_groups_t *groups, t_inputrec *ir,
t_state *state);
/*
* Reads state variables from enx file fn at time t.
* atoms and ir are required for determining which things must be read.
* Currently pcoupl and tcoupl state are read from enx.
*/
/* block funtions */
/* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
void add_blocks_enxframe(t_enxframe *ef, int n);
/* find a block by id number; if prev!=NULL, it searches from
that block's next block.
Returns NULL if no block is found with the given id. */
t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev);
/* allocate n subblocks to a block (if neccesary). Don't touch existing
subbblocks. */
void add_subblocks_enxblock(t_enxblock *eb, int n);
void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol,
const char *lastener);
/* Compare two binary energy files */
#endif
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