/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gromacs Runs On Most of All Computer Systems
*/
extern "C" {
#endif
- /**************************************************************
- * 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 {
+/**************************************************************
+ * 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 {
+} 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 */
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. */
- typedef struct
- {
- 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_large_int_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;
- } t_enxsubblock;
-
-
- /* 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 */
- typedef struct {
- double t; /* Timestamp of this frame */
- gmx_large_int_t step; /* MD step */
- gmx_large_int_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 */
- } t_enxframe;
-
- /* 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);
-
- t_fileio *enx_file_pointer(const ener_file_t ef);
-
- void close_enx(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,
- 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);
-
-
-
+ * 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. */
+typedef struct
+{
+ 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_large_int_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;
+} t_enxsubblock;
+
+
+/* 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 */
+typedef struct {
+ double t; /* Timestamp of this frame */
+ gmx_large_int_t step; /* MD step */
+ gmx_large_int_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 */
+} t_enxframe;
+
+/* 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);
+
+t_fileio *enx_file_pointer(const ener_file_t ef);
+
+void close_enx(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,
+ 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);
+
+
+
#ifdef __cplusplus
}
#endif
-#endif /* _enerio_h */
+#endif /* _enerio_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff