src/gromacs/fileio/enxio.h

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  37 #ifndef GMX_FILEIO_ENXIO_H
  38 #define GMX_FILEIO_ENXIO_H
  39
  40 #include "gromacs/fileio/xdr_datatype.h"
  41 #include "gromacs/trajectory/energy.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43
  44 struct gmx_groups_t;
  45 struct t_fileio;
  46 struct t_inputrec;
  47 class t_state;
  48
  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
  53  * during mdrun.
  54  *
  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
  59  *
  60  **************************************************************/
  61
  62 typedef struct {
  63     char *name;
  64     char *unit;
  65 } gmx_enxnm_t;
  66
  67 /*
  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.
  71  *
  72  * For backward compatibility, the order of these should not be changed.
  73  */
  74 enum {
  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                                  */
  79
  80     enxDHCOLL, /* Data about the free energy blocks in this frame.           */
  81     enxDHHIST, /* BAR histogram                                              */
  82     enxDH,     /* BAR raw delta H data                                       */
  83
  84     enxAWH,    /* AWH data */
  85
  86     enxNR      /* Total number of extra blocks in the current code,
  87                 * note that the enxio code can read files written by
  88                 * future code which contain more blocks.
  89                 */
  90 };
  91
  92 /* names for the above enum */
  93 extern const char *enx_block_id_name[];
  94
  95
  96 /* the subblocks that are contained in energy file blocks. Each of these
  97    has a number of values of a single data type in a .edr file. */
  98 struct t_enxsubblock
  99 {
 100     int          nr;        /* number of items in subblock */
 101     xdr_datatype type;      /* the block type */
 102
 103     /* the values: pointers for each type */
 104     float*             fval;
 105     double*            dval;
 106     int*               ival;
 107     gmx_int64_t*       lval;
 108     unsigned char*     cval;
 109     char**             sval;
 110
 111     /* the allocated sizes, defined separately.
 112        (nonzero sizes can be free()d later): */
 113     int fval_alloc;
 114     int dval_alloc;
 115     int ival_alloc;
 116     int lval_alloc;
 117     int cval_alloc;
 118     int sval_alloc;
 119 };
 120
 121
 122 /* the energy file blocks. Each block contains a number of sub-blocks
 123    of a single type that contain the actual data. */
 124 typedef struct t_enxblock{
 125     int            id;         /* block id, from the enx enums above */
 126     int            nsub;       /* number of subblocks */
 127     t_enxsubblock *sub;        /* the subblocks */
 128     int            nsub_alloc; /* number of allocated subblocks */
 129 } t_enxblock;
 130
 131
 132 /* The frames that are read/written */
 133 struct t_enxframe {
 134     double          t;            /* Timestamp of this frame                         */
 135     gmx_int64_t     step;         /* MD step                                 */
 136     gmx_int64_t     nsteps;       /* The number of steps between frames            */
 137     double          dt;           /* The MD time step                              */
 138     int             nsum;         /* The number of terms for the sums in ener      */
 139     int             nre;          /* Number of energies                      */
 140     int             e_size;       /* Size (in bytes) of energies                     */
 141     int             e_alloc;      /* Allocated size (in elements) of ener          */
 142     t_energy       *ener;         /* The energies                                  */
 143     int             nblock;       /* Number of following energy blocks             */
 144     t_enxblock     *block;        /* The blocks                                    */
 145     int             nblock_alloc; /* The number of blocks allocated                */
 146 };
 147
 148 /* file handle */
 149 typedef struct ener_file *ener_file_t;
 150
 151 /*
 152  * An energy file is read like this:
 153  *
 154  * ener_file_t fp;
 155  * t_enxframe *fr;
 156  *
 157  * fp = open_enx(...);
 158  * do_enxnms(fp,...);
 159  * snew(fr,1);
 160  * while (do_enx(fp,fr)) {
 161  * ...
 162  * }
 163  * free_enxframe(fr);
 164  * sfree(fr);
 165  */
 166 /* New energy reading and writing interface */
 167
 168
 169 /* initialize a pre-allocated frame */
 170 void init_enxframe(t_enxframe *ef);
 171 /* delete a frame's memory (except the ef itself) */
 172 void free_enxframe(t_enxframe *ef);
 173
 174
 175 ener_file_t open_enx(const char *fn, const char *mode);
 176
 177 struct t_fileio *enx_file_pointer(const ener_file_t ef);
 178
 179 /* Free the contents of ef */
 180 void close_enx(ener_file_t ef);
 181
 182 /* Free the contents of ef, and ef itself */
 183 void done_ener_file(ener_file_t ef);
 184
 185 void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms);
 186
 187 void free_enxnms(int n, gmx_enxnm_t *nms);
 188 /* Frees nms and all strings in it */
 189
 190 gmx_bool do_enx(ener_file_t ef, t_enxframe *fr);
 191 /* Reads enx_frames, memory in fr is (re)allocated if necessary */
 192
 193 void get_enx_state(const char *fn, real t,
 194                    const gmx_groups_t *groups, t_inputrec *ir,
 195                    t_state *state);
 196 /*
 197  * Reads state variables from enx file fn at time t.
 198  * atoms and ir are required for determining which things must be read.
 199  * Currently pcoupl and tcoupl state are read from enx.
 200  */
 201
 202
 203 /* block funtions */
 204
 205 /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
 206 void add_blocks_enxframe(t_enxframe *ef, int n);
 207
 208 /* find a block by id number; if prev!=NULL, it searches from
 209    that block's next block.
 210    Returns NULL if no block is found with the given id. */
 211 t_enxblock *find_block_id_enxframe(t_enxframe *ef, int id, t_enxblock *prev);
 212
 213
 214 /* allocate n subblocks to a block (if neccesary). Don't touch existing
 215    subbblocks. */
 216 void add_subblocks_enxblock(t_enxblock *eb, int n);
 217
 218 void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol,
 219               const char *lastener);
 220 /* Compare two binary energy files */
 221
 222 #endif