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/mdtypes/state.h"
  42 #include "gromacs/trajectory/energy.h"
  43
  44 struct gmx_groups_t;
  45 struct t_fileio;
  46 struct t_inputrec;
  47
  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
  52  * during mdrun.
  53  *
  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
  58  *
  59  **************************************************************/
  60
  61 typedef struct {
  62     char *name;
  63     char *unit;
  64 } gmx_enxnm_t;
  65
  66 /*
  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.
  70  *
  71  * For backward compatibility, the order of these should not be changed.
  72  */
  73 enum {
  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                                  */
  78
  79     enxDHCOLL, /* Data about the free energy blocks in this frame.           */
  80     enxDHHIST, /* BAR histogram                                              */
  81     enxDH,     /* BAR raw delta H data                                       */
  82
  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.
  86                 */
  87 };
  88
  89 /* names for the above enum */
  90 extern const char *enx_block_id_name[];
  91
  92
  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. */
  95 typedef struct
  96 {
  97     int          nr;        /* number of items in subblock */
  98     xdr_datatype type;      /* the block type */
  99
 100     /* the values: pointers for each type */
 101     float*             fval;
 102     double*            dval;
 103     int*               ival;
 104     gmx_int64_t*       lval;
 105     unsigned char*     cval;
 106     char**             sval;
 107
 108     /* the allocated sizes, defined separately.
 109        (nonzero sizes can be free()d later): */
 110     int fval_alloc;
 111     int dval_alloc;
 112     int ival_alloc;
 113     int lval_alloc;
 114     int cval_alloc;
 115     int sval_alloc;
 116 } t_enxsubblock;
 117
 118
 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 */
 126 } t_enxblock;
 127
 128
 129 /* The frames that are read/written */
 130 typedef struct {
 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                */
 143 } t_enxframe;
 144
 145 /* file handle */
 146 typedef struct ener_file *ener_file_t;
 147
 148 /*
 149  * An energy file is read like this:
 150  *
 151  * ener_file_t fp;
 152  * t_enxframe *fr;
 153  *
 154  * fp = open_enx(...);
 155  * do_enxnms(fp,...);
 156  * snew(fr,1);
 157  * while (do_enx(fp,fr)) {
 158  * ...
 159  * }
 160  * free_enxframe(fr);
 161  * sfree(fr);
 162  */
 163 /* New energy reading and writing interface */
 164
 165
 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);
 170
 171
 172 ener_file_t open_enx(const char *fn, const char *mode);
 173
 174 struct t_fileio *enx_file_pointer(const ener_file_t ef);
 175
 176 /* Free the contents of ef */
 177 void close_enx(ener_file_t ef);
 178
 179 /* Free the contents of ef, and ef itself */
 180 void done_ener_file(ener_file_t ef);
 181
 182 void do_enxnms(ener_file_t ef, int *nre, gmx_enxnm_t **enms);
 183
 184 void free_enxnms(int n, gmx_enxnm_t *nms);
 185 /* Frees nms and all strings in it */
 186
 187 gmx_bool do_enx(ener_file_t ef, t_enxframe *fr);
 188 /* Reads enx_frames, memory in fr is (re)allocated if necessary */
 189
 190 void get_enx_state(const char *fn, real t,
 191                    const gmx_groups_t *groups, t_inputrec *ir,
 192                    t_state *state);
 193 /*
 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.
 197  */
 198
 199
 200 /* block funtions */
 201
 202 /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
 203 void add_blocks_enxframe(t_enxframe *ef, int n);
 204
 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);
 209
 210
 211 /* allocate n subblocks to a block (if neccesary). Don't touch existing
 212    subbblocks. */
 213 void add_subblocks_enxblock(t_enxblock *eb, int n);
 214
 215 void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol,
 216               const char *lastener);
 217 /* Compare two binary energy files */
 218
 219 #endif