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/legacyheaders/types/energy.h"
  42 #include "gromacs/legacyheaders/types/inputrec.h"
  43 #include "gromacs/legacyheaders/types/state.h"
  44
  45 #ifdef __cplusplus
  46 extern "C" {
  47 #endif
  48
  49 struct gmx_groups_t;
  50 struct t_fileio;
  51
  52 /**************************************************************
  53  * These are the base datatypes + functions for reading and
  54  * writing energy files (.edr). They are either called directly
  55  * (as in the processing tools), or indirectly through mdebin.c
  56  * during mdrun.
  57  *
  58  * The routines in the corresponding c-file enxio.c
  59  * are based on the lower level routines in gmxfio.c.
  60  * The file pointer returned from open_enx
  61  * can also be used with the routines in gmxfio.h
  62  *
  63  **************************************************************/
  64
  65 typedef struct {
  66     char *name;
  67     char *unit;
  68 } gmx_enxnm_t;
  69
  70 /*
  71  * Index for the IDs of additional blocks in the energy file.
  72  * Blocks can be added without sacrificing backward and forward
  73  * compatibility of the energy files.
  74  *
  75  * For backward compatibility, the order of these should not be changed.
  76  */
  77 enum {
  78     enxOR,     /* Time and ensemble averaged data for orientation restraints */
  79     enxORI,    /* Instantaneous data for orientation restraints              */
  80     enxORT,    /* Order tensor(s) for orientation restraints                 */
  81     enxDISRE,  /* Distance restraint blocks                                  */
  82
  83     enxDHCOLL, /* Data about the free energy blocks in this frame.           */
  84     enxDHHIST, /* BAR histogram                                              */
  85     enxDH,     /* BAR raw delta H data                                       */
  86
  87     enxNR      /* Total number of extra blocks in the current code,
  88                 * note that the enxio code can read files written by
  89                 * future code which contain more blocks.
  90                 */
  91 };
  92
  93 /* names for the above enum */
  94 extern const char *enx_block_id_name[];
  95
  96
  97 /* the subblocks that are contained in energy file blocks. Each of these
  98    has a number of values of a single data type in a .edr file. */
  99 typedef struct
 100 {
 101     int          nr;        /* number of items in subblock */
 102     xdr_datatype type;      /* the block type */
 103
 104     /* the values: pointers for each type */
 105     float*             fval;
 106     double*            dval;
 107     int*               ival;
 108     gmx_int64_t*       lval;
 109     unsigned char*     cval;
 110     char**             sval;
 111
 112     /* the allocated sizes, defined separately.
 113        (nonzero sizes can be free()d later): */
 114     int fval_alloc;
 115     int dval_alloc;
 116     int ival_alloc;
 117     int lval_alloc;
 118     int cval_alloc;
 119     int sval_alloc;
 120 } t_enxsubblock;
 121
 122
 123 /* the energy file blocks. Each block contains a number of sub-blocks
 124    of a single type that contain the actual data. */
 125 typedef struct t_enxblock{
 126     int            id;         /* block id, from the enx enums above */
 127     int            nsub;       /* number of subblocks */
 128     t_enxsubblock *sub;        /* the subblocks */
 129     int            nsub_alloc; /* number of allocated subblocks */
 130 } t_enxblock;
 131
 132
 133 /* The frames that are read/written */
 134 typedef struct {
 135     double          t;            /* Timestamp of this frame                         */
 136     gmx_int64_t     step;         /* MD step                                 */
 137     gmx_int64_t     nsteps;       /* The number of steps between frames            */
 138     double          dt;           /* The MD time step                              */
 139     int             nsum;         /* The number of terms for the sums in ener      */
 140     int             nre;          /* Number of energies                      */
 141     int             e_size;       /* Size (in bytes) of energies                     */
 142     int             e_alloc;      /* Allocated size (in elements) of ener          */
 143     t_energy       *ener;         /* The energies                                  */
 144     int             nblock;       /* Number of following energy blocks             */
 145     t_enxblock     *block;        /* The blocks                                    */
 146     int             nblock_alloc; /* The number of blocks allocated                */
 147 } t_enxframe;
 148
 149 /* file handle */
 150 typedef struct ener_file *ener_file_t;
 151
 152 /*
 153  * An energy file is read like this:
 154  *
 155  * ener_file_t fp;
 156  * t_enxframe *fr;
 157  *
 158  * fp = open_enx(...);
 159  * do_enxnms(fp,...);
 160  * snew(fr,1);
 161  * while (do_enx(fp,fr)) {
 162  * ...
 163  * }
 164  * free_enxframe(fr);
 165  * sfree(fr);
 166  */
 167 /* New energy reading and writing interface */
 168
 169
 170 /* initialize a pre-allocated frame */
 171 void init_enxframe(t_enxframe *ef);
 172 /* delete a frame's memory (except the ef itself) */
 173 void free_enxframe(t_enxframe *ef);
 174
 175
 176 ener_file_t open_enx(const char *fn, const char *mode);
 177
 178 struct t_fileio *enx_file_pointer(const ener_file_t ef);
 179
 180 void close_enx(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                    struct 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
 216
 217 #ifdef __cplusplus
 218 }
 219 #endif
 220
 221 #endif