src/gromacs/fileio/enxio.h

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  38 #ifndef GMX_FILEIO_ENXIO_H
  39 #define GMX_FILEIO_ENXIO_H
  40
  41 #include "gromacs/fileio/xdr_datatype.h"
  42 #include "gromacs/utility/basedefinitions.h"
  43 #include "gromacs/utility/real.h"
  44
  45 struct SimulationGroups;
  46 struct t_energy;
  47 struct t_enxframe;
  48 struct t_fileio;
  49 struct t_inputrec;
  50 class t_state;
  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 {
  67     char* name;
  68     char* unit;
  69 } gmx_enxnm_t;
  70
  71 /*
  72  * Index for the IDs of additional blocks in the energy file.
  73  * Blocks can be added without sacrificing backward and forward
  74  * compatibility of the energy files.
  75  *
  76  * For backward compatibility, the order of these should not be changed.
  77  */
  78 enum
  79 {
  80     enxOR,    /* Time and ensemble averaged data for orientation restraints */
  81     enxORI,   /* Instantaneous data for orientation restraints              */
  82     enxORT,   /* Order tensor(s) for orientation restraints                 */
  83     enxDISRE, /* Distance restraint blocks                                  */
  84
  85     enxDHCOLL, /* Data about the free energy blocks in this frame.           */
  86     enxDHHIST, /* BAR histogram                                              */
  87     enxDH,     /* BAR raw delta H data                                       */
  88
  89     enxAWH, /* AWH data */
  90
  91     enxNR /* Total number of extra blocks in the current code,
  92            * note that the enxio code can read files written by
  93            * future code which contain more blocks.
  94            */
  95 };
  96
  97 /* names for the above enum */
  98 extern const char* enx_block_id_name[];
  99
 100
 101 /* the subblocks that are contained in energy file blocks. Each of these
 102    has a number of values of a single data type in a .edr file. */
 103 struct t_enxsubblock
 104 {
 105     int          nr;   /* number of items in subblock */
 106     xdr_datatype type; /* the block type */
 107
 108     /* the values: pointers for each type */
 109     float*         fval;
 110     double*        dval;
 111     int*           ival;
 112     int64_t*       lval;
 113     unsigned char* cval;
 114     char**         sval;
 115
 116     /* the allocated sizes, defined separately.
 117        (nonzero sizes can be free()d later): */
 118     int fval_alloc;
 119     int dval_alloc;
 120     int ival_alloc;
 121     int lval_alloc;
 122     int cval_alloc;
 123     int sval_alloc;
 124 };
 125
 126 /* the energy file blocks. Each block contains a number of sub-blocks
 127    of a single type that contain the actual data. */
 128 struct t_enxblock
 129 {
 130     int            id;         /* block id, from the enx enums above */
 131     int            nsub;       /* number of subblocks */
 132     t_enxsubblock* sub;        /* the subblocks */
 133     int            nsub_alloc; /* number of allocated subblocks */
 134 };
 135
 136 /* file handle */
 137 typedef struct ener_file* ener_file_t;
 138
 139 /*
 140  * An energy file is read like this:
 141  *
 142  * ener_file_t fp;
 143  * t_enxframe *fr;
 144  *
 145  * fp = open_enx(...);
 146  * do_enxnms(fp,...);
 147  * snew(fr,1);
 148  * while (do_enx(fp,fr)) {
 149  * ...
 150  * }
 151  * free_enxframe(fr);
 152  * sfree(fr);
 153  */
 154 /* New energy reading and writing interface */
 155
 156
 157 /* initialize a pre-allocated frame */
 158 void init_enxframe(t_enxframe* ef);
 159 /* delete a frame's memory (except the ef itself) */
 160 void free_enxframe(t_enxframe* ef);
 161
 162
 163 ener_file_t open_enx(const char* fn, const char* mode);
 164
 165 struct t_fileio* enx_file_pointer(const ener_file* ef);
 166
 167 /* Free the contents of ef */
 168 void close_enx(ener_file_t ef);
 169
 170 /* Free the contents of ef, and ef itself */
 171 void done_ener_file(ener_file_t ef);
 172
 173 void do_enxnms(ener_file_t ef, int* nre, gmx_enxnm_t** enms);
 174
 175 void free_enxnms(int n, gmx_enxnm_t* nms);
 176 /* Frees nms and all strings in it */
 177
 178 gmx_bool do_enx(ener_file_t ef, t_enxframe* fr);
 179 /* Reads enx_frames, memory in fr is (re)allocated if necessary */
 180
 181 void get_enx_state(const char* fn, real t, const SimulationGroups& groups, t_inputrec* ir, t_state* state);
 182 /*
 183  * Reads state variables from enx file fn at time t.
 184  * atoms and ir are required for determining which things must be read.
 185  * Currently pcoupl and tcoupl state are read from enx.
 186  */
 187
 188
 189 /* block funtions */
 190
 191 /* allocate n blocks to a frame (if neccesary). Don't touch existing blocks */
 192 void add_blocks_enxframe(t_enxframe* ef, int n);
 193
 194 /* find a block by id number; if prev!=NULL, it searches from
 195    that block's next block.
 196    Returns NULL if no block is found with the given id. */
 197 t_enxblock* find_block_id_enxframe(t_enxframe* ef, int id, t_enxblock* prev);
 198
 199
 200 /* allocate n subblocks to a block (if neccesary). Don't touch existing
 201    subbblocks. */
 202 void add_subblocks_enxblock(t_enxblock* eb, int n);
 203
 204 void comp_enx(const char* fn1, const char* fn2, real ftol, real abstol, const char* lastener);
 205 /* Compare two binary energy files */
 206
 207 #endif