src/gromacs/mdlib/mdebin_bar.h

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  37
  38 #ifndef _mdebin_bar_h
  39 #define _mdebin_bar_h
  40
  41 #include "gromacs/mdlib/energyoutput.h"
  42
  43 /* The functions & data structures here describe writing
  44    energy differences (or their histogram )for use with g_bar */
  45
  46 class delta_h_history_t;
  47 struct t_enxframe;
  48
  49 /* Data for one foreign lambda, or derivative. */
  50 typedef struct
  51 {
  52     real        *dh;                    /* the raw energy data. */
  53     float       *dhf;                   /* raw difference data -- in floats, for storage. */
  54     unsigned int ndh;                   /* number of data points */
  55     unsigned int ndhmax;                /* the maximum number of points */
  56
  57     int          nhist;                 /* the number of histograms. There can either be
  58                                            0 (for no histograms)
  59                                            1 (for 'foreign lambda' histograms)
  60                                            2 (for derivative histograms: there's
  61                                               a 'forward' and 'backward' histogram
  62                                               containing the minimum and maximum
  63                                               values, respectively). */
  64     int            *bin[2];             /* the histogram(s) */
  65     double          dx;                 /* the histogram spacing in kJ/mol. This is the
  66                                            same for the two histograms? */
  67     unsigned int    nbins;              /* the number of bins in the histograms*/
  68     int64_t         x0[2];              /* the starting point in units of spacing
  69                                                    of the histogram */
  70     unsigned int    maxbin[2];          /* highest bin number with data */
  71
  72     int             type;               /* the block type according to dhbtDH, etc. */
  73     int             derivative;         /* The derivative direction (as an index in the lambda
  74                                            vector) if this delta_h contains derivatives */
  75     double         *lambda;             /* lambda vector (or NULL if not applicable) */
  76     int             nlambda;            /* length of the lambda vector */
  77     gmx_bool        written;            /* whether this data has already been written out */
  78
  79     int64_t         subblock_meta_l[5]; /* metadata for an mdebin subblock for
  80                                                    I/O: for histogram counts, etc.*/
  81     double         *subblock_meta_d;    /* metadata subblock for I/O, used for
  82                                            communicating doubles (i.e. the lambda
  83                                            vector) */
  84     int subblock_meta_i[4];             /* metadata subblock for I/O, used for
  85                                            communicating ints (i.e. derivative indices,
  86                                            etc.) */
  87 } t_mde_delta_h;
  88
  89 /* the type definition is in mdebin_bar.h */
  90 struct t_mde_delta_h_coll
  91 {
  92     t_mde_delta_h *dh;                 /* the delta h data */
  93     int            ndh;                /* the number of delta_h structures */
  94
  95     int            nlambda;            /* number of bar dU delta_h structures */
  96     t_mde_delta_h *dh_du;              /* the delta h data (pointer into dh) */
  97
  98     int            ndhdl;              /* number of bar dU delta_h structures */
  99     t_mde_delta_h *dh_dhdl;            /* the dhdl data (pointer into dh) */
 100
 101     t_mde_delta_h *dh_energy;          /* energy output block (pointer into dh) */
 102     t_mde_delta_h *dh_pv;              /* pV output block (pointer into dh) */
 103     t_mde_delta_h *dh_expanded;        /* expanded ensemble output block (pointer
 104                                           into dh) */
 105
 106     double   start_time;               /* start time of the current dh collection */
 107     double   delta_time;               /* time difference between samples */
 108     gmx_bool start_time_set;           /* whether the start time has been set */
 109     double   start_lambda;             /* starting lambda for continuous motion of state*/
 110     double   delta_lambda;             /* delta lambda, for continuous motion of state */
 111     double   temperature;              /* the temperature of the samples*/
 112
 113     double  *native_lambda_vec;        /* The lambda vector describing the current
 114                                           lambda state if it is set (NULL otherwise) */
 115     int      n_lambda_vec;             /* the size of the native lambda vector */
 116     int     *native_lambda_components; /* the native lambda (and by extension,
 117                                           foreign lambda) components in terms
 118                                           of efptFEP, efptMASS, etc. */
 119     int     lambda_index;              /* the lambda_fep_state */
 120
 121     double *subblock_d;                /* for writing a metadata mdebin subblock for I/O */
 122     int    *subblock_i;                /* for writing a metadata mdebin subblock for I/O */
 123
 124     double *lambda_vec_subblock;       /* native lambda vector data subblock for
 125                                           I/O */
 126     int    *lambda_index_subblock;     /* lambda vector index data subblock for I/O */
 127 };
 128
 129
 130
 131 /* initialize a collection of delta h histograms/sets
 132     dhc = the collection
 133     ir = the input record */
 134
 135 void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc,
 136                            const t_inputrec   *ir);
 137
 138 void done_mde_delta_h_coll(t_mde_delta_h_coll *dhc);
 139
 140 /* add a bunch of samples to the delta_h collection
 141     dhc = the collection
 142     dhdl = the hamiltonian derivatives
 143     U = the array with energies: from enerd->enerpart_lambda.
 144     time = the current simulation time.
 145     current_lambda = current lambda values : primarily useful for continuous processes
 146     fep_state = current fep_state
 147  */
 148
 149 /* add a bunch of samples - note fep_state is double to allow for better data storage */
 150 void mde_delta_h_coll_add_dh(t_mde_delta_h_coll *dhc,
 151                              double              fep_state,
 152                              double              energy,
 153                              double              pV,
 154                              double             *dhdl,
 155                              double             *foreign_dU,
 156                              double              time);
 157
 158 /* write the data associated with the du blocks collection as a collection
 159     of mdebin blocks.
 160     dhc = the collection
 161     fr = the enxio frame
 162     nblock = the current number of blocks */
 163 void mde_delta_h_coll_handle_block(t_mde_delta_h_coll *dhc,
 164                                    t_enxframe *fr, int nblock);
 165
 166
 167 /* reset the collection of delta_h buffers for a new round of
 168    data gathering */
 169 void mde_delta_h_coll_reset(t_mde_delta_h_coll *dhc);
 170
 171
 172 /* set the energyhistory variables to save state */
 173 void mde_delta_h_coll_update_energyhistory(const t_mde_delta_h_coll *dhc,
 174                                            energyhistory_t          *enerhist);
 175
 176 /* restore the variables from an energyhistory */
 177 void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll      *dhc,
 178                                             const delta_h_history_t *deltaH);
 179
 180 #endif  /* _mdebin_bar_h */