src/gromacs/mdlib/mdebin_bar.h

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