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42 #include "gromacs/mdlib/energyoutput.h"
43 #include "gromacs/utility/arrayref.h"
45 /* The functions & data structures here describe writing
46 energy differences (or their histogram )for use with g_bar */
48 class delta_h_history_t;
51 /* Data for one foreign lambda, or derivative. */
54 real* dh; /* the raw energy data. */
55 float* dhf; /* raw difference data -- in floats, for storage. */
56 unsigned int ndh; /* number of data points */
57 unsigned int ndhmax; /* the maximum number of points */
59 int nhist; /* the number of histograms. There can either be
61 1 (for 'foreign lambda' histograms)
62 2 (for derivative histograms: there's
63 a 'forward' and 'backward' histogram
64 containing the minimum and maximum
65 values, respectively). */
66 int* bin[2]; /* the histogram(s) */
67 double dx; /* the histogram spacing in kJ/mol. This is the
68 same for the two histograms? */
69 unsigned int nbins; /* the number of bins in the histograms*/
70 int64_t x0[2]; /* the starting point in units of spacing
72 unsigned int maxbin[2]; /* highest bin number with data */
74 int type; /* the block type according to dhbtDH, etc. */
75 int derivative; /* The derivative direction (as an index in the lambda
76 vector) if this delta_h contains derivatives */
77 double* lambda; /* lambda vector (or NULL if not applicable) */
78 int nlambda; /* length of the lambda vector */
79 gmx_bool written; /* whether this data has already been written out */
81 int64_t subblock_meta_l[5]; /* metadata for an mdebin subblock for
82 I/O: for histogram counts, etc.*/
83 double* subblock_meta_d; /* metadata subblock for I/O, used for
84 communicating doubles (i.e. the lambda
86 int subblock_meta_i[4]; /* metadata subblock for I/O, used for
87 communicating ints (i.e. derivative indices,
91 /* the type definition is in mdebin_bar.h */
92 struct t_mde_delta_h_coll
94 t_mde_delta_h* dh; /* the delta h data */
95 int ndh; /* the number of delta_h structures */
97 int nlambda; /* number of bar dU delta_h structures */
98 t_mde_delta_h* dh_du; /* the delta h data (pointer into dh) */
100 int ndhdl; /* number of bar dU delta_h structures */
101 t_mde_delta_h* dh_dhdl; /* the dhdl data (pointer into dh) */
103 t_mde_delta_h* dh_energy; /* energy output block (pointer into dh) */
104 t_mde_delta_h* dh_pv; /* pV output block (pointer into dh) */
105 t_mde_delta_h* dh_expanded; /* expanded ensemble output block (pointer
108 double start_time; /* start time of the current dh collection */
109 double delta_time; /* time difference between samples */
110 gmx_bool start_time_set; /* whether the start time has been set */
111 double start_lambda; /* starting lambda for continuous motion of state*/
112 double delta_lambda; /* delta lambda, for continuous motion of state */
113 double temperature; /* the temperature of the samples*/
115 double* native_lambda_vec; /* The lambda vector describing the current
116 lambda state if it is set (NULL otherwise) */
117 int n_lambda_vec; /* the size of the native lambda vector */
118 int* native_lambda_components; /* the native lambda (and by extension,
119 foreign lambda) components in terms
120 of efptFEP, efptMASS, etc. */
121 int lambda_index; /* the lambda_fep_state */
123 double* subblock_d; /* for writing a metadata mdebin subblock for I/O */
124 int* subblock_i; /* for writing a metadata mdebin subblock for I/O */
126 double* lambda_vec_subblock; /* native lambda vector data subblock for
128 int* lambda_index_subblock; /* lambda vector index data subblock for I/O */
132 /* initialize a collection of delta h histograms/sets
134 inputrec = the input record */
136 void mde_delta_h_coll_init(t_mde_delta_h_coll* dhc, const t_inputrec& inputrec);
138 void done_mde_delta_h_coll(t_mde_delta_h_coll* dhc);
140 /* add a bunch of samples to the delta_h 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
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,
154 gmx::ArrayRef<double> dhdl,
158 /* write the data associated with the du blocks collection as a collection
162 nblock = the current number of blocks */
163 void mde_delta_h_coll_handle_block(t_mde_delta_h_coll* dhc, t_enxframe* fr, int nblock);
166 /* reset the collection of delta_h buffers for a new round of
168 void mde_delta_h_coll_reset(t_mde_delta_h_coll* dhc);
171 /* set the energyhistory variables to save state */
172 void mde_delta_h_coll_update_energyhistory(const t_mde_delta_h_coll* dhc, energyhistory_t* enerhist);
174 /* restore the variables from an energyhistory */
175 void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll* dhc, const delta_h_history_t* deltaH);
177 #endif /* _mdebin_bar_h */