/*
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- * This source code is part of
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- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
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+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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*/
#ifndef _mdebin_bar_h
#define _mdebin_bar_h
+#include "gromacs/legacyheaders/mdebin.h"
+
#ifdef __cplusplus
extern "C" {
#endif
-/* The functions & data structures here describe writing
+
+/* The functions & data structures here describe writing
energy differences (or their histogram )for use with g_bar */
/* Data for one foreign lambda, or derivative. */
-typedef struct
+typedef struct
{
- real *dh; /* the raw energy differences */
- unsigned int ndh; /* number of data points */
- unsigned int ndhmax; /* the maximum number of points */
-
- int nhist; /* the number of histograms. There can either be
- 0 (for no histograms)
- 1 (for 'foreign lambda' histograms)
- 2 (for derivative histograms: there's
- a 'forward' and 'backward' histogram
- containing the minimum and maximum
- values, respectively). */
- int *bin[2]; /* the histogram(s) */
- double dx; /* the histogram spacing in kJ/mol. This is the
- same for the two histograms */
- unsigned int nbins; /* the number of bins */
- gmx_large_int_t x0[2]; /* the starting point in units of spacing
- of the histogram */
- unsigned int maxbin[2]; /* highest bin number with data */
-
- gmx_bool derivative; /* whether this delta_h contains derivatives */
- double lambda; /* the 'foreign' lambda value associated with this delta H */
- gmx_bool written; /* whether this data has already been written out */
-
- double subblock_d[4]; /* data for an mdebin subblock for I/O. */
- gmx_large_int_t subblock_l[4]; /* data for an mdebin subblock for I/O. */
- int subblock_i[4]; /* data for an mdebin subblock for I/O. */
+ real *dh; /* the raw energy data. */
+ float *dhf; /* raw difference data -- in floats, for storage. */
+ unsigned int ndh; /* number of data points */
+ unsigned int ndhmax; /* the maximum number of points */
+
+ int nhist; /* the number of histograms. There can either be
+ 0 (for no histograms)
+ 1 (for 'foreign lambda' histograms)
+ 2 (for derivative histograms: there's
+ a 'forward' and 'backward' histogram
+ containing the minimum and maximum
+ values, respectively). */
+ int *bin[2]; /* the histogram(s) */
+ double dx; /* the histogram spacing in kJ/mol. This is the
+ same for the two histograms? */
+ unsigned int nbins; /* the number of bins in the histograms*/
+ gmx_int64_t x0[2]; /* the starting point in units of spacing
+ of the histogram */
+ unsigned int maxbin[2]; /* highest bin number with data */
+
+ int type; /* the block type according to dhbtDH, etc. */
+ int derivative; /* The derivative direction (as an index in the lambda
+ vector) if this delta_h contains derivatives */
+ double *lambda; /* lambda vector (or NULL if not applicable) */
+ int nlambda; /* length of the lambda vector */
+ gmx_bool written; /* whether this data has already been written out */
+
+ gmx_int64_t subblock_meta_l[5]; /* metadata for an mdebin subblock for
+ I/O: for histogram counts, etc.*/
+ double *subblock_meta_d; /* metadata subblock for I/O, used for
+ communicating doubles (i.e. the lambda
+ vector) */
+ int subblock_meta_i[4]; /* metadata subblock for I/O, used for
+ communicating ints (i.e. derivative indices,
+ etc.) */
} t_mde_delta_h;
-/* the type definition is in mdebin.h */
+/* the type definition is in mdebin_bar.h */
struct t_mde_delta_h_coll
{
- t_mde_delta_h *dh; /* the delta hs */
- int ndh; /* the number of delta_h structures */
- int ndhdl; /* number of derivative delta_hs */
-
- double start_time; /* start time of the current dh collection */
- double delta_time; /* time difference between samples */
- gmx_bool start_time_set; /* whether the start time has been set */
-
- double start_lambda; /* the native lambda associated with the free energy
- calculations (at the time of the first sample) */
- double delta_lambda; /* lambda difference between samples */
-
- double temp; /* the temperature */
- double subblock_d[5]; /* data for writing an mdebin subblock for I/O */
+ t_mde_delta_h *dh; /* the delta h data */
+ int ndh; /* the number of delta_h structures */
+
+ int nlambda; /* number of bar dU delta_h structures */
+ t_mde_delta_h *dh_du; /* the delta h data (pointer into dh) */
+
+ int ndhdl; /* number of bar dU delta_h structures */
+ t_mde_delta_h *dh_dhdl; /* the dhdl data (pointer into dh) */
+
+ t_mde_delta_h *dh_energy; /* energy output block (pointer into dh) */
+ t_mde_delta_h *dh_pv; /* pV output block (pointer into dh) */
+ t_mde_delta_h *dh_expanded; /* expanded ensemble output block (pointer
+ into dh) */
+
+ double start_time; /* start time of the current dh collection */
+ double delta_time; /* time difference between samples */
+ gmx_bool start_time_set; /* whether the start time has been set */
+ double start_lambda; /* starting lambda for continuous motion of state*/
+ double delta_lambda; /* delta lambda, for continuous motion of state */
+ double temperature; /* the temperature of the samples*/
+
+ double *native_lambda_vec; /* The lambda vector describing the current
+ lambda state if it is set (NULL otherwise) */
+ int n_lambda_vec; /* the size of the native lambda vector */
+ int *native_lambda_components; /* the native lambda (and by extension,
+ foreign lambda) components in terms
+ of efptFEP, efptMASS, etc. */
+ int lambda_index; /* the lambda_fep_state */
+
+ double *subblock_d; /* for writing a metadata mdebin subblock for I/O */
+ int *subblock_i; /* for writing a metadata mdebin subblock for I/O */
+
+ double *lambda_vec_subblock; /* native lambda vector data subblock for
+ I/O */
+ int *lambda_index_subblock; /* lambda vector index data subblock for I/O */
};
-/* initialize a collection of delta h histograms/sets
+/* initialize a collection of delta h histograms/sets
dhc = the collection
ir = the input record */
+
void mde_delta_h_coll_init(t_mde_delta_h_coll *dhc,
- const t_inputrec *ir);
+ const t_inputrec *ir);
/* add a bunch of samples to the delta_h collection
dhc = the collection
- dhdl = the hamiltonian derivative
+ dhdl = the hamiltonian derivatives
U = the array with energies: from enerd->enerpart_lambda.
- time = the current simulation time. */
-void mde_delta_h_coll_add_dh(t_mde_delta_h_coll *dhc,
- double dhdl,
- double *U, double time,
- double native_lambda);
+ time = the current simulation time.
+ current_lambda = current lambda values : primarily useful for continuous processes
+ fep_state = current fep_state
+ */
+
+/* add a bunch of samples - note fep_state is double to allow for better data storage */
+void mde_delta_h_coll_add_dh(t_mde_delta_h_coll *dhc,
+ double fep_state,
+ double energy,
+ double pV,
+ double *dhdl,
+ double *foreign_dU,
+ double time);
/* write the data associated with the du blocks collection as a collection
of mdebin blocks.
dhc = the collection
fr = the enxio frame
nblock = the current number of blocks */
-void mde_delta_h_coll_handle_block(t_mde_delta_h_coll *dhc,
+void mde_delta_h_coll_handle_block(t_mde_delta_h_coll *dhc,
t_enxframe *fr, int nblock);
-/* reset the collection of delta_h buffers for a new round of
+/* reset the collection of delta_h buffers for a new round of
data gathering */
void mde_delta_h_coll_reset(t_mde_delta_h_coll *dhc);
/* set the energyhistory variables to save state */
-void mde_delta_h_coll_update_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist);
+void mde_delta_h_coll_update_energyhistory(t_mde_delta_h_coll *dhc,
+ energyhistory_t *enerhist);
/* restore the variables from an energyhistory */
-void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist);
+void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
+ energyhistory_t *enerhist);
#ifdef __cplusplus
}
#endif
-#endif /* _mdebin_bar_h */
-
+#endif /* _mdebin_bar_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff