* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _mdebin_bar_h
-#define _mdebin_bar_h
+#ifndef GMX_MDLIB_MDEBIN_BAR_H
+#define GMX_MDLIB_MDEBIN_BAR_H
-#include "gromacs/mdlib/energyoutput.h"
-#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/real.h"
/* The functions & data structures here describe writing
energy differences (or their histogram )for use with g_bar */
class delta_h_history_t;
struct t_enxframe;
+class energyhistory_t;
+struct t_inputrec;
+
+namespace gmx
+{
+template<typename>
+class ArrayRef;
+}
/* Data for one foreign lambda, or derivative. */
typedef struct
{
- 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*/
- 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 */
- bool written; /* whether this data has already been written out */
-
- int64_t subblock_meta_l[5]; /* metadata for an mdebin subblock for
+ std::vector<real> dh; /* the raw energy data. */
+ std::vector<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). */
+ std::array<std::vector<int>, 2> bin; /* 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*/
+ std::array<int64_t, 2> x0; /* the starting point in units of spacing
+ of the histogram */
+ std::array<unsigned int, 2> maxbin; /* 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 */
+ std::vector<double> lambda; /* lambda vector (or NULL if not applicable) */
+ int nlambda; /* length of the lambda vector */
+ bool written; /* whether this data has already been written out */
+
+ std::array<int64_t, 5> subblock_meta_l; /* metadata for an mdebin subblock for
I/O: for histogram counts, etc.*/
- double* subblock_meta_d; /* metadata subblock for I/O, used for
+ std::vector<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
+ std::array<int, 4> subblock_meta_i; /* metadata subblock for I/O, used for
communicating ints (i.e. derivative indices,
etc.) */
} t_mde_delta_h;
/* the type definition is in mdebin_bar.h */
struct t_mde_delta_h_coll
{
- t_mde_delta_h* dh; /* the delta h data */
- int ndh; /* the number of delta_h structures */
+ t_mde_delta_h_coll(const t_inputrec& inputrec);
+
+ std::vector<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 */
int dh_du_index; /* the delta h data (index into dh) */
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
+ std::vector<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,
+ int n_lambda_vec; /* the size of the native lambda vector */
+ std::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 */
+ 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 */
+ std::vector<double> subblock_d; /* for writing a metadata mdebin subblock for I/O */
+ std::vector<int> subblock_i; /* for writing a metadata mdebin subblock for I/O */
};
-
-/* initialize a collection of delta h histograms/sets
- dhc = the collection
- inputrec = the input record */
-
-void mde_delta_h_coll_init(t_mde_delta_h_coll* dhc, const t_inputrec& inputrec);
-
-void done_mde_delta_h_coll(t_mde_delta_h_coll* dhc);
-
/* add a bunch of samples to the delta_h collection
dhc = the collection
dhdl = the hamiltonian derivatives
/* restore the variables from an energyhistory */
void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll* dhc, const delta_h_history_t* deltaH);
-#endif /* _mdebin_bar_h */
+#endif /* GMX_MDLIB_MDEBIN_BAR_H */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff