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colvarbias_abf.h
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Wed, Aug 28, 10:13

colvarbias_abf.h
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/************************************************************************
* Headers for the ABF and histogram biases *
************************************************************************/
#ifndef COLVARBIAS_ABF_H
#define COLVARBIAS_ABF_H
#include <vector>
#include <list>
#include <sstream>
#include <iomanip>
//#include <cmath>
#include "colvarbias.h"
#include "colvargrid.h"
typedef cvm::real* gradient_t;
/// ABF bias
class colvarbias_abf : public colvarbias {
public:
colvarbias_abf (std::string const &conf, char const *key);
~colvarbias_abf ();
cvm::real update ();
private:
/// Filename prefix for human-readable gradient/sample count output
std::string output_prefix;
/// Base filename(s) for reading previous gradient data (replaces data from restart file)
std::vector<std::string> input_prefix;
bool apply_bias;
bool update_bias;
bool hide_Jacobian;
size_t full_samples;
size_t min_samples;
/// frequency for updating output files (default: same as restartFreq?)
int output_freq;
/// Write combined files with a history of all output data?
bool b_history_files;
size_t history_freq;
// Internal data and methods
std::vector<int> bin, force_bin;
gradient_t force;
/// n-dim grid of free energy gradients
colvar_grid_gradient *gradients;
/// n-dim grid of number of samples
colvar_grid_count *samples;
/// Write human-readable FE gradients and sample count
void write_gradients_samples (const std::string &prefix, bool append = false);
/// Read human-readable FE gradients and sample count (if not using restart)
void read_gradients_samples ();
std::istream& read_restart (std::istream&);
std::ostream& write_restart (std::ostream&);
};
/// Histogram "bias" (does as the name says)
class colvarbias_histogram : public colvarbias {
public:
colvarbias_histogram (std::string const &conf, char const *key);
~colvarbias_histogram ();
cvm::real update ();
private:
/// n-dim histogram
colvar_grid_count *grid;
std::vector<int> bin;
std::string out_name;
int output_freq;
void write_grid ();
std::ofstream grid_os; /// Stream for writing grid to disk
std::istream& read_restart (std::istream&);
std::ostream& write_restart (std::ostream&);
};
#endif

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