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colvarbias_abf.h
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Tue, Jul 23, 01:20

colvarbias_abf.h
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// -*- c++ -*-
#ifndef COLVARBIAS_ABF_H
#define COLVARBIAS_ABF_H
#include <vector>
#include <list>
#include <sstream>
#include <iomanip>
#include "colvarbias.h"
#include "colvargrid.h"
typedef cvm::real* gradient_t;
/// ABF bias
class colvarbias_abf : public colvarbias {
public:
colvarbias_abf(char const *key);
virtual int init(std::string const &conf);
virtual ~colvarbias_abf();
virtual int 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 update_bias;
bool hide_Jacobian;
size_t full_samples;
size_t min_samples;
/// frequency for updating output files
int output_freq;
/// Write combined files with a history of all output data?
bool b_history_files;
size_t history_freq;
/// Cap applied biasing force?
bool cap_force;
std::vector<cvm::real> max_force;
// Internal data and methods
std::vector<int> bin, force_bin, z_bin;
gradient_t system_force, applied_force;
/// n-dim grid of free energy gradients
colvar_grid_gradient *gradients;
/// n-dim grid of number of samples
colvar_grid_count *samples;
/// n-dim grid: average force on "real" coordinate for eABF z-based estimator
colvar_grid_gradient *z_gradients;
/// n-dim grid of number of samples on "real" coordinate for eABF z-based estimator
colvar_grid_count *z_samples;
/// n-dim grid contining CZAR estimator of "real" free energy gradients
colvar_grid_gradient *czar_gradients;
// shared ABF
bool shared_on;
size_t shared_freq;
int shared_last_step;
// Share between replicas -- may be called independently of update
virtual int replica_share();
// Store the last set for shared ABF
colvar_grid_gradient *last_gradients;
colvar_grid_count *last_samples;
// For Tcl implementation of selection rules.
/// Give the total number of bins for a given bias.
virtual int bin_num();
/// Calculate the bin index for a given bias.
virtual int current_bin();
//// Give the count at a given bin index.
virtual int bin_count(int bin_index);
/// Write human-readable FE gradients and sample count
void write_gradients_samples(const std::string &prefix, bool append = false);
void write_last_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&);
};
#endif

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