forked from lijiext/lammps
96 lines
2.3 KiB
C++
96 lines
2.3 KiB
C++
/************************************************************************
|
|
* 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
|