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colvarbias_alb.h
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Wed, Jul 24, 13:24

colvarbias_alb.h
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// -*- c++ -*-
#ifndef COLVARBIAS_ALB_H
#define COLVARBIAS_ALB_H
#include "colvar.h"
#include "colvarbias_restraint.h"
class colvarbias_alb : public colvarbias {
public:
colvarbias_alb(std::string const &conf, char const *key);
virtual ~colvarbias_alb();
virtual cvm::real update();
/// Read the bias configuration from a restart file
virtual std::istream & read_restart(std::istream &is);
/// Write the bias configuration to a restart file
virtual std::ostream & write_restart(std::ostream &os);
/// Write a label to the trajectory file (comment line)
virtual std::ostream & write_traj_label(std::ostream &os);
/// Output quantities such as the bias energy to the trajectory file
virtual std::ostream & write_traj(std::ostream &os);
protected:
/// \brief Restraint centers
std::vector<colvarvalue> colvar_centers;
/// \brief colvar parameters, used for calculating the gradient/variance
std::vector<cvm::real> means;
std::vector<cvm::real> ssd; // SSD = sum of squares of differences from mean
int update_calls;
///\brief how often to update coupling constant
int update_freq;
///\brief Estimated range of coupling constant values in kT
std::vector<cvm::real> max_coupling_range;
//\brief Estimated max for how quickly the rate can change in kT / time
std::vector<cvm::real> max_coupling_rate;
/// \brief accumated couping force; used in stochastic online gradient descent algorithm
std::vector<cvm::real> coupling_accum;
/// \brief coupling constant
std::vector<cvm::real> set_coupling;
/// \brief current coupling constant, which is ramped up during equilibration to coupling
std::vector<cvm::real> current_coupling;
/// \brief how quickly to change the coupling constant
std::vector<cvm::real> coupling_rate;
// \brief if we're equilibrating our estimates or collecting data
bool b_equilibration;
// \brief If the coupling range should be increased
bool b_hard_coupling_range;
/// \brief flag for outputting colvar centers
bool b_output_centers;
/// \brief flag for outputting current gradient
bool b_output_grad;
/// \brief flag for outputting coupling constant
bool b_output_coupling;
cvm::real restraint_potential(cvm::real k, const colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
colvarvalue restraint_force(cvm::real k, const colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
#endif

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