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colvarbias.h
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Wed, Jun 19, 13:09

colvarbias.h
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/// -*- c++ -*-
#ifndef COLVARBIAS_H
#define COLVARBIAS_H
#include "colvar.h"
#include "colvarparse.h"
/// \brief Collective variable bias, base class
class colvarbias : public colvarparse {
public:
/// Name of this bias
std::string name;
/// Add a new collective variable to this bias
void add_colvar (std::string const &cv_name);
/// Retrieve colvar values and calculate their biasing forces
/// Return bias energy
virtual cvm::real update() = 0;
// TODO: move update_bias here (share with metadynamics)
/// Load new configuration - force constant and/or centers only
virtual void change_configuration(std::string const &conf);
/// Calculate change in energy from using alternate configuration
virtual cvm::real energy_difference(std::string const &conf);
/// Perform analysis tasks
virtual inline void analyse() {}
/// Send forces to the collective variables
void communicate_forces();
/// \brief Constructor
///
/// The constructor of the colvarbias base class is protected, so
/// that it can only be called from inherited classes
colvarbias (std::string const &conf, char const *key);
/// Default constructor
colvarbias();
/// Destructor
virtual ~colvarbias();
/// Read the bias configuration from a restart file
virtual std::istream & read_restart (std::istream &is) = 0;
/// Write the bias configuration to a restart file
virtual std::ostream & write_restart (std::ostream &os) = 0;
/// 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);
inline cvm::real get_energy () {
return bias_energy;
}
protected:
/// \brief Pointers to collective variables to which the bias is
/// applied; current values and metric functions will be obtained
/// through each colvar object
std::vector<colvar *> colvars;
/// \brief Current forces from this bias to the colvars
std::vector<colvarvalue> colvar_forces;
/// \brief Current energy of this bias (colvar_forces should be obtained by deriving this)
cvm::real bias_energy;
/// Whether to write the current bias energy from this bias to the trajectory file
bool b_output_energy;
/// \brief Whether this bias has already accumulated information
/// (when relevant)
bool has_data;
};
#endif

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