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colvarbias.h
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Wed, May 29, 12:22

colvarbias.h
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// -*- c++ -*-
#ifndef COLVARBIAS_H
#define COLVARBIAS_H
#include "colvar.h"
#include "colvarparse.h"
#include "colvardeps.h"
/// \brief Collective variable bias, base class
class colvarbias : public colvarparse, public cvm::deps {
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 int update();
// 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);
/// 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);
//// Share information between replicas, whatever it may be.
virtual int replica_share();
/// Perform analysis tasks
virtual void analyze() {}
/// Send forces to the collective variables
void communicate_forces();
/// \brief Constructor
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);
/// (Re)initialize the output files (does not write them yet)
virtual int setup_output() { return COLVARS_OK; }
/// Output quantities such as the bias energy to the trajectory file
virtual std::ostream & write_traj(std::ostream &os);
/// Write output files (if defined, e.g. in analysis mode)
virtual int write_output_files()
{
return COLVARS_OK;
}
inline cvm::real get_energy() {
return bias_energy;
}
/// \brief Implementation of the feature list for colvarbias
static std::vector<feature *> cvb_features;
/// \brief Implementation of the feature list accessor for colvarbias
virtual std::vector<feature *> &features() {
return cvb_features;
}
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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