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colvarbias_restraint.h
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Thu, Jul 11, 08:49

colvarbias_restraint.h
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/// -*- c++ -*-
#ifndef COLVARBIAS_RESTRAINT_H
#define COLVARBIAS_RESTRAINT_H
#include "colvarbias.h"
/// \brief Bias restraint, optionally moving towards a target
/// (implementation of \link colvarbias \endlink)
class colvarbias_restraint : public colvarbias {
public:
/// Retrieve colvar values and calculate their biasing forces
virtual cvm::real update();
/// 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);
/// 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);
/// \brief Constructor
colvarbias_restraint(std::string const &conf, char const *key);
/// Destructor
virtual ~colvarbias_restraint();
protected:
/// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const = 0;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const = 0;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const = 0;
/// \brief Restraint centers
std::vector<colvarvalue> colvar_centers;
/// \brief Restraint centers without wrapping or constraints applied
std::vector<colvarvalue> colvar_centers_raw;
/// \brief Moving target?
bool b_chg_centers;
/// \brief New restraint centers
std::vector<colvarvalue> target_centers;
/// \brief Amplitude of the restraint centers' increment at each step
/// (or stage) towards the new values (calculated from target_nsteps)
std::vector<colvarvalue> centers_incr;
/// Whether to write the current restraint centers to the trajectory file
bool b_output_centers;
/// Whether to write the current accumulated work to the trajectory file
bool b_output_acc_work;
/// \brief Accumulated work
cvm::real acc_work;
/// \brief Restraint force constant
cvm::real force_k;
/// \brief Changing force constant?
bool b_chg_force_k;
/// \brief Restraint force constant (target value)
cvm::real target_force_k;
/// \brief Restraint force constant (starting value)
cvm::real starting_force_k;
/// \brief Lambda-schedule for custom varying force constant
std::vector<cvm::real> lambda_schedule;
/// \brief Exponent for varying the force constant
cvm::real force_k_exp;
/// \brief Intermediate quantity to compute the restraint free energy
/// (in TI, would be the accumulating FE derivative)
cvm::real restraint_FE;
/// \brief Equilibration steps for restraint FE calculation through TI
cvm::real target_equil_steps;
/// \brief Number of stages over which to perform the change
/// If zero, perform a continuous change
int target_nstages;
/// \brief Number of current stage of the perturbation
int stage;
/// \brief Number of steps required to reach the target force constant
/// or restraint centers
long target_nsteps;
};
/// \brief Harmonic bias restraint
/// (implementation of \link colvarbias_restraint \endlink)
class colvarbias_restraint_harmonic : public colvarbias_restraint {
public:
colvarbias_restraint_harmonic(std::string const &conf, char const *key);
protected: /// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
/// \brief Linear bias restraint
/// (implementation of \link colvarbias_restraint \endlink)
class colvarbias_restraint_linear : public colvarbias_restraint {
public:
colvarbias_restraint_linear(std::string const &conf, char const *key);
protected: /// \brief Potential function
virtual cvm::real restraint_potential(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
/// \brief Force function
virtual colvarvalue restraint_force(cvm::real k, colvar* x, const colvarvalue& xcenter) const;
///\brief Unit scaling
virtual cvm::real restraint_convert_k(cvm::real k, cvm::real dist_measure) const;
};
#endif

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