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colvarbias_restraint_linear Class Reference

\brief Linear bias restraint (implementation of colvarbias_restraint). More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint_linear:

List of all members.

Public Methods
	colvarbias_restraint_linear (char const *key)
virtual int	init (std::string const &conf)
	\brief Parse config string and (re)initialize. More...
virtual int	update ()
virtual int	change_configuration (std::string const &conf)
	Load new configuration - force constant and/or centers only. More...
virtual cvm::real	energy_difference (std::string const &conf)
	Calculate change in energy from using alternate configuration. More...
virtual std::string const	get_state_params () const
virtual int	set_state_params (std::string const &conf)
virtual std::ostream &	write_state_data (std::ostream &os)
	Write all mutable data not already written by get_state_params(). More...
virtual std::istream &	read_state_data (std::istream &os)
	Read all mutable data not already set by set_state_params(). More...
virtual std::ostream &	write_traj_label (std::ostream &os)
	Write a label to the trajectory file (comment line). More...
virtual std::ostream &	write_traj (std::ostream &os)
	Output quantities such as the bias energy to the trajectory file. More...
Protected Methods
virtual cvm::real	restraint_potential (size_t i) const
	\brief Potential function for the i-th colvar. More...
virtual colvarvalue const	restraint_force (size_t i) const
	\brief Force function for the i-th colvar. More...
virtual cvm::real	d_restraint_potential_dk (size_t i) const
	\brief Derivative of the potential function with respect to the force constant. More...

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Detailed Description

\brief Linear bias restraint (implementation of colvarbias_restraint).

Definition at line 300 of file colvarbias_restraint.h.

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Constructor & Destructor Documentation

colvarbias_restraint_linear::colvarbias_restraint_linear (  char const *    key )

Definition at line 1168 of file colvarbias_restraint.C. References colvarbias_restraint_k::check_positive_k.

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Member Function Documentation

int colvarbias_restraint_linear::change_configuration (  std::string const &    conf )  [virtual]

Load new configuration - force constant and/or centers only. Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1230 of file colvarbias_restraint.C. References colvarbias_restraint_k::change_configuration, and conf. Referenced by energy_difference.

cvm::real colvarbias_restraint_linear::d_restraint_potential_dk (  size_t    i )  const [protected, virtual]

\brief Derivative of the potential function with respect to the force constant. Implements colvarbias_restraint. Definition at line 1269 of file colvarbias_restraint.C. References colvarbias_restraint_centers::colvar_centers, d_restraint_potential_dk, and colvarbias::variables. Referenced by d_restraint_potential_dk.

cvm::real colvarbias_restraint_linear::energy_difference (  std::string const &    conf )  [virtual]

Calculate change in energy from using alternate configuration. Reimplemented from colvarbias_restraint. Definition at line 1237 of file colvarbias_restraint.C. References colvarbias::bias_energy, change_configuration, conf, colvarbias_restraint_k::force_k, result, and update.

std::string const colvarbias_restraint_linear::get_state_params (    )  const [virtual]

Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1276 of file colvarbias_restraint.C. References colvarbias_restraint_k_moving::get_state_params, colvarbias_restraint_centers_moving::get_state_params, colvarbias_restraint_moving::get_state_params, and colvarbias_restraint::get_state_params.

int colvarbias_restraint_linear::init (  std::string const &    conf )  [virtual]

\brief Parse config string and (re)initialize. Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1182 of file colvarbias_restraint.C. References colvarmodule::cite_feature, COLVARS_INPUT_ERROR, conf, colvarmodule::error, colvardeps::f_cv_periodic, colvarbias_restraint_k::force_k, colvarbias_restraint_k_moving::init, colvarbias_restraint_centers_moving::init, colvarbias_restraint_moving::init, colvarbias_restraint::init, colvarmodule::main, colvarbias::num_variables, and colvarbias::variables.

std::istream & colvarbias_restraint_linear::read_state_data (  std::istream &    is )  [virtual]

Read all mutable data not already set by set_state_params(). Reimplemented from colvarbias. Definition at line 1302 of file colvarbias_restraint.C. References colvarbias_ti::read_state_data.

colvarvalue const colvarbias_restraint_linear::restraint_force (  size_t    i )  const [protected, virtual]

\brief Force function for the i-th colvar. Implements colvarbias_restraint. Definition at line 1261 of file colvarbias_restraint.C. References colvarbias_restraint_k::force_k, colvarvalue::set_ones, and colvarbias::variables.

cvm::real colvarbias_restraint_linear::restraint_potential (  size_t    i )  const [protected, virtual]

\brief Potential function for the i-th colvar. Implements colvarbias_restraint. Definition at line 1254 of file colvarbias_restraint.C. References colvarbias_restraint_centers::colvar_centers, colvarbias_restraint_k::force_k, and colvarbias::variables.

int colvarbias_restraint_linear::set_state_params (  std::string const &    conf )  [virtual]

Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1285 of file colvarbias_restraint.C. References conf, colvarbias_restraint_k_moving::set_state_params, colvarbias_restraint_centers_moving::set_state_params, colvarbias_restraint_moving::set_state_params, and colvarbias_restraint::set_state_params.

int colvarbias_restraint_linear::update (    )  [virtual]

Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1208 of file colvarbias_restraint.C. References colvarbias_restraint::update, colvarbias_restraint_k_moving::update, colvarbias_restraint_centers_moving::update, colvarbias_ti::update, colvarbias_restraint_k_moving::update_acc_work, and colvarbias_restraint_centers_moving::update_acc_work. Referenced by energy_difference.

std::ostream & colvarbias_restraint_linear::write_state_data (  std::ostream &    os )  [virtual]

Write all mutable data not already written by get_state_params(). Reimplemented from colvarbias. Definition at line 1296 of file colvarbias_restraint.C. References colvarbias_ti::write_state_data.

std::ostream & colvarbias_restraint_linear::write_traj (  std::ostream &    os )  [virtual]

Output quantities such as the bias energy to the trajectory file. Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1317 of file colvarbias_restraint.C. References colvarbias_restraint_k_moving::write_traj, colvarbias_restraint_centers_moving::write_traj, and colvarbias_restraint::write_traj.

std::ostream & colvarbias_restraint_linear::write_traj_label (  std::ostream &    os )  [virtual]

Write a label to the trajectory file (comment line). Reimplemented from colvarbias_restraint_centers_moving. Definition at line 1308 of file colvarbias_restraint.C. References colvarbias_restraint_k_moving::write_traj_label, colvarbias_restraint_centers_moving::write_traj_label, and colvarbias_restraint::write_traj_label.

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The documentation for this class was generated from the following files:

• colvarbias_restraint.h
• colvarbias_restraint.C

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