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colvarbias_restraint Class Reference

\brief Most general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias). More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint:

List of all members.

Public Methods
virtual int	update ()
	Retrieve colvar values and calculate their biasing forces. More...
virtual int	change_configuration (std::string const &)
	Load new configuration - force constant and/or centers only. More...
virtual cvm::real	energy_difference (std::string const &)
	Calculate change in energy from using alternate configuration. More...
virtual std::string const	get_state_params () const
	Write the values of specific mutable properties to a string. More...
virtual int	set_state_params (std::string const &conf)
	Read the values of specific mutable properties from a string. 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...
	colvarbias_restraint (char const *key)
	\brief Constructor. More...
virtual int	init (std::string const &conf)
	\brief Parse config string and (re)initialize. More...
virtual	~colvarbias_restraint ()
Protected Methods
virtual cvm::real	restraint_potential (size_t i) const=0
	\brief Potential function for the i-th colvar. More...
virtual colvarvalue const	restraint_force (size_t i) const=0
	\brief Force function for the i-th colvar. More...
virtual cvm::real	d_restraint_potential_dk (size_t i) const=0
	\brief Derivative of the potential function with respect to the force constant. More...

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Detailed Description

\brief Most general definition of a colvar restraint: see derived classes for specific types (implementation of colvarbias).

Definition at line 23 of file colvarbias_restraint.h.

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Constructor & Destructor Documentation

colvarbias_restraint::colvarbias_restraint (  char const *    key )

\brief Constructor. Definition at line 21 of file colvarbias_restraint.C. References colvarbias::state_keyword.

colvarbias_restraint::~colvarbias_restraint (    )  [virtual]

Definition at line 66 of file colvarbias_restraint.C.

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Member Function Documentation

virtual int colvarbias_restraint::change_configuration (  std::string const &    )  [inline, virtual]

Load new configuration - force constant and/or centers only. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers. Definition at line 34 of file colvarbias_restraint.h. References COLVARS_NOT_IMPLEMENTED.

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

\brief Derivative of the potential function with respect to the force constant. Implemented in colvarbias_restraint_harmonic. Referenced by colvarbias_restraint_k_moving::update, and colvarbias_restraint_k_moving::update_acc_work.

virtual cvm::real colvarbias_restraint::energy_difference (  std::string const &    )  [inline, virtual]

Calculate change in energy from using alternate configuration. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_harmonic. Definition at line 37 of file colvarbias_restraint.h.

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

Write the values of specific mutable properties to a string. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers_moving. Definition at line 71 of file colvarbias_restraint.C. References colvarbias::get_state_params. Referenced by colvarbias_restraint_linear::get_state_params, colvarbias_restraint_harmonic_walls::get_state_params, and colvarbias_restraint_harmonic::get_state_params.

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

\brief Parse config string and (re)initialize. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers. Definition at line 28 of file colvarbias_restraint.C. References conf, colvarmodule::debug, colvardeps::enable, colvardeps::f_cvb_apply_force, colvarbias_ti::init, colvarbias::init, and colvarmodule::log. Referenced by colvarbias_restraint_linear::init, colvarbias_restraint_harmonic_walls::init, and colvarbias_restraint_harmonic::init.

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

\brief Force function for the i-th colvar. Implemented in colvarbias_restraint_harmonic. Referenced by update.

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

\brief Potential function for the i-th colvar. Implemented in colvarbias_restraint_harmonic. Referenced by update.

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

Read the values of specific mutable properties from a string. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers_moving. Definition at line 77 of file colvarbias_restraint.C. References conf, and colvarbias::set_state_params. Referenced by colvarbias_restraint_linear::set_state_params, colvarbias_restraint_harmonic_walls::set_state_params, colvarbias_restraint_harmonic::set_state_params, colvarbias_restraint_k_moving::set_state_params, and colvarbias_restraint_centers_moving::set_state_params.

int colvarbias_restraint::update (    )  [virtual]

Retrieve colvar values and calculate their biasing forces. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers_moving. Definition at line 42 of file colvarbias_restraint.C. References colvarbias::bias_energy, colvarbias::colvar_forces, colvarmodule::debug, colvarmodule::log, colvarbias::num_variables, restraint_force, restraint_potential, colvarbias::update, and colvarbias::variables. Referenced by colvarbias_restraint_linear::update, colvarbias_restraint_harmonic_walls::update, and colvarbias_restraint_harmonic::update.

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

Output quantities such as the bias energy to the trajectory file. Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers_moving. Definition at line 89 of file colvarbias_restraint.C. References colvarbias::write_traj. Referenced by colvarbias_restraint_linear::write_traj, colvarbias_restraint_harmonic_walls::write_traj, and colvarbias_restraint_harmonic::write_traj.

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

Write a label to the trajectory file (comment line). Reimplemented from colvarbias. Reimplemented in colvarbias_restraint_centers_moving. Definition at line 83 of file colvarbias_restraint.C. References colvarbias::write_traj_label. Referenced by colvarbias_restraint_linear::write_traj_label, colvarbias_restraint_harmonic_walls::write_traj_label, and colvarbias_restraint_harmonic::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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