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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...

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.

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.

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.

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