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colvarbias_restraint_centers_moving Class Reference

Options to change the restraint centers over time. More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint_centers_moving:

colvarbias_restraint_centers colvarbias_restraint_moving colvarbias_restraint colvarparse colvardeps colvarbias colvarbias_ti colvarparams colvarparse colvardeps colvarbias colvarparams colvarparse colvardeps colvarparams colvarbias_restraint_harmonic colvarbias_restraint_linear List of all members.

Public Methods

 colvarbias_restraint_centers_moving (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 &)
 Load new configuration - force constant and/or centers only. More...

virtual std::string const get_state_params () const
virtual int set_state_params (std::string const &conf)
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 int update_centers (cvm::real lambda)
 \brief Update the centers by interpolating between initial and target. More...

int update_acc_work ()
 Update the accumulated work. More...


Protected Attributes

std::vector< colvarvalue > target_centers
 \brief New restraint centers. More...

std::vector< colvarvalue > initial_centers
 \brief Initial value of the restraint centers. More...

std::vector< colvarvalue > centers_incr
 \brief Increment of the restraint centers at each step. More...

bool b_output_centers
 Whether to write the current restraint centers to the trajectory file. More...

Detailed Description

Options to change the restraint centers over time.

Definition at line 152 of file colvarbias_restraint.h.

Constructor & Destructor Documentation

colvarbias_restraint_centers_moving::colvarbias_restraint_centers_moving (  char const *    key ) 
 

Definition at line 258 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_chg_centers, and b_output_centers.

Member Function Documentation

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

Load new configuration - force constant and/or centers only.

Reimplemented from colvarbias_restraint_centers.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 161 of file colvarbias_restraint.h.

References COLVARS_NOT_IMPLEMENTED.

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

Reimplemented from colvarbias_restraint_moving.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 420 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, colvarbias_restraint_centers::colvar_centers, colvardeps::f_cvb_output_acc_work, colvardeps::is_enabled, and colvarbias::num_variables.

Referenced by colvarbias_restraint_linear::get_state_params, and colvarbias_restraint_harmonic::get_state_params.

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

\brief Parse config string and (re)initialize.

Reimplemented from colvarbias_restraint_centers.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 270 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_chg_centers, b_output_centers, centers_incr, colvarbias_restraint_centers::colvar_centers, COLVARS_INPUT_ERROR, conf, colvarmodule::debug, colvarmodule::error, colvarparse::get_keyval, colvarbias_restraint_moving::init, colvarbias_restraint_centers::init, initial_centers, colvarvalue::interpolate, colvarmodule::log, midpoint, colvarbias::num_variables, and target_centers.

Referenced by colvarbias_restraint_linear::init, and colvarbias_restraint_harmonic::init.

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

Reimplemented from colvarbias_restraint_moving.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 446 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, colvarbias_restraint_centers::colvar_centers, conf, colvardeps::f_cvb_output_acc_work, colvarparse::get_keyval, colvardeps::is_enabled, colvarparse::parse_required, colvarparse::parse_restart, and colvarbias_restraint::set_state_params.

Referenced by colvarbias_restraint_linear::set_state_params, and colvarbias_restraint_harmonic::set_state_params.

int colvarbias_restraint_centers_moving::update (    )  [virtual]
 

Reimplemented from colvarbias_restraint_moving.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 342 of file colvarbias_restraint.C.

References centers_incr, colvarbias_restraint_centers::colvar_centers, colvarmodule::debug, colvarbias_restraint_moving::first_step, colvarmodule::get_error, colvarmodule::log, colvarmodule::main, colvarbias::num_variables, colvarmodule::proxy, colvarmodule::real, colvarproxy::simulation_running, colvarbias_restraint_moving::stage, colvarmodule::step_absolute, colvarmodule::step_relative, colvarbias_restraint_moving::target_nstages, colvarbias_restraint_moving::target_nsteps, and update_centers.

Referenced by colvarbias_restraint_linear::update, and colvarbias_restraint_harmonic::update.

int colvarbias_restraint_centers_moving::update_acc_work (    )  [protected]
 

Update the accumulated work.

Definition at line 400 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, centers_incr, colvarbias::colvar_forces, colvardeps::f_cvb_output_acc_work, colvarbias_restraint_moving::first_step, colvardeps::is_enabled, colvarmodule::main, colvarbias::num_variables, colvarmodule::proxy, colvarproxy::simulation_running, colvarmodule::step_absolute, colvarmodule::step_relative, and colvarbias_restraint_moving::target_nsteps.

Referenced by colvarbias_restraint_linear::update, and colvarbias_restraint_harmonic::update.

int colvarbias_restraint_centers_moving::update_centers (  cvm::real    lambda )  [protected, virtual]
 

\brief Update the centers by interpolating between initial and target.

Definition at line 319 of file colvarbias_restraint.C.

References centers_incr, colvarbias_restraint_centers::colvar_centers, colvarmodule::debug, colvarvalue::dist2_grad, colvarmodule::get_error, initial_centers, colvarvalue::interpolate, colvarmodule::log, colvarbias::num_variables, target_centers, and colvarbias::variables.

Referenced by update.

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

Output quantities such as the bias energy to the trajectory file.

Reimplemented from colvarbias_restraint.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 483 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, colvarbias_restraint_moving::b_chg_centers, colvarbias_restraint_centers::colvar_centers, colvardeps::f_cvb_output_acc_work, colvardeps::is_enabled, and colvarbias::num_variables.

Referenced by colvarbias_restraint_linear::write_traj, and colvarbias_restraint_harmonic::write_traj.

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

Write a label to the trajectory file (comment line).

Reimplemented from colvarbias_restraint.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 464 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_chg_centers, colvardeps::f_cvb_output_acc_work, colvardeps::is_enabled, colvarbias::num_variables, colvarbias::variables, and colvarmodule::wrap_string.

Referenced by colvarbias_restraint_linear::write_traj_label, and colvarbias_restraint_harmonic::write_traj_label.

Member Data Documentation

bool colvarbias_restraint_centers_moving::b_output_centers [protected]
 

Whether to write the current restraint centers to the trajectory file.

Definition at line 183 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_centers_moving, and init.

std::vector<colvarvalue> colvarbias_restraint_centers_moving::centers_incr [protected]
 

\brief Increment of the restraint centers at each step.

Definition at line 177 of file colvarbias_restraint.h.

Referenced by init, update, update_acc_work, and update_centers.

std::vector<colvarvalue> colvarbias_restraint_centers_moving::initial_centers [protected]
 

\brief Initial value of the restraint centers.

Definition at line 174 of file colvarbias_restraint.h.

Referenced by init, and update_centers.

std::vector<colvarvalue> colvarbias_restraint_centers_moving::target_centers [protected]
 

\brief New restraint centers.

Definition at line 171 of file colvarbias_restraint.h.

Referenced by init, and update_centers.

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