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colvarbias_restraint_k_moving Class Reference

Options to change the restraint force constant over time. More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint_k_moving:

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

Public Methods

 colvarbias_restraint_k_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

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


Protected Attributes

cvm::real target_force_k
 \brief Restraint force constant (target value). More...

cvm::real starting_force_k
 \brief Restraint force constant (starting value). More...

cvm::real lambda_exp
 \brief Exponent for varying the force constant. More...

cvm::real restraint_FE
 \brief Intermediate quantity to compute the restraint free energy (in TI, would be the accumulating FE derivative). More...

cvm::real target_equil_steps
 \brief Equilibration steps for restraint FE calculation through TI. More...

cvm::real force_k_incr
 \brief Increment of the force constant at each step. More...

Detailed Description

Options to change the restraint force constant over time.

Definition at line 191 of file colvarbias_restraint.h.

Constructor & Destructor Documentation

colvarbias_restraint_k_moving::colvarbias_restraint_k_moving (  char const *    key ) 
 

Definition at line 504 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_chg_force_k, colvarbias_restraint_moving::b_decoupling, force_k_incr, lambda_exp, restraint_FE, starting_force_k, target_equil_steps, and target_force_k.

Member Function Documentation

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

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

Reimplemented from colvarbias_restraint_k.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 200 of file colvarbias_restraint.h.

References COLVARS_NOT_IMPLEMENTED.

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

Reimplemented from colvarbias_restraint_moving.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 684 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, colvardeps::f_cvb_output_acc_work, colvarbias_restraint_k::force_k, and colvardeps::is_enabled.

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

\brief Parse config string and (re)initialize.

Reimplemented from colvarbias_restraint_k.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 522 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_chg_force_k, colvarbias_restraint_moving::b_decoupling, COLVARS_ERROR, COLVARS_INPUT_ERROR, conf, colvarmodule::error, colvarbias_restraint_k::force_k, colvarmodule::get_error, colvarparse::get_keyval, colvarbias_restraint_moving::init, colvarbias_restraint_k::init, lambda_exp, colvarbias_restraint_moving::lambda_schedule, colvarmodule::log, colvarparse::parse_deprecated, starting_force_k, target_equil_steps, target_force_k, and colvarbias_restraint_moving::target_nstages.

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

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

Reimplemented from colvarbias_restraint_moving.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 703 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, conf, colvardeps::f_cvb_output_acc_work, colvarbias_restraint_k::force_k, 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, colvarbias_restraint_harmonic_walls::set_state_params, and colvarbias_restraint_harmonic::set_state_params.

int colvarbias_restraint_k_moving::update (    )  [virtual]
 

Reimplemented from colvarbias_restraint_moving.

Reimplemented in colvarbias_restraint_harmonic.

Definition at line 575 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_decoupling, colvarbias_restraint::d_restraint_potential_dk, colvarbias_restraint_moving::first_step, colvarbias_restraint_k::force_k, force_k_incr, lambda_exp, colvarbias_restraint_moving::lambda_schedule, colvarmodule::log, colvarmodule::main, colvarbias::num_variables, colvarmodule::pow, colvarmodule::proxy, colvarmodule::real, restraint_FE, colvarproxy::simulation_running, colvarbias_restraint_moving::stage, starting_force_k, colvarmodule::step_absolute, target_equil_steps, target_force_k, colvarbias_restraint_moving::target_nstages, and colvarbias_restraint_moving::target_nsteps.

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

int colvarbias_restraint_k_moving::update_acc_work (    )  [protected]
 

Update the accumulated work.

Definition at line 664 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, colvarbias_restraint::d_restraint_potential_dk, colvardeps::f_cvb_output_acc_work, force_k_incr, colvardeps::is_enabled, colvarmodule::main, colvarbias::num_variables, colvarmodule::proxy, colvarproxy::simulation_running, and colvarmodule::step_relative.

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

std::ostream & colvarbias_restraint_k_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 731 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::acc_work, colvarbias_restraint_moving::b_chg_force_k, colvardeps::f_cvb_output_acc_work, and colvardeps::is_enabled.

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

std::ostream & colvarbias_restraint_k_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 721 of file colvarbias_restraint.C.

References colvarbias_restraint_moving::b_chg_force_k, colvardeps::f_cvb_output_acc_work, colvardeps::is_enabled, and colvarmodule::wrap_string.

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

Member Data Documentation

cvm::real colvarbias_restraint_k_moving::force_k_incr [protected]
 

\brief Increment of the force constant at each step.

Definition at line 226 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_k_moving, update, and update_acc_work.

cvm::real colvarbias_restraint_k_moving::lambda_exp [protected]
 

\brief Exponent for varying the force constant.

Definition at line 216 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_k_moving, init, and update.

cvm::real colvarbias_restraint_k_moving::restraint_FE [protected]
 

\brief Intermediate quantity to compute the restraint free energy (in TI, would be the accumulating FE derivative).

Definition at line 220 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_k_moving, and update.

cvm::real colvarbias_restraint_k_moving::starting_force_k [protected]
 

\brief Restraint force constant (starting value).

Definition at line 213 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_k_moving, colvarbias_restraint_harmonic_walls::init, init, and update.

cvm::real colvarbias_restraint_k_moving::target_equil_steps [protected]
 

\brief Equilibration steps for restraint FE calculation through TI.

Definition at line 223 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_k_moving, init, and update.

cvm::real colvarbias_restraint_k_moving::target_force_k [protected]
 

\brief Restraint force constant (target value).

Definition at line 210 of file colvarbias_restraint.h.

Referenced by colvarbias_restraint_k_moving, init, and update.

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