#include <colvarbias_restraint.h>
Inheritance diagram for colvarbias_restraint_harmonic_walls:
Public Methods | |
colvarbias_restraint_harmonic_walls (char const *key) | |
virtual int | init (std::string const &conf) |
\brief Parse config string and (re)initialize. More... | |
virtual int | update () |
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 | colvar_distance (size_t i) const |
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... | |
Protected Attributes | |
std::vector< colvarvalue > | lower_walls |
\brief Location of the lower walls. More... | |
std::vector< colvarvalue > | upper_walls |
\brief Location of the upper walls. More... | |
cvm::real | lower_wall_k |
\brief If both walls are defined, use this k for the lower. More... | |
cvm::real | upper_wall_k |
\brief If both walls are defined, use this k for the upper. More... |
Definition at line 262 of file colvarbias_restraint.h.
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Definition at line 897 of file colvarbias_restraint.C. References colvardeps::f_cvb_bypass_ext_lagrangian, lower_wall_k, colvardeps::provide, colvardeps::set_enabled, and upper_wall_k. |
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Definition at line 1059 of file colvarbias_restraint.C. References colvar::dist2, colvar::dist2_lgrad, colvardeps::f_cv_periodic, colvardeps::f_cvb_bypass_ext_lagrangian, colvardeps::is_enabled, lower_walls, upper_walls, and colvarbias::variables. Referenced by d_restraint_potential_dk, restraint_force, and restraint_potential. |
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\brief Derivative of the potential function with respect to the force constant.
Implements colvarbias_restraint. Definition at line 1112 of file colvarbias_restraint.C. References colvar_distance, lower_wall_k, upper_wall_k, and colvarbias::variables. |
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Reimplemented from colvarbias_restraint_k_moving. Definition at line 1121 of file colvarbias_restraint.C. References colvarbias_restraint_k_moving::get_state_params, colvarbias_restraint_moving::get_state_params, and colvarbias_restraint::get_state_params. |
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\brief Parse config string and (re)initialize.
Reimplemented from colvarbias_restraint_k_moving. Definition at line 913 of file colvarbias_restraint.C. References colvarbias_restraint_moving::b_decoupling, colvarmodule::cite_feature, COLVARS_INPUT_ERROR, conf, colvardeps::enable, colvarmodule::error, colvardeps::f_cv_periodic, colvardeps::f_cvb_scalar_variables, colvarbias_restraint_k::force_k, colvarparse::get_keyval, colvarbias_restraint_k_moving::init, colvarbias_restraint_moving::init, colvarbias_restraint::init, colvarmodule::log, lower_wall_k, lower_walls, colvarmodule::main, colvarbias::num_variables, colvarmodule::sqrt, colvarbias_restraint_k_moving::starting_force_k, upper_wall_k, upper_walls, and colvarbias::variables. |
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Read all mutable data not already set by set_state_params().
Reimplemented from colvarbias. Definition at line 1145 of file colvarbias_restraint.C. References colvarbias_ti::read_state_data. |
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\brief Force function for the i-th colvar.
Implements colvarbias_restraint. Definition at line 1104 of file colvarbias_restraint.C. References colvar_distance, colvarbias_restraint_k::force_k, lower_wall_k, upper_wall_k, and colvarbias::variables. |
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\brief Potential function for the i-th colvar.
Implements colvarbias_restraint. Definition at line 1095 of file colvarbias_restraint.C. References colvar_distance, colvarbias_restraint_k::force_k, lower_wall_k, upper_wall_k, and colvarbias::variables. |
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Reimplemented from colvarbias_restraint_k_moving. Definition at line 1129 of file colvarbias_restraint.C. References conf, colvarbias_restraint_k_moving::set_state_params, colvarbias_restraint_moving::set_state_params, and colvarbias_restraint::set_state_params. |
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Reimplemented from colvarbias_restraint_k_moving. Definition at line 1043 of file colvarbias_restraint.C. References colvarbias_restraint::update, colvarbias_restraint_k_moving::update, colvarbias_ti::update, and colvarbias_restraint_k_moving::update_acc_work. |
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Write all mutable data not already written by get_state_params().
Reimplemented from colvarbias. Definition at line 1139 of file colvarbias_restraint.C. References colvarbias_ti::write_state_data. |
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Output quantities such as the bias energy to the trajectory file.
Reimplemented from colvarbias_restraint_k_moving. Definition at line 1159 of file colvarbias_restraint.C. References colvarbias_restraint_k_moving::write_traj, and colvarbias_restraint::write_traj. |
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Write a label to the trajectory file (comment line).
Reimplemented from colvarbias_restraint_k_moving. Definition at line 1151 of file colvarbias_restraint.C. References colvarbias_restraint_k_moving::write_traj_label, and colvarbias_restraint::write_traj_label. |
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\brief If both walls are defined, use this k for the lower.
Definition at line 286 of file colvarbias_restraint.h. Referenced by colvarbias_restraint_harmonic_walls, d_restraint_potential_dk, init, restraint_force, and restraint_potential. |
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\brief Location of the lower walls.
Definition at line 280 of file colvarbias_restraint.h. Referenced by colvar_distance, and init. |
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\brief If both walls are defined, use this k for the upper.
Definition at line 289 of file colvarbias_restraint.h. Referenced by colvarbias_restraint_harmonic_walls, d_restraint_potential_dk, init, restraint_force, and restraint_potential. |
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\brief Location of the upper walls.
Definition at line 283 of file colvarbias_restraint.h. Referenced by colvar_distance, and init. |