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colvarbias_alb Class Reference

#include <colvarbias_alb.h>

Inheritance diagram for colvarbias_alb:

List of all members.

Public Methods
	colvarbias_alb (char const *key)
virtual	~colvarbias_alb ()
virtual int	init (std::string const &conf)
	\brief Parse config string and (re)initialize. More...
virtual int	update ()
	Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces(). 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...
Protected Methods
cvm::real	restraint_potential (cvm::real k, const colvar *x, const colvarvalue &xcenter) const
colvarvalue	restraint_force (cvm::real k, const colvar *x, const colvarvalue &xcenter) const
	\brief Force function. More...
cvm::real	restraint_convert_k (cvm::real k, cvm::real dist_measure) const
	\brief Unit scaling. More...
Protected Attributes
std::vector< colvarvalue >	colvar_centers
	\brief Restraint centers. More...
std::vector< cvm::real >	means
	\brief colvar parameters, used for calculating the gradient/variance. More...
std::vector< cvm::real >	ssd
int	update_calls
int	update_freq
	\brief how often to update coupling constant. More...
std::vector< cvm::real >	max_coupling_range
	\brief Estimated range of coupling constant values in kT. More...
std::vector< cvm::real >	max_coupling_rate
std::vector< cvm::real >	coupling_accum
	\brief accumated couping force; used in stochastic online gradient descent algorithm. More...
std::vector< cvm::real >	set_coupling
	\brief coupling constant. More...
std::vector< cvm::real >	current_coupling
	\brief current coupling constant, which is ramped up during equilibration to coupling. More...
std::vector< cvm::real >	coupling_rate
	\brief how quickly to change the coupling constant. More...
bool	b_equilibration
bool	b_hard_coupling_range
bool	b_output_centers
	\brief flag for outputting colvar centers. More...
bool	b_output_grad
	\brief flag for outputting current gradient. More...
bool	b_output_coupling
	\brief flag for outputting coupling constant. More...

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Constructor & Destructor Documentation

colvarbias_alb::colvarbias_alb (  char const *    key )

Definition at line 34 of file colvarbias_alb.C.

colvarbias_alb::~colvarbias_alb (    )  [virtual]

Definition at line 141 of file colvarbias_alb.C.

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Member Function Documentation

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

Write the values of specific mutable properties to a string. Reimplemented from colvarbias. Definition at line 295 of file colvarbias_alb.C. References coupling_accum, coupling_rate, current_coupling, max_coupling_range, means, colvarbias::num_variables, set_coupling, ssd, and update_calls.

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

\brief Parse config string and (re)initialize. Reimplemented from colvarbias. Definition at line 40 of file colvarbias_alb.C. References b_hard_coupling_range, b_output_centers, b_output_coupling, b_output_grad, colvarproxy_system::boltzmann, colvarmodule::cite_feature, colvar_centers, colvarbias::colvars, conf, coupling_accum, coupling_rate, current_coupling, colvarmodule::debug, colvardeps::enable, colvarmodule::error, colvardeps::f_cvb_apply_force, colvardeps::f_cvb_history_dependent, colvardeps::f_cvb_scalar_variables, colvarparse::get_keyval, colvarbias::init, colvarmodule::log, colvarmodule::main, max_coupling_range, max_coupling_rate, means, colvarbias::num_variables, colvarmodule::proxy, set_coupling, ssd, colvarproxy_system::target_temperature, and update_freq.

cvm::real colvarbias_alb::restraint_convert_k (  cvm::real    k, cvm::real    dist_measure )  const [protected]

\brief Unit scaling. Definition at line 428 of file colvarbias_alb.C. Referenced by update.

colvarvalue colvarbias_alb::restraint_force (  cvm::real    k, const colvar *    x, const colvarvalue &    xcenter )  const [protected]

\brief Force function. Referenced by update.

cvm::real colvarbias_alb::restraint_potential (  cvm::real    k, const colvar *    x, const colvarvalue &    xcenter )  const [protected]

Referenced by update.

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

Read the values of specific mutable properties from a string. Reimplemented from colvarbias. Definition at line 256 of file colvarbias_alb.C. References b_equilibration, conf, coupling_accum, coupling_rate, current_coupling, colvarmodule::error, colvarparse::get_keyval, max_coupling_range, means, set_coupling, colvarbias::set_state_params, ssd, and update_calls.

int colvarbias_alb::update (    )  [virtual]

Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces(). Reimplemented from colvarbias. Definition at line 146 of file colvarbias_alb.C. References b_equilibration, b_hard_coupling_range, colvarbias::bias_energy, colvarproxy_system::boltzmann, colvar_centers, colvarbias::colvar_forces, colvarbias::colvars, coupling_accum, coupling_rate, current_coupling, colvarmodule::debug, colvarmodule::log, colvarmodule::main, max_coupling_range, max_coupling_rate, means, colvarbias::num_variables, colvarmodule::proxy, restraint_convert_k, restraint_force, restraint_potential, set_coupling, ssd, colvarproxy_system::target_temperature, update_calls, and update_freq.

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

Output quantities such as the bias energy to the trajectory file. Reimplemented from colvarbias. Definition at line 376 of file colvarbias_alb.C. References colvarbias::bias_energy, colvar_centers, current_coupling, means, colvarbias::num_variables, ssd, and update_calls.

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

Write a label to the trajectory file (comment line). Reimplemented from colvarbias. Definition at line 344 of file colvarbias_alb.C. References colvarbias::colvars, current_coupling, means, colvarbias::name, colvarbias::num_variables, and colvarmodule::wrap_string.

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Member Data Documentation

bool colvarbias_alb::b_equilibration [protected]

Definition at line 63 of file colvarbias_alb.h. Referenced by set_state_params, and update.

bool colvarbias_alb::b_hard_coupling_range [protected]

Definition at line 66 of file colvarbias_alb.h. Referenced by init, and update.

bool colvarbias_alb::b_output_centers [protected]

\brief flag for outputting colvar centers. Definition at line 70 of file colvarbias_alb.h. Referenced by init.

bool colvarbias_alb::b_output_coupling [protected]

\brief flag for outputting coupling constant. Definition at line 76 of file colvarbias_alb.h. Referenced by init.

bool colvarbias_alb::b_output_grad [protected]

\brief flag for outputting current gradient. Definition at line 73 of file colvarbias_alb.h. Referenced by init.

std::vector<colvarvalue> colvarbias_alb::colvar_centers [protected]

\brief Restraint centers. Definition at line 34 of file colvarbias_alb.h. Referenced by init, update, and write_traj.

std::vector<cvm::real> colvarbias_alb::coupling_accum [protected]

\brief accumated couping force; used in stochastic online gradient descent algorithm. Definition at line 51 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, and update.

std::vector<cvm::real> colvarbias_alb::coupling_rate [protected]

\brief how quickly to change the coupling constant. Definition at line 60 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, and update.

std::vector<cvm::real> colvarbias_alb::current_coupling [protected]

\brief current coupling constant, which is ramped up during equilibration to coupling. Definition at line 57 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, update, write_traj, and write_traj_label.

std::vector<cvm::real> colvarbias_alb::max_coupling_range [protected]

\brief Estimated range of coupling constant values in kT. Definition at line 45 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, and update.

std::vector<cvm::real> colvarbias_alb::max_coupling_rate [protected]

Definition at line 48 of file colvarbias_alb.h. Referenced by init, and update.

std::vector<cvm::real> colvarbias_alb::means [protected]

\brief colvar parameters, used for calculating the gradient/variance. Definition at line 37 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, update, write_traj, and write_traj_label.

std::vector<cvm::real> colvarbias_alb::set_coupling [protected]

\brief coupling constant. Definition at line 54 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, and update.

std::vector<cvm::real> colvarbias_alb::ssd [protected]

Definition at line 38 of file colvarbias_alb.h. Referenced by get_state_params, init, set_state_params, update, and write_traj.

int colvarbias_alb::update_calls [protected]

Definition at line 39 of file colvarbias_alb.h. Referenced by get_state_params, set_state_params, update, and write_traj.

int colvarbias_alb::update_freq [protected]

\brief how often to update coupling constant. Definition at line 42 of file colvarbias_alb.h. Referenced by init, and update.

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

• colvarbias_alb.h
• colvarbias_alb.C

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