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colvarbias_restraint_histogram Class Reference

Restrain the 1D histogram of a set of variables (or of a multidimensional one). More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint_histogram:

List of all members.

Public Methods
	colvarbias_restraint_histogram (char const *key)
int	init (std::string const &conf)
	\brief Parse config string and (re)initialize. More...
	~colvarbias_restraint_histogram ()
virtual int	update ()
	Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces(). More...
virtual int	write_output_files ()
	Write any output files that this bias may have (e.g. PMF files). 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 Attributes
cvm::vector1d< cvm::real >	p
	Probability density. More...
cvm::vector1d< cvm::real >	ref_p
	Reference probability density. More...
cvm::vector1d< cvm::real >	p_diff
	Difference between probability density and reference. More...
cvm::real	lower_boundary
	Lower boundary of the grid. More...
cvm::real	upper_boundary
	Upper boundary of the grid. More...
cvm::real	width
	Resolution of the grid. More...
cvm::real	gaussian_width
	Width of the Gaussians. More...
cvm::real	force_k
	Restraint force constant. More...
bool	b_write_histogram
	Write the histogram to a file. More...

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Detailed Description

Restrain the 1D histogram of a set of variables (or of a multidimensional one).

Definition at line 329 of file colvarbias_restraint.h.

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Constructor & Destructor Documentation

colvarbias_restraint_histogram::colvarbias_restraint_histogram (  char const *    key )

Definition at line 1327 of file colvarbias_restraint.C. References gaussian_width, lower_boundary, upper_boundary, and width.

colvarbias_restraint_histogram::~colvarbias_restraint_histogram (    )

Definition at line 1441 of file colvarbias_restraint.C. References p, p_diff, and ref_p.

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Member Function Documentation

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

\brief Parse config string and (re)initialize. Reimplemented from colvarbias. Definition at line 1337 of file colvarbias_restraint.C. References b_write_histogram, colvarmodule::cite_feature, colvarproxy_io::close_input_stream, COLVARS_FILE_ERROR, COLVARS_INPUT_ERROR, conf, data, colvardeps::enable, colvarmodule::error, colvardeps::f_cvb_apply_force, colvarmodule::fabs, force_k, gaussian_width, colvarparse::get_keyval, colvarparse::getline_nocomments, colvarbias::init, colvarproxy_io::input_stream, colvarmodule::log, lower_boundary, colvarmodule::main, p, p_diff, colvarparse::parse_silent, colvarmodule::proxy, ref_p, upper_boundary, and width.

int colvarbias_restraint_histogram::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 1449 of file colvarbias_restraint.C. References colvarbias::bias_energy, colvarbias::colvar_forces, COLVARS_NOT_IMPLEMENTED, colvarmodule::debug, colvarmodule::error, colvarmodule::exp, force, force_k, gaussian_width, colvarmodule::log, lower_boundary, colvarbias::num_variables, p, p_diff, PI, colvarvalue::real_value, ref_p, colvarvalue::reset, colvarmodule::sqrt, colvarvalue::type, colvarvalue::type_scalar, colvarvalue::type_vector, colvarbias::variables, colvarvalue::vector1d_value, and width.

int colvarbias_restraint_histogram::write_output_files (    )  [virtual]

Write any output files that this bias may have (e.g. PMF files). Reimplemented from colvarbias. Definition at line 1539 of file colvarbias_restraint.C. References colvarproxy_io::close_output_stream, lower_boundary, colvarmodule::main, colvarbias::name, colvarproxy_io::output_stream, p, colvarmodule::proxy, colvarbias::variables, width, and colvarmodule::wrap_string.

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

Output quantities such as the bias energy to the trajectory file. Reimplemented from colvarbias. Definition at line 1581 of file colvarbias_restraint.C. References colvarbias::bias_energy.

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

Write a label to the trajectory file (comment line). Reimplemented from colvarbias. Definition at line 1570 of file colvarbias_restraint.C. References colvarmodule::wrap_string.

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Member Data Documentation

bool colvarbias_restraint_histogram::b_write_histogram [protected]

Write the histogram to a file. Definition at line 370 of file colvarbias_restraint.h. Referenced by init.

cvm::real colvarbias_restraint_histogram::force_k [protected]

Restraint force constant. Definition at line 367 of file colvarbias_restraint.h. Referenced by init, and update.

cvm::real colvarbias_restraint_histogram::gaussian_width [protected]

Width of the Gaussians. Definition at line 364 of file colvarbias_restraint.h. Referenced by colvarbias_restraint_histogram, init, and update.

cvm::real colvarbias_restraint_histogram::lower_boundary [protected]

Lower boundary of the grid. Definition at line 355 of file colvarbias_restraint.h. Referenced by colvarbias_restraint_histogram, init, update, and write_output_files.

cvm::vector1d<cvm::real> colvarbias_restraint_histogram::p [protected]

Probability density. Definition at line 346 of file colvarbias_restraint.h. Referenced by init, update, write_output_files, and ~colvarbias_restraint_histogram.

cvm::vector1d<cvm::real> colvarbias_restraint_histogram::p_diff [protected]

Difference between probability density and reference. Definition at line 352 of file colvarbias_restraint.h. Referenced by init, update, and ~colvarbias_restraint_histogram.

cvm::vector1d<cvm::real> colvarbias_restraint_histogram::ref_p [protected]

Reference probability density. Definition at line 349 of file colvarbias_restraint.h. Referenced by init, update, and ~colvarbias_restraint_histogram.

cvm::real colvarbias_restraint_histogram::upper_boundary [protected]

Upper boundary of the grid. Definition at line 358 of file colvarbias_restraint.h. Referenced by colvarbias_restraint_histogram, and init.

cvm::real colvarbias_restraint_histogram::width [protected]

Resolution of the grid. Definition at line 361 of file colvarbias_restraint.h. Referenced by colvarbias_restraint_histogram, init, update, and write_output_files.

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

• colvarbias_restraint.h
• colvarbias_restraint.C

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