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colvarbias_histogram Class Reference

Histogram "bias" (does as the name says). More...

#include <colvarbias_histogram.h>

Inheritance diagram for colvarbias_histogram:

List of all members.

Public Methods
	colvarbias_histogram (char const *key)
	~colvarbias_histogram ()
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 int	write_output_files ()
	Write any output files that this bias may have (e.g. PMF files). More...
Protected Methods
virtual std::istream &	read_state_data (std::istream &is)
	Read all mutable data not already set by set_state_params(). More...
virtual std::ostream &	write_state_data (std::ostream &os)
	Write all mutable data not already written by get_state_params(). More...
Protected Attributes
colvar_grid_scalar *	grid
	n-dim histogram. More...
std::vector< int >	bin
std::string	out_name
std::string	out_name_dx
size_t	colvar_array_size
	If one or more of the variables are colvarvalue::type_vector, treat them as arrays of this length. More...
std::vector< cvm::real >	weights
	If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram. More...

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Detailed Description

Histogram "bias" (does as the name says).

Definition at line 22 of file colvarbias_histogram.h.

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Constructor & Destructor Documentation

colvarbias_histogram::colvarbias_histogram (  char const *    key )

Definition at line 16 of file colvarbias_histogram.C. References colvardeps::f_cvb_bypass_ext_lagrangian, NULL, and colvardeps::provide.

colvarbias_histogram::~colvarbias_histogram (    )

Definition at line 106 of file colvarbias_histogram.C. References grid, and NULL.

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Member Function Documentation

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

\brief Parse config string and (re)initialize. Reimplemented from colvarbias. Reimplemented in colvarbias_reweightaMD. Definition at line 24 of file colvarbias_histogram.C. References colvarparse::check_keywords, colvarmodule::cite_feature, colvar_array_size, colvarbias::colvars, COLVARS_INPUT_ERROR, conf, colvardeps::enable, colvarmodule::error, colvardeps::f_cv_grid, colvardeps::f_cvb_bypass_ext_lagrangian, colvardeps::f_cvb_history_dependent, colvardeps::f_cvb_scalar_variables, colvarparse::get_keyval, grid, colvarbias::init, colvar_grid< cvm::real >::init_from_colvars, colvardeps::is_enabled, colvarparse::key_lookup, colvarmodule::main, colvarbias::num_variables, out_name, out_name_dx, colvar_grid< cvm::real >::parse_params, colvar_grid< cvm::real >::request_actual_value, colvarvalue::type_scalar, colvarvalue::type_vector, and weights. Referenced by colvarbias_reweightaMD::init.

std::istream & colvarbias_histogram::read_state_data (  std::istream &    is )  [protected, virtual]

Read all mutable data not already set by set_state_params(). Reimplemented from colvarbias. Reimplemented in colvarbias_reweightaMD. Definition at line 198 of file colvarbias_histogram.C. References grid, colvar_grid< cvm::real >::read_raw, and colvarbias::read_state_data_key.

int colvarbias_histogram::update (    )  [virtual]

Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces(). Reimplemented from colvarbias. Reimplemented in colvarbias_reweightaMD. Definition at line 115 of file colvarbias_histogram.C. References colvar_grid_scalar::acc_value, bin, colvarbias::can_accumulate_data, colvar_array_size, colvar_grid< cvm::real >::current_bin_scalar, colvarmodule::debug, colvarmodule::get_error, grid, colvar_grid< cvm::real >::index_ok, colvarmodule::log, colvarbias::name, colvarbias::num_variables, out_name, out_name_dx, colvarmodule::output_prefix, colvarmodule::step_relative, colvarbias::update, and weights.

int colvarbias_histogram::write_output_files (    )  [virtual]

Write any output files that this bias may have (e.g. PMF files). Reimplemented from colvarbias. Reimplemented in colvarbias_reweightaMD. Definition at line 175 of file colvarbias_histogram.C. References grid, colvarbias::has_data, colvarmodule::log, out_name, out_name_dx, colvar_grid_scalar::write_multicol, and colvar_grid_scalar::write_opendx.

std::ostream & colvarbias_histogram::write_state_data (  std::ostream &    os )  [protected, virtual]

Write all mutable data not already written by get_state_params(). Reimplemented from colvarbias. Reimplemented in colvarbias_reweightaMD. Definition at line 211 of file colvarbias_histogram.C. References grid, and colvar_grid< cvm::real >::write_raw.

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Member Data Documentation

std::vector<int> colvarbias_histogram::bin [protected]

Definition at line 36 of file colvarbias_histogram.h. Referenced by colvarbias_reweightaMD::update, and update.

size_t colvarbias_histogram::colvar_array_size [protected]

If one or more of the variables are colvarvalue::type_vector, treat them as arrays of this length. Definition at line 40 of file colvarbias_histogram.h. Referenced by init, colvarbias_reweightaMD::update, and update.

colvar_grid_scalar* colvarbias_histogram::grid [protected]

n-dim histogram. Definition at line 35 of file colvarbias_histogram.h. Referenced by colvarbias_reweightaMD::init, init, colvarbias_reweightaMD::read_state_data, read_state_data, colvarbias_reweightaMD::update, update, colvarbias_reweightaMD::write_exponential_reweighted_pmf, write_output_files, colvarbias_reweightaMD::write_state_data, write_state_data, and ~colvarbias_histogram.

std::string colvarbias_histogram::out_name [protected]

Definition at line 37 of file colvarbias_histogram.h. Referenced by init, update, and write_output_files.

std::string colvarbias_histogram::out_name_dx [protected]

Definition at line 37 of file colvarbias_histogram.h. Referenced by init, update, and write_output_files.

std::vector<cvm::real> colvarbias_histogram::weights [protected]

If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram. Definition at line 42 of file colvarbias_histogram.h. Referenced by init, and update.

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

• colvarbias_histogram.h
• colvarbias_histogram.C

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