colvarbias_abf Class Reference

ABF bias. More...

#include <colvarbias_abf.h>

Inheritance diagram for colvarbias_abf:

Collaboration diagram for colvarbias_abf:

Public Member Functions
	colvarbias_abf (char const *key)
	Constructor for ABF bias.
int	init (std::string const &conf) override
	Initializer for ABF bias. More...
	~colvarbias_abf () override
	Default destructor for ABF bias. More...
int	update () override
	Per-timestep update of ABF bias. More...
std::ostream &	write_state_data (std::ostream &os) override
	Write all mutable data not already written by get_state_params() to a formatted stream. More...
cvm::memory_stream &	write_state_data (cvm::memory_stream &os) override
	Write all mutable data not already written by get_state_params() to an unformatted stream. More...
std::istream &	read_state_data (std::istream &is) override
	Read all mutable data not already set by set_state_params() from a formatted stream. More...
cvm::memory_stream &	read_state_data (cvm::memory_stream &is) override
	Read all mutable data not already set by set_state_params() from an unformatted stream. More...
int	write_output_files () override
	Write any output files that this bias may have (e.g. PMF files) More...
int	calc_energy (std::vector< colvarvalue > const *values) override
	Calculate the bias energy for 1D ABF. More...
Public Member Functions inherited from colvarbias
int	add_colvar (std::string const &cv_name)
	Add a new collective variable to this bias.
size_t	num_variables () const
	How many variables are defined for this bias.
std::vector< colvar * > *	variables ()
	Access the variables vector.
colvar *	variables (int i) const
	Access the i-th variable.
virtual int	update ()
virtual bool	can_accumulate_data ()
virtual int	calc_energy (std::vector< colvarvalue > const *values)
virtual int	calc_forces (std::vector< colvarvalue > const *values)
int	communicate_forces ()
	Send forces to the collective variables.
virtual int	end_of_step ()
	Carry out operations needed before next step is run.
virtual int	change_configuration (std::string const &conf)
	Load new configuration - force constant and/or centers only. More...
virtual cvm::real	energy_difference (std::string const &conf)
	Calculate change in energy from using alternate configuration. More...
virtual int	bin_num ()
	Give the total number of bins for a given bias. More...
virtual int	current_bin ()
	Calculate the bin index for a given bias. More...
virtual int	bin_count (int bin_index)
virtual int	local_sample_count (int radius)
	Return the average number of samples in a given "radius" around current bin. More...
virtual int	replica_share ()
virtual size_t	replica_share_freq () const
	Report the frequency at which this bias needs to communicate with replicas. More...
virtual void	analyze ()
	Perform analysis tasks.
	colvarbias (char const *key)
	Constructor.
virtual int	init (std::string const &conf)
	Parse config string and (re)initialize. More...
virtual int	init_dependencies ()
	Initialize dependency tree. More...
virtual int	reset ()
	Set to zero all mutable data.
virtual int	clear ()
	Delete everything.
virtual int	clear_state_data ()
	Delete only the allocatable data (save memory) More...
virtual	~colvarbias ()
	Destructor.
virtual std::string const	get_state_params () const
	Write the values of specific mutable properties to a string. More...
int	check_matching_state (std::string const &conf)
	Check the name of the bias vs. the given string, set the matching_state flag accordingly.
virtual int	set_state_params (std::string const &state_conf)
	Read the values of specific mutable properties from a string. More...
virtual std::ostream &	write_state_data (std::ostream &os)
	Write all mutable data not already written by get_state_params() to a formatted stream. More...
virtual cvm::memory_stream &	write_state_data (cvm::memory_stream &os)
	Write all mutable data not already written by get_state_params() to an unformatted stream. More...
virtual std::istream &	read_state_data (std::istream &is)
	Read all mutable data not already set by set_state_params() from a formatted stream. More...
virtual cvm::memory_stream &	read_state_data (cvm::memory_stream &is)
	Read all mutable data not already set by set_state_params() from an unformatted stream. More...
std::ostream &	write_state_data_key (std::ostream &os, std::string const &key, bool header=true) const
cvm::memory_stream &	write_state_data_key (cvm::memory_stream &os, std::string const &key, bool header=true) const
std::istream &	read_state_data_key (std::istream &is, std::string const &key)
cvm::memory_stream &	read_state_data_key (cvm::memory_stream &is, std::string const &key)
std::ostream &	write_state (std::ostream &os)
	Write the bias configuration to a formatted stream.
cvm::memory_stream &	write_state (cvm::memory_stream &os)
	Write the bias configuration to an unformatted stream.
std::istream &	read_state (std::istream &is)
	Read the bias configuration from a formatted stream.
cvm::memory_stream &	read_state (cvm::memory_stream &is)
	Read the bias configuration from an unformatted stream.
int	write_state_prefix (std::string const &prefix)
	Write the bias state to a file with the given prefix.
int	write_state_string (std::string &output)
	Write the bias state to a string.
int	read_state_prefix (std::string const &prefix)
	Read the bias state from a file with this name or prefix.
int	read_state_string (char const *buffer)
	Read the bias state from this string buffer.
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...
virtual int	setup_output ()
	(Re)initialize the output files (does not write them yet) More...
virtual int	write_output_files ()
	Write any output files that this bias may have (e.g. PMF files) More...
virtual int	write_state_to_replicas ()
	If this bias is communicating with other replicas through files, send it to them. More...
cvm::real	get_energy ()
virtual const std::vector< feature * > &	features () const
	Implementation of the feature list accessor for colvarbias. More...
virtual std::vector< feature * > &	modify_features ()
Public Member Functions inherited from colvarparse
	colvarparse ()
	Default constructor.
	colvarparse (const std::string &conf)
	Constructor that stores the object's config string.
void	clear ()
	Set the object ready to parse a new configuration string.
void	set_string (std::string const &conf)
	Set a new config string for this object.
	~colvarparse () override
	Default destructor.
std::string const &	get_config () const
	Get the configuration string (includes comments)
int	check_keywords (std::string &conf, char const *key)
	Check that all the keywords within "conf" are in the list of allowed keywords; this will invoke strip_values() first and then loop over all words.
void	clear_keyword_registry ()
	Use this after parsing a config string (note that check_keywords() calls it already)
bool	get_keyval (std::string const &conf, char const *key, int &value, int const &def_value=0, Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, size_t &value, size_t const &def_value=0, Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, long &value, long const &def_value=0, Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, cvm::step_number &value, cvm::step_number const &def_value=0, Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::string &value, std::string const &def_value=std::string(""), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, cvm::real &value, cvm::real const &def_value=0.0, Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, cvm::rvector &value, cvm::rvector const &def_value=cvm::rvector(), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, cvm::quaternion &value, cvm::quaternion const &def_value=cvm::quaternion(), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, colvarvalue &value, colvarvalue const &def_value=colvarvalue(colvarvalue::type_notset), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, bool &value, bool const &def_value=false, Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< int > &values, std::vector< int > const &def_values=std::vector< int >(0, 0), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< size_t > &values, std::vector< size_t > const &def_values=std::vector< size_t >(0, 0), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< long > &values, std::vector< long > const &def_values=std::vector< long >(0, 0), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< std::string > &values, std::vector< std::string > const &def_values=std::vector< std::string >(0, std::string("")), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::real > &values, std::vector< cvm::real > const &def_values=std::vector< cvm::real >(0, 0.0), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::rvector > &values, std::vector< cvm::rvector > const &def_values=std::vector< cvm::rvector >(0, cvm::rvector()), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< cvm::quaternion > &values, std::vector< cvm::quaternion > const &def_values=std::vector< cvm::quaternion >(0, cvm::quaternion()), Parse_Mode const parse_mode=parse_normal)
bool	get_keyval (std::string const &conf, char const *key, std::vector< colvarvalue > &values, std::vector< colvarvalue > const &def_values=std::vector< colvarvalue >(0, colvarvalue(colvarvalue::type_notset)), Parse_Mode const parse_mode=parse_normal)
bool	key_lookup (std::string const &conf, char const *key, std::string *data=nullptr, size_t *save_pos=nullptr)
	Low-level function for parsing configuration strings; automatically adds the requested keyword to the list of valid ones. More...
std::istream &	read_config_line (std::istream &is, std::string &line)
	Reads a configuration line, adds it to config_string, and returns the stream. More...
template<>
int	_get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, bool &value, bool const &)
template<>
int	_get_keyval_scalar_novalue_ (std::string const &key_str, bool &value, Parse_Mode const &parse_mode)
Public Member Functions inherited from colvarparams
int	param_exists (std::string const &param_name)
	Whether the parameter param_name exists.
virtual std::vector< std::string >	get_param_names ()
	Get a copy of the names of registered parameters.
virtual std::vector< std::string >	get_param_grad_names ()
	Get a copy of the names of registered parameter gradients.
virtual void const *	get_param_ptr (std::string const &param_name)
	Pointer to the parameter param_name.
virtual void const *	get_param_grad_ptr (std::string const &param_name)
	Pointer to the gradient of parameter param_name.
virtual cvm::real	get_param (std::string const &param_name)
	Value of the parameter param_name (must be a scalar)
virtual int	set_param (std::string const &param_name, void const *new_value)
	Set the named parameter to the given value. More...
Public Member Functions inherited from colvardeps
int	get_time_step_factor () const
	returns time_step_factor
void	init_feature (int feature_id, const char *description, feature_type type)
	Pair a numerical feature ID with a description and type.
bool	is_not_set (int id)
bool	is_dynamic (int id)
bool	is_static (int id)
bool	is_user (int id)
virtual const std::vector< feature * > &	features () const =0
virtual std::vector< feature * > &	modify_features ()=0
void	add_child (colvardeps *child)
void	remove_child (colvardeps *child)
void	remove_all_children ()
bool	is_enabled (int f=f_cv_active) const
bool	is_available (int f=f_cv_active) const
void	provide (int feature_id, bool truefalse=true)
void	set_enabled (int feature_id, bool truefalse=true)
	Enable or disable, depending on flag value.
int	enable (int f, bool dry_run=false, bool toplevel=true)
int	disable (int f)
void	free_children_deps ()
void	restore_children_deps ()
	re-enable children features (to be used when object becomes active)
int	decr_ref_count (int f)
virtual void	do_feature_side_effects (int)
virtual int	init_dependencies ()=0
	Initialize dependency tree for object of a derived class. More...
void	require_feature_self (int f, int g)
	Make feature f require feature g within the same object.
void	exclude_feature_self (int f, int g)
	Make features f and g mutually exclusive within the same object.
void	require_feature_children (int f, int g)
	Make feature f require feature g within children.
void	require_feature_alt (int f, int g, int h)
	Make feature f require either g or h within the same object.
void	require_feature_alt (int f, int g, int h, int i)
	Make feature f require any of g, h, or i within the same object.
void	require_feature_alt (int f, int g, int h, int i, int j)
	Make feature f require any of g, h, i, or j within the same object.
void	print_state ()
	print all enabled features and those of children, for debugging
void	check_enabled (int f, std::string const &reason) const
	Check that a feature is enabled, raising COLVARS_BUG_ERROR if not.

Private Member Functions
int	update_system_force ()
	Calculate system force for all colvars.
int	calc_biasing_force (std::vector< cvm::real > &force)
	Calulate the biasing force for the current bin.
cvm::real	smoothing_factor (cvm::real weight)
	Calulate the smoothing factor to apply to biasing forces for given local count.
int	replica_share () override
int	replica_share_CZAR ()
size_t	replica_share_freq () const override
	Report the frequency at which this bias needs to communicate with replicas. More...
int	bin_num () override
	Give the total number of bins for a given bias. More...
int	current_bin () override
	Calculate the bin index for a given bias. More...
int	bin_count (int bin_index) override
	Give the count at a given bin index. More...
int	local_sample_count (int radius) override
	Return the average number of samples in a given "radius" around current bin. More...
void	write_gradients_samples (const std::string &prefix, bool close=true, bool local=false)
int	read_gradients_samples ()
	Read human-readable FE gradients and sample count (if not using restart)
template<class T >
int	write_grid_to_file (T const *grid, std::string const &name, bool close)
	Shorthand template used in write_gradient_samples()
template<typename OST >
OST &	write_state_data_template_ (OST &os)
	Generic stream writing function (formatted and not)
template<typename IST >
IST &	read_state_data_template_ (IST &is)
	Generic stream readingx function (formatted and not)

Private Attributes
std::vector< std::string >	input_prefix
	Base filename(s) for reading previous gradient data (replaces data from restart file)
bool	update_bias
	Adapt the bias at each time step (as opposed to keeping it constant)?
bool	hide_Jacobian
bool	b_integrate
	Integrate gradients into a PMF on output.
size_t	full_samples
	Number of samples per bin before applying the full biasing force.
size_t	min_samples
	Number of samples per bin before applying a scaled-down biasing force.
cvm::step_number	history_last_step
	Latest absolute time step at which history files were written.
bool	b_czar_window_file
	Write CZAR output file for stratified eABF (.zgrad)
size_t	history_freq
	Number of timesteps between recording data in history files (if non-zero)
UIestimator::UIestimator	eabf_UI
	Umbrella Integration estimator of free energy from eABF.
bool	b_UI_estimator
	Run UI estimator?
bool	b_CZAR_estimator
	Run CZAR estimator?
int	pabf_freq
	Frequency for updating pABF PMF (if zero, pABF is not used)
int	integrate_iterations
	Max number of CG iterations for integrating PMF at startup and for file output.
cvm::real	integrate_tol
	Tolerance for integrating PMF at startup and for file output.
int	pabf_integrate_iterations
	Max number of CG iterations for integrating PMF at on-the-fly pABF updates.
cvm::real	pabf_integrate_tol
	Tolerance for integrating PMF at on-the-fly pABF updates.
bool	cap_force
	Cap the biasing force to be applied? (option maxForce)
std::vector< cvm::real >	max_force
	Maximum force to be applied.
std::vector< int >	bin
	Current bin in sample grid.
std::vector< int >	force_bin
	Current bin in force grid.
std::vector< int >	z_bin
	Cuurent bin in "actual" coordinate, when running extended Lagrangian dynamics.
gradient_t	system_force
	Measured instantaneous system force.
std::shared_ptr< colvar_grid_gradient >	gradients
	n-dim grid of free energy gradients
std::shared_ptr< colvar_grid_count >	samples
	n-dim grid of number of samples
std::shared_ptr< integrate_potential >	pmf
	n-dim grid of pmf (dimension 1 to 3)
std::shared_ptr< colvar_grid_gradient >	z_gradients
	n-dim grid: average force on "real" coordinate for eABF z-based estimator
std::shared_ptr< colvar_grid_count >	z_samples
	n-dim grid of number of samples on "real" coordinate for eABF z-based estimator
std::shared_ptr< colvar_grid_gradient >	czar_gradients
	n-dim grid containing CZAR estimatr of "real" free energy gradients
std::shared_ptr< integrate_potential >	czar_pmf
	n-dim grid of CZAR pmf (dimension 1 to 3)
bool	shared_on
size_t	shared_freq
cvm::step_number	shared_last_step
std::unique_ptr< colvar_grid_gradient >	last_gradients
std::shared_ptr< colvar_grid_count >	last_samples
std::unique_ptr< colvar_grid_gradient >	z_gradients_in
std::shared_ptr< colvar_grid_count >	z_samples_in
std::shared_ptr< colvar_grid_gradient >	local_gradients
std::shared_ptr< colvar_grid_count >	local_samples
std::unique_ptr< integrate_potential >	local_pmf
std::shared_ptr< colvar_grid_gradient >	global_z_gradients
std::shared_ptr< colvar_grid_count >	global_z_samples
std::shared_ptr< colvar_grid_gradient >	global_czar_gradients
std::shared_ptr< integrate_potential >	global_czar_pmf

Additional Inherited Members
Public Types inherited from colvarparse
enum	Parse_Mode {   parse_null = 0 , parse_echo = (1<<1) , parse_echo_default = (1<<2) , parse_deprecation_warning = (1<<3) ,   parse_silent = 0 , parse_required = (1<<16) , parse_override = (1<<17) , parse_restart = (1<<18) ,   parse_normal = (1<<1) | (1<<2) | (1<<17) , parse_deprecated = (1<<1) | (1<<3) | (1<<17) }
	How a keyword is parsed in a string. More...
Public Types inherited from colvardeps
enum	features_biases {   f_cvb_active , f_cvb_awake , f_cvb_step_zero_data , f_cvb_apply_force ,   f_cvb_bypass_ext_lagrangian , f_cvb_get_total_force , f_cvb_output_acc_work , f_cvb_history_dependent ,   f_cvb_time_dependent , f_cvb_scalar_variables , f_cvb_calc_pmf , f_cvb_calc_ti_samples ,   f_cvb_write_ti_samples , f_cvb_write_ti_pmf , f_cvb_scale_biasing_force , f_cvb_extended ,   f_cvb_ntot }
enum	features_colvar {   f_cv_active , f_cv_awake , f_cv_gradient , f_cv_collect_gradient ,   f_cv_collect_atom_ids , f_cv_fdiff_velocity , f_cv_total_force , f_cv_total_force_calc ,   f_cv_subtract_applied_force , f_cv_Jacobian , f_cv_hide_Jacobian , f_cv_extended_Lagrangian ,   f_cv_external , f_cv_Langevin , f_cv_output_energy , f_cv_output_value ,   f_cv_output_velocity , f_cv_output_applied_force , f_cv_output_total_force , f_cv_lower_boundary ,   f_cv_upper_boundary , f_cv_hard_lower_boundary , f_cv_hard_upper_boundary , f_cv_reflecting_lower_boundary ,   f_cv_reflecting_upper_boundary , f_cv_grid , f_cv_runave , f_cv_corrfunc ,   f_cv_scripted , f_cv_custom_function , f_cv_periodic , f_cv_single_cvc ,   f_cv_scalar , f_cv_linear , f_cv_homogeneous , f_cv_multiple_ts ,   f_cv_ntot }
enum	features_cvc {   f_cvc_active , f_cvc_scalar , f_cvc_periodic , f_cvc_width ,   f_cvc_lower_boundary , f_cvc_upper_boundary , f_cvc_explicit_atom_groups , f_cvc_gradient ,   f_cvc_explicit_gradient , f_cvc_inv_gradient , f_cvc_Jacobian , f_cvc_one_site_total_force ,   f_cvc_debug_gradient , f_cvc_pbc_minimum_image , f_cvc_com_based , f_cvc_scalable ,   f_cvc_scalable_com , f_cvc_collect_atom_ids , f_cvc_ntot }
enum	features_atomgroup {   f_ag_active , f_ag_center , f_ag_center_origin , f_ag_rotate ,   f_ag_fitting_group , f_ag_explicit_gradient , f_ag_fit_gradients , f_ag_atom_forces ,   f_ag_scalable , f_ag_scalable_com , f_ag_collect_atom_ids , f_ag_ntot }
Static Public Member Functions inherited from colvarbias
static void	delete_features ()
Static Public Member Functions inherited from colvarparse
static std::string	to_lower_cppstr (std::string const &in)
	Return a lowercased copy of the string.
static std::istream &	getline_nocomments (std::istream &is, std::string &s)
	Works as std::getline() but also removes everything between a comment character and the following newline.
static int	check_braces (std::string const &conf, size_t const start_pos)
	Check if the content of a config string has matching braces. More...
static int	check_ascii (std::string const &conf)
	Check that a config string contains non-ASCII characters. More...
static void	split_string (const std::string &data, const std::string &delim, std::vector< std::string > &dest)
	Split a string with a specified delimiter into a vector. More...
Public Attributes inherited from colvarbias
std::string	name
	Name of this bias.
std::string	bias_type
	Keyword indicating the type of this bias.
std::string	state_keyword
	Keyword used in state files (== bias_type most of the time)
int	rank
	Track how many times a bias of this type was defined.
size_t	output_freq
	Frequency for writing output files.
std::string	output_prefix
	Use this prefix for all output files.
Public Attributes inherited from colvardeps
std::string	description
Static Public Attributes inherited from colvarbias
static std::vector< feature * >	cvb_features
	Implementation of the feature list for colvarbias.
Static Public Attributes inherited from colvarparse
static const char *const	white_space = " \t"
	Accepted white space delimiters, used in key_lookup()
Protected Types inherited from colvarparse
enum	key_set_mode { key_not_set = 0 , key_set_user = 1 , key_set_default = 2 }
	How a keyword has been set.
Protected Types inherited from colvardeps
enum	feature_type { f_type_not_set , f_type_dynamic , f_type_user , f_type_static }
	Enum of possible feature types.
Protected Member Functions inherited from colvarparse
bool	get_key_string_value (std::string const &conf, char const *key, std::string &data)
	Get the string value of a keyword, and save it for later parsing.
bool	get_key_string_multi_value (std::string const &conf, char const *key, std::vector< std::string > &data)
	Get multiple strings from repeated instances of a same keyword.
template<typename TYPE >
bool	_get_keyval_scalar_ (std::string const &conf, char const *key, TYPE &value, TYPE const &def_value, Parse_Mode const &parse_mode)
	Template for single-value keyword parsers.
template<typename TYPE >
bool	_get_keyval_vector_ (std::string const &conf, char const *key, std::vector< TYPE > &values, std::vector< TYPE > const &def_values, Parse_Mode const &parse_mode)
	Template for multiple-value keyword parsers.
template<typename TYPE >
int	_get_keyval_scalar_value_ (std::string const &key_str, std::string const &data, TYPE &value, TYPE const &def_value)
	Extract the value of a variable from a string.
template<typename TYPE >
int	_get_keyval_scalar_novalue_ (std::string const &key_str, TYPE &value, Parse_Mode const &parse_mode)
	Handle the case where the user provides a keyword without value.
template<typename TYPE >
void	mark_key_set_user (std::string const &key_str, TYPE const &value, Parse_Mode const &parse_mode)
	Record that the keyword has just been user-defined.
template<typename TYPE >
void	mark_key_set_default (std::string const &key_str, TYPE const &def_value, Parse_Mode const &parse_mode)
	Record that the keyword has just been set to its default value.
void	error_key_required (std::string const &key_str, Parse_Mode const &parse_mode)
	Raise error condition due to the keyword being required!
bool	key_already_set (std::string const &key_str)
	True if the keyword has been set already.
void	add_keyword (char const *key)
	Add a new valid keyword to the list.
void	strip_values (std::string &conf)
	Remove all the values from the config string.
Protected Member Functions inherited from colvarparams
	colvarparams ()
	Default constructor.
virtual	~colvarparams ()
	Default destructor.
void	register_param (std::string const &param_name, void *param_ptr)
	Register the given parameter.
void	register_param_grad (std::string const &param_name, colvarvalue *param_grad_ptr)
	Register the gradient of the given parameter.
Protected Member Functions inherited from colvardeps
bool	get_keyval_feature (colvarparse *cvp, std::string const &conf, char const *key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)
	Parse a keyword and enable a feature accordingly.
Protected Attributes inherited from colvarbias
std::vector< colvar * >	colvars
	Pointers to collective variables to which the bias is applied; current values and metric functions will be obtained through each colvar object.
std::vector< colvarvalue >	colvar_values
	Up to date value of each colvar.
std::vector< colvarvalue >	colvar_forces
	Current forces from this bias to the variables.
std::vector< colvarvalue >	previous_colvar_forces
	Forces last applied by this bias to the variables.
cvm::real	bias_energy
	Current energy of this bias (colvar_forces should be obtained by deriving this)
bool	b_output_energy
	Whether to write the current bias energy from this bias to the trajectory file.
bool	has_data
	Whether this bias has already accumulated information (for history-dependent biases)
cvm::step_number	state_file_step
	Step number read from the last state file.
bool	matching_state
	Flag used to tell if the state string being read is for this bias.
colvar_grid_scalar *	biasing_force_scaling_factors
	The biasing forces will be scaled by the factor in this grid if b_bias_force_scaled is true.
std::vector< int >	biasing_force_scaling_factors_bin
Protected Attributes inherited from colvarparse
std::string const	keyword_delimiters_left
	Characters allowed immediately to the left of a kewyord.
std::string const	keyword_delimiters_right
	Characters allowed immediately to the right of a kewyord.
std::list< std::string >	allowed_keywords
	List of legal keywords for this object: this is updated by each call to colvarparse::get_keyval() or colvarparse::key_lookup()
std::map< std::string, key_set_mode >	key_set_modes
	Track which keywords have been already set, and how.
std::list< size_t >	data_begin_pos
	List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.
std::list< size_t >	data_end_pos
	List of delimiters for the values of each keyword in the configuration string; all keywords will be stripped of their values before the keyword check is performed.
std::string	config_string
	Configuration string of the object (includes comments)
Protected Attributes inherited from colvarparams
std::map< std::string, void const * >	param_map
	Pointers to relevant parameters that may be accessed by other objects.
std::map< std::string, colvarvalue const * >	param_grad_map
	Derivatives of the object with respect to internal parameters.
Protected Attributes inherited from colvardeps
int	time_step_factor
std::vector< feature_state >	feature_states
	List of the states of all features.

Detailed Description

ABF bias.

Constructor & Destructor Documentation

~colvarbias_abf()

colvarbias_abf::~colvarbias_abf ( )

override

Default destructor for ABF bias.

Destructor.

Member Function Documentation

bin_count()

int colvarbias_abf::bin_count ( int  bin_index )

overrideprivatevirtual

Give the count at a given bin index.

Reimplemented from colvarbias.

bin_num()

int colvarbias_abf::bin_num ( )

overrideprivatevirtual

Give the total number of bins for a given bias.

Reimplemented from colvarbias.

calc_energy()

int colvarbias_abf::calc_energy ( std::vector< colvarvalue > const *  values )

overridevirtual

Calculate the bias energy for 1D ABF.

Reimplemented from colvarbias.

current_bin()

int colvarbias_abf::current_bin ( )

overrideprivatevirtual

Calculate the bin index for a given bias.

Reimplemented from colvarbias.

init()

int colvarbias_abf::init ( std::string const &  conf )

overridevirtual

Initializer for ABF bias.

Reimplemented from colvarbias.

local_sample_count()

int colvarbias_abf::local_sample_count ( int  radius )

overrideprivatevirtual

Return the average number of samples in a given "radius" around current bin.

Reimplemented from colvarbias.

read_state_data() [1/2]

cvm::memory_stream & colvarbias_abf::read_state_data ( cvm::memory_stream &  is )

overridevirtual

Read all mutable data not already set by set_state_params() from an unformatted stream.

Reimplemented from colvarbias.

read_state_data() [2/2]

std::istream & colvarbias_abf::read_state_data ( std::istream &  is )

overridevirtual

Read all mutable data not already set by set_state_params() from a formatted stream.

Reimplemented from colvarbias.

replica_share()

int colvarbias_abf::replica_share ( )

overrideprivatevirtual

Reimplemented from colvarbias.

replica_share_freq()

size_t colvarbias_abf::replica_share_freq ( ) const

overrideprivatevirtual

Report the frequency at which this bias needs to communicate with replicas.

Reimplemented from colvarbias.

update()

int colvarbias_abf::update ( )

overridevirtual

Per-timestep update of ABF bias.

Update the FE gradient, compute and apply biasing force.

Compute the bias energy

Reimplemented from colvarbias.

write_gradients_samples()

void colvarbias_abf::write_gradients_samples ( const std::string &  prefix, bool  close = true, bool  local = false  )

private

Write human-readable FE gradients and sample count, and DX file in dim > 2

Parameters

local

write grids contining replica-local data in shared ABF

write_output_files()

int colvarbias_abf::write_output_files ( )

overridevirtual

Write any output files that this bias may have (e.g. PMF files)

Reimplemented from colvarbias.

write_state_data() [1/2]

cvm::memory_stream & colvarbias_abf::write_state_data ( cvm::memory_stream &  os )

overridevirtual

Write all mutable data not already written by get_state_params() to an unformatted stream.

Reimplemented from colvarbias.

write_state_data() [2/2]

std::ostream & colvarbias_abf::write_state_data ( std::ostream &  os )

overridevirtual

Write all mutable data not already written by get_state_params() to a formatted stream.

Reimplemented from colvarbias.

Member Data Documentation

hide_Jacobian

bool colvarbias_abf::hide_Jacobian

private

Use normalized definition of PMF for distance functions? (flat at long distances) by including the Jacobian term separately of the recorded PMF

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

• colvarbias_abf.h
• colvarbias_abf.cpp