Collective variable bias, base class. More...

#include <colvarbias.h>

Inheritance diagram for colvarbias:

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Collaboration diagram for colvarbias:

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Public Member Functions
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 (colvarmodule cvmodule_in, char const key)
	Constructor.

virtual int	init (std::string const &conf)
	Parse config string and (re)initialize. More...

virtual int	init_mts (std::string const &conf)
	Initialize multiple-time-stepping options.

int	init_dependencies () override
	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 override
	Implementation of the feature list accessor for colvarbias. More...

virtual std::vector< feature * > &	modify_features () override

Public Member Functions inherited from colvardeps
	colvardeps (colvarmodule *cvmodule_in)

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, bool error=false)

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

std::vector< colvardeps * >	get_parents () const
	Return the parents.

std::vector< colvardeps * >	get_children () const
	Return the children.

Public Member Functions inherited from colvarparse
colvarmodule *	get_cvmodule ()

	colvarparse (colvarmodule *cvmodule_in)
	Default constructor. More...

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...

int	check_ascii (std::string const &conf)
	Check that a config string contains non-ASCII characters. 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...

Static Public Member Functions
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 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
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
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 Member Functions
	colvarbias ()
	Default constructor.

	colvarbias (colvarbias &)
	Copy constructor.

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 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 Attributes
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 colvardeps
int	time_step_factor = 1

std::vector< feature_state >	feature_states
	List of the states of all features.

Protected Attributes inherited from colvarparse
colvarmodule *	cvmodule = nullptr

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.

Private Member Functions
template<typename IST >
IST &	read_state_data_key_template_ (IST &is, std::string const &key)

template<typename IST >
IST &	read_state_template_ (IST &is, colvarmodule *cvmodule_in)
	Generic stream reading function (formatted and not)

Additional Inherited Members
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_smp , f_cvb_ntot }

enum	features_colvar { f_cv_active , f_cv_awake , f_cv_apply_force , 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_total_force_current_step , 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_require_cpu_buffers , 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 }

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...

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 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.

Detailed Description

Collective variable bias, base class.

Member Function Documentation

◆ bin_count()

int colvarbias::bin_count ( int bin_index )

virtual

Reimplemented in colvarbias_abf.

◆ bin_num()

int colvarbias::bin_num ( )

virtual

Give the total number of bins for a given bias.

Reimplemented in colvarbias_abf.

◆ calc_energy()

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

virtual

Compute the energy of the bias Uses the vector of colvar values provided if not NULL, and the values currently cached in the bias instance otherwise

Reimplemented in colvarbias_abf, and colvarbias_meta.

◆ calc_forces()

int colvarbias::calc_forces ( std::vector< colvarvalue > const * values )

virtual

Compute the forces due to the bias Uses the vector of colvar values provided if not NULL, and the values currently cached in the bias instance otherwise

Reimplemented in colvarbias_meta.

◆ can_accumulate_data()

bool colvarbias::can_accumulate_data ( )

virtual

Returns true if the current step represent a valid increment, whose data can be recorded (as opposed to e.g. a continuation step from a restart)

◆ change_configuration()

int colvarbias::change_configuration ( std::string const & conf )

virtual

Load new configuration - force constant and/or centers only.

Reimplemented in colvarbias_restraint, colvarbias_restraint_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, colvarbias_restraint_centers, colvarbias_restraint_k, colvarbias_restraint_harmonic, colvarbias_restraint_linear, and colvarbias_restraint_harmonic_walls.

◆ clear_state_data()

int colvarbias::clear_state_data ( )

virtual

Delete only the allocatable data (save memory)

Reimplemented in colvarbias_meta.

◆ current_bin()

int colvarbias::current_bin ( )

virtual

Calculate the bin index for a given bias.

Reimplemented in colvarbias_abf.

◆ energy_difference()

cvm::real colvarbias::energy_difference ( std::string const & conf )

virtual

Calculate change in energy from using alternate configuration.

Reimplemented in colvarbias_restraint, colvarbias_restraint_harmonic, and colvarbias_restraint_linear.

◆ features()

virtual const std::vector< feature * > & colvarbias::features ( ) const

inlineoverridevirtual

Implementation of the feature list accessor for colvarbias.

Implements colvardeps.

◆ get_state_params()

std::string const colvarbias::get_state_params ( ) const

virtual

Write the values of specific mutable properties to a string.

Reimplemented in colvarbias_ti, colvarbias_alb, colvarbias_restraint, colvarbias_restraint_harmonic, colvarbias_restraint_linear, colvarbias_abmd, colvarbias_meta, colvarbias_restraint_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, and colvarbias_restraint_harmonic_walls.

◆ init()

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

virtual

Parse config string and (re)initialize.

Reimplemented in colvarbias_ti, colvarbias_alb, colvarbias_histogram, colvarbias_restraint, colvarbias_restraint_centers, colvarbias_restraint_k, colvarbias_restraint_harmonic, colvarbias_restraint_linear, colvarbias_restraint_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, colvarbias_opes, colvarbias_restraint_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, and colvarbias_restraint_harmonic_walls.

◆ init_dependencies()

int colvarbias::init_dependencies ( )

overridevirtual

Initialize dependency tree.

Implements colvardeps.

◆ local_sample_count()

int colvarbias::local_sample_count ( int radius )

virtual

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

Reimplemented in colvarbias_abf.

◆ modify_features()

virtual std::vector< feature * > & colvarbias::modify_features ( )

inlineoverridevirtual

Implements colvardeps.

◆ read_state_data() [1/2]

virtual cvm::memory_stream & colvarbias::read_state_data ( cvm::memory_stream & is )

inlinevirtual

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

Reimplemented in colvarbias_ti, colvarbias_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, and colvarbias_opes.

◆ read_state_data() [2/2]

virtual std::istream & colvarbias::read_state_data ( std::istream & is )

inlinevirtual

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

Reimplemented in colvarbias_ti, colvarbias_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, and colvarbias_opes.

◆ read_state_data_key() [1/2]

cvm::memory_stream & colvarbias::read_state_data_key	(	cvm::memory_stream &	is,
		std::string const &	key
	)

Read a keyword header for a data sequence from an unformatted stream

Parameters

[in,out]	Input	stream
[in]	Keyword	labeling the header block; an error will be raised if not matching

◆ read_state_data_key() [2/2]

std::istream & colvarbias::read_state_data_key	(	std::istream &	is,
		std::string const &	key
	)

Read a keyword header for a data sequence from a formatted stream

Parameters

[in,out]	Input	stream
[in]	Keyword	labeling the header block; an error will be raised if not matching

◆ read_state_data_key_template_()

template<typename IST >

IST & colvarbias::read_state_data_key_template_	(	IST &	is,
		std::string const &	key
	)

private

Read a keyword header for a data sequence from a stream

Parameters

[in,out]	Input	stream
[in]	Keyword	labeling the header block; an error will be raised if not matching

◆ replica_share_freq()

size_t colvarbias::replica_share_freq ( ) const

virtual

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

Reimplemented in colvarbias_abf, and colvarbias_meta.

◆ set_state_params()

int colvarbias::set_state_params ( std::string const & state_conf )

virtual

Read the values of specific mutable properties from a string.

Reimplemented in colvarbias_alb, colvarbias_restraint, colvarbias_restraint_harmonic, colvarbias_restraint_linear, colvarbias_abmd, colvarbias_restraint_moving, colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, colvarbias_restraint_harmonic_walls, colvarbias_ti, and colvarbias_meta.

◆ setup_output()

virtual int colvarbias::setup_output ( )

inlinevirtual

(Re)initialize the output files (does not write them yet)

Reimplemented in colvarbias_meta.

◆ update()

int colvarbias::update ( )

virtual

Retrieve colvar values and calculate their biasing forces Some implementations may use calc_energy() and calc_forces()

Reimplemented in colvarbias_ti, colvarbias_alb, colvarbias_histogram, colvarbias_restraint, colvarbias_restraint_harmonic, colvarbias_restraint_linear, colvarbias_restraint_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, colvarbias_opes, colvarbias_restraint_moving, and colvarbias_restraint_harmonic_walls.

◆ write_output_files()

virtual int colvarbias::write_output_files ( )

inlinevirtual

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

Reimplemented in colvarbias_ti, colvarbias_histogram, colvarbias_restraint_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, and colvarbias_opes.

◆ write_state_data() [1/2]

virtual cvm::memory_stream & colvarbias::write_state_data ( cvm::memory_stream & os )

inlinevirtual

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

Reimplemented in colvarbias_ti, colvarbias_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, and colvarbias_opes.

◆ write_state_data() [2/2]

virtual std::ostream & colvarbias::write_state_data ( std::ostream & os )

inlinevirtual

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

Reimplemented in colvarbias_ti, colvarbias_histogram, colvarbias_abf, colvarbias_abmd, colvarbias_reweightaMD, colvarbias_meta, and colvarbias_opes.

◆ write_state_data_key() [1/2]

cvm::memory_stream & colvarbias::write_state_data_key	(	cvm::memory_stream &	os,
		std::string const &	key,
		bool	header = `true`
	)		const

Write a keyword header for a data sequence to an unformatted stream

Parameters

[in,out]	os	Output stream
[in]	key	Keyword labeling the header block
[in]	header	Ignored

◆ write_state_data_key() [2/2]

std::ostream & colvarbias::write_state_data_key	(	std::ostream &	os,
		std::string const &	key,
		bool	header = `true`
	)		const

Write a keyword header for a data sequence to a formatted stream

Parameters

[in,out]	os	Output stream
[in]	key	Keyword labeling the header block
[in]	header	Whether this is the header of a multi-line segment vs a single line

◆ write_state_to_replicas()

virtual int colvarbias::write_state_to_replicas ( )

inlinevirtual

If this bias is communicating with other replicas through files, send it to them.

Reimplemented in colvarbias_meta.

◆ write_traj()

std::ostream & colvarbias::write_traj ( std::ostream & os )

virtual

Output quantities such as the bias energy to the trajectory file.

Reimplemented in colvarbias_alb, colvarbias_restraint, colvarbias_restraint_harmonic, colvarbias_restraint_linear, colvarbias_restraint_histogram, colvarbias_abmd, colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, and colvarbias_restraint_harmonic_walls.

◆ write_traj_label()

std::ostream & colvarbias::write_traj_label ( std::ostream & os )

virtual

Write a label to the trajectory file (comment line)

Reimplemented in colvarbias_alb, colvarbias_restraint, colvarbias_restraint_harmonic, colvarbias_restraint_linear, colvarbias_restraint_histogram, colvarbias_abmd, colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, and colvarbias_restraint_harmonic_walls.

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

colvarbias.h
colvarbias.cpp

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ bin_count()

◆ bin_num()

◆ calc_energy()

◆ calc_forces()

◆ can_accumulate_data()

◆ change_configuration()

◆ clear_state_data()

◆ current_bin()

◆ energy_difference()

◆ features()

◆ get_state_params()

◆ init()

◆ init_dependencies()

◆ local_sample_count()

◆ modify_features()

◆ read_state_data() [1/2]

◆ read_state_data() [2/2]

◆ read_state_data_key() [1/2]

◆ read_state_data_key() [2/2]

◆ read_state_data_key_template_()

◆ replica_share_freq()

◆ set_state_params()

◆ setup_output()

◆ update()

◆ write_output_files()

◆ write_state_data() [1/2]

◆ write_state_data() [2/2]

◆ write_state_data_key() [1/2]

◆ write_state_data_key() [2/2]

◆ write_state_to_replicas()

◆ write_traj()

◆ write_traj_label()