Options to change the restraint configuration over time (shared between centers and k moving) More...

#include <colvarbias_restraint.h>

Inheritance diagram for colvarbias_restraint_moving:

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Collaboration diagram for colvarbias_restraint_moving:

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Public Member Functions
	colvarbias_restraint_moving (char const *key)

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

virtual int	update ()

virtual int	change_configuration (std::string const &)

virtual std::string const	get_state_params () const

virtual int	set_state_params (std::string const &conf)

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.

Protected Attributes
bool	b_chg_centers
	Moving target?

bool	b_chg_force_k
	Changing force constant?

bool	b_decoupling
	Perform decoupling of the restraint?

int	target_nstages
	Number of stages over which to perform the change If zero, perform a continuous change.

int	stage
	Number of current stage of the perturbation.

std::vector< cvm::real >	lambda_schedule
	Lambda-schedule for custom varying force constant.

cvm::step_number	target_nsteps
	Number of steps required to reach the target force constant or restraint centers.

cvm::step_number	first_step
	Timestep at which the restraint starts moving.

cvm::real	acc_work
	Accumulated work (computed when outputAccumulatedWork == true)

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.

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 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 colvardeps
std::string	description

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.

Detailed Description

Options to change the restraint configuration over time (shared between centers and k moving)

Member Function Documentation

◆ change_configuration()

virtual int colvarbias_restraint_moving::change_configuration ( std::string const & )

inlinevirtual

Reimplemented in colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, colvarbias_restraint_harmonic, and colvarbias_restraint_linear.

◆ init()

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

virtual

Reimplemented in colvarbias_restraint_centers_moving, colvarbias_restraint_k_moving, colvarbias_restraint_harmonic, colvarbias_restraint_harmonic_walls, and colvarbias_restraint_linear.

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

colvarbias_restraint.h
colvarbias_restraint.cpp

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ change_configuration()

◆ init()