Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses colvar::orientation to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*)) More...

#include <colvarcomp.h>

Inheritance diagram for colvar::rmsd:

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Collaboration diagram for colvar::rmsd:

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Public Member Functions
virtual int	init (std::string const &conf)

virtual void	calc_value ()
	Calculate the variable. More...

virtual void	calc_gradients ()
	Calculate the atomic gradients, to be reused later in order to apply forces. More...

virtual void	calc_force_invgrads ()
	Calculate the total force from the system using the inverse atomic gradients. More...

virtual void	calc_Jacobian_derivative ()
	Calculate the divergence of the inverse atomic gradients. More...

Public Member Functions inherited from colvar::cvc
std::string	function_type () const
	String identifier for the type of collective variable.

	cvc ()
	Constructor.

virtual	~cvc ()
	Destructor.

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

virtual int	init_dependencies ()
	Initialize dependency tree. More...

int	setup ()
	After construction, set data related to dependency handling.

virtual const std::vector< feature * > &	features () const
	Implementation of the feature list accessor for colvar. More...

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

virtual std::vector< std::vector< int > >	get_atom_lists ()
	Get vector of vectors of atom IDs for all atom groups.

virtual void	read_data ()
	Obtain data needed for the calculation for the backend.

virtual void	calc_value ()=0
	Calculate the variable. More...

virtual void	calc_gradients ()
	Calculate the atomic gradients, to be reused later in order to apply forces. More...

void	calc_fit_gradients ()
	Calculate the atomic fit gradients.

virtual void	debug_gradients ()
	Calculate finite-difference gradients alongside the analytical ones, for each Cartesian component.

virtual void	collect_gradients (std::vector< int > const &atom_ids, std::vector< cvm::rvector > &atomic_gradients)
	Calculate atomic gradients and add them to the corresponding item in gradient vector May be overridden by CVCs that do not store their gradients in the classic way, see dihedPC. More...

virtual void	calc_force_invgrads ()
	Calculate the total force from the system using the inverse atomic gradients. More...

virtual void	calc_Jacobian_derivative ()
	Calculate the divergence of the inverse atomic gradients. More...

colvarvalue const &	value () const
	Return the previously calculated value.

colvarvalue const &	total_force () const
	Return the previously calculated total force.

colvarvalue const &	Jacobian_derivative () const
	Return the previously calculated divergence of the inverse atomic gradients.

virtual void	apply_force (colvarvalue const &cvforce)
	Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) More...

virtual cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const

virtual colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities) More...

virtual colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities) More...

virtual void	wrap (colvarvalue &x_unwrapped) const
	Wrap value (for periodic/symmetric cvcs) More...

void	register_atom_group (cvm::atom_group *ag)
	Store a pointer to new atom group, and list as child for dependencies.

virtual colvarvalue const *	get_param_grad (std::string const &param_name)
	Pointer to the gradient of parameter param_name.

virtual int	set_param (std::string const &param_name, void const *new_value)
	Set the named parameter to the given value. More...

void	set_value (colvarvalue const &new_value)

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, 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

void	check_enabled (int f, std::string const &reason) const
	Check that a feature is enabled, raising COLVARS_BUG_ERROR if not.

Protected Member Functions
int	init_permutation (std::string const &conf)
	Permutation RMSD input parsing.

Protected Member Functions inherited from colvar::cvc
int	set_function_type (std::string const &type)
	Set the value of function_type and its dependencies.

int	update_description ()
	Update the description string based on name and type.

cvm::atom_group *	parse_group (std::string const &conf, char const *group_key, bool optional=false)
	Parse a group definition.

virtual int	init_total_force_params (std::string const &conf)
	Parse options pertaining to total force calculation.

void	init_as_distance ()
	Set data types for a scalar distance (convenience function)

void	init_as_angle ()
	Set data types for a bounded angle (0° to 180°)

void	init_as_periodic_angle ()
	Set data types for a periodic angle (-180° to 180°)

void	init_scalar_boundaries (cvm::real lb, cvm::real ub)
	Set two scalar boundaries (convenience function)

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
cvm::atom_group *	atoms = nullptr
	Atom group.

std::vector< cvm::atom_pos >	ref_pos

size_t	n_permutations = 1
	Number of permutations of symmetry-related atoms.

size_t	best_perm_index = 0
	Index of the permutation yielding the smallest RMSD (0 for identity)

Protected Attributes inherited from colvar::cvc
std::vector< std::string >	function_types
	Record the type of this class as well as those it is derived from.

colvarvalue	x
	Cached value.

colvarvalue	x_old
	Value at the previous step.

colvarvalue	ft
	Calculated total force (Note: this is calculated from the total atomic forces read from the program, subtracting fromt the "internal" forces of the system the "external" forces from the colvar biases)

colvarvalue	jd
	Calculated Jacobian derivative (divergence of the inverse gradients): serves to calculate the phase space correction.

colvarvalue	lower_boundary
	Location of the lower boundary (not defined by user choice)

colvarvalue	upper_boundary
	Location of the upper boundary (not defined by user choice)

cvm::real	width = 0.0
	CVC-specific default colvar width (default: not provided)

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_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_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 colvar::cvc
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 colvar::cvc
std::string	name
	The name of the object (helps to identify this cvc instance when debugging)

std::string	config_key
	Keyword used in the input to denote this CVC.

cvm::real	sup_coeff = 1.0
	Coefficient in the polynomial combination (default: 1.0)

int	sup_np = 1
	Exponent in the polynomial combination (default: 1)

cvm::real	period = 0.0
	Period of the values of this CVC (default: 0.0, non periodic)

cvm::real	wrap_center = 0.0
	If the component is periodic, wrap around this value (default: 0.0)

std::vector< cvm::atom_group * >	atom_groups
	Pointers to all atom groups, to let colvars collect info e.g. atomic gradients.

bool	b_try_scalable = true
	Whether or not this CVC will be computed in parallel whenever possible.

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.

Static Protected Attributes inherited from colvar::cvc
static std::vector< feature * >	cvc_features
	Implementation of the feature list for colvar.

Detailed Description

Colvar component: root mean square deviation (RMSD) of a group with respect to a set of reference coordinates; uses colvar::orientation to calculate the rotation matrix (colvarvalue::type_scalar type, range [0:*))

Member Function Documentation

◆ calc_force_invgrads()

void colvar::rmsd::calc_force_invgrads ( )

virtual

Calculate the total force from the system using the inverse atomic gradients.

Reimplemented from colvar::cvc.

◆ calc_gradients()

void colvar::rmsd::calc_gradients ( )

virtual

Calculate the atomic gradients, to be reused later in order to apply forces.

Reimplemented from colvar::cvc.

◆ calc_Jacobian_derivative()

void colvar::rmsd::calc_Jacobian_derivative ( )

virtual

Calculate the divergence of the inverse atomic gradients.

Reimplemented from colvar::cvc.

◆ calc_value()

void colvar::rmsd::calc_value ( )

virtual

Calculate the variable.

Implements colvar::cvc.

◆ init()

int colvar::rmsd::init ( std::string const & conf )

virtual

An init function should be defined for every class inheriting from cvc

Parameters

conf	Contents of the configuration file pertaining to this cvc

Reimplemented from colvar::cvc.

Member Data Documentation

◆ ref_pos

std::vector<cvm::atom_pos> colvar::rmsd::ref_pos

protected

Reference coordinates (for RMSD calculation only) Includes sets with symmetry permutations (n_permutations * n_atoms)

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

colvarcomp.h
colvarcomp_distances.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ calc_force_invgrads()

◆ calc_gradients()

◆ calc_Jacobian_derivative()

◆ calc_value()

◆ init()

Member Data Documentation

◆ ref_pos