A collective variable (main class); to be defined, it needs at least one object of a derived class of colvar::cvc; it calculates and returns a colvarvalue object. More...

#include <colvar.h>

Inheritance diagram for colvar:

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Collaboration diagram for colvar:

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Classes
class	alch_Flambda

class	alch_lambda

class	alpha_angles
	Colvar component: alpha helix content of a contiguous segment of 5 or more residues, implemented as a sum of Ca-Ca-Ca angles and hydrogen bonds (colvarvalue::type_scalar type, range [0:1]) More...

class	angle
	Colvar component: angle between the centers of mass of three groups (colvarvalue::type_scalar type, range [0:PI]) More...

class	aspath

class	aspathCV

class	azpath

class	azpathCV

class	cartesian

class	CartesianBasedPath

class	coordnum
	Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) More...

class	customColvar
	custom expression of colvars More...

class	CVBasedPath

class	cvc
	Colvar component (base class for collective variables) More...

class	dihedPC
	Colvar component: dihedPC Projection of the config onto a dihedral principal component See e.g. Altis et al., J. Chem. Phys 126, 244111 (2007) Based on a set of 'dihedral' cvcs. More...

class	dihedral
	Colvar component: dihedral between the centers of mass of four groups (colvarvalue::type_scalar type, range [-PI:PI]) More...

class	dipole_angle
	Colvar component: angle between the dipole of a molecule and an axis formed by two groups of atoms(colvarvalue::type_scalar type, range [0:PI]) More...

class	dipole_magnitude
	Colvar component: dipole magnitude of a molecule. More...

class	distance
	Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)) More...

class	distance_dir
	Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unit3vector type, range [-1:1]x[-1:1]x[-1:1]) More...

class	distance_inv
	Colvar component: average distance between two groups of atoms, weighted as the sixth power, as in NMR refinements(colvarvalue::type_scalar type, range (0:*)) More...

class	distance_pairs
	Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component) More...

class	distance_vec

class	distance_xy
	Colvar component: projection of the distance vector on a plane (colvarvalue::type_scalar type, range [0:*)) More...

class	distance_z
	Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-:)) More...

class	eigenvector
	Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-:)) More...

class	euler_phi

class	euler_psi

class	euler_theta

class	groupcoordnum
	Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]) More...

class	gspath
	Colvar component: alternative path collective variable using geometry, variable s For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html Diaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601. More...

class	gspathCV
	Colvar component: alternative path collective variable using geometry, variable s Allow any combination of existing (scalar) CVs For more information see https://plumed.github.io/doc-v2.5/user-doc/html/_p_a_t_h.html Diaz Leines, G.; Ensing, B. Path Finding on High-Dimensional Free Energy Landscapes. Phys. Rev. Lett. 2012, 109 (2), 020601. https://doi.org/10.1103/PhysRevLett.109.020601. More...

class	gyration
	Colvar component: Radius of gyration of an atom group (colvarvalue::type_scalar type, range [0:*)) More...

class	gzpath
	Colvar component: alternative path collective variable using geometry, variable z This should be merged with gspath in the same class by class inheritance or something else. More...

class	gzpathCV

class	h_bond
	Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]) More...

class	inertia
	Colvar component: moment of inertia of an atom group (colvarvalue::type_scalar type, range [0:*)) More...

class	inertia_z
	Colvar component: moment of inertia of an atom group around a user-defined axis (colvarvalue::type_scalar type, range [0:*)) More...

class	linearCombination
	Current only linear combination of sub-CVCs is available. More...

class	map_total

class	neuralNetwork

class	orientation
	Colvar component: orientation in space of an atom group, with respect to a set of reference coordinates (colvarvalue::type_quaternion type, range [-1:1]x[-1:1]x[-1:1]x[-1:1]) More...

class	orientation_angle

class	orientation_proj
	Colvar component: cosine of the angle of rotation with respect to a set of reference coordinates (colvarvalue::type_scalar type, range [-1:1]) More...

class	polar_phi
	Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180]) More...

class	polar_theta
	Colvar component: polar coordinate theta of a group (colvarvalue::type_scalar type, range [0:180]) More...

class	rmsd
	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...

class	selfcoordnum
	Colvar component: self-coordination number within a group (colvarvalue::type_scalar type, range [0:N*(N-1)/2]) More...

class	spin_angle
	Colvar component: angle of rotation around a predefined axis (colvarvalue::type_scalar type, range [-PI:PI]) More...

class	tilt
	Colvar component: projection of the orientation vector onto a predefined axis (colvarvalue::type_scalar type, range [-1:1]) More...

class	torchANN

Public Member Functions
colvarvalue const &	value () const
	Current value (previously set by calc() or by read_traj())

colvarvalue const &	actual_value () const
	Current actual value (not extended DOF)

colvarvalue const &	run_ave () const
	Current running average (if calculated as set by analysis flag)

cvm::real const &	force_constant () const
	Force constant of the spring.

colvarvalue const &	velocity () const
	Current velocity (previously set by calc() or by read_traj())

colvarvalue const &	total_force () const
	Current total force (previously obtained from calc() or read_traj()). Note: this is calculated using the atomic forces from the last simulation step. More...

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

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

void	do_feature_side_effects (int id)

bool	periodic_boundaries () const
	Is the interval defined by the two boundaries periodic?

bool	periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub) const
	Is the interval defined by the two boundaries periodic?

	colvar ()
	Constructor.

int	init (std::string const &conf)
	Main init function.

void	define_component_types ()
	Populate the map of available CVC types.

int	init_components (std::string const &conf)
	Parse the CVC configuration and allocate their data.

int	init_custom_function (std::string const &conf)
	Parse parameters for custom function with Lepton.

int	init_grid_parameters (std::string const &conf)
	Init defaults for grid options.

int	check_grid_parameters ()
	Consistency check for the grid paramaters.

int	parse_legacy_wall_params (std::string const &conf)
	Read legacy wall keyword (these are biases now)

int	init_extended_Lagrangian (std::string const &conf)
	Init extended Lagrangian parameters.

int	init_output_flags (std::string const &conf)
	Init output flags.

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

void	setup ()
	Get ready for a run and re-initialize internal data if needed.

	~colvar ()
	Destructor.

int	calc ()
	Calculate the colvar's value and related quantities.

int	end_of_step ()
	Carry out operations needed before next step is run.

int	calc_cvcs (int first=0, size_t num_cvcs=0)
	Calculate a subset of the colvar components (CVCs) currently active (default: all active CVCs) Note: both arguments refer to the sect of active CVCs, not all CVCs.

int	check_cvc_range (int first_cvc, size_t num_cvcs)
	Ensure that the selected range of CVCs is consistent.

int	calc_cvc_values (int first, size_t num_cvcs)
	Calculate the values of the given subset of CVCs.

int	calc_cvc_gradients (int first, size_t num_cvcs)
	Same as colvar::calc_cvc_values but for gradients.

int	calc_cvc_total_force (int first, size_t num_cvcs)
	Same as colvar::calc_cvc_values but for total forces.

int	calc_cvc_Jacobians (int first, size_t num_cvcs)
	Same as colvar::calc_cvc_values but for Jacobian derivatives/forces.

int	collect_cvc_data ()
	Collect quantities from CVCs and update aggregated data for the colvar.

int	collect_cvc_values ()
	Collect the values of the CVCs.

int	collect_cvc_gradients ()
	Same as colvar::collect_cvc_values but for gradients.

int	collect_cvc_total_forces ()
	Same as colvar::collect_cvc_values but for total forces.

int	collect_cvc_Jacobians ()
	Same as colvar::collect_cvc_values but for Jacobian derivatives/forces.

int	calc_colvar_properties ()
	Calculate the quantities associated to the colvar (but not to the CVCs)

colvarvalue const	applied_force () const
	Get the current applied force.

void	reset_bias_force ()
	Set the total biasing force to zero.

void	add_bias_force (colvarvalue const &force)
	Add to the total force from biases.

void	add_bias_force_actual_value (colvarvalue const &force)
	Apply a force to the actual value (only meaningful with extended Lagrangian)

cvm::real	update_forces_energy ()
	Collect all forces on this colvar, integrate internal equations of motion of internal degrees of freedom; see also colvar::communicate_forces() return colvar energy if extended Lagrandian active.

void	update_extended_Lagrangian ()
	Integrate equations of motion of extended Lagrangian coordinate if needed.

void	communicate_forces ()
	Communicate forces (previously calculated in colvar::update()) to the external degrees of freedom.

int	set_cvc_flags (std::vector< bool > const &flags)
	Enables and disables individual CVCs based on the given array.

int	update_cvc_flags ()
	Updates the flags in the CVC objects, and their number.

int	update_cvc_config (std::vector< std::string > const &confs)
	Modify the configuration of CVCs (currently, only base class data)

int	cvc_param_exists (std::string const &param_name)
	Whether this named parameter exists (in the first and only component)

cvm::real	get_cvc_param (std::string const &param_name)
	Get the value of the named parameter (from the first and only component)

void const *	get_cvc_param_ptr (std::string const &param_name)
	Get a pointer to the named parameter (from the first and only component)

colvarvalue const *	get_cvc_param_grad (std::string const &param_name)
	Pointer to the derivative of the variable with respect to param_name.

int	set_cvc_param (std::string const &param_name, void const *new_value)
	Set the named parameter in the first and only component to the given value.

size_t	num_dimensions () const
	Number of dimensions of the value of this colvar.

size_t	num_cvcs () const
	Number of CVC objects defined.

size_t	num_active_cvcs () const
	number of CVC objects with an active flag (as set by update_cvc_flags)

cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const
	Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients. More...

colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients. More...

colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients. More...

void	wrap (colvarvalue &x_unwrapped) const
	Use the internal metrics (as from colvar::cvc objects) to wrap a value into a standard interval. More...

int	parse_analysis (std::string const &conf)
	Read the analysis tasks.

int	analyze ()
	Perform analysis tasks.

std::istream &	read_traj (std::istream &is)
	Read the value from a collective variable trajectory file.

std::ostream &	write_traj (std::ostream &os)
	Output formatted values to the trajectory file.

std::ostream &	write_traj_label (std::ostream &os)
	Write a label to the trajectory file (comment line)

std::istream &	read_state (std::istream &is)
	Read the colvar's state from a formatted input stream.

cvm::memory_stream &	read_state (cvm::memory_stream &is)
	Read the colvar's state from an unformatted input stream.

int	check_matching_state (std::string const &state_conf)
	Check the name of the bias vs. the given string, set the matching_state flag accordingly.

int	set_state_params (std::string const &state_conf)
	Read the values of colvar mutable data from a string (used by both versions of read_state())

std::string const	get_state_params () const
	Write the state information of this colvar in a block of text, suitable for later parsing.

std::ostream &	write_state (std::ostream &os) const
	Write the colvar's state to a formatted output stream.

cvm::memory_stream &	write_state (cvm::memory_stream &os) const
	Write the colvar's state to an unformatted output stream.

int	write_output_files ()
	Write output files (if defined, e.g. in analysis mode)

const std::vector< std::shared_ptr< colvar::cvc > > &	get_cvcs () const
	Get all colvarcomp objects.

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

std::vector< int > const &	get_volmap_ids ()
	Volmap numeric IDs, one for each CVC (-1 if not available)

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.

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

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

Static Public Member Functions
static void	delete_features ()

static const std::map< std::string, std::function< colvar::cvc *()> > &	get_global_cvc_map ()
	A global mapping of cvc names to the cvc constructors.

static bool	compare_cvc (const colvar::cvc const i, const colvar::cvc const j)
	function for sorting cvcs by their names More...

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
std::string	name
	Name.

cvm::real	width = 1.0
	Typical fluctuation amplitude for this collective variable (e.g. local width of a free energy basin) More...

std::vector< colvarbias * >	biases
	List of biases that depend on this colvar.

colvarvalue	fb
	Bias force; reset_bias_force() should be called before the biases are updated.

colvarvalue	fb_actual
	Bias force to the actual value (only useful with extended Lagrangian)

colvarvalue	f
	Total applied force; fr (if extended_lagrangian is defined), fb (if biases are applied) and the walls' forces (if defined) contribute to it.

colvarvalue	f_old
	Applied force at the previous step (to be subtracted from total force if needed)

colvarvalue	ft
	Total force, as derived from the atomic trajectory; should equal the system force plus f.

cvm::real	period = 0.0
	Period, if this variable is periodic.

cvm::real	wrap_center = 0.0
	Center of wrapping, if this variable is periodic.

bool	expand_boundaries = false
	Expand the boundaries of multiples of width, to keep the value always within range.

colvarvalue	lower_boundary
	Location of the lower boundary.

colvarvalue	upper_boundary
	Location of the upper boundary.

std::vector< int >	atom_ids
	Sorted array of (zero-based) IDs for all atoms involved.

std::vector< cvm::rvector >	atomic_gradients
	Array of atomic gradients collected from all cvcs with appropriate components, rotations etc. For scalar variables only!

Public Attributes inherited from colvardeps
std::string	description

Static Public Attributes
static std::vector< feature * >	cv_features
	Implementation of the feature list for colvar.

Static Public Attributes inherited from colvarparse
static const char *const	white_space = " \t"
	Accepted white space delimiters, used in key_lookup()

Protected Types
enum	acf_type_e { acf_notset , acf_vel , acf_coor , acf_p2coor }
	Type of autocorrelation function (ACF) More...

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
colvarvalue	fdiff_velocity (colvarvalue const &xold, colvarvalue const &xnew)

void	update_active_cvc_square_norm ()
	Update the sum of square coefficients for active cvcs.

void	calc_vel_acf (std::list< colvarvalue > &v_history, colvarvalue const &v)
	Velocity ACF, scalar product between v(0) and v(t)

void	calc_coor_acf (std::list< colvarvalue > &x_history, colvarvalue const &x)
	Coordinate ACF, scalar product between x(0) and x(t) (does not work with scalar numbers)

void	calc_p2coor_acf (std::list< colvarvalue > &x_history, colvarvalue const &x)
	Coordinate ACF, second order Legendre polynomial between x(0) and x(t) (does not work with scalar numbers)

int	calc_acf ()
	Calculate the auto-correlation function (ACF)

int	write_acf (std::ostream &os)
	Save the ACF to a file.

int	calc_runave ()
	Calculate the running average and its standard deviation.

void	build_atom_list (void)
	Initialize the sorted list of atom IDs for atoms involved in all cvcs (called when enabling f_cv_collect_gradients)

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
colvarvalue	x
	Value of the colvar.

colvarvalue	x_reported
	Cached reported value (x may be manipulated)

colvarvalue	v_fdiff
	Finite-difference velocity.

colvarvalue	v_reported
	Cached reported velocity.

colvarvalue	x_ext
	Restraint center.

colvarvalue	prev_x_ext
	Previous value of the restraint center;.

colvarvalue	v_ext
	Velocity of the restraint center.

colvarvalue	prev_v_ext
	Previous velocity of the restraint center.

cvm::real	ext_mass = 0.0
	Mass of the restraint center.

cvm::real	ext_force_k = 0.0
	Restraint force constant.

cvm::real	ext_gamma = 0.0
	Friction coefficient for Langevin extended dynamics.

cvm::real	ext_sigma = 0.0
	Amplitude of Gaussian white noise for Langevin extended dynamics.

colvarvalue	fr
	Applied force on extended DOF, for output (unscaled if using MTS)

colvarvalue	fj
	Jacobian force, when Jacobian_force is enabled.

colvarvalue	ft_reported
	Cached reported total force.

size_t	n_active_cvcs = 0
	Number of CVC objects with an active flag.

cvm::real	active_cvc_square_norm = 0.0
	Sum of square coefficients for active cvcs.

cvm::step_number	prev_timestep
	Absolute timestep number when this colvar was last updated.

bool	matching_state
	Flag used to tell if the state string being read is for this colvar.

colvarvalue	x_old
	Previous value (to calculate velocities during analysis)

colvarvalue	x_restart
	Value read from the most recent state file (if any)

bool	after_restart
	True if a state file was just read.

std::list< std::list< colvarvalue > >	acf_x_history

std::list< std::list< colvarvalue > >	acf_v_history

std::list< std::list< colvarvalue > >::iterator	acf_x_history_p

std::list< std::list< colvarvalue > >::iterator	acf_v_history_p

std::list< std::list< colvarvalue > >	x_history
	Time series of values and velocities used in running averages.

std::list< std::list< colvarvalue > >::iterator	x_history_p

std::string	acf_colvar_name
	Collective variable with which the correlation is calculated (default: itself)

size_t	acf_length
	Length of autocorrelation function (ACF)

size_t	acf_offset
	After how many steps the ACF starts.

size_t	acf_stride
	How many timesteps separate two ACF values.

size_t	acf_nframes
	Number of frames for each ACF point.

bool	acf_normalize
	Normalize the ACF to a maximum value of 1?

std::vector< cvm::real >	acf
	ACF values.

std::string	acf_outfile
	Name of the file to write the ACF.

acf_type_e	acf_type
	Type of autocorrelation function (ACF)

size_t	runave_length
	Length of running average series.

size_t	runave_stride
	Timesteps to skip between two values in the running average series.

std::string	runave_outfile
	Name of the file to write the running average.

colvarvalue	runave
	Current value of the running average.

cvm::real	runave_variance = 0.0
	Current value of the square deviation from the running average.

cvm::real	kinetic_energy = 0.0
	If extended Lagrangian active: colvar kinetic energy.

cvm::real	potential_energy = 0.0
	If extended Lagrangian active: colvar harmonic potential.

std::vector< std::shared_ptr< colvar::cvc > >	cvcs
	Array of components objects.

std::vector< bool >	cvc_flags
	Flags to enable or disable cvcs at next colvar evaluation.

std::string	scripted_function
	Name of scripted function to be used.

std::vector< const colvarvalue * >	sorted_cvc_values

std::vector< int >	volmap_ids_
	Volmap numeric IDs, one for each CVC (-1 if not available)

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 = 1

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

Static Protected Attributes
static std::map< std::string, std::function< colvar::cvc *()> >	global_cvc_map
	A global mapping of cvc names to the cvc constructors. More...

static std::map< std::string, std::string >	global_cvc_desc_map
	A global mapping of cvc names to the corresponding descriptions. More...

Private Member Functions
template<typename def_class_name >
void	add_component_type (char const description, char const config_key)
	Declare an available CVC type and its description, register them in the global map.

int	init_components_type (const std::string &conf, const char *config_key)
	Initialize any CVC objects matching the given key.

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_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 }

Detailed Description

A collective variable (main class); to be defined, it needs at least one object of a derived class of colvar::cvc; it calculates and returns a colvarvalue object.

This class parses the configuration, defines the behaviour and stores the value (colvar::x) and all related data of a collective variable. How the value is calculated is defined in colvar::cvc and its derived classes. The colvar object contains pointers to multiple colvar::cvc derived objects, which can be combined together into one collective variable. This makes possible to implement new collective variables at runtime based on the existing ones. Currently, this possibility is limited to a polynomial, using the coefficients cvc::sup_coeff and the exponents cvc::sup_np. In case of non-scalar variables, only exponents equal to 1 are accepted.

Please note that most of its members are colvarvalue objects, i.e. they can handle different data types together, and must all be set to the same type of colvar::value() before using them together in assignments or other operations; this is usually done automatically in the constructor. If you add a new member of colvarvalue type, you should also add its initialization line in the colvar constructor.

Member Enumeration Documentation

◆ acf_type_e

enum colvar::acf_type_e

protected

Type of autocorrelation function (ACF)

Enumerator
acf_notset	Unset type.
acf_vel	Velocity ACF, scalar product between v(0) and v(t)
acf_coor	Coordinate ACF, scalar product between x(0) and x(t)
acf_p2coor	Coordinate ACF, second order Legendre polynomial between x(0) and x(t) (does not work with scalar numbers)

Member Function Documentation

◆ compare_cvc()

bool colvar::compare_cvc	(	const colvar::cvc *const	i,
		const colvar::cvc *const	j
	)

static

function for sorting cvcs by their names

Compare two cvcs using their names Used to sort CVC array in scripted coordinates

◆ dist2()

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

Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients.

Handles correctly symmetries and periodic boundary conditions

◆ dist2_lgrad()

colvarvalue colvar::dist2_lgrad	(	colvarvalue const &	x1,
		colvarvalue const &	x2
	)		const

Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients.

Handles correctly symmetries and periodic boundary conditions

◆ dist2_rgrad()

colvarvalue colvar::dist2_rgrad	(	colvarvalue const &	x1,
		colvarvalue const &	x2
	)		const

Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients.

Handles correctly symmetries and periodic boundary conditions

◆ do_feature_side_effects()

void colvar::do_feature_side_effects ( int id )

virtual

Implements possible actions to be carried out when a given feature is enabled This overloads the base function in colvardeps

Reimplemented from colvardeps.

◆ features()

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

inlinevirtual

Implementation of the feature list accessor for colvar.

Implements colvardeps.

◆ init_dependencies()

int colvar::init_dependencies ( )

virtual

Initialize dependency tree.

Implements colvardeps.

◆ modify_features()

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

inlinevirtual

Implements colvardeps.

◆ total_force()

colvarvalue const & colvar::total_force ( ) const

inline

Current total force (previously obtained from calc() or read_traj()). Note: this is calculated using the atomic forces from the last simulation step.

Total atom forces are read from the MD program, the total force acting on the collective variable is calculated summing those from all colvar components, the bias and walls forces are subtracted.

◆ wrap()

void colvar::wrap ( colvarvalue & x_unwrapped ) const

Use the internal metrics (as from colvar::cvc objects) to wrap a value into a standard interval.

Handles correctly symmetries and periodic boundary conditions

Member Data Documentation

◆ acf_x_history

std::list< std::list<colvarvalue> > colvar::acf_x_history

protected

Time series of values and velocities used in correlation functions

◆ acf_x_history_p

std::list<std::list<colvarvalue>>::iterator colvar::acf_x_history_p

protected

Time series of values and velocities used in correlation functions (pointers)x

◆ global_cvc_desc_map

std::map< std::string, std::string > colvar::global_cvc_desc_map

staticprotected

Initial value:

=

std::map<std::string, std::string>()

A global mapping of cvc names to the corresponding descriptions.

◆ global_cvc_map

std::map< std::string, std::function< colvar::cvc *()> > colvar::global_cvc_map

staticprotected

Initial value:

=

std::map<std::string, std::function<colvar::cvc *()>>()

colvar::cvc

Colvar component (base class for collective variables)

Definition: colvarcomp.h:71

A global mapping of cvc names to the cvc constructors.

◆ sorted_cvc_values

std::vector<const colvarvalue *> colvar::sorted_cvc_values

protected

Current cvc values in the order requested by script when using scriptedFunction

◆ width

cvm::real colvar::width = 1.0

Typical fluctuation amplitude for this collective variable (e.g. local width of a free energy basin)

In metadynamics calculations, colvarbias_meta, this value is used to calculate the width of a gaussian. In ABF calculations, colvarbias_abf, it is used to calculate the grid spacing in the direction of this collective variable.

◆ x_history_p

std::list<std::list<colvarvalue>>::iterator colvar::x_history_p

protected

Time series of values and velocities used in correlation functions (pointers)x

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

colvar.h
colvar.cpp

Classes

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Types

Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ acf_type_e

Member Function Documentation

◆ compare_cvc()

◆ dist2()

◆ dist2_lgrad()

◆ dist2_rgrad()

◆ do_feature_side_effects()

◆ features()

◆ init_dependencies()

◆ modify_features()

◆ total_force()

◆ wrap()

Member Data Documentation

◆ acf_x_history

◆ acf_x_history_p

◆ global_cvc_desc_map

◆ global_cvc_map

◆ sorted_cvc_values

◆ width

◆ x_history_p