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colvar Class Reference

\brief 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. More...

#include <colvar.h>

Inheritance diagram for colvar:

List of all members.

Public Methods
colvarvalue const &	value () const
	\brief Current value (previously set by calc() or by read_traj()). More...
colvarvalue const &	actual_value () const
	\brief Current actual value (not extended DOF). More...
colvarvalue const &	run_ave () const
	\brief Current running average (if calculated as set by analysis flag). More...
cvm::real const &	force_constant () const
	\brief Force constant of the spring. More...
colvarvalue const &	velocity () const
	\brief Current velocity (previously set by calc() or by read_traj()). More...
colvarvalue const &	total_force () const
	\brief 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. More...
virtual const std::vector< feature * > &	features () const
	\brief Implementation of the feature list accessor for colvar. More...
virtual std::vector< feature * > &	modify_features ()
void	do_feature_side_effects (int id)
	Implements possible actions to be carried out when a given feature is enabled This overloads the base function in colvardeps. More...
bool	periodic_boundaries () const
	\brief Is the interval defined by the two boundaries periodic? More...
bool	periodic_boundaries (colvarvalue const &lb, colvarvalue const &ub) const
	\brief Is the interval defined by the two boundaries periodic? More...
	colvar ()
	Constructor. More...
int	init (std::string const &conf)
	Main init function. More...
int	init_components (std::string const &conf)
	Parse the CVC configuration and allocate their data. More...
int	init_custom_function (std::string const &conf)
	Parse parameters for custom function with Lepton. More...
int	init_grid_parameters (std::string const &conf)
	Init defaults for grid options. More...
int	init_extended_Lagrangian (std::string const &conf)
	Init extended Lagrangian parameters. More...
int	init_output_flags (std::string const &conf)
	Init output flags. More...
virtual int	init_dependencies ()
	\brief Initialize dependency tree. More...
void	setup ()
	Get ready for a run and re-initialize internal data if needed. More...
	~colvar ()
	Destructor. More...
int	calc ()
	\brief Calculate the colvar's value and related quantities. More...
int	end_of_step ()
	Carry out operations needed before next step is run. More...
int	calc_cvcs (int first=0, size_t num_cvcs=0)
	\brief 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.* More...
int	check_cvc_range (int first_cvc, size_t num_cvcs)
	Ensure that the selected range of CVCs is consistent. More...
int	calc_cvc_values (int first, size_t num_cvcs)
	\brief Calculate the values of the given subset of CVCs. More...
int	calc_cvc_gradients (int first, size_t num_cvcs)
	\brief Same as colvar::calc_cvc_values but for gradients. More...
int	calc_cvc_total_force (int first, size_t num_cvcs)
	\brief Same as colvar::calc_cvc_values but for total forces. More...
int	calc_cvc_Jacobians (int first, size_t num_cvcs)
	\brief Same as colvar::calc_cvc_values but for Jacobian derivatives/forces. More...
int	collect_cvc_data ()
	\brief Collect quantities from CVCs and update aggregated data for the colvar. More...
int	collect_cvc_values ()
	\brief Collect the values of the CVCs. More...
int	collect_cvc_gradients ()
	\brief Same as colvar::collect_cvc_values but for gradients. More...
int	collect_cvc_total_forces ()
	\brief Same as colvar::collect_cvc_values but for total forces. More...
int	collect_cvc_Jacobians ()
	\brief Same as colvar::collect_cvc_values but for Jacobian derivatives/forces. More...
int	calc_colvar_properties ()
	\brief Calculate the quantities associated to the colvar (but not to the CVCs). More...
colvarvalue const	applied_force () const
	Get the current applied force. More...
void	reset_bias_force ()
	Set the total biasing force to zero. More...
void	add_bias_force (colvarvalue const &force)
	Add to the total force from biases. More...
void	add_bias_force_actual_value (colvarvalue const &force)
	Apply a force to the actual value (only meaningful with extended Lagrangian). More...
cvm::real	update_forces_energy ()
	\brief 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. More...
void	update_extended_Lagrangian ()
	\brief Integrate equations of motion of extended Lagrangian coordinate if needed. More...
void	communicate_forces ()
	\brief Communicate forces (previously calculated in colvar::update()) to the external degrees of freedom. More...
int	set_cvc_flags (std::vector< bool > const &flags)
	\brief Enables and disables individual CVCs based on the given array. More...
int	update_cvc_flags ()
	\brief Updates the flags in the CVC objects, and their number. More...
int	update_cvc_config (std::vector< std::string > const &confs)
	\brief Modify the configuration of CVCs (currently, only base class data). More...
int	cvc_param_exists (std::string const &param_name)
	Whether this named parameter exists (in the first and only component). More...
cvm::real	get_cvc_param (std::string const &param_name)
	Get the value of the named parameter (from the first and only component). More...
void const *	get_cvc_param_ptr (std::string const &param_name)
	Get a pointer to the named parameter (from the first and only component). More...
colvarvalue const *	get_cvc_param_grad (std::string const &param_name)
	Pointer to the derivative of the variable with respect to param_name. More...
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. More...
size_t	num_dimensions () const
	\brief Number of dimensions of the value of this colvar. More...
size_t	num_cvcs () const
	\brief Number of CVC objects defined. More...
size_t	num_active_cvcs () const
	\brief number of CVC objects with an active flag (as set by update_cvc_flags). More...
cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const
	\brief Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients Handles correctly symmetries and periodic boundary conditions. More...
colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	\brief Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients Handles correctly symmetries and periodic boundary conditions. More...
colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	\brief Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients Handles correctly symmetries and periodic boundary conditions. More...
void	wrap (colvarvalue &x_unwrapped) const
	\brief Use the internal metrics (as from colvar::cvc objects) to wrap a value into a standard interval Handles correctly symmetries and periodic boundary conditions. More...
int	parse_analysis (std::string const &conf)
	Read the analysis tasks. More...
int	analyze ()
	Perform analysis tasks. More...
std::istream &	read_traj (std::istream &is)
	Read the value from a collective variable trajectory file. More...
std::ostream &	write_traj (std::ostream &os)
	Output formatted values to the trajectory file. More...
std::ostream &	write_traj_label (std::ostream &os)
	Write a label to the trajectory file (comment line). More...
std::istream &	read_state (std::istream &is)
	Read the collective variable from a restart file. More...
std::ostream &	write_state (std::ostream &os)
	Write the collective variable to a restart file. More...
int	write_output_files ()
	Write output files (if defined, e.g. in analysis mode). More...
virtual std::vector< std::vector< int > >	get_atom_lists ()
	\brief Get vector of vectors of atom IDs for all atom groups. More...
std::vector< int > const &	get_volmap_ids ()
	Volmap numeric IDs, one for each CVC (-1 if not available). More...
Static Public Methods
void	delete_features ()
bool	compare_cvc (const colvar::cvc const i, const colvar::cvc const j)
	getter of the global cvc map \brief function for sorting cvcs by their names. More...
Public Attributes
std::string	name
	Name. More...
cvm::real	width
	\brief 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. More...
std::vector< colvarbias * >	biases
	List of biases that depend on this colvar. More...
colvarvalue	fb
	\brief Bias force; reset_bias_force() should be called before the biases are updated. More...
colvarvalue	fb_actual
	\brief Bias force to the actual value (only useful with extended Lagrangian). More...
colvarvalue	f
	\brief Total applied* force; fr (if extended_lagrangian is defined), fb (if biases are applied) and the walls' forces (if defined) contribute to it.* More...
colvarvalue	f_old
	Applied force at the previous step (to be subtracted from total force if needed). More...
colvarvalue	ft
	\brief Total force, as derived from the atomic trajectory; should equal the system force plus f. More...
cvm::real	period
	Period, if this variable is periodic. More...
cvm::real	wrap_center
	Center of wrapping, if this variable is periodic. More...
bool	expand_boundaries
	\brief Expand the boundaries of multiples of width, to keep the value always within range. More...
colvarvalue	lower_boundary
	\brief Location of the lower boundary. More...
colvarvalue	upper_boundary
	\brief Location of the upper boundary. More...
std::vector< int >	atom_ids
	\brief Sorted array of (zero-based) IDs for all atoms involved. More...
std::vector< cvm::rvector >	atomic_gradients
	\brief Array of atomic gradients collected from all cvcs with appropriate components, rotations etc. For scalar variables only! More...
Static Public Attributes
std::vector< feature * >	cv_features
	\brief Implementation of the feature list for colvar. More...
Protected Types
enum	acf_type_e { acf_notset, acf_vel, acf_coor, acf_p2coor }
	Type of autocorrelation function (ACF). More...
Protected Methods
colvarvalue	fdiff_velocity (colvarvalue const &xold, colvarvalue const &xnew)
void	update_active_cvc_square_norm ()
	Update the sum of square coefficients for active cvcs. More...
void	calc_vel_acf (std::list< colvarvalue > &v_history, colvarvalue const &v)
	\brief Velocity ACF, scalar product between v(0) and v(t). More...
void	calc_coor_acf (std::list< colvarvalue > &x_history, colvarvalue const &x)
	\brief Coordinate ACF, scalar product between x(0) and x(t) (does not work with scalar numbers). More...
void	calc_p2coor_acf (std::list< colvarvalue > &x_history, colvarvalue const &x)
	\brief Coordinate ACF, second order Legendre polynomial between x(0) and x(t) (does not work with scalar numbers). More...
int	calc_acf ()
	Calculate the auto-correlation function (ACF). More...
int	write_acf (std::ostream &os)
	Save the ACF to a file. More...
int	calc_runave ()
	Calculate the running average and its standard deviation. More...
void	build_atom_list (void)
	\brief Initialize the sorted list of atom IDs for atoms involved in all cvcs (called when enabling f_cv_collect_gradients). More...
Protected Attributes
colvarvalue	x
	Value of the colvar. More...
colvarvalue	x_reported
	Cached reported value (x may be manipulated). More...
colvarvalue	v_fdiff
	Finite-difference velocity. More...
colvarvalue	v_reported
	Cached reported velocity. More...
colvarvalue	x_ext
	Restraint center. More...
colvarvalue	prev_x_ext
	Previous value of the restraint center;. More...
colvarvalue	v_ext
	Velocity of the restraint center. More...
colvarvalue	prev_v_ext
	Previous velocity of the restraint center. More...
cvm::real	ext_mass
	Mass of the restraint center. More...
cvm::real	ext_force_k
	Restraint force constant. More...
cvm::real	ext_gamma
	Friction coefficient for Langevin extended dynamics. More...
cvm::real	ext_sigma
	Amplitude of Gaussian white noise for Langevin extended dynamics. More...
colvarvalue	fr
	\brief Applied force on extended DOF, for output (unscaled if using MTS). More...
colvarvalue	fj
	\brief Jacobian force, when Jacobian_force is enabled. More...
colvarvalue	ft_reported
	Cached reported total force. More...
size_t	n_active_cvcs
	\brief Number of CVC objects with an active flag. More...
cvm::real	active_cvc_square_norm
	Sum of square coefficients for active cvcs. More...
cvm::step_number	prev_timestep
	\brief Absolute timestep number when this colvar was last updated. More...
colvarvalue	x_old
	Previous value (to calculate velocities during analysis). More...
colvarvalue	x_restart
	Value read from the most recent state file (if any). More...
bool	after_restart
	True if a state file was just read. More...
std::list< std::list< colvarvalue > >	acf_x_history
	Time series of values and velocities used in correlation functions. More...
std::list< std::list< colvarvalue > >	acf_v_history
	Time series of values and velocities used in correlation functions. More...
std::list< std::list< colvarvalue > >::iterator	acf_x_history_p
	Time series of values and velocities used in correlation functions (pointers)x. More...
std::list< std::list< colvarvalue > >::iterator	acf_v_history_p
	Time series of values and velocities used in correlation functions (pointers)x. More...
std::list< std::list< colvarvalue > >	x_history
	Time series of values and velocities used in running averages. More...
std::list< std::list< colvarvalue > >::iterator	x_history_p
	Time series of values and velocities used in correlation functions (pointers)x. More...
std::string	acf_colvar_name
	\brief Collective variable with which the correlation is calculated (default: itself). More...
size_t	acf_length
	Length of autocorrelation function (ACF). More...
size_t	acf_offset
	After how many steps the ACF starts. More...
size_t	acf_stride
	How many timesteps separate two ACF values. More...
size_t	acf_nframes
	Number of frames for each ACF point. More...
bool	acf_normalize
	Normalize the ACF to a maximum value of 1? More...
std::vector< cvm::real >	acf
	ACF values. More...
std::string	acf_outfile
	Name of the file to write the ACF. More...
acf_type_e	acf_type
	Type of autocorrelation function (ACF). More...
size_t	runave_length
	Length of running average series. More...
size_t	runave_stride
	Timesteps to skip between two values in the running average series. More...
std::string	runave_outfile
	Name of the file to write the running average. More...
colvarvalue	runave
	Current value of the running average. More...
cvm::real	runave_variance
	Current value of the square deviation from the running average. More...
cvm::real	kinetic_energy
	If extended Lagrangian active: colvar kinetic energy. More...
cvm::real	potential_energy
	If extended Lagrangian active: colvar harmonic potential. More...
std::vector< cvc * >	cvcs
	\brief Array of colvar::cvc objects. More...
std::vector< bool >	cvc_flags
	\brief Flags to enable or disable cvcs at next colvar evaluation. More...
std::string	scripted_function
	Name of scripted function to be used. More...
std::vector< const colvarvalue * >	sorted_cvc_values
	Current cvc values in the order requested by script when using scriptedFunction. More...
std::vector< int >	volmap_ids_
	Volmap numeric IDs, one for each CVC (-1 if not available). More...

Detailed Description

Definition at line 54 of file colvar.h.

Member Enumeration Documentation

enum colvar::acf_type_e [protected]

Type of autocorrelation function (ACF).

Enumeration values:

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 \brief Coordinate ACF, second order Legendre polynomial between x(0) and x(t) (does not work with scalar numbers).

Definition at line 514 of file colvar.h.

Constructor & Destructor Documentation

colvar::colvar ( )

Constructor.

Definition at line 27 of file colvar.C.
References after_restart, colvardeps::description, expand_boundaries, init_dependencies, kinetic_energy, potential_energy, and prev_timestep.

colvar::~colvar ( )

Destructor.

Definition at line 1275 of file colvar.C.
References biases, colvarmodule::config_changed, cvcs, colvarmodule::log, colvarmodule::main, name, NULL, colvardeps::remove_all_children, and colvarmodule::variables.

Member Function Documentation

colvarvalue const & colvar::actual_value ( ) const [inline]

\brief Current actual value (not extended DOF).

Definition at line 713 of file colvar.h.
References x.

void colvar::add_bias_force ( colvarvalue const & force ) [inline]

Add to the total force from biases.

Definition at line 737 of file colvar.h.
References colvardeps::check_enabled, colvarmodule::debug, colvardeps::f_cv_gradient, fb, force, colvarmodule::log, and name.

void colvar::add_bias_force_actual_value ( colvarvalue const & force ) [inline]

Apply a force to the actual value (only meaningful with extended Lagrangian).

Definition at line 748 of file colvar.h.
References colvarmodule::debug, fb_actual, force, colvarmodule::log, and name.

int colvar::analyze ( )

Perform analysis tasks.

Definition at line 2559 of file colvar.C.
References calc_acf, calc_runave, colvardeps::f_cv_corrfunc, colvardeps::f_cv_runave, and colvardeps::is_enabled.

colvarvalue const colvar::applied_force ( ) const [inline]

Get the current applied force.

Definition at line 333 of file colvar.h.
References colvardeps::f_cv_extended_Lagrangian, and colvardeps::is_enabled.
Referenced by write_traj.

void colvar::build_atom_list ( void ) [protected]

\brief Initialize the sorted list of atom IDs for atoms involved in all cvcs (called when enabling f_cv_collect_gradients).

Definition at line 973 of file colvar.C.
References atom_ids, atomic_gradients, cvcs, colvarmodule::debug, colvardeps::f_ag_fit_gradients, colvardeps::f_ag_fitting_group, and colvarmodule::log.
Referenced by do_feature_side_effects.

int colvar::calc ( )

\brief Calculate the colvar's value and related quantities.

Definition at line 1340 of file colvar.C.
References calc_cvcs, collect_cvc_data, colvardeps::f_cv_active, colvardeps::is_enabled, and update_cvc_flags.

int colvar::calc_acf ( ) [protected]

Calculate the auto-correlation function (ACF).

Definition at line 2593 of file colvar.C.
References acf, acf_colvar_name, acf_coor, acf_length, acf_nframes, acf_notset, acf_offset, acf_p2coor, acf_stride, acf_v_history, acf_v_history_p, acf_vel, acf_x_history, acf_x_history_p, calc_coor_acf, calc_p2coor_acf, calc_vel_acf, colvarvalue::check_types, colvarmodule::colvar_by_name, COLVARS_INPUT_ERROR, colvarmodule::error, history_add_value, history_incr, colvarmodule::log, name, NULL, prev_timestep, colvarmodule::step_relative, value, and velocity.
Referenced by analyze.

int colvar::calc_colvar_properties ( )

\brief Calculate the quantities associated to the colvar (but not to the CVCs).

Definition at line 1688 of file colvar.C.
References after_restart, colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_fdiff_velocity, colvardeps::f_cv_reflecting_lower_boundary, colvardeps::f_cv_reflecting_upper_boundary, colvardeps::f_cv_subtract_applied_force, f_old, fdiff_velocity, ft, ft_reported, colvardeps::is_enabled, colvarmodule::log, lower_boundary, colvarvalue::norm2, prev_timestep, prev_v_ext, prev_x_ext, colvarvalue::reset, colvarmodule::step_relative, colvarvalue::type, colvarvalue::type_notset, upper_boundary, v_ext, v_fdiff, v_reported, x, x_ext, x_old, and x_reported.
Referenced by collect_cvc_data.

void colvar::calc_coor_acf ( std::list< colvarvalue > & x_history,

colvarvalue const & x

) [protected]

\brief Coordinate ACF, scalar product between x(0) and x(t) (does not work with scalar numbers).

Definition at line 2713 of file colvar.C.
References acf, acf_length, acf_nframes, acf_offset, colvarvalue::inner_opt, colvarvalue::norm2, and x.
Referenced by calc_acf.

int colvar::calc_cvc_gradients ( int first,

size_t num_cvcs

)

\brief Same as colvar::calc_cvc_values but for gradients.

Definition at line 1532 of file colvar.C.
References cvcs, colvarmodule::debug, colvarmodule::decrease_depth, colvardeps::f_cvc_debug_gradient, colvardeps::f_cvc_gradient, colvarmodule::increase_depth, colvarmodule::log, num_active_cvcs, and num_cvcs.
Referenced by calc_cvcs.

int colvar::calc_cvc_Jacobians ( int first,

size_t num_cvcs

)

\brief Same as colvar::calc_cvc_values but for Jacobian derivatives/forces.

Definition at line 1645 of file colvar.C.
References cvcs, colvarmodule::decrease_depth, colvardeps::f_cv_Jacobian, colvarmodule::increase_depth, colvardeps::is_enabled, num_active_cvcs, and num_cvcs.
Referenced by calc_cvcs.

int colvar::calc_cvc_total_force ( int first,

size_t num_cvcs

)

\brief Same as colvar::calc_cvc_values but for total forces.

Definition at line 1584 of file colvar.C.
References cvcs, colvarmodule::debug, colvarmodule::decrease_depth, colvardeps::f_cv_total_force_calc, colvarmodule::increase_depth, colvardeps::is_enabled, colvarmodule::log, num_active_cvcs, and num_cvcs.
Referenced by calc_cvcs.

int colvar::calc_cvc_values ( int first,

size_t num_cvcs

)

\brief Calculate the values of the given subset of CVCs.

Definition at line 1429 of file colvar.C.
References cvcs, colvarmodule::debug, colvarmodule::decrease_depth, colvarmodule::increase_depth, colvarmodule::log, num_active_cvcs, and num_cvcs.
Referenced by calc_cvcs.

int colvar::calc_cvcs ( int first = 0,

size_t num_cvcs = 0

)

\brief 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.

Definition at line 1355 of file colvar.C.
References calc_cvc_gradients, calc_cvc_Jacobians, calc_cvc_total_force, calc_cvc_values, check_cvc_range, colvarmodule::debug, colvarmodule::log, colvarmodule::main, num_cvcs, colvarmodule::proxy, colvarmodule::step_relative, and colvarproxy_system::total_forces_same_step.
Referenced by calc, and colvarproxy_smp::smp_colvars_loop.

void colvar::calc_p2coor_acf ( std::list< colvarvalue > & x_history,

colvarvalue const & x

) [protected]

\brief Coordinate ACF, second order Legendre polynomial between x(0) and x(t) (does not work with scalar numbers).

Definition at line 2733 of file colvar.C.
References acf, acf_length, acf_nframes, acf_offset, and colvarvalue::p2leg_opt.
Referenced by calc_acf.

int colvar::calc_runave ( ) [protected]

Calculate the running average and its standard deviation.

Definition at line 2813 of file colvar.C.
References acf_nframes, colvarvalue::apply_constraints, colvarmodule::debug, dist2, history_add_value, colvarmodule::log, colvarmodule::main, colvarproxy_io::output_stream, colvarproxy_io::output_stream_exists, colvarvalue::output_width, prev_timestep, colvarmodule::proxy, colvarmodule::real, colvarvalue::reset, runave, runave_length, runave_outfile, runave_stride, runave_variance, colvarmodule::sqrt, colvarmodule::step_relative, string, colvarvalue::type, value, colvarmodule::wrap_string, x, x_history, and x_history_p.
Referenced by analyze.

void colvar::calc_vel_acf ( std::list< colvarvalue > & v_history,

colvarvalue const & v

) [protected]

\brief Velocity ACF, scalar product between v(0) and v(t).

Definition at line 2688 of file colvar.C.
References acf, acf_length, acf_nframes, acf_offset, colvarvalue::inner_opt, and colvarvalue::norm2.
Referenced by calc_acf.

int colvar::check_cvc_range ( int first_cvc,

size_t num_cvcs

)

Ensure that the selected range of CVCs is consistent.

Definition at line 1418 of file colvar.C.
References COLVARS_BUG_ERROR, cvcs, colvarmodule::error, and name.
Referenced by calc_cvcs.

int colvar::collect_cvc_data ( )

\brief Collect quantities from CVCs and update aggregated data for the colvar.

Definition at line 1389 of file colvar.C.
References calc_colvar_properties, collect_cvc_gradients, collect_cvc_Jacobians, collect_cvc_total_forces, collect_cvc_values, colvarmodule::debug, colvarmodule::log, colvarmodule::main, colvarmodule::proxy, colvarmodule::step_relative, and colvarproxy_system::total_forces_same_step.
Referenced by calc.

int colvar::collect_cvc_gradients ( )

\brief Same as colvar::collect_cvc_values but for gradients.

Definition at line 1567 of file colvar.C.
References atom_ids, atomic_gradients, cvcs, colvardeps::f_cv_collect_gradient, and colvardeps::is_enabled.
Referenced by collect_cvc_data.

int colvar::collect_cvc_Jacobians ( )

\brief Same as colvar::collect_cvc_values but for Jacobian derivatives/forces.

Definition at line 1666 of file colvar.C.
References active_cvc_square_norm, colvarproxy_system::boltzmann, cvcs, colvarmodule::debug, colvardeps::f_cv_Jacobian, fj, colvardeps::is_enabled, colvarmodule::log, colvarmodule::main, colvarmodule::proxy, colvarvalue::reset, and colvarproxy_system::target_temperature.
Referenced by collect_cvc_data.

int colvar::collect_cvc_total_forces ( )

\brief Same as colvar::collect_cvc_values but for total forces.

Definition at line 1613 of file colvar.C.
References active_cvc_square_norm, cvcs, colvarmodule::debug, colvardeps::f_cv_hide_Jacobian, colvardeps::f_cv_subtract_applied_force, colvardeps::f_cv_total_force_calc, fj, ft, colvardeps::is_enabled, colvarmodule::log, colvarvalue::reset, and colvarmodule::step_relative.
Referenced by collect_cvc_data.

int colvar::collect_cvc_values ( )

\brief Collect the values of the CVCs.

Definition at line 1460 of file colvar.C.
References COLVARS_INPUT_ERROR, COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::debug, dist2, colvarmodule::error, colvardeps::f_cv_custom_function, colvardeps::f_cv_scripted, colvarmodule::integer_power, colvardeps::is_enabled, colvarmodule::log, name, colvarvalue::reset, scripted_function, colvarvalue::size, sorted_cvc_values, colvarvalue::type, colvarvalue::type_scalar, value, width, x, and x_restart.
Referenced by collect_cvc_data.

void colvar::communicate_forces ( )

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

Definition at line 1930 of file colvar.C.
References colvarvalue::as_vector, COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::debug, colvarmodule::error, f, colvardeps::f_cv_custom_function, colvardeps::f_cv_scripted, colvardeps::is_enabled, colvarmodule::log, scripted_function, colvarvalue::size, sorted_cvc_values, colvarvalue::type, colvarvalue::type_scalar, value, and x.

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

const colvar::cvc *const j

) [static]

getter of the global cvc map \brief function for sorting cvcs by their names.

Definition at line 47 of file colvar.C.
References colvar::cvc::name.
Referenced by init.

int colvar::cvc_param_exists ( std::string const & param_name )

Whether this named parameter exists (in the first and only component).

Definition at line 2099 of file colvar.C.
References COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::error, colvardeps::f_cv_single_cvc, and colvardeps::is_enabled.

void colvar::delete_features ( ) [inline, static]

Definition at line 108 of file colvar.h.
References cv_features.
Referenced by colvarmodule::~colvarmodule.

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

colvarvalue const & x2

) const

\brief Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients Handles correctly symmetries and periodic boundary conditions.

Definition at line 2179 of file colvar.C.
References cvcs, colvarvalue::dist2, colvardeps::f_cv_custom_function, colvardeps::f_cv_homogeneous, colvardeps::f_cv_periodic, colvardeps::f_cv_scalar, colvardeps::f_cv_scripted, colvardeps::is_enabled, period, colvarvalue::real_value, and wrap_center.
Referenced by calc_runave, collect_cvc_values, colvarbias_restraint_harmonic_walls::colvar_distance, and update_extended_Lagrangian.

colvarvalue colvar::dist2_lgrad ( colvarvalue const & x1,

colvarvalue const & x2

) const

\brief Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients Handles correctly symmetries and periodic boundary conditions.

Definition at line 2198 of file colvar.C.
References cvcs, colvarvalue::dist2_grad, colvardeps::f_cv_custom_function, colvardeps::f_cv_homogeneous, colvardeps::f_cv_periodic, colvardeps::f_cv_scalar, colvardeps::f_cv_scripted, colvardeps::is_enabled, period, colvarvalue::real_value, and wrap_center.
Referenced by colvarbias_restraint_harmonic_walls::colvar_distance, fdiff_velocity, and update_extended_Lagrangian.

colvarvalue colvar::dist2_rgrad ( colvarvalue const & x1,

colvarvalue const & x2

) const

\brief Use the internal metrics (as from colvar::cvc objects) to calculate square distances and gradients Handles correctly symmetries and periodic boundary conditions.

Definition at line 2217 of file colvar.C.
References cvcs, colvarvalue::dist2_grad, colvardeps::f_cv_custom_function, colvardeps::f_cv_homogeneous, colvardeps::f_cv_periodic, colvardeps::f_cv_scalar, colvardeps::f_cv_scripted, colvardeps::is_enabled, period, colvarvalue::real_value, and wrap_center.

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.
Definition at line 956 of file colvar.C.
References atom_ids, build_atom_list, colvardeps::f_cv_collect_atom_ids, colvardeps::f_cv_total_force_calc, and colvarmodule::request_total_force.

int colvar::end_of_step ( )

Carry out operations needed before next step is run.

Definition at line 1911 of file colvar.C.
References colvarmodule::debug, f, colvardeps::f_cv_fdiff_velocity, colvardeps::f_cv_subtract_applied_force, f_old, colvardeps::is_enabled, colvarmodule::log, prev_timestep, colvarmodule::step_relative, x, and x_old.

colvarvalue colvar::fdiff_velocity ( colvarvalue const & xold,

colvarvalue const & xnew

) [inline, protected]

Definition at line 163 of file colvar.h.
References dist2_lgrad, and colvarmodule::dt.
Referenced by calc_colvar_properties.

virtual const std::vector<feature *>& colvar::features ( ) const [inline, virtual]

\brief Implementation of the feature list accessor for colvar.

Implements colvardeps.
Definition at line 100 of file colvar.h.
References cv_features.
Referenced by init_dependencies.

cvm::real const & colvar::force_constant ( ) const [inline]

\brief Force constant of the spring.

Definition at line 701 of file colvar.h.
References ext_force_k.

std::vector< std::vector< int > > colvar::get_atom_lists ( ) [virtual]

\brief Get vector of vectors of atom IDs for all atom groups.

Definition at line 1249 of file colvar.C.
References cvcs.

cvm::real colvar::get_cvc_param ( std::string const & param_name )

Get the value of the named parameter (from the first and only component).

Definition at line 2109 of file colvar.C.
References COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::error, colvardeps::f_cv_single_cvc, and colvardeps::is_enabled.

colvarvalue const * colvar::get_cvc_param_grad ( std::string const & param_name )

Pointer to the derivative of the variable with respect to param_name.

Definition at line 2131 of file colvar.C.
References COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::error, colvardeps::f_cv_single_cvc, colvardeps::is_enabled, and NULL.

void const * colvar::get_cvc_param_ptr ( std::string const & param_name )

Get a pointer to the named parameter (from the first and only component).

Definition at line 2120 of file colvar.C.
References COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::error, colvardeps::f_cv_single_cvc, colvardeps::is_enabled, and NULL.

std::vector< int > const & colvar::get_volmap_ids ( )

Volmap numeric IDs, one for each CVC (-1 if not available).

Definition at line 1260 of file colvar.C.
References cvcs, and volmap_ids_.

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

Main init function.

Definition at line 53 of file colvar.C.
References active_cvc_square_norm, colvarvalue::check_types, colvarmodule::cite_feature, colvarmodule::colvar_by_name, COLVARS_ERROR, COLVARS_INPUT_ERROR, compare_cvc, conf, cvcs, colvarmodule::debug, colvardeps::description, colvardeps::enable, colvarmodule::error, f, colvardeps::f_cv_active, colvardeps::f_cv_custom_function, colvardeps::f_cv_external, colvardeps::f_cv_gradient, colvardeps::f_cv_homogeneous, colvardeps::f_cv_linear, colvardeps::f_cv_multiple_ts, colvardeps::f_cv_periodic, colvardeps::f_cv_scalar, colvardeps::f_cv_scripted, colvardeps::f_cv_single_cvc, colvardeps::f_cvc_periodic, f_old, colvarmodule::fabs, fj, ft, ft_reported, colvarmodule::get_error, colvarparse::get_keyval, init_components, init_custom_function, init_extended_Lagrangian, init_grid_parameters, init_output_flags, colvardeps::is_enabled, colvarmodule::log, colvarmodule::main, name, NULL, parse_analysis, colvarparse::parse_silent, period, colvarvalue::reset, reset_bias_force, colvarmodule::scripted_forces, scripted_function, colvardeps::set_enabled, colvarparse::set_string, colvarvalue::size, size, sorted_cvc_values, colvardeps::time_step_factor, colvarmodule::to_str, colvarvalue::Type, colvarvalue::type, colvarvalue::type_all, colvarvalue::type_desc, colvarvalue::type_keyword, colvarvalue::type_notset, colvarvalue::type_scalar, colvarvalue::type_vector, v_fdiff, v_reported, value, colvarmodule::variables, colvarvalue::vector1d_value, wrap_center, x, x_old, x_reported, and x_restart.

int colvar::init_components ( std::string const & conf )

Parse the CVC configuration and allocate their data.

Definition at line 841 of file colvar.C.
References colvardeps::add_child, COLVARS_INPUT_ERROR, conf, cvcs, colvarmodule::error, it, colvarmodule::log, n_active_cvcs, and name.
Referenced by init.

int colvar::init_custom_function ( std::string const & conf )

Parse parameters for custom function with Lepton.

Definition at line 463 of file colvar.C.
References COLVARS_NOT_IMPLEMENTED, conf, colvarmodule::error, colvarparse::key_lookup, and string.
Referenced by init.

int colvar::init_extended_Lagrangian ( std::string const & conf )

Init extended Lagrangian parameters.

Definition at line 634 of file colvar.C.
References colvarproxy_system::boltzmann, COLVARS_INPUT_ERROR, conf, colvarmodule::dt, colvardeps::enable, colvarmodule::error, ext_force_k, ext_gamma, ext_mass, ext_sigma, colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_external, colvardeps::f_cv_Langevin, colvardeps::f_cv_output_energy, colvardeps::f_cv_reflecting_lower_boundary, colvardeps::f_cv_reflecting_upper_boundary, fr, colvarparse::get_keyval, colvardeps::get_keyval_feature, colvardeps::is_enabled, colvarmodule::log, colvarmodule::main, PI, colvarmodule::proxy, colvarmodule::real, colvarmodule::sqrt, colvarproxy_system::target_temperature, colvardeps::time_step_factor, colvarvalue::type, colvarvalue::type_notset, v_ext, value, and x_ext.
Referenced by init.

int colvar::init_grid_parameters ( std::string const & conf )

Init defaults for grid options.

Definition at line 486 of file colvar.C.
References colvarmodule::append_new_config, COLVARS_INPUT_ERROR, conf, cvcs, colvardeps::disable, colvardeps::enable, colvarmodule::error, expand_boundaries, colvardeps::f_cv_hard_lower_boundary, colvardeps::f_cv_hard_upper_boundary, colvardeps::f_cv_lower_boundary, colvardeps::f_cv_scalar, colvardeps::f_cv_single_cvc, colvardeps::f_cv_upper_boundary, colvardeps::f_cvc_lower_boundary, colvardeps::f_cvc_upper_boundary, colvardeps::f_cvc_width, colvarparse::get_keyval, colvardeps::get_keyval_feature, colvardeps::is_enabled, colvarparse::key_already_set, colvarmodule::log, lower_boundary, colvarmodule::main, colvarparse::parse_silent, periodic_boundaries, colvarvalue::real_value, string, colvardeps::time_step_factor, colvarvalue::type, upper_boundary, value, and width.
Referenced by init.

int colvar::init_output_flags ( std::string const & conf )

Init output flags.

Definition at line 712 of file colvar.C.
References COLVARS_INPUT_ERROR, conf, colvardeps::enable, colvarmodule::error, colvardeps::f_cv_output_applied_force, colvardeps::f_cv_output_total_force, colvardeps::f_cv_output_value, colvardeps::f_cv_output_velocity, colvardeps::f_cv_subtract_applied_force, colvarparse::get_keyval, colvardeps::get_keyval_feature, and colvarparse::parse_silent.
Referenced by init.

virtual std::vector<feature *>& colvar::modify_features ( ) [inline, virtual]

Implements colvardeps.
Definition at line 104 of file colvar.h.
References cv_features.
Referenced by init_dependencies.

size_t colvar::num_active_cvcs ( ) const [inline]

\brief number of CVC objects with an active flag (as set by update_cvc_flags).

Definition at line 417 of file colvar.h.
References n_active_cvcs.
Referenced by calc_cvc_gradients, calc_cvc_Jacobians, calc_cvc_total_force, and calc_cvc_values.

size_t colvar::num_cvcs ( ) const [inline]

\brief Number of CVC objects defined.

Definition at line 410 of file colvar.h.
References cvcs.
Referenced by calc_cvc_gradients, calc_cvc_Jacobians, calc_cvc_total_force, calc_cvc_values, and calc_cvcs.

size_t colvar::num_dimensions ( ) const [inline]

\brief Number of dimensions of the value of this colvar.

Definition at line 404 of file colvar.h.
References colvarvalue::size, and value.

int colvar::parse_analysis ( std::string const & conf )

Read the analysis tasks.

Definition at line 1013 of file colvar.C.
References acf_colvar_name, acf_coor, acf_length, acf_normalize, acf_offset, acf_outfile, acf_p2coor, acf_stride, acf_type, acf_vel, colvarmodule::colvar_by_name, COLVARS_ERROR, COLVARS_INPUT_ERROR, conf, colvardeps::enable, colvarmodule::error, colvardeps::f_cv_corrfunc, colvardeps::f_cv_fdiff_velocity, colvardeps::f_cv_runave, colvarmodule::get_error, colvarparse::get_keyval, colvarmodule::log, name, NULL, runave_length, runave_outfile, runave_stride, colvarmodule::set_error_bits, and colvarparse::to_lower_cppstr.
Referenced by init.

bool colvar::periodic_boundaries ( colvarvalue const & lb,

colvarvalue const & ub

) const

\brief Is the interval defined by the two boundaries periodic?

Definition at line 2156 of file colvar.C.
References period, colvarmodule::sqrt, and width.

bool colvar::periodic_boundaries ( ) const

\brief Is the interval defined by the two boundaries periodic?

Definition at line 2168 of file colvar.C.
References colvardeps::f_cv_lower_boundary, colvardeps::f_cv_upper_boundary, colvardeps::is_enabled, lower_boundary, and upper_boundary.
Referenced by init_grid_parameters.

std::istream & colvar::read_state ( std::istream & is )

Read the collective variable from a restart file.

Definition at line 2256 of file colvar.C.
References after_restart, COLVARS_INPUT_ERROR, conf, colvarmodule::debug, colvarmodule::error, colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_output_velocity, colvarparse::get_keyval, colvardeps::is_enabled, colvarmodule::log, name, colvarparse::parse_silent, colvarvalue::type, v_ext, v_fdiff, v_reported, x, x_ext, x_reported, and x_restart.

std::istream & colvar::read_traj ( std::istream & is )

Read the value from a collective variable trajectory file.

Definition at line 2337 of file colvar.C.
References f, colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_output_applied_force, colvardeps::f_cv_output_total_force, colvardeps::f_cv_output_value, colvardeps::f_cv_output_velocity, ft, ft_reported, colvardeps::is_enabled, colvarmodule::log, v_ext, v_fdiff, v_reported, x, x_ext, and x_reported.

void colvar::reset_bias_force ( ) [inline]

Set the total biasing force to zero.

Definition at line 757 of file colvar.h.
References fb, fb_actual, colvarvalue::reset, colvarvalue::type, and value.
Referenced by init.

colvarvalue const & colvar::run_ave ( ) const [inline]

\brief Current running average (if calculated as set by analysis flag).

Definition at line 719 of file colvar.h.
References runave.

int colvar::set_cvc_flags ( std::vector< bool > const & flags )

\brief Enables and disables individual CVCs based on the given array.

Definition at line 2016 of file colvar.C.
References COLVARS_ERROR, cvc_flags, cvcs, and colvarmodule::error.

int colvar::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.

Definition at line 2142 of file colvar.C.
References COLVARS_NOT_IMPLEMENTED, cvcs, colvarmodule::error, colvardeps::f_cv_single_cvc, and colvardeps::is_enabled.

void colvar::setup ( )

Get ready for a run and re-initialize internal data if needed.

Definition at line 1235 of file colvar.C.
References atoms, cvcs, and name.

colvarvalue const & colvar::total_force ( ) const [inline]

\brief 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.

Definition at line 731 of file colvar.h.
References ft_reported.

void colvar::update_active_cvc_square_norm ( ) [protected]

Update the sum of square coefficients for active cvcs.

Definition at line 2029 of file colvar.C.
References active_cvc_square_norm, and cvcs.
Referenced by update_cvc_config, and update_cvc_flags.

int colvar::update_cvc_config ( std::vector< std::string > const & confs )

\brief Modify the configuration of CVCs (currently, only base class data).

Definition at line 2064 of file colvar.C.
References COLVARS_INPUT_ERROR, conf, cvcs, colvarmodule::decrease_depth, colvarmodule::error, colvarmodule::increase_depth, colvarmodule::log, name, and update_active_cvc_square_norm.

int colvar::update_cvc_flags ( )

\brief Updates the flags in the CVC objects, and their number.

Definition at line 2040 of file colvar.C.
References COLVARS_ERROR, cvc_flags, cvcs, colvarmodule::error, colvardeps::f_cvc_active, n_active_cvcs, and update_active_cvc_square_norm.
Referenced by calc.

void colvar::update_extended_Lagrangian ( )

\brief Integrate equations of motion of extended Lagrangian coordinate if needed.

Definition at line 1800 of file colvar.C.
References colvarvalue::apply_constraints, cvcs, colvarmodule::debug, colvardeps::description, dist2, dist2_lgrad, colvarmodule::dt, colvarmodule::error, ext_force_k, ext_gamma, ext_mass, ext_sigma, f, colvardeps::f_cv_external, colvardeps::f_cv_Langevin, colvardeps::f_cv_reflecting_lower_boundary, colvardeps::f_cv_reflecting_upper_boundary, colvardeps::f_cv_subtract_applied_force, fb_actual, fr, ft_reported, colvardeps::is_enabled, kinetic_energy, colvarmodule::log, lower_boundary, potential_energy, prev_timestep, prev_v_ext, prev_x_ext, colvarmodule::real, colvarvalue::reset, colvarvalue::set_random, colvarmodule::step_relative, colvardeps::time_step_factor, colvarvalue::type, upper_boundary, v_ext, wrap, x, and x_ext.
Referenced by update_forces_energy.

cvm::real colvar::update_forces_energy ( )

\brief 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.

Definition at line 1754 of file colvar.C.
References colvarmodule::debug, f, colvardeps::f_cv_active, colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_external, colvardeps::f_cv_hide_Jacobian, colvardeps::f_cv_Jacobian, fb, fb_actual, fj, fr, colvardeps::is_enabled, kinetic_energy, colvarmodule::log, potential_energy, colvarmodule::real, colvarvalue::reset, colvardeps::time_step_factor, colvarvalue::type, update_extended_Lagrangian, and value.

colvarvalue const & colvar::value ( ) const [inline]

\brief Current value (previously set by calc() or by read_traj()).

Definition at line 707 of file colvar.h.
References x_reported.
Referenced by colvarbias::add_colvar, calc_acf, calc_runave, collect_cvc_values, communicate_forces, init, init_extended_Lagrangian, init_grid_parameters, num_dimensions, colvarmodule::read_colvar, reset_bias_force, and update_forces_energy.

colvarvalue const & colvar::velocity ( ) const [inline]

\brief Current velocity (previously set by calc() or by read_traj()).

Definition at line 725 of file colvar.h.
References v_reported.
Referenced by calc_acf.

void colvar::wrap ( colvarvalue & x_unwrapped ) const

\brief Use the internal metrics (as from colvar::cvc objects) to wrap a value into a standard interval Handles correctly symmetries and periodic boundary conditions.

Definition at line 2237 of file colvar.C.
References cvcs, colvardeps::f_cv_custom_function, colvardeps::f_cv_periodic, colvardeps::f_cv_scripted, colvarmodule::floor, colvardeps::is_enabled, period, colvarvalue::real_value, and wrap_center.
Referenced by update_extended_Lagrangian.

int colvar::write_acf ( std::ostream & os ) [protected]

Save the ACF to a file.

Definition at line 2755 of file colvar.C.
References acf, acf_colvar_name, acf_coor, acf_nframes, acf_normalize, acf_notset, acf_offset, acf_p2coor, acf_stride, acf_vel, COLVARS_FILE_ERROR, it, name, colvarmodule::real, and colvarmodule::wrap_string.
Referenced by write_output_files.

int colvar::write_output_files ( )

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

Definition at line 2529 of file colvar.C.
References acf, acf_outfile, colvarmodule::backup_file, COLVARS_FILE_ERROR, colvardeps::f_cv_corrfunc, colvardeps::is_enabled, colvarmodule::log, string, and write_acf.

std::ostream & colvar::write_state ( std::ostream & os )

Write the collective variable to a restart file.

Definition at line 2387 of file colvar.C.
References colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_output_velocity, colvarproxy_io::flush_output_stream, colvardeps::is_enabled, colvarmodule::main, name, colvarmodule::proxy, runave_outfile, v_reported, x, and x_reported.

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

Output formatted values to the trajectory file.

Definition at line 2475 of file colvar.C.
References applied_force, colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_external, colvardeps::f_cv_output_applied_force, colvardeps::f_cv_output_energy, colvardeps::f_cv_output_total_force, colvardeps::f_cv_output_value, colvardeps::f_cv_output_velocity, ft_reported, colvardeps::is_enabled, kinetic_energy, potential_energy, v_fdiff, v_reported, x, and x_reported.

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

Write a label to the trajectory file (comment line).

Definition at line 2424 of file colvar.C.
References colvardeps::f_cv_extended_Lagrangian, colvardeps::f_cv_external, colvardeps::f_cv_output_applied_force, colvardeps::f_cv_output_energy, colvardeps::f_cv_output_total_force, colvardeps::f_cv_output_value, colvardeps::f_cv_output_velocity, colvardeps::is_enabled, colvarvalue::output_width, colvarmodule::wrap_string, and x.

Member Data Documentation

std::vector<cvm::real> colvar::acf [protected]

ACF values.

Definition at line 509 of file colvar.h.
Referenced by calc_acf, calc_coor_acf, calc_p2coor_acf, calc_vel_acf, write_acf, and write_output_files.

std::string colvar::acf_colvar_name [protected]

\brief Collective variable with which the correlation is calculated (default: itself).

Definition at line 497 of file colvar.h.
Referenced by calc_acf, parse_analysis, and write_acf.

size_t colvar::acf_length [protected]

Length of autocorrelation function (ACF).

Definition at line 499 of file colvar.h.
Referenced by calc_acf, calc_coor_acf, calc_p2coor_acf, calc_vel_acf, and parse_analysis.

size_t colvar::acf_nframes [protected]

Number of frames for each ACF point.

Definition at line 505 of file colvar.h.
Referenced by calc_acf, calc_coor_acf, calc_p2coor_acf, calc_runave, calc_vel_acf, and write_acf.

bool colvar::acf_normalize [protected]

Normalize the ACF to a maximum value of 1?

Definition at line 507 of file colvar.h.
Referenced by parse_analysis, and write_acf.

size_t colvar::acf_offset [protected]

After how many steps the ACF starts.

Definition at line 501 of file colvar.h.
Referenced by calc_acf, calc_coor_acf, calc_p2coor_acf, calc_vel_acf, parse_analysis, and write_acf.

std::string colvar::acf_outfile [protected]

Name of the file to write the ACF.

Definition at line 511 of file colvar.h.
Referenced by parse_analysis, and write_output_files.

size_t colvar::acf_stride [protected]

How many timesteps separate two ACF values.

Definition at line 503 of file colvar.h.
Referenced by calc_acf, parse_analysis, and write_acf.

acf_type_e colvar::acf_type [protected]

Type of autocorrelation function (ACF).

Definition at line 527 of file colvar.h.
Referenced by parse_analysis.

std::list< std::list<colvarvalue> > colvar::acf_v_history [protected]

Time series of values and velocities used in correlation functions.

Definition at line 484 of file colvar.h.
Referenced by calc_acf.

std::list< std::list<colvarvalue> >::iterator colvar::acf_v_history_p [protected]

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

Definition at line 487 of file colvar.h.
Referenced by calc_acf.

std::list< std::list<colvarvalue> > colvar::acf_x_history [protected]

Time series of values and velocities used in correlation functions.

Definition at line 484 of file colvar.h.
Referenced by calc_acf.

std::list< std::list<colvarvalue> >::iterator colvar::acf_x_history_p [protected]

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

Definition at line 487 of file colvar.h.
Referenced by calc_acf.

cvm::real colvar::active_cvc_square_norm [protected]

Sum of square coefficients for active cvcs.

Definition at line 393 of file colvar.h.
Referenced by collect_cvc_Jacobians, collect_cvc_total_forces, init, and update_active_cvc_square_norm.

bool colvar::after_restart [protected]

True if a state file was just read.

Definition at line 480 of file colvar.h.
Referenced by calc_colvar_properties, colvar, and read_state.

std::vector<int> colvar::atom_ids

\brief Sorted array of (zero-based) IDs for all atoms involved.

Definition at line 685 of file colvar.h.
Referenced by build_atom_list, collect_cvc_gradients, colvar::dihedPC::collect_gradients, colvar::alpha_angles::collect_gradients, colvar::cvc::collect_gradients, and do_feature_side_effects.

std::vector<cvm::rvector> colvar::atomic_gradients

\brief Array of atomic gradients collected from all cvcs with appropriate components, rotations etc. For scalar variables only!

Definition at line 690 of file colvar.h.
Referenced by build_atom_list, collect_cvc_gradients, colvar::dihedPC::collect_gradients, colvar::alpha_angles::collect_gradients, and colvar::cvc::collect_gradients.

std::vector<colvarbias *> colvar::biases

List of biases that depend on this colvar.

Definition at line 121 of file colvar.h.
Referenced by colvarbias::add_colvar, and ~colvar.

std::vector< colvardeps::feature * > colvar::cv_features [static]

\brief Implementation of the feature list for colvar.

Definition at line 2898 of file colvar.C.
Referenced by delete_features, features, and modify_features.

std::vector<bool> colvar::cvc_flags [protected]

\brief Flags to enable or disable cvcs at next colvar evaluation.

Definition at line 646 of file colvar.h.
Referenced by set_cvc_flags, and update_cvc_flags.

std::vector<cvc *> colvar::cvcs [protected]

\brief Array of colvar::cvc objects.

Definition at line 643 of file colvar.h.
Referenced by build_atom_list, calc_cvc_gradients, calc_cvc_Jacobians, calc_cvc_total_force, calc_cvc_values, check_cvc_range, collect_cvc_gradients, collect_cvc_Jacobians, collect_cvc_total_forces, collect_cvc_values, communicate_forces, cvc_param_exists, dist2, dist2_lgrad, dist2_rgrad, get_atom_lists, get_cvc_param, get_cvc_param_grad, get_cvc_param_ptr, get_volmap_ids, init, init_components, init_grid_parameters, num_cvcs, set_cvc_flags, set_cvc_param, setup, update_active_cvc_square_norm, update_cvc_config, update_cvc_flags, update_extended_Lagrangian, wrap, and ~colvar.

bool colvar::expand_boundaries

\brief Expand the boundaries of multiples of width, to keep the value always within range.

Definition at line 234 of file colvar.h.
Referenced by colvar, and init_grid_parameters.

cvm::real colvar::ext_force_k [protected]

Restraint force constant.

Definition at line 189 of file colvar.h.
Referenced by force_constant, init_extended_Lagrangian, and update_extended_Lagrangian.

cvm::real colvar::ext_gamma [protected]

Friction coefficient for Langevin extended dynamics.

Definition at line 191 of file colvar.h.
Referenced by init_extended_Lagrangian, and update_extended_Lagrangian.

cvm::real colvar::ext_mass [protected]

Mass of the restraint center.

Definition at line 187 of file colvar.h.
Referenced by init_extended_Lagrangian, and update_extended_Lagrangian.

cvm::real colvar::ext_sigma [protected]

Amplitude of Gaussian white noise for Langevin extended dynamics.

Definition at line 193 of file colvar.h.
Referenced by init_extended_Lagrangian, and update_extended_Lagrangian.

colvarvalue colvar::f

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

Definition at line 217 of file colvar.h.
Referenced by communicate_forces, end_of_step, energythread, init, read_traj, shader_template, update_extended_Lagrangian, and update_forces_energy.

colvarvalue colvar::f_old

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

Definition at line 220 of file colvar.h.
Referenced by calc_colvar_properties, end_of_step, and init.

colvarvalue colvar::fb

\brief Bias force; reset_bias_force() should be called before the biases are updated.

Definition at line 209 of file colvar.h.
Referenced by add_bias_force, reset_bias_force, and update_forces_energy.

colvarvalue colvar::fb_actual

\brief Bias force to the actual value (only useful with extended Lagrangian).

Definition at line 212 of file colvar.h.
Referenced by add_bias_force_actual_value, reset_bias_force, update_extended_Lagrangian, and update_forces_energy.

colvarvalue colvar::fj [protected]

\brief Jacobian force, when Jacobian_force is enabled.

Definition at line 199 of file colvar.h.
Referenced by collect_cvc_Jacobians, collect_cvc_total_forces, init, and update_forces_energy.

colvarvalue colvar::fr [protected]

\brief Applied force on extended DOF, for output (unscaled if using MTS).

Definition at line 196 of file colvar.h.
Referenced by init_extended_Lagrangian, update_extended_Lagrangian, and update_forces_energy.

colvarvalue colvar::ft

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

Definition at line 224 of file colvar.h.
Referenced by calc_colvar_properties, collect_cvc_total_forces, init, and read_traj.

colvarvalue colvar::ft_reported [protected]

Cached reported total force.

Definition at line 202 of file colvar.h.
Referenced by calc_colvar_properties, init, read_traj, total_force, update_extended_Lagrangian, and write_traj.

cvm::real colvar::kinetic_energy [protected]

If extended Lagrangian active: colvar kinetic energy.

Definition at line 563 of file colvar.h.
Referenced by colvar, update_extended_Lagrangian, update_forces_energy, and write_traj.

colvarvalue colvar::lower_boundary

\brief Location of the lower boundary.

Definition at line 237 of file colvar.h.
Referenced by calc_colvar_properties, init_grid_parameters, periodic_boundaries, and update_extended_Lagrangian.

size_t colvar::n_active_cvcs [protected]

\brief Number of CVC objects with an active flag.

Definition at line 390 of file colvar.h.
Referenced by init_components, num_active_cvcs, and update_cvc_flags.

std::string colvar::name

Name.

Definition at line 59 of file colvar.h.
Referenced by add_bias_force, add_bias_force_actual_value, colvarbias::add_colvar, calc_acf, check_cvc_range, collect_cvc_values, init, init_components, parse_analysis, read_state, setup, colvarproxy_smp::smp_colvars_loop, update_cvc_config, write_acf, write_state, and ~colvar.

cvm::real colvar::period

Period, if this variable is periodic.

Definition at line 227 of file colvar.h.
Referenced by dist2, dist2_lgrad, dist2_rgrad, init, periodic_boundaries, and wrap.

cvm::real colvar::potential_energy [protected]

If extended Lagrangian active: colvar harmonic potential.

Definition at line 565 of file colvar.h.
Referenced by colvar, update_extended_Lagrangian, update_forces_energy, and write_traj.

cvm::step_number colvar::prev_timestep [protected]

\brief Absolute timestep number when this colvar was last updated.

Definition at line 399 of file colvar.h.
Referenced by calc_acf, calc_colvar_properties, calc_runave, colvar, end_of_step, and update_extended_Lagrangian.

colvarvalue colvar::prev_v_ext [protected]

Previous velocity of the restraint center.

Definition at line 185 of file colvar.h.
Referenced by calc_colvar_properties, and update_extended_Lagrangian.

colvarvalue colvar::prev_x_ext [protected]

Previous value of the restraint center;.

Definition at line 181 of file colvar.h.
Referenced by calc_colvar_properties, and update_extended_Lagrangian.

colvarvalue colvar::runave [protected]

Current value of the running average.

Definition at line 555 of file colvar.h.
Referenced by calc_runave, and run_ave.

size_t colvar::runave_length [protected]

Length of running average series.

Definition at line 549 of file colvar.h.
Referenced by calc_runave, and parse_analysis.

std::string colvar::runave_outfile [protected]

Name of the file to write the running average.

Definition at line 553 of file colvar.h.
Referenced by calc_runave, parse_analysis, and write_state.

size_t colvar::runave_stride [protected]

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

Definition at line 551 of file colvar.h.
Referenced by calc_runave, and parse_analysis.

cvm::real colvar::runave_variance [protected]

Current value of the square deviation from the running average.

Definition at line 557 of file colvar.h.
Referenced by calc_runave.

std::string colvar::scripted_function [protected]

Name of scripted function to be used.

Definition at line 653 of file colvar.h.
Referenced by collect_cvc_values, communicate_forces, and init.

std::vector<const colvarvalue *> colvar::sorted_cvc_values [protected]

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

Definition at line 657 of file colvar.h.
Referenced by collect_cvc_values, communicate_forces, and init.

colvarvalue colvar::upper_boundary

\brief Location of the upper boundary.

Definition at line 240 of file colvar.h.
Referenced by calc_colvar_properties, init_grid_parameters, periodic_boundaries, and update_extended_Lagrangian.

colvarvalue colvar::v_ext [protected]

Velocity of the restraint center.

Definition at line 183 of file colvar.h.
Referenced by calc_colvar_properties, init_extended_Lagrangian, read_state, read_traj, and update_extended_Lagrangian.

colvarvalue colvar::v_fdiff [protected]

Finite-difference velocity.

Definition at line 161 of file colvar.h.
Referenced by calc_colvar_properties, init, read_state, read_traj, and write_traj.

colvarvalue colvar::v_reported [protected]

Cached reported velocity.

Definition at line 175 of file colvar.h.
Referenced by calc_colvar_properties, init, read_state, read_traj, velocity, write_state, and write_traj.

std::vector<int> colvar::volmap_ids_ [protected]

Volmap numeric IDs, one for each CVC (-1 if not available).

Definition at line 680 of file colvar.h.
Referenced by get_volmap_ids.

cvm::real colvar::width

\brief 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.

Definition at line 94 of file colvar.h.
Referenced by collect_cvc_values, init_grid_parameters, and periodic_boundaries.

cvm::real colvar::wrap_center

Center of wrapping, if this variable is periodic.

Definition at line 230 of file colvar.h.
Referenced by dist2, dist2_lgrad, dist2_rgrad, init, and wrap.

colvarvalue colvar::x [protected]

Value of the colvar.

Definition at line 148 of file colvar.h.
Referenced by actual_value, calc_colvar_properties, calc_coor_acf, calc_runave, collect_cvc_values, communicate_forces, end_of_step, init, read_state, read_traj, colvar::cvc::set_value, update_extended_Lagrangian, write_state, write_traj, and write_traj_label.

colvarvalue colvar::x_ext [protected]

Restraint center.

Definition at line 179 of file colvar.h.
Referenced by calc_colvar_properties, init_extended_Lagrangian, read_state, read_traj, and update_extended_Lagrangian.

std::list< std::list<colvarvalue> > colvar::x_history [protected]

Time series of values and velocities used in running averages.

Definition at line 490 of file colvar.h.
Referenced by calc_runave.

std::list< std::list<colvarvalue> >::iterator colvar::x_history_p [protected]

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

Definition at line 493 of file colvar.h.
Referenced by calc_runave.

colvarvalue colvar::x_old [protected]

Previous value (to calculate velocities during analysis).

Definition at line 474 of file colvar.h.
Referenced by calc_colvar_properties, end_of_step, and init.

colvarvalue colvar::x_reported [protected]

Cached reported value (x may be manipulated).

Definition at line 158 of file colvar.h.
Referenced by calc_colvar_properties, init, read_state, read_traj, value, write_state, and write_traj.

colvarvalue colvar::x_restart [protected]

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

Definition at line 477 of file colvar.h.
Referenced by collect_cvc_values, init, and read_state.

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

Generated on Sun Sep 15 02:46:09 2024 for VMD (current) by

colvar Class Reference

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