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colvardeps Class Referenceabstract

Parent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution. More...

#include <colvardeps.h>

Inheritance diagram for colvardeps:
Inheritance graph


class  feature
struct  feature_state
 This contains the current state of each feature for each object. More...

Public Types

enum  features_biases {
  f_cvb_active, f_cvb_apply_force, f_cvb_get_total_force, f_cvb_history_dependent,
  f_cvb_scalar_variables, f_cvb_calc_pmf, f_cvb_ntot
enum  features_colvar {
  f_cv_active, f_cv_gradient, f_cv_collect_gradient, f_cv_fdiff_velocity,
  f_cv_total_force, f_cv_total_force_calc, f_cv_subtract_applied_force, f_cv_Jacobian,
  f_cv_hide_Jacobian, f_cv_extended_Lagrangian, f_cv_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_grid, f_cv_runave,
  f_cv_corrfunc, f_cv_scripted, f_cv_periodic, f_cv_scalar,
  f_cv_linear, f_cv_homogeneous, f_cv_ntot
enum  features_cvc {
  f_cvc_active, f_cvc_scalar, f_cvc_gradient, f_cvc_inv_gradient,
  f_cvc_debug_gradient, f_cvc_Jacobian, f_cvc_one_site_total_force, f_cvc_com_based,
  f_cvc_scalable, f_cvc_scalable_com, f_cvc_ntot
enum  features_atomgroup {
  f_ag_active, f_ag_center, f_ag_rotate, f_ag_fitting_group,
  f_ag_fit_gradient_group, f_ag_fit_gradient_ref, f_ag_atom_forces, f_ag_scalable,
  f_ag_scalable_com, f_ag_ntot

Public Member Functions

void init_feature (int feature_id, const char *description, feature_type type=f_type_not_set)
 Pair a numerical feature ID with a description and type.
bool is_dynamic (int id)
bool is_static (int id)
bool is_user (int id)
virtual std::vector< feature * > & 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)
int enable (int f, bool dry_run=false, bool toplevel=true)
virtual int refresh_deps ()
void init_cvb_requires ()
void init_cv_requires ()
void init_cvc_requires ()
void init_ag_requires ()
void print_state ()
 print all enabled features and those of children, for debugging

Public Attributes

std::string description

Protected Member Functions

bool get_keyval_feature (colvarparse *cvp, std::string const &conf, char const *key, int feature_id, bool const &def_value, colvarparse::Parse_Mode const parse_mode=colvarparse::parse_normal)
 Parse a keyword and enable a feature accordingly.

Detailed Description

Parent class for a member object of a bias, cv or cvc etc. containing features and their dependencies, and handling dependency resolution.

There are 3 kinds of features:

  1. Dynamic features are under the control of the dependency resolution system. They may be enabled or disabled depending on dependencies.
  2. User features may be enabled based on user input (they may trigger a failure upon dependency resolution, though)
  3. Static features are static properties of the object, determined programatically at initialization time.

Member Enumeration Documentation


Perform a standard minimum msd fit for given atoms ie. not using refpositionsgroup


Bias is active.


Calculate colvar.


Gradients are calculated and temporarily stored, so that external forces can be applied.


Collect atomic gradient data from all cvcs into vector atomic_gradient.


Calculate the velocity with finite differences.


The total force is calculated, projecting the atomic forces on the inverse gradient.


Calculate total force from atomic forces.


Subtract the applied force from the total force.


Estimate Jacobian derivative.


Do not report the Jacobian force as part of the total force instead, apply a correction internally to cancel it.


The variable has a harmonic restraint around a moving center with fictitious mass; bias forces will be applied to the center.


The extended system coordinate undergoes Langevin dynamics.


Output the potential and kinetic energies (for extended Lagrangian colvars only)


Output the value to the trajectory file (on by default)


Output the velocity to the trajectory file.


Output the applied force to the trajectory file.


Output the total force to the trajectory file.


A lower boundary is defined.


An upper boundary is defined.


Provide a discretization of the values of the colvar to be used by the biases or in analysis (needs lower and upper boundary)


Compute running average.


Compute time correlation function.


Value and gradient computed by user script.


Colvar is periodic.


is scalar


Number of colvar features.


If enabled, calc_gradients() will call debug_gradients() for every group needed.

Member Function Documentation

void colvardeps::provide ( int  feature_id,
bool  truefalse = true 

Set the feature's available flag, without checking To be used for dynamic properties dependencies will be checked by enable()

virtual int colvardeps::refresh_deps ( )

This function is called whenever feature states are changed outside of the object's control, that is, by parents Eventually it may also be used when properties of children change

Reimplemented in colvar.

void colvardeps::remove_all_children ( )

Used before deleting an object, if not handled by that object's destructor (useful for cvcs because their children are member objects)

void colvardeps::set_enabled ( int  feature_id,
bool  truefalse = true 

Set the feature's enabled flag, without dependency check or resolution To be used for static properties only Checking for availability is up to the caller

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