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colvardeps Class Reference

\brief 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 programmatically at initialization time. The following diagram summarizes the dependency tree at the bias, colvar, and colvarcomp levels. Isolated and atom group features are not shown to save space. More...

#include <colvardeps.h>

Inheritance diagram for colvardeps:

colvar colvar::cvc colvarbias colvarbias_restraint_moving colvarmodule::atom_group colvar::alch_Flambda colvar::alch_lambda colvar::alpha_angles colvar::angle colvar::cartesian colvar::componentDisabled colvar::coordnum colvar::dihedPC colvar::dihedral colvar::dipole_angle colvar::dipole_magnitude colvar::distance colvar::distance_inv colvar::distance_pairs colvar::distance_z colvar::eigenvector colvar::gyration colvar::h_bond colvar::map_total colvar::orientation colvar::polar_phi colvar::polar_theta colvar::rmsd colvar::selfcoordnum colvarbias_abf colvarbias_alb colvarbias_histogram colvarbias_meta colvarbias_restraint colvarbias_restraint_histogram colvarbias_ti colvarbias_restraint_centers_moving colvarbias_restraint_k_moving List of all members.

Public Types

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_ntot
}
enum  features_colvar {
  f_cv_active, f_cv_awake, f_cv_gradient, f_cv_collect_gradient,
  f_cv_collect_atom_ids, f_cv_fdiff_velocity, f_cv_total_force, f_cv_total_force_calc,
  f_cv_subtract_applied_force, f_cv_Jacobian, f_cv_hide_Jacobian, f_cv_extended_Lagrangian,
  f_cv_external, f_cv_Langevin, f_cv_output_energy, f_cv_output_value,
  f_cv_output_velocity, f_cv_output_applied_force, f_cv_output_total_force, f_cv_lower_boundary,
  f_cv_upper_boundary, f_cv_hard_lower_boundary, f_cv_hard_upper_boundary, f_cv_reflecting_lower_boundary,
  f_cv_reflecting_upper_boundary, f_cv_grid, f_cv_runave, f_cv_corrfunc,
  f_cv_scripted, f_cv_custom_function, f_cv_periodic, f_cv_single_cvc,
  f_cv_scalar, f_cv_linear, f_cv_homogeneous, f_cv_multiple_ts,
  f_cv_ntot
}
enum  features_cvc {
  f_cvc_active, f_cvc_scalar, f_cvc_periodic, f_cvc_width,
  f_cvc_lower_boundary, f_cvc_upper_boundary, f_cvc_gradient, f_cvc_explicit_gradient,
  f_cvc_inv_gradient, f_cvc_Jacobian, f_cvc_one_site_total_force, f_cvc_debug_gradient,
  f_cvc_pbc_minimum_image, f_cvc_com_based, f_cvc_scalable, f_cvc_scalable_com,
  f_cvc_collect_atom_ids, f_cvc_ntot
}
enum  features_atomgroup {
  f_ag_active, f_ag_center, f_ag_center_origin, f_ag_rotate,
  f_ag_fitting_group, f_ag_explicit_gradient, f_ag_fit_gradients, f_ag_atom_forces,
  f_ag_scalable, f_ag_scalable_com, f_ag_collect_atom_ids, f_ag_ntot
}

Public Methods

 colvardeps ()
virtual ~colvardeps ()
int get_time_step_factor () const
 \brief returns time_step_factor. More...

void init_feature (int feature_id, const char *description, feature_type type)
 Pair a numerical feature ID with a description and type. More...

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

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

void set_enabled (int feature_id, bool truefalse=true)
 Enable or disable, depending on flag value. More...

int enable (int f, bool dry_run=false, bool toplevel=true)
 Enable a feature and recursively solve its dependencies. For accurate reference counting, do not add spurious calls to enable()
Parameters:
dry_run  Recursively test whether a feature is available, without enabling it
toplevel  False if this is called as part of a chain of dependency resolution. This is used to diagnose failed dependencies by displaying the full stack: only the toplevel dependency will throw a fatal error.
 More...

int disable (int f)
 Disable a feature, decrease the reference count of its dependencies and recursively disable them as applicable. More...

void free_children_deps ()
 disable all enabled features to free their dependencies to be done when deleting the object Cannot be in the base class destructor because it needs the derived class features(). More...

void restore_children_deps ()
 re-enable children features (to be used when object becomes active). More...

int decr_ref_count (int f)
 Decrement the reference count of a feature disabling it if it's dynamic and count reaches zero. More...

virtual void do_feature_side_effects (int)
 Implements possible actions to be carried out when a given feature is enabled Base function does nothing, can be overloaded. More...

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. More...

void exclude_feature_self (int f, int g)
 Make features f and g mutually exclusive within the same object. More...

void require_feature_children (int f, int g)
 Make feature f require feature g within children. More...

void require_feature_alt (int f, int g, int h)
 Make feature f require either g or h within the same object. More...

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. More...

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. More...

void print_state ()
 \brief print all enabled features and those of children, for debugging. More...

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


Public Attributes

std::string description

Protected Types

enum  feature_type { f_type_not_set, f_type_dynamic, f_type_user, f_type_static }
 Enum of possible feature types. More...


Protected Methods

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. More...


Protected Attributes

int time_step_factor
 Time step multiplier (for coarse-timestep biases & colvars) Biases and colvars will only be calculated at those times (f_cvb_awake and f_cv_awake); a Biases use this to apply "impulse" biasing forces at the outer timestep Unused by lower-level objects (cvcs and atom groups). More...

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

Detailed Description

\brief 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 programmatically at initialization time. The following diagram summarizes the dependency tree at the bias, colvar, and colvarcomp levels. Isolated and atom group features are not shown to save space.

Definition at line 34 of file colvardeps.h.

Member Enumeration Documentation

enum colvardeps::feature_type [protected]
 

Enum of possible feature types.

Enumeration values:
f_type_not_set 
f_type_dynamic 
f_type_user 
f_type_static 

Definition at line 83 of file colvardeps.h.

enum colvardeps::features_atomgroup
 

Enumeration values:
f_ag_active 
f_ag_center 
f_ag_center_origin 
f_ag_rotate 
f_ag_fitting_group 
f_ag_explicit_gradient  \brief Does not have explicit atom gradients from parent CVC.
f_ag_fit_gradients 
f_ag_atom_forces 
f_ag_scalable 
f_ag_scalable_com 
f_ag_collect_atom_ids  \brief Build list of atoms involved in atom group.
f_ag_ntot 

Definition at line 385 of file colvardeps.h.

enum colvardeps::features_biases
 

Enumeration values:
f_cvb_active  \brief Bias is active.
f_cvb_awake  \brief Bias is awake (active on its own accord) this timestep.
f_cvb_step_zero_data  Accumulates data starting from step 0 of a simulation run.
f_cvb_apply_force  \brief will apply forces.
f_cvb_bypass_ext_lagrangian  \brief force this bias to act on actual value for extended-Lagrangian coordinates.
f_cvb_get_total_force  \brief requires total forces.
f_cvb_output_acc_work  \brief whether this bias should record the accumulated work.
f_cvb_history_dependent  \brief depends on simulation history.
f_cvb_time_dependent  \brief depends on time.
f_cvb_scalar_variables  \brief requires scalar colvars.
f_cvb_calc_pmf  \brief whether this bias will compute a PMF.
f_cvb_calc_ti_samples  \brief whether this bias will compute TI samples.
f_cvb_write_ti_samples  \brief whether this bias will write TI samples.
f_cvb_write_ti_pmf  \brief whether this bias should write the TI PMF.
f_cvb_scale_biasing_force  \brief whether this bias uses an external grid to scale the biasing forces.
f_cvb_ntot 

Definition at line 225 of file colvardeps.h.

enum colvardeps::features_colvar
 

Enumeration values:
f_cv_active  \brief Calculate colvar.
f_cv_awake  \brief Colvar is awake (active on its own accord) this timestep.
f_cv_gradient  \brief Gradients are calculated and temporarily stored, so that external forces can be applied.
f_cv_collect_gradient  \brief Collect atomic gradient data from all cvcs into vector atomic_gradient.
f_cv_collect_atom_ids  \brief Build list of atoms involved in CV calculation.
f_cv_fdiff_velocity  \brief Calculate the velocity with finite differences.
f_cv_total_force  \brief The total force is calculated, projecting the atomic forces on the inverse gradient.
f_cv_total_force_calc  \brief Calculate total force from atomic forces.
f_cv_subtract_applied_force  \brief Subtract the applied force from the total force.
f_cv_Jacobian  \brief Estimate Jacobian derivative.
f_cv_hide_Jacobian  \brief Do not report the Jacobian force as part of the total force instead, apply a correction internally to cancel it.
f_cv_extended_Lagrangian  \brief The variable has a harmonic restraint around a moving center with fictitious mass; bias forces will be applied to the center.
f_cv_external  \brief An extended variable that sets an external variable in the back-end (eg. an alchemical coupling parameter for lambda-dynamics) Can have a single component.
f_cv_Langevin  \brief The extended system coordinate undergoes Langevin dynamics.
f_cv_output_energy  \brief Output the potential and kinetic energies (for extended Lagrangian colvars only).
f_cv_output_value  \brief Output the value to the trajectory file (on by default).
f_cv_output_velocity  \brief Output the velocity to the trajectory file.
f_cv_output_applied_force  \brief Output the applied force to the trajectory file.
f_cv_output_total_force  \brief Output the total force to the trajectory file.
f_cv_lower_boundary  \brief A lower boundary is defined.
f_cv_upper_boundary  \brief An upper boundary is defined.
f_cv_hard_lower_boundary  \brief The lower boundary is not defined from user's choice.
f_cv_hard_upper_boundary  \brief The upper boundary is not defined from user's choice.
f_cv_reflecting_lower_boundary  \brief Reflecting lower boundary condition.
f_cv_reflecting_upper_boundary  \brief Reflecting upper boundary condition.
f_cv_grid  \brief Provide a discretization of the values of the colvar to be used by the biases or in analysis (needs lower and upper boundary).
f_cv_runave  \brief Compute running average.
f_cv_corrfunc  \brief Compute time correlation function.
f_cv_scripted  \brief Value and gradient computed by user script.
f_cv_custom_function  \brief Value and gradient computed by user function through Lepton.
f_cv_periodic  \brief Colvar is periodic.
f_cv_single_cvc  \brief The colvar has only one component.
f_cv_scalar  \brief is scalar.
f_cv_linear 
f_cv_homogeneous 
f_cv_multiple_ts  \brief multiple timestep through time_step_factor.
f_cv_ntot  \brief Number of colvar features.

Definition at line 259 of file colvardeps.h.

enum colvardeps::features_cvc
 

Enumeration values:
f_cvc_active  Computation of this CVC is enabled.
f_cvc_scalar  This CVC computes a scalar value.
f_cvc_periodic  Values of this CVC lie in a periodic interval.
f_cvc_width  This CVC provides a default value for the colvar's width.
f_cvc_lower_boundary  This CVC provides a default value for the colvar's lower boundary.
f_cvc_upper_boundary  This CVC provides a default value for the colvar's upper boundary.
f_cvc_gradient  CVC calculates atom gradients.
f_cvc_explicit_gradient  CVC calculates and stores explicit atom gradients on rank 0.
f_cvc_inv_gradient  CVC calculates and stores inverse atom gradients (used for total force).
f_cvc_Jacobian  CVC calculates the Jacobian term of the total-force expression.
f_cvc_one_site_total_force  The total force for this CVC will be computed from one group only.
f_cvc_debug_gradient  calc_gradients() will call debug_gradients() for every group needed.
f_cvc_pbc_minimum_image  With PBCs, minimum-image convention will be used for distances (does not affect the periodicity of CVC values, e.g. angles).
f_cvc_com_based  This CVC is a function of centers of mass.
f_cvc_scalable  This CVC can be computed in parallel.
f_cvc_scalable_com  Centers-of-mass used in this CVC can be computed in parallel.
f_cvc_collect_atom_ids  \brief Build list of atoms involved in CVC calculation.
f_cvc_ntot  Number of CVC features.

Definition at line 345 of file colvardeps.h.

Constructor & Destructor Documentation

colvardeps::colvardeps (    ) 
 

Definition at line 16 of file colvardeps.C.

References time_step_factor.

colvardeps::~colvardeps (    )  [virtual]
 

Definition at line 22 of file colvardeps.C.

References description, colvarmodule::log, and remove_all_children.

Member Function Documentation

void colvardeps::add_child (  colvardeps *    child ) 
 

Definition at line 450 of file colvardeps.C.

References colvarmodule::debug, colvarmodule::decrease_depth, enable, feature_states, features, colvarmodule::increase_depth, is_enabled, colvarmodule::log, and parents.

Referenced by colvarbias::add_colvar, colvar::init_components, and colvar::cvc::register_atom_group.

void colvardeps::check_enabled (  int    f,
std::string const &    reason
)  const [inline]
 

\brief Check that a feature is enabled, raising COLVARS_BUG_ERROR if not.

Definition at line 430 of file colvardeps.h.

References COLVARS_BUG_ERROR, description, colvarmodule::error, features, and is_enabled.

Referenced by colvar::add_bias_force.

int colvardeps::decr_ref_count (  int    f ) 
 

Decrement the reference count of a feature disabling it if it's dynamic and count reaches zero.

Definition at line 357 of file colvardeps.C.

References COLVARS_ERROR, colvarmodule::debug, description, disable, colvarmodule::error, feature, feature_states, features, and colvarmodule::log.

Referenced by disable.

int colvardeps::disable (  int    f ) 
 

Disable a feature, decrease the reference count of its dependencies and recursively disable them as applicable.

Definition at line 294 of file colvardeps.C.

References COLVARS_ERROR, colvarmodule::debug, decr_ref_count, colvarmodule::decrease_depth, description, colvarmodule::error, feature, feature_states, features, free_children_deps, colvarmodule::increase_depth, is_enabled, and colvarmodule::log.

Referenced by colvar::alch_lambda::alch_lambda, decr_ref_count, colvar::distance_dir::distance_dir, colvar::distance_pairs::distance_pairs, colvar::distance_vec::distance_vec, colvar::cvc::init, colvar::init_grid_parameters, colvar::orientation::orientation, colvar::cvc::parse_group, set_enabled, and simple_scalar_dist_functions.

virtual void colvardeps::do_feature_side_effects (  int    )  [inline, virtual]
 

Implements possible actions to be carried out when a given feature is enabled Base function does nothing, can be overloaded.

Reimplemented in colvar.

Definition at line 222 of file colvardeps.h.

Referenced by enable.

int colvardeps::enable (  int    f,
bool    dry_run = false,
bool    toplevel = true
) 
 

Enable a feature and recursively solve its dependencies. For accurate reference counting, do not add spurious calls to enable()

Parameters:
dry_run  Recursively test whether a feature is available, without enabling it
toplevel  False if this is called as part of a chain of dependency resolution. This is used to diagnose failed dependencies by displaying the full stack: only the toplevel dependency will throw a fatal error.

Definition at line 125 of file colvardeps.C.

References COLVARS_ERROR, colvarmodule::debug, colvarmodule::decrease_depth, description, do_feature_side_effects, colvarmodule::error, feature, feature_states, features, colvarmodule::increase_depth, is_dynamic, is_enabled, is_static, is_user, colvarmodule::log, and restore_children_deps.

Referenced by add_child, colvar::alpha_angles::alpha_angles, colvar::angle::angle, colvar::dihedPC::dihedPC, colvar::dihedral::dihedral, colvar::distance::distance, colvar::distance_dir::distance_dir, colvar::distance_vec::distance_vec, colvar::distance_xy::distance_xy, colvar::distance_z::distance_z, colvar::euler_phi::euler_phi, colvar::euler_psi::euler_psi, colvar::euler_theta::euler_theta, colvar::cvc::init, colvarbias_restraint_histogram::init, colvarbias_restraint_harmonic_walls::init, colvarbias_restraint::init, colvarbias_meta::init, colvarbias_histogram::init, colvarbias_alb::init, colvarbias_abf::init, colvarbias_ti::init, colvarbias::init, colvar::init, colvar::cvc::init_as_distance, colvar::cvc::init_as_periodic_angle, colvar::cvc::init_dependencies, colvar::init_extended_Lagrangian, colvar::init_grid_parameters, colvar::init_output_flags, colvar::cvc::init_scalar_boundaries, colvar::orientation_angle::orientation_angle, colvar::parse_analysis, colvar::cvc::parse_group, colvar::polar_theta::polar_theta, set_enabled, simple_scalar_dist_functions, and colvar::spin_angle::spin_angle.

void colvardeps::exclude_feature_self (  int    f,
int    g
) 
 

Make features f and g mutually exclusive within the same object.

Definition at line 396 of file colvardeps.C.

References features.

Referenced by colvar::cvc::init_dependencies, colvarbias::init_dependencies, and colvar::init_dependencies.

virtual const std::vector<feature *>& colvardeps::features (    )  const [pure virtual]
 

Implemented in colvar.

Referenced by add_child, check_enabled, decr_ref_count, disable, enable, exclude_feature_self, free_children_deps, get_keyval_feature, is_dynamic, is_not_set, is_static, is_user, print_state, require_feature_alt, require_feature_children, require_feature_self, and restore_children_deps.

void colvardeps::free_children_deps (    ) 
 

disable all enabled features to free their dependencies to be done when deleting the object Cannot be in the base class destructor because it needs the derived class features().

Definition at line 43 of file colvardeps.C.

References colvarmodule::debug, colvarmodule::decrease_depth, description, feature_states, features, colvarmodule::increase_depth, is_enabled, and colvarmodule::log.

Referenced by colvarbias::clear, disable, and colvar::cvc::~cvc.

bool colvardeps::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
)  [protected]
 

Parse a keyword and enable a feature accordingly.

Definition at line 107 of file colvardeps.C.

References conf, description, colvarmodule::error, features, colvarparse::get_keyval, is_user, colvarparse::Parse_Mode, and set_enabled.

Referenced by colvar::cvc::init, colvarbias_restraint_moving::init, colvarbias_abf::init, colvarbias_ti::init, colvarbias::init, colvar::init_extended_Lagrangian, colvar::init_grid_parameters, colvar::init_output_flags, and colvar::cvc::init_total_force_params.

int colvardeps::get_time_step_factor (    )  const [inline]
 

\brief returns time_step_factor.

Definition at line 92 of file colvardeps.h.

References time_step_factor.

Referenced by colvarbias_abf::init.

virtual int colvardeps::init_dependencies (    )  [pure virtual]
 

Initialize dependency tree for object of a derived class.

Implemented in colvar.

void colvardeps::init_feature (  int    feature_id,
const char *    description,
feature_type    type
) 
 

Pair a numerical feature ID with a description and type.

Definition at line 383 of file colvardeps.C.

References modify_features.

Referenced by colvar::cvc::init_dependencies, colvarbias::init_dependencies, and colvar::init_dependencies.

bool colvardeps::is_available (  int    f = f_cv_active )  const [inline]
 

Definition at line 173 of file colvardeps.h.

References f_cv_active, and feature_states.

Referenced by colvar::cvc::parse_group.

bool colvardeps::is_dynamic (  int    id )  [inline]
 

Definition at line 133 of file colvardeps.h.

References f_type_dynamic, and features.

Referenced by enable, and colvar::cvc::init_dependencies.

bool colvardeps::is_enabled (  int    f = f_cv_active )  const [inline]
 

Definition at line 167 of file colvardeps.h.

References f_cv_active, and feature_states.

Referenced by add_child, colvar::analyze, colvar::applied_force, colvar::distance_pairs::apply_force, colvar::calc, colvar::calc_colvar_properties, colvar::calc_cvc_Jacobians, colvar::calc_cvc_total_force, colvar::distance_xy::calc_force_invgrads, colvar::distance_z::calc_force_invgrads, colvar::distance::calc_force_invgrads, colvar::dihedral::calc_force_invgrads, colvar::angle::calc_force_invgrads, colvar::distance_xy::calc_gradients, colvar::distance_z::calc_gradients, colvar::map_total::calc_value, colvar::orientation::calc_value, colvar::distance_pairs::calc_value, colvar::distance_inv::calc_value, colvar::distance_dir::calc_value, colvar::distance_xy::calc_value, colvar::distance_z::calc_value, colvar::distance_vec::calc_value, colvar::distance::calc_value, colvar::selfcoordnum::calc_value, colvar::coordnum::calc_value, colvar::dihedral::calc_value, colvar::dipole_angle::calc_value, colvar::angle::calc_value, colvarbias::can_accumulate_data, check_enabled, colvar::collect_cvc_gradients, colvar::collect_cvc_Jacobians, colvar::collect_cvc_total_forces, colvar::collect_cvc_values, colvarbias_restraint_harmonic_walls::colvar_distance, colvarbias::communicate_forces, colvar::communicate_forces, colvar::coordnum::coordnum, colvar::cvc_param_exists, disable, colvar::distance_z::dist2, colvar::dist2, colvar::distance_z::dist2_lgrad, colvar::dist2_lgrad, colvar::distance_z::dist2_rgrad, colvar::dist2_rgrad, colvar::distance_inv::distance_inv, colvar::distance_z::distance_z, enable, colvar::end_of_step, free_children_deps, colvar::get_cvc_param, colvar::get_cvc_param_grad, colvar::get_cvc_param_ptr, colvarbias_restraint_k_moving::get_state_params, colvarbias_restraint_centers_moving::get_state_params, colvar::cvc::init, colvarbias_restraint_moving::init, colvarbias_histogram::init, colvarbias_abf::init, colvarbias_ti::init, colvarbias::init, colvar::init, colvar::init_extended_Lagrangian, colvar::init_grid_parameters, colvarbias_ti::init_grids, colvar::cvc::init_total_force_params, colvar::cvc::parse_group, colvar::periodic_boundaries, print_state, colvar::read_state, colvarbias_ti::read_state_data, colvar::read_traj, restore_children_deps, colvar::set_cvc_param, colvar::cvc::set_param, colvarbias_restraint_k_moving::set_state_params, colvarbias_restraint_centers_moving::set_state_params, simple_scalar_dist_functions, colvarbias_abf::update, colvarbias_restraint_k_moving::update_acc_work, colvarbias_restraint_centers_moving::update_acc_work, colvarbias_meta::update_bias, colvar::update_extended_Lagrangian, colvar::update_forces_energy, colvarbias_meta::update_replicas_registry, colvarbias_ti::update_system_forces, colvar::distance_z::wrap, colvar::wrap, colvarbias_ti::write_output_files, colvar::write_output_files, colvar::write_state, colvarbias_ti::write_state_data, colvarbias_restraint_k_moving::write_traj, colvarbias_restraint_centers_moving::write_traj, colvar::write_traj, colvarbias_restraint_k_moving::write_traj_label, colvarbias_restraint_centers_moving::write_traj_label, and colvar::write_traj_label.

bool colvardeps::is_not_set (  int    id )  [inline]
 

Definition at line 132 of file colvardeps.h.

References f_type_not_set, and features.

Referenced by colvar::cvc::init_dependencies, colvarbias::init_dependencies, and colvar::init_dependencies.

bool colvardeps::is_static (  int    id )  [inline]
 

Definition at line 134 of file colvardeps.h.

References f_type_static, and features.

Referenced by enable.

bool colvardeps::is_user (  int    id )  [inline]
 

Definition at line 135 of file colvardeps.h.

References f_type_user, and features.

Referenced by enable, and get_keyval_feature.

virtual std::vector<feature *>& colvardeps::modify_features (    )  [pure virtual]
 

Implemented in colvar.

Referenced by init_feature.

void colvardeps::print_state (    ) 
 

\brief print all enabled features and those of children, for debugging.

Definition at line 431 of file colvardeps.C.

References colvarmodule::decrease_depth, description, feature_states, features, colvarmodule::increase_depth, is_enabled, colvarmodule::log, and colvarmodule::to_str.

Referenced by colvarbias::init.

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().

Definition at line 93 of file colvardeps.C.

References feature_states.

Referenced by colvar::angle::angle, colvarbias_histogram::colvarbias_histogram, colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls, colvarbias_ti::colvarbias_ti, colvar::dihedral::dihedral, colvar::distance::distance, colvar::distance_xy::distance_xy, colvar::distance_z::distance_z, and colvar::cvc::init_total_force_params.

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).

Definition at line 502 of file colvardeps.C.

References description, and colvarmodule::error.

Referenced by colvar::~colvar, ~colvardeps, and colvar::cvc::~cvc.

void colvardeps::remove_child (  colvardeps *    child ) 
 

Definition at line 474 of file colvardeps.C.

References description, colvarmodule::error, and parents.

void colvardeps::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.

Definition at line 422 of file colvardeps.C.

References features.

void colvardeps::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.

Definition at line 414 of file colvardeps.C.

References features.

void colvardeps::require_feature_alt (  int    f,
int    g,
int    h
) 
 

Make feature f require either g or h within the same object.

Definition at line 407 of file colvardeps.C.

References features.

Referenced by colvar::init_dependencies.

void colvardeps::require_feature_children (  int    f,
int    g
) 
 

Make feature f require feature g within children.

Definition at line 402 of file colvardeps.C.

References features.

Referenced by colvar::cvc::init_dependencies, colvarbias::init_dependencies, and colvar::init_dependencies.

void colvardeps::require_feature_self (  int    f,
int    g
) 
 

Make feature f require feature g within the same object.

Definition at line 390 of file colvardeps.C.

References features.

Referenced by colvar::cvc::init_dependencies, colvarbias::init_dependencies, and colvar::init_dependencies.

void colvardeps::restore_children_deps (    ) 
 

re-enable children features (to be used when object becomes active).

Definition at line 73 of file colvardeps.C.

References colvarmodule::debug, colvarmodule::decrease_depth, description, feature_states, features, colvarmodule::increase_depth, is_enabled, and colvarmodule::log.

Referenced by enable.

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

Enable or disable, depending on flag value.

Definition at line 98 of file colvardeps.C.

References disable, and enable.

Referenced by colvarbias_restraint_harmonic_walls::colvarbias_restraint_harmonic_walls, get_keyval_feature, and colvar::init.

Member Data Documentation

std::string colvardeps::description
 

Definition at line 42 of file colvardeps.h.

Referenced by check_enabled, colvar::colvar, colvarbias::colvarbias, colvar::cvc::cvc, colvar::cvc::debug_gradients, decr_ref_count, disable, enable, free_children_deps, get_keyval_feature, colvar::cvc::init, colvarbias_abf::init, colvarbias::init, colvar::init, colvar::cvc::init_dependencies, colvarbias::init_dependencies, colvar::init_dependencies, print_state, remove_all_children, remove_child, restore_children_deps, colvar::cvc::setup, colvar::update_extended_Lagrangian, and ~colvardeps.

std::vector<feature_state> colvardeps::feature_states [protected]
 

List of the states of all features.

Definition at line 80 of file colvardeps.h.

Referenced by add_child, colvarbias_abf::colvarbias_abf, colvarbias_ti::colvarbias_ti, decr_ref_count, disable, enable, free_children_deps, colvar::cvc::init_dependencies, colvarbias::init_dependencies, colvar::init_dependencies, is_available, is_enabled, print_state, provide, and restore_children_deps.

int colvardeps::time_step_factor [protected]
 

Time step multiplier (for coarse-timestep biases & colvars) Biases and colvars will only be calculated at those times (f_cvb_awake and f_cv_awake); a Biases use this to apply "impulse" biasing forces at the outer timestep Unused by lower-level objects (cvcs and atom groups).

Definition at line 77 of file colvardeps.h.

Referenced by colvarbias::colvarbias, colvardeps, colvarbias::communicate_forces, get_time_step_factor, colvarbias_abf::init, colvarbias::init, colvar::init, colvar::init_extended_Lagrangian, colvar::init_grid_parameters, colvar::update_extended_Lagrangian, and colvar::update_forces_energy.

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