Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/lib/colvars/colvardeps.h
a2b4a794d9a2lammm-master-deprecated

Last Change
Raw File

colvardeps.h
View Options

// -*- c++ -*-
#ifndef COLVARDEPS_H
#define COLVARDEPS_H
#include "colvarmodule.h"
#include "colvarparse.h"
/// Parent class for a member object of a bias, cv or cvc etc. containing dependencies
/// (features) and handling dependency resolution
// Some features like colvar::f_linear have no dependencies, require() doesn't enable anything but fails if unavailable
// Policy: those features are unavailable at all times
// Other features are under user control
// They are unavailable unless requested by the user, then they may be enabled subject to
// satisfied dependencies
// It seems important to have available default to false (for safety) and enabled to false (for efficiency)
class colvardeps {
public:
colvardeps() {}
virtual ~colvardeps();
// Subclasses should initialize the following members:
std::string description; // reference to object name (cv, cvc etc.)
/// This contains the current state of each feature for each object
struct feature_state {
feature_state(bool a, bool e)
: available(a), enabled(e) {}
/// Available means: supported, subject to dependencies as listed,
/// MAY BE ENABLED AS A RESULT OF DEPENDENCY SOLVING
/// Remains false for passive flags that are set based on other object properties,
/// eg. f_cv_linear
/// Is set to true upon user request for features that are implemented by the user
/// or under his/her direct control, e.g. f_cv_scripted or f_cv_extended_Lagrangian
bool available;
/// Currently enabled - this flag is subject to change dynamically
/// TODO consider implications for dependency solving: anyone who disables
/// it should trigger a refresh of parent objects
bool enabled; // see if this should be private depending on implementation
// bool enabledOnce; // this should trigger an update when object is evaluated
};
/// List of the state of all features
std::vector<feature_state *> feature_states;
/// Describes a feature and its dependecies
/// used in a static array within each subclass
class feature {
public:
feature() {}
~feature() {}
std::string description; // Set by derived object initializer
// features that this feature requires in the same object
// NOTE: we have no safety mechanism against circular dependencies, however, they would have to be internal to an object (ie. requires_self or requires_alt)
std::vector<int> requires_self;
// Features that are incompatible, ie. required disabled
// if enabled, they will cause a dependency failure (they will not be disabled)
// To enforce these dependencies regardless of the order in which they
// are enabled, they are always set in a symmetric way, so whichever is enabled
// second will cause the dependency to fail
std::vector<int> requires_exclude;
// sets of features that are required in an alternate way
// when parent feature is enabled, if none are enabled, the first one listed that is available will be enabled
std::vector<std::vector<int> > requires_alt;
// features that this feature requires in children
std::vector<int> requires_children;
};
// Accessor to array of all features with deps, static in most derived classes
// Subclasses with dynamic dependency trees may override this
// with a non-static array
// Intermediate classes (colvarbias and colvarcomp, which are also base classes)
// implement this as virtual to allow overriding
virtual std::vector<feature *>&features() = 0;
void add_child(colvardeps *child);
void remove_child(colvardeps *child);
/// Used before deleting an object, if not handled by that object's destructor
/// (useful for cvcs because their children are member objects)
void remove_all_children();
private:
// pointers to objects this object depends on
// list should be maintained by any code that modifies the object
// this could be secured by making lists of colvars / cvcs / atom groups private and modified through accessor functions
std::vector<colvardeps *> children;
// pointers to objects that depend on this object
// the size of this array is in effect a reference counter
std::vector<colvardeps *> parents;
public:
// disabling a feature f:
// if parents depend on f, tell them to refresh / check that they are ok?
// if children provide features to satisfy f ONLY, disable that
// When the state of this object has changed, recursively tell parents
// to enforce their dependencies
// void refresh_parents() {
//
// }
// std::vector<colvardeps *> parents; // Needed to trigger a refresh if capabilities of this object change
// End of members to be initialized by subclasses
// Checks whether given feature is enabled
// Defaults to querying f_*_active
inline bool is_enabled(int f = f_cv_active) const {
return feature_states[f]->enabled;
}
// Checks whether given feature is available
// Defaults to querying f_*_active
inline bool is_available(int f = f_cv_active) const {
return feature_states[f]->available;
}
void provide(int feature_id); // set the feature's flag to available in local object
/// Parse a keyword and enable a feature accordingly
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);
int enable(int f, bool dry_run = false, bool toplevel = true); // enable a feature and recursively solve its dependencies
// dry_run is set to true to recursively test if a feature is available, without enabling it
// int disable(int f);
/// 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
virtual int refresh_deps() { return COLVARS_OK; }
// NOTE that all feature enums should start with f_*_active
enum features_biases {
/// \brief Bias is active
f_cvb_active,
f_cvb_apply_force, // will apply forces
f_cvb_get_total_force, // requires total forces
f_cvb_history_dependent, // depends on simulation history
f_cvb_ntot
};
enum features_colvar {
/// \brief Calculate colvar
f_cv_active,
/// \brief Gradients are calculated and temporarily stored, so
/// that external forces can be applied
f_cv_gradient,
/// \brief Collect atomic gradient data from all cvcs into vector
/// atomic_gradient
f_cv_collect_gradient,
/// \brief Calculate the velocity with finite differences
f_cv_fdiff_velocity,
/// \brief The total force is calculated, projecting the atomic
/// forces on the inverse gradient
f_cv_total_force,
/// \brief Calculate total force from atomic forces
f_cv_total_force_calc,
/// \brief Estimate Jacobian derivative
f_cv_Jacobian,
/// \brief Do not report the Jacobian force as part of the total force
/// instead, apply a correction internally to cancel it
f_cv_hide_Jacobian,
/// \brief The variable has a harmonic restraint around a moving
/// center with fictitious mass; bias forces will be applied to
/// the center
f_cv_extended_Lagrangian,
/// \brief The extended system coordinate undergoes Langevin dynamics
f_cv_Langevin,
/// \brief Output the potential and kinetic energies
/// (for extended Lagrangian colvars only)
f_cv_output_energy,
/// \brief Output the value to the trajectory file (on by default)
f_cv_output_value,
/// \brief Output the velocity to the trajectory file
f_cv_output_velocity,
/// \brief Output the applied force to the trajectory file
f_cv_output_applied_force,
/// \brief Output the total force to the trajectory file
f_cv_output_total_force,
/// \brief A lower boundary is defined
f_cv_lower_boundary,
/// \brief An upper boundary is defined
f_cv_upper_boundary,
/// \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_grid,
/// \brief Apply a restraining potential (|x-xb|^2) to the colvar
/// when it goes below the lower wall
f_cv_lower_wall,
/// \brief Apply a restraining potential (|x-xb|^2) to the colvar
/// when it goes above the upper wall
f_cv_upper_wall,
/// \brief Compute running average
f_cv_runave,
/// \brief Compute time correlation function
f_cv_corrfunc,
/// \brief Value and gradient computed by user script
f_cv_scripted,
/// \brief Colvar is periodic
f_cv_periodic,
/// \brief is scalar
f_cv_scalar,
f_cv_linear,
f_cv_homogeneous,
/// \brief Number of colvar features
f_cv_ntot
};
enum features_cvc {
f_cvc_active,
f_cvc_scalar,
f_cvc_gradient,
f_cvc_inv_gradient,
/// \brief If enabled, calc_gradients() will call debug_gradients() for every group needed
f_cvc_debug_gradient,
f_cvc_Jacobian,
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,
/// Perform a standard minimum msd fit for given atoms
/// ie. not using refpositionsgroup
// f_ag_min_msd_fit,
f_ag_fit_gradient_group,// TODO check that these are sometimes needed separately
// maybe for minimum RMSD?
f_ag_fit_gradient_ref,
f_ag_atom_forces,
f_ag_scalable,
f_ag_scalable_com,
f_ag_ntot
};
void init_cvb_requires();
void init_cv_requires();
void init_cvc_requires();
void init_ag_requires();
/// \brief print all enabled features and those of children, for debugging
void print_state();
};
#endif
c4science · Help