\brief Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) Note: multiple calls to this function within the same simulation step will add the forces altogether
Parameters:

cvforce The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object.

More...

virtual cvm::real

dist2 (colvarvalue const &x1, colvarvalue const &x2) const

\brief Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities) colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the colvarvalue types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the colvarvalue member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar colvarvalue type. More...

virtual colvarvalue

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

\brief Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). More...

virtual colvarvalue

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

\brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). More...

Protected Attributes

cvm::atom_group *

atoms

Atoms involved. More...

Detailed Description

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

Definition at line 637 of file colvarcomp.h.

Constructor & Destructor Documentation

colvar::gyration::gyration ( std::string const & conf )

virtual colvar::gyration::~gyration ( ) [inline, virtual]

Definition at line 645 of file colvarcomp.h.

Member Function Documentation

void colvar::gyration::apply_force ( colvarvalue const & force ) [virtual]

\brief Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the ft member is not altered by this function) Note: multiple calls to this function within the same simulation step will add the forces altogether
Parameters:

cvforce The collective variable force, usually coming from the biases and eventually manipulated by the parent colvar object.

Implements colvar::cvc.
Reimplemented in colvar::inertia.
Definition at line 860 of file colvarcomp_distances.C.
References atoms, force, and colvarvalue::real_value.

void colvar::gyration::calc_force_invgrads ( ) [virtual]

\brief Calculate the total force from the system using the inverse atomic gradients.

Reimplemented from colvar::cvc.
Definition at line 841 of file colvarcomp_distances.C.
References atoms, colvar::cvc::ft, colvarvalue::real_value, and colvar::cvc::x.

void colvar::gyration::calc_gradients ( ) [virtual]

\brief Calculate the atomic gradients, to be reused later in order to apply forces.

Reimplemented from colvar::cvc.
Reimplemented in colvar::inertia.
Definition at line 832 of file colvarcomp_distances.C.
References atoms, colvarmodule::real, colvarvalue::real_value, and colvar::cvc::x.

void colvar::gyration::calc_Jacobian_derivative ( ) [virtual]

\brief Calculate the divergence of the inverse atomic gradients.

Reimplemented from colvar::cvc.
Definition at line 854 of file colvarcomp_distances.C.
References atoms, colvar::cvc::jd, colvarmodule::real, colvarvalue::real_value, and colvar::cvc::x.

void colvar::gyration::calc_value ( ) [virtual]

\brief Calculate the variable.

Implements colvar::cvc.
Reimplemented in colvar::inertia.
Definition at line 822 of file colvarcomp_distances.C.
References atoms, colvarvalue::real_value, colvarmodule::sqrt, and colvar::cvc::x.

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

colvarvalue const & x2

) const [virtual]

\brief Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities) colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the colvarvalue types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the colvarvalue member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar colvarvalue type.

Reimplemented from colvar::cvc.
Reimplemented in colvar::inertia.

virtual colvarvalue colvar::gyration::dist2_lgrad ( colvarvalue const & x1,

colvarvalue const & x2

) const [virtual]

\brief Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::cvc.
Reimplemented in colvar::inertia.

virtual colvarvalue colvar::gyration::dist2_rgrad ( colvarvalue const & x1,

colvarvalue const & x2

) const [virtual]

\brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).

Reimplemented from colvar::cvc.
Reimplemented in colvar::inertia.

Member Data Documentation

cvm::atom_group* colvar::gyration::atoms [protected]

Atoms involved.

Definition at line 642 of file colvarcomp.h.
Referenced by colvar::inertia_z::apply_force, colvar::inertia::apply_force, apply_force, calc_force_invgrads, colvar::inertia_z::calc_gradients, colvar::inertia::calc_gradients, calc_gradients, calc_Jacobian_derivative, colvar::inertia_z::calc_value, colvar::inertia::calc_value, and calc_value.

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

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