\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

Atom group. More...

std::vector< cvm::atom_pos >

ref_pos

Reference coordinates. More...

std::vector< cvm::rvector >

eigenvec

Eigenvector (of a normal or essential mode): will always have zero center. More...

cvm::real

eigenvec_invnorm2

Inverse square norm of the eigenvector. More...

Detailed Description

\brief Colvar component: projection of 3N coordinates onto an eigenvector(colvarvalue::type_scalar type, range (-*:*)).

Definition at line 712 of file colvarcomp.h.

Constructor & Destructor Documentation

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

Constructor.

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

Definition at line 733 of file colvarcomp.h.

Member Function Documentation

void colvar::eigenvector::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.
Definition at line 1439 of file colvarcomp_distances.C.
References atoms, force, and colvarvalue::real_value.

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

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

Reimplemented from colvar::cvc.
Definition at line 1446 of file colvarcomp_distances.C.
References atoms, eigenvec_invnorm2, colvar::cvc::ft, and colvarvalue::real_value.

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

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

Reimplemented from colvar::cvc.
Definition at line 1431 of file colvarcomp_distances.C.
References atoms, and eigenvec.

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

\brief Calculate the divergence of the inverse atomic gradients.

Reimplemented from colvar::cvc.
Definition at line 1458 of file colvarcomp_distances.C.
References atoms, eigenvec, eigenvec_invnorm2, colvar::cvc::jd, colvarvalue::real_value, and colvarmodule::sqrt.

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

\brief Calculate the variable.

Implements colvar::cvc.
Definition at line 1422 of file colvarcomp_distances.C.
References atoms, eigenvec, colvarvalue::real_value, ref_pos, and colvar::cvc::x.

virtual cvm::real colvar::eigenvector::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.

virtual colvarvalue colvar::eigenvector::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.

virtual colvarvalue colvar::eigenvector::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.

Member Data Documentation

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

Atom group.

Definition at line 718 of file colvarcomp.h.
Referenced by apply_force, calc_force_invgrads, calc_gradients, calc_Jacobian_derivative, and calc_value.

std::vector<cvm::rvector> colvar::eigenvector::eigenvec [protected]

Eigenvector (of a normal or essential mode): will always have zero center.

Definition at line 724 of file colvarcomp.h.
Referenced by calc_gradients, calc_Jacobian_derivative, and calc_value.

cvm::real colvar::eigenvector::eigenvec_invnorm2 [protected]

Inverse square norm of the eigenvector.

Definition at line 727 of file colvarcomp.h.
Referenced by calc_force_invgrads, and calc_Jacobian_derivative.

std::vector<cvm::atom_pos> colvar::eigenvector::ref_pos [protected]

Reference coordinates.

Definition at line 721 of file colvarcomp.h.
Referenced by calc_value.

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

Generated on Thu Sep 19 02:45:43 2024 for VMD (current) by