\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 *

group1

First atom group. More...

cvm::atom_group *

group2

Second atom group. More...

cvm::rvector

dist_v

Vector distance, cached to be recycled. More...

Detailed Description

\brief Colvar component: distance between the centers of mass of two groups (colvarvalue::type_scalar type, range [0:*)).

Definition at line 350 of file colvarcomp.h.

Constructor & Destructor Documentation

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

Definition at line 20 of file colvarcomp_distances.C.
References conf, colvardeps::enable, colvardeps::f_cvc_com_based, colvardeps::f_cvc_inv_gradient, colvardeps::f_cvc_Jacobian, group1, group2, colvar::cvc::init_as_distance, colvar::cvc::init_total_force_params, colvar::cvc::parse_group, colvardeps::provide, and colvar::cvc::set_function_type.

colvar::distance::distance ( )

Definition at line 37 of file colvarcomp_distances.C.
References colvardeps::enable, colvardeps::f_cvc_com_based, colvardeps::f_cvc_inv_gradient, colvardeps::f_cvc_Jacobian, colvar::cvc::init_as_distance, colvardeps::provide, and colvar::cvc::set_function_type.

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

Definition at line 363 of file colvarcomp.h.

Member Function Documentation

void colvar::distance::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::distance_vec.
Definition at line 87 of file colvarcomp_distances.C.
References force, group1, group2, and colvarvalue::real_value.

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

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

Reimplemented from colvar::cvc.
Definition at line 69 of file colvarcomp_distances.C.
References dist_v, colvardeps::f_cvc_one_site_total_force, colvar::cvc::ft, group1, group2, colvardeps::is_enabled, and colvarvalue::real_value.

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

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

Reimplemented from colvar::cvc.
Reimplemented in colvar::distance_vec.
Definition at line 61 of file colvarcomp_distances.C.
References dist_v, group1, and group2.

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

\brief Calculate the divergence of the inverse atomic gradients.

Reimplemented from colvar::cvc.
Definition at line 81 of file colvarcomp_distances.C.
References colvar::cvc::jd, colvarvalue::real_value, and colvar::cvc::x.

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

\brief Calculate the variable.

Implements colvar::cvc.
Reimplemented in colvar::distance_vec.
Definition at line 49 of file colvarcomp_distances.C.
References dist_v, colvardeps::f_cvc_pbc_minimum_image, group1, group2, colvardeps::is_enabled, colvarmodule::position_distance, colvarvalue::real_value, and colvar::cvc::x.

virtual cvm::real colvar::distance::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::distance_vec.

virtual colvarvalue colvar::distance::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::distance_vec.

virtual colvarvalue colvar::distance::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::distance_vec.

Member Data Documentation

cvm::rvector colvar::distance::dist_v [protected]

Vector distance, cached to be recycled.

Definition at line 359 of file colvarcomp.h.
Referenced by calc_force_invgrads, calc_gradients, colvar::distance_dir::calc_value, and calc_value.

cvm::atom_group* colvar::distance::group1 [protected]

First atom group.

Definition at line 355 of file colvarcomp.h.
Referenced by colvar::distance_dir::apply_force, colvar::distance_vec::apply_force, apply_force, colvar::groupcoordnum::apply_force, calc_force_invgrads, calc_gradients, colvar::groupcoordnum::calc_gradients, colvar::distance_dir::calc_value, colvar::distance_vec::calc_value, calc_value, colvar::groupcoordnum::calc_value, and distance.

cvm::atom_group* colvar::distance::group2 [protected]

Second atom group.

Definition at line 357 of file colvarcomp.h.
Referenced by colvar::distance_dir::apply_force, colvar::distance_vec::apply_force, apply_force, colvar::groupcoordnum::apply_force, calc_force_invgrads, calc_gradients, colvar::groupcoordnum::calc_gradients, colvar::distance_dir::calc_value, colvar::distance_vec::calc_value, calc_value, colvar::groupcoordnum::calc_value, and distance.

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

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