\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...

virtual void

wrap (colvarvalue &x_unwrapped) const

\brief Redefined to make use of the user-provided period. More...

Protected Attributes

cvm::atom_group *

main

Main atom group. More...

cvm::atom_group *

ref1

Reference atom group. More...

cvm::atom_group *

ref2

Optional, second ref atom group. More...

cvm::rvector

axis

Vector on which the distance vector is projected. More...

cvm::real

axis_norm

Norm of the axis. More...

cvm::rvector

dist_v

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

bool

fixed_axis

Flag: using a fixed axis vector? More...

Detailed Description

\brief Colvar component: projection of the distance vector along an axis(colvarvalue::type_scalar type, range (-*:*)).

Definition at line 433 of file colvarcomp.h.

Constructor & Destructor Documentation

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

Definition at line 171 of file colvarcomp_distances.C.
References conf, colvardeps::enable, colvarmodule::error, colvardeps::f_cvc_com_based, colvardeps::f_cvc_inv_gradient, colvardeps::f_cvc_Jacobian, colvardeps::f_cvc_periodic, fixed_axis, colvarparse::get_keyval, colvar::cvc::init_total_force_params, colvardeps::is_enabled, colvarparse::key_lookup, colvarmodule::log, main, colvar::cvc::parse_group, colvar::cvc::period, colvardeps::provide, ref1, ref2, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, colvar::cvc::wrap_center, and colvar::cvc::x.
Referenced by colvar::distance_xy::distance_xy.

colvar::distance_z::distance_z ( )

Definition at line 221 of file colvarcomp_distances.C.
References colvardeps::enable, colvardeps::f_cvc_com_based, colvardeps::f_cvc_inv_gradient, colvardeps::f_cvc_Jacobian, colvardeps::provide, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_scalar, and colvar::cvc::x.

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

Definition at line 454 of file colvarcomp.h.

Member Function Documentation

void colvar::distance_z::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_xy.
Definition at line 306 of file colvarcomp_distances.C.
References force, main, colvarvalue::real_value, ref1, and ref2.

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

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

Reimplemented from colvar::cvc.
Reimplemented in colvar::distance_xy.
Definition at line 287 of file colvarcomp_distances.C.
References colvardeps::f_cvc_one_site_total_force, fixed_axis, colvar::cvc::ft, colvardeps::is_enabled, main, colvarvalue::real_value, and ref1.

void colvar::distance_z::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_xy.
Definition at line 261 of file colvarcomp_distances.C.
References axis_norm, colvardeps::f_cvc_pbc_minimum_image, colvardeps::is_enabled, main, colvarvalue::real_value, ref1, ref2, and colvar::cvc::x.

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

\brief Calculate the divergence of the inverse atomic gradients.

Reimplemented from colvar::cvc.
Reimplemented in colvar::distance_xy.
Definition at line 300 of file colvarcomp_distances.C.
References colvar::cvc::jd, and colvarvalue::real_value.

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

\brief Calculate the variable.

Implements colvar::cvc.
Reimplemented in colvar::distance_xy.
Definition at line 231 of file colvarcomp_distances.C.
References axis_norm, dist_v, colvardeps::f_cvc_pbc_minimum_image, colvardeps::is_enabled, main, colvarmodule::position_distance, colvarvalue::real_value, ref1, ref2, wrap, and colvar::cvc::x.

cvm::real colvar::distance_z::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_xy.
Definition at line 320 of file colvarcomp_distances.C.
References colvardeps::f_cvc_periodic, colvarmodule::floor, colvardeps::is_enabled, colvar::cvc::period, and colvarvalue::real_value.

colvarvalue colvar::distance_z::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_xy.
Definition at line 332 of file colvarcomp_distances.C.
References colvardeps::f_cvc_periodic, colvarmodule::floor, colvardeps::is_enabled, colvar::cvc::period, and colvarvalue::real_value.

colvarvalue colvar::distance_z::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_xy.
Definition at line 344 of file colvarcomp_distances.C.
References colvardeps::f_cvc_periodic, colvarmodule::floor, colvardeps::is_enabled, colvar::cvc::period, and colvarvalue::real_value.

void colvar::distance_z::wrap ( colvarvalue & x_unwrapped ) const [virtual]

\brief Redefined to make use of the user-provided period.

Reimplemented from colvar::cvc.
Definition at line 356 of file colvarcomp_distances.C.
References colvardeps::f_cvc_periodic, colvarmodule::floor, colvardeps::is_enabled, colvar::cvc::period, colvarvalue::real_value, and colvar::cvc::wrap_center.
Referenced by calc_value.

Member Data Documentation

cvm::rvector colvar::distance_z::axis [protected]

Vector on which the distance vector is projected.

Definition at line 444 of file colvarcomp.h.

cvm::real colvar::distance_z::axis_norm [protected]

Norm of the axis.

Definition at line 446 of file colvarcomp.h.
Referenced by colvar::distance_xy::calc_gradients, calc_gradients, colvar::distance_xy::calc_value, and calc_value.

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

Vector distance, cached to be recycled.

Definition at line 448 of file colvarcomp.h.
Referenced by colvar::distance_xy::calc_gradients, colvar::distance_xy::calc_value, and calc_value.

bool colvar::distance_z::fixed_axis [protected]

Flag: using a fixed axis vector?

Definition at line 450 of file colvarcomp.h.
Referenced by colvar::distance_xy::calc_force_invgrads, calc_force_invgrads, colvar::distance_xy::calc_value, and distance_z.

cvm::atom_group* colvar::distance_z::main [protected]

Main atom group.

Definition at line 438 of file colvarcomp.h.
Referenced by colvar::distance_xy::apply_force, apply_force, colvar::distance_xy::calc_force_invgrads, calc_force_invgrads, colvar::distance_xy::calc_gradients, calc_gradients, colvar::distance_xy::calc_value, calc_value, and distance_z.

cvm::atom_group* colvar::distance_z::ref1 [protected]

Reference atom group.

Definition at line 440 of file colvarcomp.h.
Referenced by colvar::distance_xy::apply_force, apply_force, colvar::distance_xy::calc_force_invgrads, calc_force_invgrads, colvar::distance_xy::calc_gradients, calc_gradients, colvar::distance_xy::calc_value, calc_value, and distance_z.

cvm::atom_group* colvar::distance_z::ref2 [protected]

Optional, second ref atom group.

Definition at line 442 of file colvarcomp.h.
Referenced by colvar::distance_xy::apply_force, apply_force, colvar::distance_xy::calc_gradients, calc_gradients, colvar::distance_xy::calc_value, calc_value, and distance_z.

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

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