colvar::distance_dir Class Reference

Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unitvector type, range [-1:1]x[-1:1]x[-1:1]). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::distance_dir:

List of all members.

Public Member Functions
	distance_dir (std::string const &conf)
	distance_dir ()
virtual	~distance_dir ()
virtual void	calc_value ()
	Calculate the variable.
virtual void	calc_gradients ()
	Calculate the atomic gradients, to be reused later in order to apply forces.
virtual void	apply_force (colvarvalue const &force)
	Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function).

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Detailed Description

Colvar component: distance unit vector (direction) between centers of mass of two groups (colvarvalue::type_unitvector type, range [-1:1]x[-1:1]x[-1:1]).

Definition at line 362 of file colvarcomp.h.

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Constructor & Destructor Documentation

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

Definition at line 412 of file colvarcomp_distances.C. References colvarvalue::type(). : distance (conf) { function_type = "distance_dir"; x.type (colvarvalue::type_unitvector); }

colvar::distance_dir::distance_dir (   )

Definition at line 420 of file colvarcomp_distances.C. References colvarvalue::type(). : distance() { function_type = "distance_dir"; x.type (colvarvalue::type_unitvector); }

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

Definition at line 368 of file colvarcomp.h. {}

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Member Function Documentation

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

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the 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 object Reimplemented from colvar::distance. Definition at line 448 of file colvarcomp_distances.C. References colvarmodule::atom_group::apply_force(), colvarmodule::atom_group::noforce, and colvarvalue::rvector_value. { // remove the radial force component cvm::real const iprod = force.rvector_value * x.rvector_value; cvm::rvector const force_tang = (1.0 - iprod) * force.rvector_value; if (!group1.noforce) group1.apply_force (-1.0 * force_tang); if (!group2.noforce) group2.apply_force ( force_tang); }

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

Calculate the atomic gradients, to be reused later in order to apply forces. Reimplemented from colvar::distance. Definition at line 442 of file colvarcomp_distances.C. { // gradients are computed on the fly within apply_force() }

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

Calculate the variable. Reimplemented from colvar::distance. Definition at line 428 of file colvarcomp_distances.C. References colvarmodule::atom_group::center_of_mass(), colvarmodule::position_distance(), colvarmodule::atom_group::read_positions(), colvarmodule::atom_group::reset_atoms_data(), colvarvalue::rvector_value, and colvarmodule::rvector::unit(). { group1.reset_atoms_data(); group2.reset_atoms_data(); group1.read_positions(); group2.read_positions(); dist_v = cvm::position_distance (group1.center_of_mass(), group2.center_of_mass()); x.rvector_value = dist_v.unit(); }

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

• colvarcomp.h
• colvarcomp_distances.C

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