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colvar::distance_pairs Class Reference

\brief Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::distance_pairs:

List of all members.

Public Methods
	distance_pairs (std::string const &conf)
	distance_pairs ()
virtual	~distance_pairs ()
virtual void	calc_value ()
	\brief Calculate the variable. More...
virtual void	calc_gradients ()
	\brief Calculate the atomic gradients, to be reused later in order to apply forces. More...
virtual void	apply_force (colvarvalue const &force)
	\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...
Protected Attributes
cvm::atom_group *	group1
	First atom group. More...
cvm::atom_group *	group2
	Second atom group. More...

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Detailed Description

\brief Colvar component: N1xN2 vector of pairwise distances (colvarvalue::type_vector type, range (0:*) for each component).

Definition at line 587 of file colvarcomp.h.

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Constructor & Destructor Documentation

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

colvar::distance_pairs::distance_pairs (    )

Definition at line 673 of file colvarcomp_distances.C. References colvardeps::disable, colvardeps::f_cvc_explicit_gradient, colvar::cvc::set_function_type, colvarvalue::type, colvarvalue::type_vector, and colvar::cvc::x.

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

Definition at line 598 of file colvarcomp.h.

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Member Function Documentation

void colvar::distance_pairs::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 718 of file colvarcomp_distances.C. References colvardeps::f_cvc_pbc_minimum_image, force, group1, group2, colvardeps::is_enabled, and colvarmodule::position_distance.

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

\brief Calculate the atomic gradients, to be reused later in order to apply forces. Reimplemented from colvar::cvc. Definition at line 712 of file colvarcomp_distances.C.

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

\brief Calculate the variable. Implements colvar::cvc. Definition at line 681 of file colvarcomp_distances.C. References colvardeps::f_cvc_pbc_minimum_image, group1, group2, colvardeps::is_enabled, colvarmodule::position_distance, colvarvalue::vector1d_value, and colvar::cvc::x.

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Member Data Documentation

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

First atom group. Definition at line 592 of file colvarcomp.h. Referenced by apply_force, and calc_value.

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

Second atom group. Definition at line 594 of file colvarcomp.h. Referenced by apply_force, and calc_value.

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

• colvarcomp.h
• colvarcomp_distances.C

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