colvar::distance Class Reference

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

#include <colvarcomp.h>

Inheritance diagram for colvar::distance:

List of all members.

Public Member Functions
	distance (std::string const &conf)
	distance ()
virtual	~distance ()
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	calc_force_invgrads ()
	Calculate the total force from the system using the inverse atomic gradients.
virtual void	calc_Jacobian_derivative ()
	Calculate the divergence of the inverse atomic gradients.
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).
virtual cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const
	Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual cvm::real	compare (colvarvalue const &x1, colvarvalue const &x2) const
	Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error.
Protected Attributes
cvm::atom_group	group1
	First atom group.
cvm::atom_group	group2
	Second atom group.
cvm::rvector	dist_v
	Vector distance, cached to be recycled.
bool	b_1site_force

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Detailed Description

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

This class also serves as the template for many collective variables with two atom groups: in this case, the distance::distance() constructor should be called on the same configuration string, to make the same member data and functions available to the derived object

Definition at line 298 of file colvarcomp.h.

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Constructor & Destructor Documentation

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

Definition at line 15 of file colvarcomp_distances.C. References b_1site_force, group1, group2, colvarmodule::log(), colvar::cvc::parse_group(), and colvarvalue::type(). : cvc (conf) { function_type = "distance"; b_inverse_gradients = true; b_Jacobian_derivative = true; if (get_keyval (conf, "oneSiteSystemForce", b_1site_force, false)) { cvm::log ("Computing system force on group 1 only"); } parse_group (conf, "group1", group1); parse_group (conf, "group2", group2); x.type (colvarvalue::type_scalar); }

colvar::distance::distance (   )

Definition at line 29 of file colvarcomp_distances.C. References b_1site_force, and colvarvalue::type(). : cvc () { function_type = "distance"; b_inverse_gradients = true; b_Jacobian_derivative = true; b_1site_force = false; x.type (colvarvalue::type_scalar); }

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

Definition at line 314 of file colvarcomp.h. {}

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Member Function Documentation

void colvar::distance::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 Implements colvar::cvc. Reimplemented in colvar::distance_dir, colvar::min_distance, and colvar::coordnum. Definition at line 75 of file colvarcomp_distances.C. References colvarmodule::atom_group::apply_colvar_force(), group1, group2, and colvarmodule::atom_group::noforce. { if (!group1.noforce) group1.apply_colvar_force (force); if (!group2.noforce) group2.apply_colvar_force (force); }

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

Calculate the total force from the system using the inverse atomic gradients. Reimplemented from colvar::cvc. Definition at line 59 of file colvarcomp_distances.C. References dist_v, group1, group2, colvarmodule::atom_group::read_system_forces(), colvarvalue::real_value, colvarmodule::atom_group::system_force(), and colvarmodule::rvector::unit(). { group1.read_system_forces(); if ( b_1site_force ) { ft.real_value = -1.0 * (group1.system_force() * dist_v.unit()); } else { group2.read_system_forces(); ft.real_value = 0.5 * ((group2.system_force() - group1.system_force()) * dist_v.unit()); } }

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

Calculate the atomic gradients, to be reused later in order to apply forces. Implements colvar::cvc. Reimplemented in colvar::distance_dir, colvar::min_distance, and colvar::coordnum. Definition at line 52 of file colvarcomp_distances.C. References dist_v, group1, group2, colvarmodule::atom_group::set_weighted_gradient(), and colvarmodule::rvector::unit(). { cvm::rvector const u = dist_v.unit(); group1.set_weighted_gradient (-1.0 * u); group2.set_weighted_gradient ( u); }

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

Calculate the divergence of the inverse atomic gradients. Reimplemented from colvar::cvc. Definition at line 70 of file colvarcomp_distances.C. References colvarvalue::real_value. { jd.real_value = x.real_value ? (2.0 / x.real_value) : 0.0; }

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

Calculate the variable. Implements colvar::cvc. Reimplemented in colvar::distance_dir, colvar::min_distance, and colvar::coordnum. Definition at line 39 of file colvarcomp_distances.C. References colvarmodule::atom_group::center_of_mass(), dist_v, group1, group2, colvarmodule::rvector::norm(), colvarmodule::position_distance(), colvarmodule::atom_group::read_positions(), colvarvalue::real_value, and colvarmodule::atom_group::reset_atoms_data(). { 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.real_value = dist_v.norm(); }

virtual cvm::real colvar::distance::compare (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error. Reimplemented from colvar::cvc. Reimplemented in colvar::min_distance, and colvar::coordnum.

virtual cvm::real colvar::distance::dist2 (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

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 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 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 type. Reimplemented from colvar::cvc. Reimplemented in colvar::min_distance, and colvar::coordnum.

virtual colvarvalue colvar::distance::dist2_lgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

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::min_distance, and colvar::coordnum.

virtual colvarvalue colvar::distance::dist2_rgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

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::min_distance, and colvar::coordnum.

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Member Data Documentation

bool colvar::distance::b_1site_force [protected]

Compute system force on first site only to avoid unwanted coupling to other colvars (see e.g. Ciccotti et al., 2005) Definition at line 310 of file colvarcomp.h. Referenced by distance().

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

Vector distance, cached to be recycled. Definition at line 307 of file colvarcomp.h. Referenced by calc_force_invgrads(), calc_gradients(), and calc_value().

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

First atom group. Definition at line 303 of file colvarcomp.h. Referenced by apply_force(), calc_force_invgrads(), calc_gradients(), calc_value(), and distance().

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

Second atom group. Definition at line 305 of file colvarcomp.h. Referenced by apply_force(), calc_force_invgrads(), calc_gradients(), calc_value(), and distance().

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

• colvarcomp.h
• colvarcomp_distances.C

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