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colvar::groupcoordnum Class Reference

\brief Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::groupcoordnum:

colvar::distance colvar::cvc colvarparse colvardeps colvarparams List of all members.

Public Methods

 groupcoordnum (std::string const &conf)
 Constructor. More...

virtual ~groupcoordnum ()
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...


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::real r0
 \brief "Cutoff" for isotropic calculation (default). More...

cvm::rvector r0_vec
 \brief "Cutoff vector" for anisotropic calculation. More...

bool b_anisotropic
 \brief Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be used. More...

int en
 Integer exponent of the function numerator. More...

int ed
 Integer exponent of the function denominator. More...


Detailed Description

\brief Colvar component: coordination number between two groups (colvarvalue::type_scalar type, range [0:N1*N2]).

Definition at line 1018 of file colvarcomp.h.


Constructor & Destructor Documentation

colvar::groupcoordnum::groupcoordnum std::string const &    conf
 

Constructor.

virtual colvar::groupcoordnum::~groupcoordnum   [inline, virtual]
 

Definition at line 1036 of file colvarcomp.h.


Member Function Documentation

void colvar::groupcoordnum::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.

Reimplemented from colvar::distance.

Definition at line 645 of file colvarcomp_coordnums.C.

References force, colvar::distance::group1, colvar::distance::group2, and colvarvalue::real_value.

void colvar::groupcoordnum::calc_gradients   [virtual]
 

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

Reimplemented from colvar::distance.

Definition at line 619 of file colvarcomp_coordnums.C.

References ed, en, colvar::distance::group1, colvar::distance::group2, NULL, r0, and r0_vec.

void colvar::groupcoordnum::calc_value   [virtual]
 

\brief Calculate the variable.

Reimplemented from colvar::distance.

Definition at line 596 of file colvarcomp_coordnums.C.

References ed, en, colvar::distance::group1, colvar::distance::group2, NULL, r0, r0_vec, colvarvalue::real_value, and colvar::cvc::x.

virtual cvm::real colvar::groupcoordnum::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::distance.

virtual colvarvalue colvar::groupcoordnum::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::distance.

virtual colvarvalue colvar::groupcoordnum::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::distance.


Member Data Documentation

bool colvar::groupcoordnum::b_anisotropic [protected]
 

\brief Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be used.

Definition at line 1028 of file colvarcomp.h.

int colvar::groupcoordnum::ed [protected]
 

Integer exponent of the function denominator.

Definition at line 1032 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.

int colvar::groupcoordnum::en [protected]
 

Integer exponent of the function numerator.

Definition at line 1030 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.

cvm::real colvar::groupcoordnum::r0 [protected]
 

\brief "Cutoff" for isotropic calculation (default).

Definition at line 1023 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.

cvm::rvector colvar::groupcoordnum::r0_vec [protected]
 

\brief "Cutoff vector" for anisotropic calculation.

Definition at line 1025 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.


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