#include <colvarcomp.h>
Inheritance diagram for colvar::dipole_angle:
Public Methods  
dipole_angle (std::string const &conf)  
Initialize by parsing the configuration. More...  
dipole_angle (cvm::atom const &a1, cvm::atom const &a2, cvm::atom const &a3)  
\brief Initialize the three groups after three atoms. More...  
dipole_angle ()  
virtual  ~dipole_angle ()  
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
 
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_valuex1.real_value)*(x2.real_valuex1.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::atom_group *  group1  
Dipole atom group. More...  
cvm::atom_group *  group2  
Atom group. More...  
cvm::atom_group *  group3  
Atom group. More...  
cvm::rvector  r21  
Inter site vectors. More...  
cvm::rvector  r23  
Inter site vectors. More...  
cvm::real  r21l  
Inter site vector norms. More...  
cvm::real  r23l  
Inter site vector norms. More...  
cvm::rvector  dxdr1  
Derivatives wrt group centers of mass. More...  
cvm::rvector  dxdr3  
Derivatives wrt group centers of mass. More...  
bool  b_1site_force  
Compute total force on first site only to avoid unwanted coupling to other colvars (see e.g. Ciccotti et al., 2005) (or to allow dummy atoms). More... 
Definition at line 798 of file colvarcomp.h.

Initialize by parsing the configuration.


\brief Initialize the three groups after three atoms.
Definition at line 154 of file colvarcomp_angles.C. References colvarmodule::atom_group, group1, group2, group3, colvar::cvc::init_as_angle, colvar::cvc::register_atom_group, and colvar::cvc::set_function_type. 

Definition at line 170 of file colvarcomp_angles.C. References colvar::cvc::init_as_angle, and colvar::cvc::set_function_type. 

Definition at line 828 of file colvarcomp.h. 

\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
Implements colvar::cvc. Definition at line 232 of file colvarcomp_angles.C. References force, group1, group2, group3, and colvarvalue::real_value. 

\brief Calculate the atomic gradients, to be reused later in order to apply forces.
Reimplemented from colvar::cvc. Definition at line 201 of file colvarcomp_angles.C. References dxdr1, dxdr3, group1, group2, group3, PI, r21, r21l, r23, r23l, and colvarmodule::sqrt. 

\brief Calculate the variable.
Implements colvar::cvc. Definition at line 177 of file colvarcomp_angles.C. References colvarmodule::acos, colvardeps::f_cvc_pbc_minimum_image, group1, group2, group3, colvardeps::is_enabled, PI, colvarmodule::position_distance, r21, r21l, r23, r23l, colvarvalue::real_value, and colvar::cvc::x. 

\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_valuex1.real_value)*(x2.real_valuex1.real_value) in case of a scalar colvarvalue type.
Reimplemented from colvar::cvc. 

\brief Gradient(with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
Reimplemented from colvar::cvc. 

\brief Gradient(with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
Reimplemented from colvar::cvc. 

Compute total force on first site only to avoid unwanted coupling to other colvars (see e.g. Ciccotti et al., 2005) (or to allow dummy atoms).
Definition at line 820 of file colvarcomp.h. 

Derivatives wrt group centers of mass.
Definition at line 815 of file colvarcomp.h. Referenced by calc_gradients. 

Derivatives wrt group centers of mass.
Definition at line 815 of file colvarcomp.h. Referenced by calc_gradients. 

Dipole atom group.
Definition at line 804 of file colvarcomp.h. Referenced by apply_force, calc_gradients, calc_value, and dipole_angle. 

Atom group.
Definition at line 806 of file colvarcomp.h. Referenced by apply_force, calc_gradients, calc_value, and dipole_angle. 

Atom group.
Definition at line 808 of file colvarcomp.h. Referenced by apply_force, calc_gradients, calc_value, and dipole_angle. 

Inter site vectors.
Definition at line 811 of file colvarcomp.h. Referenced by calc_gradients, and calc_value. 

Inter site vector norms.
Definition at line 813 of file colvarcomp.h. Referenced by calc_gradients, and calc_value. 

Inter site vectors.
Definition at line 811 of file colvarcomp.h. Referenced by calc_gradients, and calc_value. 

Inter site vector norms.
Definition at line 813 of file colvarcomp.h. Referenced by calc_gradients, and calc_value. 