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colvar::polar_phi Class Reference

\brief Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180]). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::polar_phi:

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

Public Methods

 polar_phi (std::string const &conf)
 polar_phi ()
virtual ~polar_phi ()
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
 Redefined to handle the 2*PI periodicity. More...

virtual colvarvalue dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
 Redefined to handle the 2*PI periodicity. More...

virtual colvarvalue dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
 Redefined to handle the 2*PI periodicity. More...

virtual void wrap (colvarvalue &x_unwrapped) const
 Redefined to handle the 2*PI periodicity. More...


Protected Attributes

cvm::atom_group * atoms
cvm::real r
cvm::real theta
cvm::real phi

Detailed Description

\brief Colvar component: polar coordinate phi of a group (colvarvalue::type_scalar type, range [-180:180]).

Definition at line 502 of file colvarcomp.h.


Constructor & Destructor Documentation

colvar::polar_phi::polar_phi std::string const &    conf
 

colvar::polar_phi::polar_phi  
 

Definition at line 565 of file colvarcomp_angles.C.

References colvar::cvc::init_as_periodic_angle, and colvar::cvc::set_function_type.

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

Definition at line 508 of file colvarcomp.h.


Member Function Documentation

void colvar::polar_phi::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 592 of file colvarcomp_angles.C.

References atoms, force, and colvarvalue::real_value.

void colvar::polar_phi::calc_gradients   [virtual]
 

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

Reimplemented from colvar::cvc.

Definition at line 583 of file colvarcomp_angles.C.

References atoms, phi, PI, r, and theta.

void colvar::polar_phi::calc_value   [virtual]
 

\brief Calculate the variable.

Implements colvar::cvc.

Definition at line 572 of file colvarcomp_angles.C.

References colvarmodule::acos, colvarmodule::atan2, atoms, phi, PI, r, colvarvalue::real_value, theta, and colvar::cvc::x.

cvm::real colvar::polar_phi::dist2 colvarvalue const &    x1,
colvarvalue const &    x2
const [virtual]
 

Redefined to handle the 2*PI periodicity.

Reimplemented from colvar::cvc.

Definition at line 601 of file colvarcomp_angles.C.

References colvarvalue::real_value.

colvarvalue colvar::polar_phi::dist2_lgrad colvarvalue const &    x1,
colvarvalue const &    x2
const [virtual]
 

Redefined to handle the 2*PI periodicity.

Reimplemented from colvar::cvc.

Definition at line 610 of file colvarcomp_angles.C.

References colvarvalue::real_value.

colvarvalue colvar::polar_phi::dist2_rgrad colvarvalue const &    x1,
colvarvalue const &    x2
const [virtual]
 

Redefined to handle the 2*PI periodicity.

Reimplemented from colvar::cvc.

Definition at line 619 of file colvarcomp_angles.C.

References colvarvalue::real_value.

void colvar::polar_phi::wrap colvarvalue   x_unwrapped const [virtual]
 

Redefined to handle the 2*PI periodicity.

Reimplemented from colvar::cvc.

Definition at line 628 of file colvarcomp_angles.C.

References colvarvalue::real_value, and colvar::cvc::wrap_center.


Member Data Documentation

cvm::atom_group* colvar::polar_phi::atoms [protected]
 

Definition at line 510 of file colvarcomp.h.

Referenced by apply_force, calc_gradients, and calc_value.

cvm::real colvar::polar_phi::phi [protected]
 

Definition at line 511 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.

cvm::real colvar::polar_phi::r [protected]
 

Definition at line 511 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.

cvm::real colvar::polar_phi::theta [protected]
 

Definition at line 511 of file colvarcomp.h.

Referenced by calc_gradients, and calc_value.


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