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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:

List of all members.

Public Methods

polar_phi (std::string const &conf)

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 theta

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.

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

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