meshi.symmetryComplex.energy.cylinder
Class CylinderEnergyElement

java.lang.Object
  meshi.energy.EnergyElement
      meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement

public class CylinderEnergyElement
extends EnergyElement

Responsible for energy and forces calculations of the Cylinder energy function on a single atom.
The atom's cartesian coordinates are transformed to Cylindrical Coordinates and forces are transformed back to cartesian coordinates.

Field Summary

protected Atom	atom The atom which is kept in the cylinder.
protected double	atomHeight The atom's cylindrical coordinates.
protected double	atomR The atom's cylindrical coordinates.
protected double	atomTheta The atom's cylindrical coordinates.
protected double	force Force constants.
protected double	force2 Force constants.
protected double	height The cylinder's dimensions.
protected double	innerR The cylinder's dimensions.
protected double	outerR The cylinder's dimensions.
protected double	weight

Fields inherited from class meshi.energy.EnergyElement

atoms, dFormatSrt, dFormatStd, DX, frozen, relativeDiffTolerance, VERY_SMALL, XYZ

Constructor Summary

CylinderEnergyElement(Atom atom, CylinderParameters parameters, double weight)
Constructs an energy elements for the given atom.

Method Summary

double	evaluate() Calculates the cylinder energy and updates forces on the atom.
static boolean	isPointInCylinder(Coordinates coordinates, double outerR, double innerR, double height) For loops building.
void	setAtoms()
private void	updateCylindricalCoors() Updates the cylindrical coordinates according to the cartesian coordinates.
private void	updateForces(double forceOnR, double forceOnHeight) Updates the forces on the atom.

Methods inherited from class meshi.energy.EnergyElement

atoms, evaluateAtoms, frozen, test, updateFrozen

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

atom

protected final Atom atom

The atom which is kept in the cylinder.

weight

protected final double weight

innerR

protected final double innerR

The cylinder's dimensions.

outerR

protected final double outerR

The cylinder's dimensions.

height

protected final double height

The cylinder's dimensions.

atomR

protected double atomR

The atom's cylindrical coordinates.

atomTheta

protected double atomTheta

The atom's cylindrical coordinates.

atomHeight

protected double atomHeight

The atom's cylindrical coordinates.

force

protected final double force

Force constants. Currently both equal to 1 for all atoms but can be changed to atom-specific.

force2

protected final double force2

Force constants. Currently both equal to 1 for all atoms but can be changed to atom-specific.

Constructor Detail

CylinderEnergyElement

public CylinderEnergyElement(Atom atom,
                             CylinderParameters parameters,
                             double weight)

Constructs an energy elements for the given atom.

Method Detail

updateCylindricalCoors

private void updateCylindricalCoors()

Updates the cylindrical coordinates according to the cartesian coordinates.

setAtoms

public void setAtoms()

Specified by:

setAtoms in class EnergyElement

evaluate

public double evaluate()

Calculates the cylinder energy and updates forces on the atom.

Specified by:

evaluate in class EnergyElement

updateForces

private void updateForces(double forceOnR,
                          double forceOnHeight)

Updates the forces on the atom. The parameters are forces in cylidrical coordinates and are transformed to cartesian coordinates.

isPointInCylinder

public static boolean isPointInCylinder(Coordinates coordinates,
                                        double outerR,
                                        double innerR,
                                        double height)

For loops building. Should be changed.