electronDensity
Class ElectronDensity

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  electronDensity.ElectronDensity

All Implemented Interfaces:

java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable, java.lang.Runnable, javax.accessibility.Accessible

public class ElectronDensity
extends java.applet.Applet
implements java.lang.Runnable

Electron Density Plot

Copyright (c) 2000-2001,2009 David N. Blauch

ElectronDensity.class is an applet that displays electron density plots for a wave function.

Applet Parameters

NAME	Variable Type	Default	Description
AutoPlot	boolean	true	If true, the plot is automatically updated after every change in settings. Otherwise the plot is updated only when the replot method is called.
BackgroundMode	boolean	true	If true, the background is black; otherwise, the background is white.
Brightness	double	1.0	Adjusts the brightness of the display.
ComplexMode	int	0	This parameter controls the electron density plot when the wave function itself is being displayed. 0 = display real component of the wave function (default) 1 = display imaginary component of the wave function 2 = display the absolute value of the wave function For mode 2 (absolute value of the wave function), if the display sign option is false, the electron density plot is displayed in the positive color in all regions. If the display sign option is true, the color is based upon the phase angle. The pure positive color represents a purely real wave function (Im = 0); the pure negative color represents a purely imaginary wave function (Re = 0).
DensityMode	int	0	0 = display psi*psi (default) (psi = wave function) 1 = display the wave function itself
DisplaySign	boolean	true	If true, different colors are used to represent regions where the wave function is positive and negative in value. If false, the same color (that for positive regions) is used throughout the plot.
Interpolate	int	-1	For large displays and complicated wave functions, the time required to create the electron density plot can be lengthy. To speed execution, the wave function is evaluated on a coarse grid and interpolation is used to estimate the wave function at intervening points. The value of the Interpolate parameter is the number of points in a linear interval that are obtained by interpolation for every explicit evaluation of the wave function. A value of 0 correponds to no interpolation. A value of -1 (default) instructs the applet to select a value (0, 1, 2, 3, or 4). For plots with intricate detail, no interpolation (0) should be employed. Unless a plot is very large, requires extensive computations for the evaluation of the wave function, and has no fine features, interpolations above 2 should be avoided. For problems sufficiently large that the majority of the computational time is required to compute the wave function at each point, the following speed-up factors may be expected: 0 = 1x, 1 = 4x, 2 = 9x, 3 = 16x, and 4 = 25x. For small problems, the performance enhancement will be smaller, because the overhead for computing the pixel map is independent of the degree of interpolation. For even simple wave functions (e.g., 1s orbital), over 95% of the computational time is devoted to computing wave function values when no interpolation (0) is employed. For very complicated problems, more than 99% of the computational time is devoted to computing wave function values. Thus interpolation, even with a setting of 1 or 2, provides a very significant increase in speed.
IsReady	String		JavaScript variable that will be set to true when applet has initialized. Must use MAYSCRIPT in APPLET tag to use this feature.
Orbital	String	1s	This parameter specifies the orbital used to construct the electron density plot. The string follows the usual chemical notation for hydrogen atom orbitals: 1s (default), 2s, 2px, 3dz2, 4dx2-y2, etc. The following hybrid orbitals are available: sp, sp2, sp3, dsp2, dsp3ax (the axial orbital), dsp3eq (the equitorial orbital), and d2sp3. Not all hydrogen orbitals orbitals are available.
NegativeColor	String	#00FFFF	This parameter specifies the color used to display regions where the wave function is negative. The string is converted to an integer, which is used to create the color. The default color is a light blue.
PositiveColor	String	#FFFF00	This parameter specifies the color used to display regions where the wave function is positive. The string is converted to an integer, which is used to create the color. The default color is yellow.
ShowControls	boolean	true	If true, controls are provided at the bottom of the applet to manually enter values for n, l, and m (i.e., the quantum numbers). If false, no controls are displayed.
ShowAxes	boolean	false	If true, vertical and horizontal axes are shown. Regardless of the value of this parameter, no axes are shown if the plot does not lie in the xy, xz, or yz plane.
ViewAlong	char	Y	Sets axis (x, y, or z) along which the display is viewed.

Version:

2.2

Author:

David N. Blauch

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.awt.Component

java.awt.Component.BaselineResizeBehavior

Field Summary

Fields inherited from class java.awt.Component

BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT

Fields inherited from interface java.awt.image.ImageObserver

ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH

Constructor Summary

ElectronDensity()

Method Summary

void	addCircle(double _x, double _y, int _dia, boolean _fill) Adds a circle to the electron density plot.
void	addCircle(double _x, double _y, int _dia, boolean _fill, int _red, int _green, int _blue) Adds a circle to the electron density plot.
void	addGaussian(int id, double _coefReal, double _coefImag) Adds an existing gaussian wave function to the collection of wave functions used to construct the hybrid orbital.
void	addNLM(int _n, int _l, int _m, double _coefReal, double _coefImag) Adds a new hydrogenic wave function using the user-supplied quantum numbers.
void	addWaveFunction(WaveFunction _waveFunction, double _coefReal, double _coefImag) Adds a new wave function to the collection of wave functions used to construct the hybrid orbital.
void	clearCircles() Clears all circles
void	createGaussian(int id, int nbr, java.lang.String geometry) Creates a Gaussian basis function with the given id number.
void	defineGaussian(int basisID, int functionID, double alpha, double scale, double coef) Defines the parameters for a gaussian function in a gaussian basis function
void	destroy()
java.lang.String	getAppletInfo()
double	getMaxR() Returns the current maximum displacement (in units of Zr/a)
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
double	getRotationAngle() Returns angle of rotation
double	getRotationX() Returns the x coordinate for the axis of rotation.
double	getRotationY() Returns the y coordinate for the axis of rotation.
double	getRotationZ() Returns the z coordinate for the axis of rotation.
void	init()
void	paint(java.awt.Graphics g)
void	replot() Replots the electron density plot.
void	resetView() Resets the rotation vector to the default xy plane view
void	run()
void	setAutoMaxR(boolean _autoMaxR) Determines whether the maximum displacement is automatically estimated or is supplied by the user (default 3.0)
void	setAutoPlot(boolean _autoPlot) Determines whether the plot is updated after every change in setting.
void	setBackgroundMode(boolean _backgroundMode) Sets the background mode.
void	setBrightness(double _brightness) Sets the brightness factor.
void	setColors(java.awt.Color _pos, java.awt.Color _neg) Sets the colors used in the electron density plot.
void	setColors(int _posRed, int _posGreen, int _posBlue, int _negRed, int _negGreen, int _negBlue) Sets the colors used in the electron density plot.
void	setComplexMode(int _mode) Sets the display mode for complex values (occurs only when the density mode is 1, which displays the wave function itself).
void	setDensityMode(int _mode) Sets the display mode (psi = wave function).
void	setDisplaySign(boolean _displaySign) Determines whether the display shows the sign of the wave function.
void	setGaussian(int id) Sets the wave function to be the previously defined gaussian basis function with the indicated id.
void	setGaussian(int id, double _coefReal, double _coefImag) Sets the wave function to be the previously defined gaussian basis function with the indicated id.
void	setGaussianOrigin(int id, double _r, double _theta, double _phi) Sets the origin (in spherical coordinates) for the gaussian basis function
void	setGaussianOriginXYZ(int id, double _x, double _y, double _z) Sets the origin (in cartesian coordinates) for the gaussian basis function
void	setInterpolation(int _nbr) Sets the interpolation level.
void	setMaxR(double _maxR) Sets the maximum displacement to be used is autoMaxR = false.
void	setNLM(int _n, int _l, int _m) Creates a new hydrogenic wave function using the user-supplied quantum numbers.
void	setNLM(int _n, int _l, int _m, double _coefReal, double _coefImag) Creates a new hydrogenic wave function using the user-supplied quantum numbers.
void	setOrbital(java.lang.String _orbital) Sets the orbital to be displayed.
void	setRotation(double _x, double _y, double _z, double _a) Sets the rotation parameters for the display.
void	setShowAxes(boolean _showAxes) Sets the showAxes property.
void	setViewXY() Sets the plot to display the xy plane
void	setViewXZ() Sets the plot to display the xz plane
void	setViewYZ() Sets the plot to display the xz plane
void	setWaveFunction(WaveFunction _waveFunction, double _coefReal, double _coefImag) Creates a new hybrid wave function using the user-supplied wave function.
void	start()
void	stop()

Methods inherited from class java.applet.Applet

getAccessibleContext, getAppletContext, getAudioClip, getAudioClip, getCodeBase, getDocumentBase, getImage, getImage, getLocale, getParameter, isActive, newAudioClip, play, play, resize, resize, setStub, showStatus

Methods inherited from class java.awt.Panel

addNotify

Methods inherited from class java.awt.Container

add, add, add, add, add, addContainerListener, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getAlignmentX, getAlignmentY, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getInsets, getLayout, getListeners, getMaximumSize, getMinimumSize, getMousePosition, getPreferredSize, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, print, printComponents, remove, remove, removeAll, removeContainerListener, removeNotify, setComponentZOrder, setFocusCycleRoot, setFocusTraversalKeys, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setFont, setLayout, transferFocusBackward, transferFocusDownCycle, update, validate

Methods inherited from class java.awt.Component

action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, contains, contains, createImage, createImage, createVolatileImage, createVolatileImage, disable, dispatchEvent, enable, enable, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBaseline, getBaselineResizeBehavior, getBounds, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getFontMetrics, getForeground, getGraphics, getGraphicsConfiguration, getHeight, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocation, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPeer, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getSize, getToolkit, getTreeLock, getWidth, getX, getY, gotFocus, handleEvent, hasFocus, hide, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isDoubleBuffered, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isOpaque, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, printAll, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, repaint, requestFocus, requestFocusInWindow, reshape, setBackground, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setEnabled, setFocusable, setFocusTraversalKeysEnabled, setForeground, setIgnoreRepaint, setLocale, setLocation, setLocation, setMaximumSize, setMinimumSize, setName, setPreferredSize, setSize, setSize, setVisible, show, show, size, toString, transferFocus, transferFocusUpCycle

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

ElectronDensity

public ElectronDensity()

Method Detail

getParameter

public java.lang.String getParameter(java.lang.String key,
                                     java.lang.String def)

init

public void init()

Overrides:

init in class java.applet.Applet

start

public void start()

Overrides:

start in class java.applet.Applet

stop

public void stop()

Overrides:

stop in class java.applet.Applet

paint

public void paint(java.awt.Graphics g)

Overrides:

paint in class java.awt.Container

run

public void run()

Specified by:

run in interface java.lang.Runnable

destroy

public void destroy()

Overrides:

destroy in class java.applet.Applet

getAppletInfo

public java.lang.String getAppletInfo()

Overrides:

getAppletInfo in class java.applet.Applet

getParameterInfo

public java.lang.String[][] getParameterInfo()

Overrides:

getParameterInfo in class java.applet.Applet

addCircle

public void addCircle(double _x,
                      double _y,
                      int _dia,
                      boolean _fill)

Adds a circle to the electron density plot. The circle position is specified by x,y position on the screen in units of distance/Bohr radius. The circle is white in color. The position of the circle is not subject to rotation.

Parameters:

_x - x position of circle center in normalized coordinates

_y - y position of circle center in normalized coordinates

_dia - diameter of circle in pixels

_fill - if true the circle is filled

addCircle

public void addCircle(double _x,
                      double _y,
                      int _dia,
                      boolean _fill,
                      int _red,
                      int _green,
                      int _blue)

Adds a circle to the electron density plot. The circle position is specified by x,y position on the screen in units of distance/Bohr radius. The position of the circle is not subject to rotation.

Parameters:

_x - x position of circle center in normalized coordinates

_y - y position of circle center in normalized coordinates

_dia - diameter of circle in pixels

_fill - if true the circle is filled

_red - red component of the color

_green - green component of the color

_blue - blue component of the color

addGaussian

public void addGaussian(int id,
                        double _coefReal,
                        double _coefImag)

Adds an existing gaussian wave function to the collection of wave functions used to construct the hybrid orbital.

Parameters:

id - id number for a previously created gaussian basis function

_coefReal - real component of the coefficient for constructing the hybrid wave function

_coefImag - imaginary component of the coefficient for constructing the hybrid wave function

addNLM

public void addNLM(int _n,
                   int _l,
                   int _m,
                   double _coefReal,
                   double _coefImag)

Adds a new hydrogenic wave function using the user-supplied quantum numbers. The electron density plot for the new hybrid wave function is NOT displayed.

Parameters:

_n - principal quantum number

_l - angular momentum quantum number

_m - magnetic quantum number

_coefReal - real component of the coefficient for constructing the hybrid wave function

_coefImag - imaginary component of the coefficient for constructing the hybrid wave function

See Also:

replot()

addWaveFunction

public void addWaveFunction(WaveFunction _waveFunction,
                            double _coefReal,
                            double _coefImag)

Adds a new wave function to the collection of wave functions used to construct the hybrid orbital. It is assumed that the individual wave functions used to construct the hybrid wave function are orthogonal. If the orthogonality relation is not obeyed, the resulting hybrid orbital will not be normalized.

The electron density plot for the new hybrid wave function is NOT displayed.

Parameters:

_coefReal - real component of the coefficient for constructing the hybrid wave function

_coefImag - imaginary component of the coefficient for constructing the hybrid wave function

See Also:

replot()

clearCircles

public void clearCircles()

Clears all circles

createGaussian

public void createGaussian(int id,
                           int nbr,
                           java.lang.String geometry)

Creates a Gaussian basis function with the given id number. It is necessary to specify the number of component gaussian functions in the basis function and the geometry of the basis function. The individual gaussian functions are defined using the defineGaussian method.

Parameters:

id - identification number for this gaussian basis function

nbr - number of gaussian functions in the basis function

geometry - basis function geometry: s, x, y, z, xx, xy, xz, yy, yz, zz

See Also:

defineGaussian(int, int, double, double, double)

defineGaussian

public void defineGaussian(int basisID,
                           int functionID,
                           double alpha,
                           double scale,
                           double coef)

Defines the parameters for a gaussian function in a gaussian basis function

Parameters:

basisID - id of the gaussian basis function

functionID - id of the gaussian function in the gaussian basis function

alpha - alpha parameter in exp argument

scale - scale factor

coef - coefficient for this gaussian function

getMaxR

public double getMaxR()

Returns the current maximum displacement (in units of Zr/a)

getRotationAngle

public double getRotationAngle()

Returns angle of rotation

getRotationX

public double getRotationX()

Returns the x coordinate for the axis of rotation.

getRotationY

public double getRotationY()

Returns the y coordinate for the axis of rotation.

getRotationZ

public double getRotationZ()

Returns the z coordinate for the axis of rotation.

replot

public void replot()

Replots the electron density plot.

resetView

public void resetView()

Resets the rotation vector to the default xy plane view

setAutoMaxR

public void setAutoMaxR(boolean _autoMaxR)

Determines whether the maximum displacement is automatically estimated or is supplied by the user (default 3.0)

setAutoPlot

public void setAutoPlot(boolean _autoPlot)

Determines whether the plot is updated after every change in setting. If false, the plot is updated only when the replot method is called.

See Also:

replot()

setBackgroundMode

public void setBackgroundMode(boolean _backgroundMode)

Sets the background mode. If true, the background is black. If false, the background is white.

setBrightness

public void setBrightness(double _brightness)

Sets the brightness factor. The larger this value, the brighter the display will be. The default value is 1.0

setColors

public void setColors(java.awt.Color _pos,
                      java.awt.Color _neg)

Sets the colors used in the electron density plot. These colors loosely represent the colors in regions where the electron density is near a maximum.

Parameters:

_pos - Color for the regions where the wave function is positive

_neg - Color for the regions where the wave function is negative

setColors

public void setColors(int _posRed,
                      int _posGreen,
                      int _posBlue,
                      int _negRed,
                      int _negGreen,
                      int _negBlue)

Sets the colors used in the electron density plot. These colors loosely represent the colors in regions where the electron density is near a maximum.

Parameters:

_posRed - red component for positive regions

_posGreen - green component for positive regions

_posBlue - blue component for positive regions

_negRed - red component for negative regions

_negGreen - green component for negative regions

_negBlue - blue component for negative regions

setComplexMode

public void setComplexMode(int _mode)

Sets the display mode for complex values (occurs only when the density mode is 1, which displays the wave function itself).

0 = Display the real component of the wave function

1 = Display the imaginary component of the wave function

2 = Display the absolute value of the wave function

For mode 2 (absolute value of the wave function), if the display sign option is false, the electron density plot is displayed in the positive color in all regions. If the display sign option is true, the color is based upon the phase angle. The pure positive color represents a purely real wave function (Im = 0); the pure negative color represents a purely imaginary wave function (Re = 0).

See Also:

setDensityMode(int), setDisplaySign(boolean)

setDensityMode

public void setDensityMode(int _mode)

Sets the display mode (psi = wave function).

0 = Display psi*psi (that is, the electron density)

1 = Display psi

See Also:

setComplexMode(int), setDisplaySign(boolean)

setDisplaySign

public void setDisplaySign(boolean _displaySign)

Determines whether the display shows the sign of the wave function. For displays of psi*psi (psi = wave function) the real component of the wave function is used to determine the sign if complex mode = 0 or 2 and the imaginary component is used if complex mode = 1. For displays of |psi|, if display sign is true, the color describes the phase angle, with the positive color representing a pure real number and the negative color representing a pure imaginary number.

setGaussian

public void setGaussian(int id)

Sets the wave function to be the previously defined gaussian basis function with the indicated id. The coefficient for the gaussian basis function is 1.0

setGaussian

public void setGaussian(int id,
                        double _coefReal,
                        double _coefImag)

Sets the wave function to be the previously defined gaussian basis function with the indicated id.

Parameters:

_coefReal - real component of the coefficient

_coefImag - imaginary component of the coefficient

setGaussianOrigin

public void setGaussianOrigin(int id,
                              double _r,
                              double _theta,
                              double _phi)

Sets the origin (in spherical coordinates) for the gaussian basis function

Parameters:

id - id for the gaussian basis function

setGaussianOriginXYZ

public void setGaussianOriginXYZ(int id,
                                 double _x,
                                 double _y,
                                 double _z)

Sets the origin (in cartesian coordinates) for the gaussian basis function

Parameters:

id - id for the gaussian basis function

setInterpolation

public void setInterpolation(int _nbr)

Sets the interpolation level.

-1 = computer selects an "appropriate" value

0 = no interpolation

1 = 5/9 of the points are interpolated

2 = 11/16 of the points are interpolated, etc.

setMaxR

public void setMaxR(double _maxR)

Sets the maximum displacement to be used is autoMaxR = false.

setNLM

public void setNLM(int _n,
                   int _l,
                   int _m)

Creates a new hydrogenic wave function using the user-supplied quantum numbers. The coefficient for the new wave function is 1.0. The electron density plot for the new wave function is displayed.

Parameters:

_n - principal quantum number

_l - angular momentum quantum number

_m - magnetic quantum number

setNLM

public void setNLM(int _n,
                   int _l,
                   int _m,
                   double _coefReal,
                   double _coefImag)

Creates a new hydrogenic wave function using the user-supplied quantum numbers. The electron density plot for the new wave function is NOT displayed.

Parameters:

_n - principal quantum number

_l - angular momentum quantum number

_m - magnetic quantum number

_coefReal - real component of the coefficient for constructing the hybrid wave function

_coefImag - imaginary component of the coefficient for constructing the hybrid wave function

setOrbital

public void setOrbital(java.lang.String _orbital)

Sets the orbital to be displayed. The display is automatically updated. Available orbitals are:

1s, 2s, 2px, 2py, 2pz, 3s, 3px, 3py, 3pz, 3dz2, 3dxz, 3dyz, 3dxy, 3dx2-y2, 4s, 4px, 4py, 4pz, 4dz2, 4dxz, 4dyz, 4dxy, 4dx2-y2, 4f5xz2-xr2, 4f5yz2-yr2, 4f5z3-3zr2, 4fx3-3xy2, 4fxyz, 4fy3-3yx2, 4fzx2-zy2, sp, sp2, sp3, dsp2, dsp3ax, dsp3eq, d2sp3

Parameters:

_orbital - String identifying the orbital (from the above list) to be displayed

setRotation

public void setRotation(double _x,
                        double _y,
                        double _z,
                        double _a)

Sets the rotation parameters for the display. The parameters _x, _y, and _z define the axis of rotation. All points are rotated an angle _a (in radians) about this axis. The rotation follows the right-hand rule.

setShowAxes

public void setShowAxes(boolean _showAxes)

Sets the showAxes property. If true, axes and labels are drawn on the electron density plot. If false (default), no axes are drawn. Axes may only be drawn when the view is of the xz, yz, or xy plane.

See Also:

setViewXY(), setViewXZ(), setViewYZ(), resetView()

setViewXY

public void setViewXY()

Sets the plot to display the xy plane

setViewXZ

public void setViewXZ()

Sets the plot to display the xz plane

setViewYZ

public void setViewYZ()

Sets the plot to display the xz plane

setWaveFunction

public void setWaveFunction(WaveFunction _waveFunction,
                            double _coefReal,
                            double _coefImag)

Creates a new hybrid wave function using the user-supplied wave function.

The electron density plot for the new hybrid wave function is NOT displayed.

Parameters:

_coefReal - real component of the coefficient for constructing the hybrid wave function

_coefImag - imaginary component of the coefficient for constructing the hybrid wave function

See Also:

replot()