showStructure
Class ShowStructure

java.lang.Object
  java.awt.Component
      java.awt.Container
          java.awt.Panel
              java.applet.Applet
                  showStructure.ShowStructure

All Implemented Interfaces:

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

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

Displays unit cell structure.

Applet Parameters

NAME	Variable Type	Default	Description
Animation	boolean	false	Configures system for animation of atom segments for the specified unit cell.
A	Float	1.0	Length for unit cell axis a.
B	Float	1.0	Length for unit cell axis b.
C	Float	1.0	Length for unit cell axis c.
CellType	Integer	1	Specifies the cell type: 1 simple cubic (default) 2 body-centered cubic 3 face-centered cubic 4 hexagonal
IsReady	String		JavaScript variable that will be set to true when applet has initialized. Must use MAYSCRIPT in APPLET tag to use this feature.
Offset	float	2.0	Offset for positioning pieces and assembled pieces.
Red	Float	0.0	RGB red component for animated pieces.
Green	Float	1.0	RGB green component for animated pieces.
Blue	Float	0.0	RGB blue component for animated pieces.
Time	long	2000	Duration of each animation stage in milliseconds.
ViewDistance	float	10.0	Distance of view from origin. Set to keep entire scene in view.

Version:

1.0

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

ShowStructure()

Method Summary

void	addCellAtoms(float r, float dRed, float dGreen, float dBlue, float eRed, float eGreen, float eBlue) Adds atoms centered on cell positions
void	addHoleAtoms(int s, float r, float dRed, float dGreen, float dBlue, float eRed, float eGreen, float eBlue) Adds atoms centered on hole positions
void	addLayer(int nx, int ny, float r, float dRed, float dGreen, float dBlue, float eRed, float eGreen, float eBlue) Creates a layer of closest-packed atoms in the plane at z = 0;
void	addLineGroup(double x0, double y0, double z0, double x1, double y1, double z1)
void	addLineGroup(javax.vecmath.Point3d[] pts)
void	addPoints(float r, int nx, int ny) Adds a layer of points for a closest-packed structure
void	addSegments(int ns, float r, float dRed, float dGreen, float dBlue, float eRed, float eGreen, float eBlue) Creates a set of sphere segments (sphere center at the origin) ns = -1 atoms in center unit cell layer of an hcp structure ns = 0 atoms on vertices of hexagonal cell ns = 2 sphere cut into halves by xy plane ns = 4 sphere cut into quarters by xy and xz planes ns = 6 sphere cut into sixths by xy plane and phi = 0, 120, and 240 degrees ns = 8 sphere cut into eighths by xy, xz, and yz planes
void	addSegmentsD(float r, float d, float dRed, float dGreen, float dBlue, float eRed, float eGreen, float eBlue) Creates a set of sphere segments (sphere center at the origin) for atoms in center unit cell layer of an hcp structure
void	addSegmentsS(float r, float d, float dRed, float dGreen, float dBlue, float eRed, float eGreen, float eBlue) Creates a set of sphere segments (sphere center at the origin) for atoms in center unit cell layer in a tetragonal cell
void	alignAtomAndPoint(int grp, int idx, int pt)
void	assemblePieces()
void	destroy()
java.lang.String	getAppletInfo()
javax.vecmath.Vector3f	getAtomGroupTranslation()
boolean	getIsAnimate()
java.lang.String	getParameter(java.lang.String key, java.lang.String def)
java.lang.String[][]	getParameterInfo()
void	init()
void	mulUnitCellRotation(float x, float y, float z, float a)
void	mulUnitCellTranslation(float x, float y, float z)
void	resetAnimation()
void	run()
void	setAtomGroupRotation(float x, float y, float z, float a) Sets the rotation for the entire set of AtomGroups
void	setAtomGroupRotation(int grp, float x, float y, float z, float a) Sets the rotation for a specific AtomGroup
void	setAtomGroupTranslation(float x, float y, float z) Sets the translation for the entire set of AtomGroups
void	setAtomGroupTranslation(int grp, float x, float y, float z) Sets the translation for a specific AtomGroup
void	setAtomGroupVisible(int grp, boolean s) Sets the visibility of all atoms in a group
void	setAtomVisible(int grp, int idx, boolean s) Sets the visibility of the indicated atom
void	setCellGroupRotation(float x, float y, float z, float a) Sets the rotation for the cell group
void	setCellGroupTranslation(float x, float y, float z) Sets the translation of the cell group
void	setFacesVisible(boolean s) Sets the visibility of the unit cell faces
void	setLineGroupRotation(float x, float y, float z, float a) Sets the rotation for the entire set of LineGroups
void	setLineGroupRotation(int grp, float x, float y, float z, float a) Sets the rotation for a specific LineGroup
void	setLineGroupsVisible(boolean s) Sets the visibility of all LineGroups
void	setLineGroupTranslation(float x, float y, float z) Sets the translation for the entire set of LineGroups
void	setLineGroupTranslation(int grp, float x, float y, float z) Sets the translation for a specific LineGroup
void	setLineGroupVisible(int idx, boolean s) Sets the visibility of the indicated LineGroup
void	setLinesVisible(boolean s) Sets the visibility of the unit cell lines
void	setPointGroupRotation(float x, float y, float z, float a) Sets the rotation for the entire set of PointGroups
void	setPointGroupRotation(int grp, float x, float y, float z, float a) Sets the rotation for a specific PointGroup
void	setPointGroupTranslation(float x, float y, float z) Sets the translation for the entire set of PointGroups
void	setPointGroupTranslation(int grp, float x, float y, float z) Sets the translation for a specific PointGroup
void	setPointGroupVisible(boolean s) Sets the visibility of all points in all groups
void	setPointGroupVisible(int grp, boolean s) Sets the visibility of all points in a group
void	setRotation(float x, float y, float z, float a) Set rotation for the entire structure.
void	setSegmentGroupRotation(float x, float y, float z, float a) Sets the rotation for the entire set of SegmentGroups
void	setSegmentGroupRotation(int grp, float x, float y, float z, float a) Sets the rotation for a specific SegmentGroup
void	setSegmentGroupRotation(int grp, int idx, float x, float y, float z, float a) Sets the rotation for a specific SegmentGroup
void	setSegmentGroupTranslation(float x, float y, float z) Sets the translation for the entire set of SegmentGroups
void	setSegmentGroupTranslation(int grp, float x, float y, float z) Sets the translation for a specific SegmentGroup
void	setSegmentGroupTranslation(int grp, int idx, float x, float y, float z) Sets the translation for a specific SegmentGroup
void	setSegmentGroupVisible(int grp, boolean s) Sets the visibility of all segments in a group
void	setSegmentVisible(int grp, int idx, boolean s) Sets the visibility of the indicated segment
void	setTranslation(float x, float y, float z) Set the translation for the entire structure.
void	setUnitCellRotation(float x, float y, float z, float a)
void	setUnitCellTranslation(float x, float y, float z)
void	setViewDistance(float r) Sets the viewing distance.
void	showPieces()
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, paint, 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

ShowStructure

public ShowStructure()

Method Detail

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

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

destroy

public void destroy()

Overrides:

destroy in class java.applet.Applet

addCellAtoms

public void addCellAtoms(float r,
                         float dRed,
                         float dGreen,
                         float dBlue,
                         float eRed,
                         float eGreen,
                         float eBlue)

Adds atoms centered on cell positions

Parameters:

r - atom radius

dRed - diffuse color red component

dGreen - diffuse color green component

dBlue - diffuse color blue component

eRed - emissive color red component

eGreen - emissive color green component

eBlue - emissive color blue component

addHoleAtoms

public void addHoleAtoms(int s,
                         float r,
                         float dRed,
                         float dGreen,
                         float dBlue,
                         float eRed,
                         float eGreen,
                         float eBlue)

Adds atoms centered on hole positions

Parameters:

s - type of hole, where multiple holes geometries exist

r - atom radius

dRed - diffuse color red component

dGreen - diffuse color green component

dBlue - diffuse color blue component

eRed - emissive color red component

eGreen - emissive color green component

eBlue - emissive color blue component

addPoints

public void addPoints(float r,
                      int nx,
                      int ny)

Adds a layer of points for a closest-packed structure

Parameters:

r - atom radius

nx - number of unit cells along x direction

ny - number of unit cells along y direction

addLayer

public void addLayer(int nx,
                     int ny,
                     float r,
                     float dRed,
                     float dGreen,
                     float dBlue,
                     float eRed,
                     float eGreen,
                     float eBlue)

Creates a layer of closest-packed atoms in the plane at z = 0;

Parameters:

nx - number of atoms along x axis

ny - number of atoms along y axis

r - atom radius

dRed - diffuse color red component

dGreen - diffuse color green component

dBlue - diffuse color blue component

eRed - emissive color red component

eGreen - emissive color green component

eBlue - emissive color blue component

addSegments

public void addSegments(int ns,
                        float r,
                        float dRed,
                        float dGreen,
                        float dBlue,
                        float eRed,
                        float eGreen,
                        float eBlue)

Creates a set of sphere segments (sphere center at the origin) ns = -1 atoms in center unit cell layer of an hcp structure ns = 0 atoms on vertices of hexagonal cell ns = 2 sphere cut into halves by xy plane ns = 4 sphere cut into quarters by xy and xz planes ns = 6 sphere cut into sixths by xy plane and phi = 0, 120, and 240 degrees ns = 8 sphere cut into eighths by xy, xz, and yz planes

Parameters:

ns - number of sphere segments

r - sphere radius

dRed - diffuse color red component

dGreen - diffuse color green component

dBlue - diffuse color blue component

eRed - emissive color red component

eGreen - emissive color green component

eBlue - emissive color blue component

addSegmentsD

public void addSegmentsD(float r,
                         float d,
                         float dRed,
                         float dGreen,
                         float dBlue,
                         float eRed,
                         float eGreen,
                         float eBlue)

Creates a set of sphere segments (sphere center at the origin) for atoms in center unit cell layer of an hcp structure

Parameters:

r - sphere radius

d - distance from origin of sphere to planes

dRed - diffuse color red component

dGreen - diffuse color green component

dBlue - diffuse color blue component

eRed - emissive color red component

eGreen - emissive color green component

eBlue - emissive color blue component

addSegmentsS

public void addSegmentsS(float r,
                         float d,
                         float dRed,
                         float dGreen,
                         float dBlue,
                         float eRed,
                         float eGreen,
                         float eBlue)

Creates a set of sphere segments (sphere center at the origin) for atoms in center unit cell layer in a tetragonal cell

Parameters:

r - sphere radius

d - distance from origin of sphere to planes

dRed - diffuse color red component

dGreen - diffuse color green component

dBlue - diffuse color blue component

eRed - emissive color red component

eGreen - emissive color green component

eBlue - emissive color blue component

addLineGroup

public void addLineGroup(javax.vecmath.Point3d[] pts)

addLineGroup

public void addLineGroup(double x0,
                         double y0,
                         double z0,
                         double x1,
                         double y1,
                         double z1)

getAtomGroupTranslation

public javax.vecmath.Vector3f getAtomGroupTranslation()

alignAtomAndPoint

public void alignAtomAndPoint(int grp,
                              int idx,
                              int pt)

setAtomVisible

public void setAtomVisible(int grp,
                           int idx,
                           boolean s)

Sets the visibility of the indicated atom

Parameters:

grp - group index

idx - atom index

s - visibility state

setAtomGroupVisible

public void setAtomGroupVisible(int grp,
                                boolean s)

Sets the visibility of all atoms in a group

Parameters:

grp - group index

s - visibility state

setAtomGroupRotation

public void setAtomGroupRotation(float x,
                                 float y,
                                 float z,
                                 float a)

Sets the rotation for the entire set of AtomGroups

setAtomGroupTranslation

public void setAtomGroupTranslation(float x,
                                    float y,
                                    float z)

Sets the translation for the entire set of AtomGroups

setAtomGroupRotation

public void setAtomGroupRotation(int grp,
                                 float x,
                                 float y,
                                 float z,
                                 float a)

Sets the rotation for a specific AtomGroup

Parameters:

grp - index of AtomGroup

setAtomGroupTranslation

public void setAtomGroupTranslation(int grp,
                                    float x,
                                    float y,
                                    float z)

Sets the translation for a specific AtomGroup

Parameters:

grp - index of AtomGroup

setCellGroupRotation

public void setCellGroupRotation(float x,
                                 float y,
                                 float z,
                                 float a)

Sets the rotation for the cell group

setCellGroupTranslation

public void setCellGroupTranslation(float x,
                                    float y,
                                    float z)

Sets the translation of the cell group

setFacesVisible

public void setFacesVisible(boolean s)

Sets the visibility of the unit cell faces

Parameters:

s - visibility state

setLinesVisible

public void setLinesVisible(boolean s)

Sets the visibility of the unit cell lines

Parameters:

s - visibility state

setLineGroupRotation

public void setLineGroupRotation(float x,
                                 float y,
                                 float z,
                                 float a)

Sets the rotation for the entire set of LineGroups

setLineGroupTranslation

public void setLineGroupTranslation(float x,
                                    float y,
                                    float z)

Sets the translation for the entire set of LineGroups

setLineGroupRotation

public void setLineGroupRotation(int grp,
                                 float x,
                                 float y,
                                 float z,
                                 float a)

Sets the rotation for a specific LineGroup

Parameters:

grp - index of LineGroup

setLineGroupTranslation

public void setLineGroupTranslation(int grp,
                                    float x,
                                    float y,
                                    float z)

Sets the translation for a specific LineGroup

Parameters:

grp - index of LineGroup

setLineGroupVisible

public void setLineGroupVisible(int idx,
                                boolean s)

Sets the visibility of the indicated LineGroup

Parameters:

idx - LineGroup index

s - visibility state

setLineGroupsVisible

public void setLineGroupsVisible(boolean s)

Sets the visibility of all LineGroups

Parameters:

s - visibility state

setPointGroupRotation

public void setPointGroupRotation(float x,
                                  float y,
                                  float z,
                                  float a)

Sets the rotation for the entire set of PointGroups

setPointGroupTranslation

public void setPointGroupTranslation(float x,
                                     float y,
                                     float z)

Sets the translation for the entire set of PointGroups

setPointGroupRotation

public void setPointGroupRotation(int grp,
                                  float x,
                                  float y,
                                  float z,
                                  float a)

Sets the rotation for a specific PointGroup

Parameters:

grp - index of PointGroup

setPointGroupTranslation

public void setPointGroupTranslation(int grp,
                                     float x,
                                     float y,
                                     float z)

Sets the translation for a specific PointGroup

Parameters:

grp - index of PointGroup

setPointGroupVisible

public void setPointGroupVisible(boolean s)

Sets the visibility of all points in all groups

Parameters:

s - visibility state

setPointGroupVisible

public void setPointGroupVisible(int grp,
                                 boolean s)

Sets the visibility of all points in a group

Parameters:

grp - group index

s - visibility state

setSegmentVisible

public void setSegmentVisible(int grp,
                              int idx,
                              boolean s)

Sets the visibility of the indicated segment

Parameters:

grp - group index

idx - segment index

s - visibility state

setSegmentGroupVisible

public void setSegmentGroupVisible(int grp,
                                   boolean s)

Sets the visibility of all segments in a group

Parameters:

grp - group index

s - visibility state

setSegmentGroupRotation

public void setSegmentGroupRotation(float x,
                                    float y,
                                    float z,
                                    float a)

Sets the rotation for the entire set of SegmentGroups

setSegmentGroupTranslation

public void setSegmentGroupTranslation(float x,
                                       float y,
                                       float z)

Sets the translation for the entire set of SegmentGroups

setSegmentGroupRotation

public void setSegmentGroupRotation(int grp,
                                    float x,
                                    float y,
                                    float z,
                                    float a)

Sets the rotation for a specific SegmentGroup

Parameters:

grp - index of SegmentGroup

setSegmentGroupTranslation

public void setSegmentGroupTranslation(int grp,
                                       float x,
                                       float y,
                                       float z)

Sets the translation for a specific SegmentGroup

Parameters:

grp - index of SegmentGroup

setSegmentGroupRotation

public void setSegmentGroupRotation(int grp,
                                    int idx,
                                    float x,
                                    float y,
                                    float z,
                                    float a)

Sets the rotation for a specific SegmentGroup

Parameters:

grp - index of SegmentGroup

idx - index of the segment

setSegmentGroupTranslation

public void setSegmentGroupTranslation(int grp,
                                       int idx,
                                       float x,
                                       float y,
                                       float z)

Sets the translation for a specific SegmentGroup

Parameters:

grp - index of SegmentGroup

idx - index of the segment

setRotation

public void setRotation(float x,
                        float y,
                        float z,
                        float a)

Set rotation for the entire structure.

setTranslation

public void setTranslation(float x,
                           float y,
                           float z)

Set the translation for the entire structure.

mulUnitCellRotation

public void mulUnitCellRotation(float x,
                                float y,
                                float z,
                                float a)

mulUnitCellTranslation

public void mulUnitCellTranslation(float x,
                                   float y,
                                   float z)

setUnitCellRotation

public void setUnitCellRotation(float x,
                                float y,
                                float z,
                                float a)

setUnitCellTranslation

public void setUnitCellTranslation(float x,
                                   float y,
                                   float z)

setViewDistance

public void setViewDistance(float r)

Sets the viewing distance.

Parameters:

r - new viewing distance (along z axis)

showPieces

public void showPieces()

assemblePieces

public void assemblePieces()

resetAnimation

public void resetAnimation()

getIsAnimate

public boolean getIsAnimate()

run

public void run()

Specified by:

run in interface java.lang.Runnable