package ndcp1; // // Viewer for nuclear lattice models // // Written by: R. W. Gray // Date: 02-23-1999 // Version: 0.01 // import java.awt.*; import java.awt.event.*; import com.sun.j3d.utils.applet.MainFrame; import com.sun.j3d.utils.universe.*; import com.sun.j3d.utils.geometry.*; import javax.media.j3d.*; import javax.vecmath.*; import javax.swing.*; import javax.swing.event.*; import javax.swing.tree.*; import java.util.*; //import java.awt.AWTEvent; import java.util.Enumeration; //import com.sun.j3d.utils.behaviors.keyboard.*; public class ndcp extends JFrame implements Constants { static Dimension windowSize; JPanel contentPane; BorderLayout borderLayout1 = new BorderLayout(); static ndcp theApp; // The application object static JFrame theFrame; // The application frame static NDCPMenu theMenu; // The nucleon tables are [nucleon][x,y,z][p,n] static int[][][] FCC = new int[MAX_NUCLEONS][3][2]; static int[][][] SCP = new int[MAX_NUCLEONS][3][2]; static int[][][] IPLG = new int[MAX_NUCLEONS][3][2]; // [which-nucleon][0=currently-displayed, 1=transparence-value] MySphere[] theProtons = new MySphere[MAX_NUCLEONS]; MySphere[] theNeutrons = new MySphere[MAX_NUCLEONS]; Shape3D[] allFCCBonds = new Shape3D[2500]; Bond[] fccBonds = new Bond[2500]; int numFCCBonds; int cntFCCppBonds = 0; int cntFCCnnBonds = 0; int cntFCCpnBonds = 0; Shape3D[] allSCPBonds = new Shape3D[2500]; Bond[] scpBonds = new Bond[2500]; int numSCPBonds; int cntSCPppBonds = 0; int cntSCPnnBonds = 0; int cntSCPpnBonds = 0; double bondRadius = 0.10; int showBondType = 0; // 0=none, 1=PP, 2=NN, 3=PN, 4=PP&NN, 5=PP*PN, 6=NN&PN, 7=all // 21 Fission planes Shape3D[] theFissionPlanes = new Shape3D[21]; FissionPlane[] fPlanes = new FissionPlane[21]; int whichFissionPlane = -1; // -1=none, 0, 1, ..., 20 int cntFissionPP = 0; int cntFissionNN = 0; int cntFissionPN = 0; int cntFissionLeft = 0; int cntFissionRight = 0; float FPCr = 0.0f; // fission plane color: red component float FPCg = 0.0f; // fission plane color: green component float FPCb = 0.0f; // fission plane color: blue component float FPTransparency = 0.7f; // fission plane transparency // TransformGroup[] objPPosition = new TransformGroup[MAX_NUCLEONS]; TransformGroup[] objNPosition = new TransformGroup[MAX_NUCLEONS]; TransformGroup[] objPSize = new TransformGroup[MAX_NUCLEONS]; TransformGroup[] objNSize = new TransformGroup[MAX_NUCLEONS]; RandomBehavior myRandomBehavior; AutoRotBehavior myAutoRotBehavior; Switch groupProtons; Switch groupNeutrons; Switch groupAxes; Switch groupFCCBonds; Switch groupSCPBonds; Switch groupFissionPlanes; Switch groupNSpheres; Switch groupJCylinders; Switch groupMCones; Switch groupSCircles; Switch groupICircles; Switch groupAlphas; DirectionalLight lightD1; int cntP; // the number of protons in the array int cntN; // the number of neutrons in the array // Current options/state values, i.e. what model is selected, etc. char model; // G=IPM, L=LDM, F=FCC, S=SCP, A=Alpha, B=IBM, Q=Quarks String modelName; // Display status info boolean DisplayStatus; String[] nucleusName = {"(H) Hydrogen", "(He) Helium", "(Li) Lithium", "(Be) Beryllium", "(B) Boron", "(C) Carbon", "(N) Nitrogen", "(O) Oxygen", "(F) Fluorine", "(Ne) Neon", "(Na) Sodium", "(Mg) Magnesium", "(Al) Aluminum", "(Si) Silicon", "(P) Phosphorus", "(S) Sulfur", "(Cl) Chlorine", "(Ar) Argon", "(K) Potassium", "(Ca) Calcium", "(Sc) Scandium", "(Ti) Titanium", "(V) Vanadium", "(Cr) Chromium", "(Mn) Manganese", "(Fe) Iron", "(Co) Cobalt", "(Ni) Nickel", "(Cu) Copper", "(Zn) Zinc", "(Ga) Gallium", "(Ge) Germanium", "(As) Arsenic", "(Se) Selenium", "(Br) Bromine", "(Kr) Krypton", "(Rb) Rubidium", "(Sr) Strontium", "(Y) Yttrium", "(Zr) Zirconium", "(Nb) Niobium", "(Mo) Molybdenum", "(Tc) Technetium", "(Ru) Ruthenium", "(Rh) Rhodium", "(Pd) Palladium", "(Ag) Silver", "(Cd) Cadmium", "(In) Indium", "(Sn) Tin", "(Sb) Antimony", "(Te) Tellurium", "(I) Iodine", "(Xe) Xenon", "(Cs) Cesium", "(Ba) Barium", "(La) Lanthanum", "(Ce) Cerium", "(Pr) Praseodymium", "(Nd) Neodymium", "(Pr) Promethium", "(Sm) Samarium", "(Eu) Europium", "(Gd) Gadolinium", "(Tb) Terbium", "(Dy) Dysprosium", "(Ho) Holmium", "(Er) Erbium", "(Tm) Thulium", "(Yb) Ytterbium", "(Lu) Lutecium", "(Hf) Hafnium", "(Ta) Tantalum", "(W) Tungsten", "(Re) Rhenium", "(Os) Osmium", "(Ir) Iridium", "(Pt) Platinum", "(Au) Gold", "(Hg) Mercury", "(Tl) Thallium", "(Pb) Lead", "(Bi) Bismuth", "(Po) Polonium", "(At) Astatine", "(Rn) Radon", "(Fr) Francium", "(Ra) Radium", "(Ac) Actinium", "(Th) Thorium", "(Pa) Protactinium", "(U) Uranium", "(Np) Neptunium", "(Pu) Plutonium", "(Am) Americium", "(Cm) Curium", "(Bk) Berkelium", "(Cf) Californium", "(Es) Einsteinium", "(Fm) Fermium", "(Md) Mendelevium", "(No) Nobelium", "(Lr) Lawrencium" }; int currentZ; int currentN; double fccSpacing; // with the fcc coordinates used, this is 2 * sqrt(2) double currentLatticeSpacing; // in fm units, distance to nearest nucleon double currentNucleonRadius; // in fm units // view platform location float vInitZLoc; // initial Z-axis location float vpX = 0.0f; float vpY = 0.0f; float vpZ = 25.0f; float vpRadiusInc = 0.025f; // Pecentage of radius for change float voX = 0.0f; float voY = 1.0f; float voZ = 0.0f; // Revolve parameters double revolveSpeed = 5.0; // in degrees boolean revolveOn = false; boolean revolveX = true; boolean revolveY = false; boolean revolveZ = false; boolean zoomR = false; // Axes parameters // 0=x, 1=y, 2=z, 3=xy, 4=yz, 5=xz Shape3D[] theAxes = new Shape3D[6]; float AXISCr = 0.0f; // axis color: red component float AXISCg = 0.0f; // axis color: green component float AXISCb = 0.0f; // axis color: blue component float axisLength = 5.0f; boolean xOn = false; boolean yOn = false; boolean zOn = false; boolean xyOn = false; boolean yzOn = false; boolean xzOn = false; // Shells: Sub-Structure Parameters // Quantum Number Color Options: Which quantum numbers to color. int QNCOption = 6; // 0=none, 1=n, 2=j, 3=m, 4=l, 5=s, 6=i // At most, there are 7 sub-structures to be displayed, e.g. n=0, 1, ..., 6 // Each sub-structure/shell needs a different color. // Each type of shell (n, j, m, s, i) can share the sam appearance. float[][] theColors = new float[7][3]; // [level][r,g,b] Appearance[] theShellAppearances = new Appearance[7]; boolean showSubstructure = false; float SubStructureTransparency = 0.3f; Sphere[] nSpheres = new Sphere[7]; float[] nRadius = new float[7]; // radius for each n value float[] jRadius = new float[7]; // radius for each j vlaue Shape3D[] jCylinders = new Shape3D[7]; Shape3D[] mCones = new Shape3D[7]; Shape3D[] iCircles = new Shape3D[7]; Shape3D[] sCircles = new Shape3D[7]; // alpha clusters int MAXALPHA = 10; Sphere[] alphaSphere = new Sphere[MAXALPHA]; // use the same sphere for all alpha clusters float[][] alphaCenter = new float[MAXALPHA][3]; // (x, y, z) for each alpha int numAlphas; // number of alphas defined float alphaRadius; // current alpha radius TransformGroup AlphaTG; // Used to set and change the size of all alpha spheres boolean DisplayAlpahaAsWire = false; Appearance alphaWire; Appearance alphaSolid; // Background Parameters Background BG; // the background; float BGCr = 0.0f; // background color: red component float BGCg = 0.0f; // background color: green component float BGCb = 0.0f; // background color: blue component // Text Colors float TCr = 1.0f; // text color: red component float TCg = 1.0f; // text color: green component float TCb = 1.0f; // text color: blue component // main() is only called if running as an application /* public static void main(String[] args) { theApp = new NDCP(); theApp.init(); // call the init method } // end main */ public static void main(String[] p) { theApp = new ndcp(); } /**Construct the frame*/ public ndcp() { enableEvents(AWTEvent.WINDOW_EVENT_MASK); try { jbInit(); } catch(Exception e) { e.printStackTrace(); } } /**Overridden so we can exit when window is closed*/ protected void processWindowEvent(WindowEvent e) { super.processWindowEvent(e); if (e.getID() == WindowEvent.WINDOW_CLOSING) { System.exit(0); } } private void jbInit() throws Exception { //setIconImage(Toolkit.getDefaultToolkit().createImage(ndcp.class.getResource("[Your Icon]"))); contentPane = (JPanel) this.getContentPane(); contentPane.setLayout(borderLayout1); this.setSize(new Dimension(400, 300)); this.setTitle("Nuclear Display Computer Program"); theApp = this; currentZ = 0; currentN = 0; model = 'G'; // Start with IPM modelName = new String("Independent Particle"); fccSpacing = 2.0 * Math.sqrt(2.0); currentLatticeSpacing = 2.026; // 2.026 fm between nearest fcc lattice sites. currentNucleonRadius = 0.86; // in fm units. showBondType = 0; DisplayStatus = true; // The structures/substructures are to be colored in the // following color order. // red theColors[0][0] = 1.0f; theColors[0][1] = 0.0f; theColors[0][2] = 0.0f; // yellow theColors[1][0] = 1.0f; theColors[1][1] = 1.0f; theColors[1][2] = 0.0f; // purple theColors[2][0] = 219.0f / 255.0f; theColors[2][1] = 0.0f / 255.0f; theColors[2][2] = 219.0f / 255.0f; // green theColors[3][0] = 0.0f; theColors[3][1] = 1.0f; theColors[3][2] = 0.0f; // blue theColors[4][0] = 0.0f; theColors[4][1] = 0.0f; theColors[4][2] = 1.0f; // tan theColors[5][0] = 255.0f / 255.0f; theColors[5][1] = 180.0f / 255.0f; theColors[5][2] = 104.0f / 255.0f; // magenta theColors[6][0] = 1.0f; theColors[6][1] = 0.0f; theColors[6][2] = 1.0f; for (int i = 0; i < 7; i++) { theShellAppearances[i] = createShellAppearance(theColors[i][0], theColors[i][1], theColors[i][2]); } // end for statement // initial view platform location vInitZLoc = 25.0f; // Initial view platform z-axis location // before we do *anything*, get the window size. theFrame = new JFrame("Nuclear Display Computer Program"); theFrame.getContentPane().setBackground(Color.black); theFrame.getContentPane().setLayout(new BorderLayout()); Toolkit theKit = theFrame.getToolkit(); windowSize = theKit.getScreenSize(); theFrame.setBounds(0, 0, windowSize.width, windowSize.height); FCCcoordinates(); SCPcoordinates(); // define all bonds; // FCC Bonds numFCCBonds = 0; // PP bonds for (int i = 0; i < (cntP-1); i++) { double x1 = theProtons[i].fccX; double y1 = theProtons[i].fccY; double z1 = theProtons[i].fccZ; for (int j = i+1; j < cntP; j++) { double x2 = theProtons[j].fccX; double y2 = theProtons[j].fccY; double z2 = theProtons[j].fccZ; double d = Math.sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1)); if (d < 3.0) { fccBonds[numFCCBonds] = new Bond(theApp, i, j, 1); numFCCBonds++; } // end if statement } // end for statement } // end for statement // NN bonds for (int i = 0; i < (cntN-1); i++) { double x1 = theNeutrons[i].fccX; double y1 = theNeutrons[i].fccY; double z1 = theNeutrons[i].fccZ; for (int j = i+1; j < cntN; j++) { double x2 = theNeutrons[j].fccX; double y2 = theNeutrons[j].fccY; double z2 = theNeutrons[j].fccZ; double d = Math.sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1)); if (d < 3.0) { fccBonds[numFCCBonds] = new Bond(theApp, i, j, 2); numFCCBonds++; } // end if statement } // end for statement } // end for statement // PN bonds for (int i = 0; i < cntP; i++) { double x1 = theProtons[i].fccX; double y1 = theProtons[i].fccY; double z1 = theProtons[i].fccZ; for (int j = 0; j < cntN; j++) { double x2 = theNeutrons[j].fccX; double y2 = theNeutrons[j].fccY; double z2 = theNeutrons[j].fccZ; double d = Math.sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1)); if (d < 3.0) { fccBonds[numFCCBonds] = new Bond(theApp, i, j, 3); numFCCBonds++; } // end if statement } // end for statement } // end for statement // // SCP Bonds // numSCPBonds = 0; // PP bonds for (int i = 0; i < (cntP-1); i++) { double x1 = theProtons[i].scpX; double y1 = theProtons[i].scpY; double z1 = theProtons[i].scpZ; for (int j = i+1; j < cntP; j++) { double x2 = theProtons[j].scpX; double y2 = theProtons[j].scpY; double z2 = theProtons[j].scpZ; double d = Math.sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1)); if (d < 2.1) { scpBonds[numSCPBonds] = new Bond(theApp, i, j, 4); numSCPBonds++; } // end if statement } // end for statement } // end for statement // NN bonds for (int i = 0; i < (cntN-1); i++) { double x1 = theNeutrons[i].scpX; double y1 = theNeutrons[i].scpY; double z1 = theNeutrons[i].scpZ; for (int j = i+1; j < cntN; j++) { double x2 = theNeutrons[j].scpX; double y2 = theNeutrons[j].scpY; double z2 = theNeutrons[j].scpZ; double d = Math.sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1)); if (d < 2.1) { scpBonds[numSCPBonds] = new Bond(theApp, i, j, 5); numSCPBonds++; } // end if statement } // end for statement } // end for statement // PN bonds for (int i = 0; i < cntP; i++) { double x1 = theProtons[i].scpX; double y1 = theProtons[i].scpY; double z1 = theProtons[i].scpZ; for (int j = 0; j < cntN; j++) { double x2 = theNeutrons[j].scpX; double y2 = theNeutrons[j].scpY; double z2 = theNeutrons[j].scpZ; double d = Math.sqrt((x2 - x1)*(x2 - x1) + (y2 - y1)*(y2 - y1) + (z2 - z1)*(z2 - z1)); if (d < 2.1) { scpBonds[numSCPBonds] = new Bond(theApp, i, j, 6); numSCPBonds++; if ((i == 3) && (j == 12)) { System.out.println("P3-N12 SCP bond found: #"+(numSCPBonds-1)); } if ((i == 12) && (j == 1)) { System.out.println("P12-N1 SCP bond found #"+(numSCPBonds-1)); } } // end if statement } // end for statement } // end for statement System.out.println("Num fcc bonds: "+numFCCBonds); System.out.println("Num scp bonds: "+numSCPBonds); // define radii for each n value float[] accumR = new float[7]; int[] countsR = {0, 0, 0, 0, 0, 0, 0}; for (int i = 0; i < cntP; i++) { float x = theProtons[i].fccX; float y = theProtons[i].fccY; float z = theProtons[i].fccZ; accumR[theProtons[i].n] += Math.sqrt(x * x + y * y + z * z); countsR[theProtons[i].n]++; } // end for statement for (int i = 0; i < cntN; i++) { float x = theNeutrons[i].fccX; float y = theNeutrons[i].fccY; float z = theNeutrons[i].fccZ; accumR[theNeutrons[i].n] += Math.sqrt(x * x + y * y + z * z); countsR[theNeutrons[i].n]++; } // end for statement for (int i = 0; i < 7; i++) { nRadius[i] = accumR[i] / countsR[i]; } // end for statement // define cylinder radii for each j value float[] accumX = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}; float[] accumY = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}; int[] counts = {0, 0, 0, 0, 0, 0, 0}; float[] accumRr = {0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f, 0.0f}; for (int i = 0; i < cntP; i++) { int j = (int)((theProtons[i].j / 2.0f) + 0.5f) - 1; accumRr[j] += Math.sqrt(theProtons[i].fccX * theProtons[i].fccX + theProtons[i].fccY * theProtons[i].fccY); counts[j]++; } // end for statement i for (int i = 0; i < cntN; i++) { int j = (int)((theNeutrons[i].j / 2.0f) + 0.5f) - 1; accumRr[j] += Math.sqrt(theNeutrons[i].fccX * theNeutrons[i].fccX + theNeutrons[i].fccY * theNeutrons[i].fccY); counts[j]++; } // end for statement i for (int i = 0; i < 7; i++) { jRadius[i] = accumRr[i] / counts[i]; } // end for statement // Define all alpha clusters numAlphas = 0; alphaWire = createAlphaWire(); alphaSolid = createAlphaSolid(); alphaRadius = (float)Math.sqrt(2.0); alphaSphere[0] = new Sphere(alphaRadius, Sphere.ENABLE_APPEARANCE_MODIFY | Sphere.GENERATE_NORMALS, null); alphaSphere[0].setAppearance(alphaWire); alphaCenter[numAlphas][0] = 0.0f; // (x, y, z) for each alpha alphaCenter[numAlphas][1] = 0.0f; alphaCenter[numAlphas][2] = 0.0f; numAlphas++; alphaSphere[1] = new Sphere(alphaRadius, Sphere.ENABLE_APPEARANCE_MODIFY | Sphere.GENERATE_NORMALS, null); alphaSphere[1].setAppearance(alphaWire); alphaCenter[numAlphas][0] = 2.0f; // (x, y, z) for each alpha alphaCenter[numAlphas][1] = 0.0f; alphaCenter[numAlphas][2] = 0.0f; numAlphas++; // Start Testing float hz = 0.0f; for (int i = 0; i < cntN; i++) { float x = theNeutrons[i].fccX; float y = theNeutrons[i].fccY; float z = theNeutrons[i].fccZ; if (theNeutrons[i].fccZ == 13.0f) { System.out.println("("+theNeutrons[i].fccX+", "+theNeutrons[i].fccY+", "+theNeutrons[i].fccZ+")"); hz = theNeutrons[i].fccZ; } // end if statement } // end for statement // End Testing // SimpleUniverse is a Convenience Utility class MyCanvas3D canvas3D = new MyCanvas3D(theApp); SimpleUniverse simpleU = new SimpleUniverse(canvas3D); // creat the menu // This is required! Otherwise the heaveyweight canvas3D // sits on to of the lightweight menus and you never see them. JPopupMenu.setDefaultLightWeightPopupEnabled(false); theMenu = new NDCPMenu(theApp); // create all the geometry BranchGroup scene = createSceneGraph(simpleU); simpleU.addBranchGraph(scene); theFrame.setJMenuBar(theMenu); theFrame.getContentPane().add("Center", canvas3D); theFrame.setVisible(true); } // end init() public BranchGroup createSceneGraph(SimpleUniverse SU) { // Create the root of the branch graph BranchGroup objRoot = new BranchGroup(); // setup the background color BoundingSphere worldBounds = new BoundingSphere(new Point3d( 0.0, 0.0, 0.0 ), 1000.0 ); BG = new Background(BGCr, BGCg, BGCb); BG.setCapability(Background.ALLOW_COLOR_WRITE); BG.setApplicationBounds(worldBounds); objRoot.addChild(BG); // Create a light source AmbientLight lightA = new AmbientLight(); lightA.setInfluencingBounds(new BoundingSphere(new Point3d(0.0,0.0,0.0), 1000.0)); objRoot.addChild(lightA); lightD1 = new DirectionalLight(); lightD1.setInfluencingBounds(new BoundingSphere(new Point3d(0.0,0.0,0.0), 1000.0)); lightD1.setCapability(DirectionalLight.ALLOW_DIRECTION_WRITE); objRoot.addChild(lightD1); // Construct the FCC model // ***** Sphere branch ****** // add a transform object to allow scaling the spheres // Transform3D T3DScale = new Transform3D(); // T3DScale.setScale(currentNucleonRadius); TransformGroup objBehave = new TransformGroup(); objBehave.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE); objRoot.addChild(objBehave); myRandomBehavior = new RandomBehavior(objBehave, theApp); myRandomBehavior.setSchedulingBounds(worldBounds); objBehave.addChild(myRandomBehavior); // Add switch to allow render picking of protons groupProtons = new Switch(); groupProtons.setCapability(Switch.ALLOW_SWITCH_WRITE); objBehave.addChild(groupProtons); for (int i = 0; i < cntP; i++) { // add a transform group to give location of sphere float x = theProtons[i].fccX; float y = theProtons[i].fccY; float z = theProtons[i].fccZ; Transform3D T3DP = new Transform3D(); T3DP.setTranslation(new Vector3f(x, y, z)); objPPosition[i] = new TransformGroup(T3DP); objPPosition[i].setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE); groupProtons.addChild(objPPosition[i]); Transform3D T3DPSize = new Transform3D(); T3DPSize.setScale(currentNucleonRadius / currentLatticeSpacing); objPSize[i] = new TransformGroup(T3DPSize); objPSize[i].setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE); objPPosition[i].addChild(objPSize[i]); theProtons[i].setAppearance(createAppearanceProton()); theProtons[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); theProtons[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); objPSize[i].addChild(theProtons[i]); } // end for statement // Add switch to allow render picking of neutrons groupNeutrons = new Switch(); groupNeutrons.setCapability(Switch.ALLOW_SWITCH_WRITE); objBehave.addChild(groupNeutrons); for (int i = 0; i < cntN; i++) { // add a transform group to give location of sphere float x = theNeutrons[i].fccX; float y = theNeutrons[i].fccY; float z = theNeutrons[i].fccZ; Transform3D T3DN = new Transform3D(); T3DN.setTranslation(new Vector3f(x, y, z)); objNPosition[i] = new TransformGroup(T3DN); objNPosition[i].setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE); groupNeutrons.addChild(objNPosition[i]); Transform3D T3DNSize = new Transform3D(); T3DNSize.setScale(currentNucleonRadius / currentLatticeSpacing); objNSize[i] = new TransformGroup(T3DNSize); objNSize[i].setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE); objNPosition[i].addChild(objNSize[i]); theNeutrons[i].setAppearance(createAppearanceNeutron()); theNeutrons[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); theNeutrons[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); objNSize[i].addChild(theNeutrons[i]); } // end for statement // Determine which to make visible groupProtons.setWhichChild(Switch.CHILD_MASK); groupProtons.setChildMask(getProtonMask()); groupNeutrons.setWhichChild(Switch.CHILD_MASK); groupNeutrons.setChildMask(getNeutronMask()); // Set the initial viewing platform location TransformGroup vpTrans = null; Transform3D T3D = new Transform3D(); Vector3f translate = new Vector3f(); vpTrans = SU.getViewingPlatform().getViewPlatformTransform(); translate.set(0.0f, 0.0f, vInitZLoc); T3D.setTranslation(translate); vpTrans.setTransform(T3D); myAutoRotBehavior = new AutoRotBehavior(vpTrans, theApp); myAutoRotBehavior.setSchedulingBounds(worldBounds); myAutoRotBehavior.setEnable(false); objRoot.addChild(myAutoRotBehavior); SimpleBehaviorZ myKeyInputBehavior = new SimpleBehaviorZ(theApp, SU, vpTrans, vpZ); myKeyInputBehavior.setSchedulingBounds(worldBounds); objRoot.addChild(myKeyInputBehavior); SimpleMouseBehavior myMouseBehavior = new SimpleMouseBehavior(theApp, SU, vpTrans, vpZ); myMouseBehavior.setSchedulingBounds(worldBounds); objRoot.addChild(myMouseBehavior); SU.getViewer().getView().setDepthBufferFreezeTransparent(false); // set up the axes and planes groupAxes = new Switch(); groupAxes.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupAxes); MyAxes anAxis = new MyAxes(theApp, 'X'); theAxes[0] = new Shape3D(); theAxes[0].setGeometry(anAxis.Line()); theAxes[0].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theAxes[0].setAppearance(anAxis.createAppearanceLine()); groupAxes.addChild(theAxes[0]); anAxis = new MyAxes(theApp, 'Y'); theAxes[1] = new Shape3D(); theAxes[1].setGeometry(anAxis.Line()); theAxes[1].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theAxes[1].setAppearance(anAxis.createAppearanceLine()); groupAxes.addChild(theAxes[1]); anAxis = new MyAxes(theApp, 'Z'); theAxes[2] = new Shape3D(); theAxes[2].setGeometry(anAxis.Line()); theAxes[2].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theAxes[2].setAppearance(anAxis.createAppearanceLine()); groupAxes.addChild(theAxes[2]); MyXYZPlane aPlane = new MyXYZPlane(theApp, "XY"); theAxes[3] = new Shape3D(); theAxes[3].setGeometry(aPlane.Solid()); theAxes[3].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theAxes[3].setAppearance(aPlane.createAppearanceSolid()); groupAxes.addChild(theAxes[3]); aPlane = new MyXYZPlane(theApp, "YZ"); theAxes[4] = new Shape3D(); theAxes[4].setGeometry(aPlane.Solid()); theAxes[4].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theAxes[4].setAppearance(aPlane.createAppearanceSolid()); groupAxes.addChild(theAxes[4]); aPlane = new MyXYZPlane(theApp, "XZ"); theAxes[5] = new Shape3D(); theAxes[5].setGeometry(aPlane.Solid()); theAxes[5].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theAxes[5].setAppearance(aPlane.createAppearanceSolid()); groupAxes.addChild(theAxes[5]); // Determine which to make visible groupAxes.setWhichChild(Switch.CHILD_MASK); groupAxes.setChildMask(getAxesMask()); // Define all bonds // FCC Bonds groupFCCBonds = new Switch(); groupFCCBonds.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupFCCBonds); Appearance anApp; Material theMaterial; for (int i = 0; i < numFCCBonds; i++) { allFCCBonds[i] = new Shape3D(); allFCCBonds[i].setGeometry(fccBonds[i].Solid()); allFCCBonds[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); anApp = fccBonds[i].createAppearanceSolid(); theMaterial = anApp.getMaterial(); if (fccBonds[i].type == 1) theMaterial.setDiffuseColor(1.0f, 0.0f, 0.0f); if (fccBonds[i].type == 2) theMaterial.setDiffuseColor(0.0f, 0.0f, 1.0f); if (fccBonds[i].type == 3) theMaterial.setDiffuseColor(0.7f, 0.7f, 0.7f); allFCCBonds[i].setAppearance(anApp); groupFCCBonds.addChild(allFCCBonds[i]); } // end for statement // Determine which bonds to display groupFCCBonds.setWhichChild(Switch.CHILD_MASK); groupFCCBonds.setChildMask(getFCCBondMask()); // SCP Bonds groupSCPBonds = new Switch(); groupSCPBonds.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupSCPBonds); for (int i = 0; i < numSCPBonds; i++) { allSCPBonds[i] = new Shape3D(); allSCPBonds[i].setGeometry(scpBonds[i].Solid()); allSCPBonds[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); anApp = scpBonds[i].createAppearanceSolid(); theMaterial = anApp.getMaterial(); if (scpBonds[i].type == 4) theMaterial.setDiffuseColor(1.0f, 0.0f, 0.0f); if (scpBonds[i].type == 5) theMaterial.setDiffuseColor(0.0f, 0.0f, 1.0f); if (scpBonds[i].type == 6) theMaterial.setDiffuseColor(0.7f, 0.7f, 0.7f); allSCPBonds[i].setAppearance(anApp); groupSCPBonds.addChild(allSCPBonds[i]); } // end for statement // Determine which bonds to display groupSCPBonds.setWhichChild(Switch.CHILD_MASK); groupSCPBonds.setChildMask(getSCPBondMask()); // // there are 21 plans for fission: 12 assym, 9 sym = 21. // groupFissionPlanes = new Switch(); groupFissionPlanes.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupFissionPlanes); for (int i = 0; i < 21; i++) { fPlanes[i] = new FissionPlane(theApp, i); theFissionPlanes[i] = new Shape3D(); theFissionPlanes[i].setGeometry(fPlanes[i].Solid()); theFissionPlanes[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); theFissionPlanes[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); theFissionPlanes[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); theFissionPlanes[i].setAppearance(fPlanes[i].createAppearanceSolid()); groupFissionPlanes.addChild(theFissionPlanes[i]); } // end for statement groupFissionPlanes.setWhichChild(Switch.CHILD_MASK); groupFissionPlanes.setChildMask(getFissionPlaneMask()); // setup the initial substructure spheres, cylinders, cones, circles. // 7 N spheres: groupNSpheres = new Switch(); groupNSpheres.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupNSpheres); for (int i = 0; i < 7; i++) { nSpheres[i] = new Sphere(nRadius[i], Sphere.ENABLE_APPEARANCE_MODIFY | Sphere.GENERATE_NORMALS, null); nSpheres[i].setAppearance(theShellAppearances[i]); groupNSpheres.addChild(nSpheres[i]); } // end for statement groupNSpheres.setWhichChild(Switch.CHILD_MASK); groupNSpheres.setChildMask(getNSpheresMask()); // 7 J Cylinders groupJCylinders = new Switch(); groupJCylinders.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupJCylinders); for (int i = 0; i < 7; i++) { MyCylinder myCyl = new MyCylinder(0.0f, 0.0f, -2.0f, 0.0f, 0.0f, 2.0f, jRadius[i]); jCylinders[i] = new Shape3D(); jCylinders[i].setGeometry(myCyl.Solid()); jCylinders[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); jCylinders[i].setAppearance(theShellAppearances[i]); jCylinders[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); jCylinders[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); groupJCylinders.addChild(jCylinders[i]); } // end for statement groupJCylinders.setWhichChild(Switch.CHILD_MASK); groupJCylinders.setChildMask(getJCylindersMask()); // M Cones: groupMCones = new Switch(); groupMCones.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupMCones); for (int i = 0; i < 7; i++) { MyCone myCone = new MyCone((float)(2*i + 1), 2.0f); mCones[i] = new Shape3D(); mCones[i].setGeometry(myCone.Solid()); mCones[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); mCones[i].setAppearance(theShellAppearances[i]); mCones[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); mCones[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); groupMCones.addChild(mCones[i]); } // end for statement groupMCones.setWhichChild(Switch.CHILD_MASK); groupMCones.setChildMask(getMConesMask()); // S Circles groupSCircles = new Switch(); groupSCircles.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupSCircles); for (int i = 0; i < 7; i++) { MyCircle myCircle = new MyCircle('X', 1.0f*(i+1), 1.0f); sCircles[i] = new Shape3D(); sCircles[i].setGeometry(myCircle.Solid()); sCircles[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); sCircles[i].setAppearance(theShellAppearances[i]); sCircles[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); sCircles[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); groupSCircles.addChild(sCircles[i]); } // end for statement groupSCircles.setWhichChild(Switch.CHILD_MASK); groupSCircles.setChildMask(getSCirclesMask()); // I Circles groupICircles = new Switch(); groupICircles.setCapability(Switch.ALLOW_SWITCH_WRITE); objRoot.addChild(groupICircles); for (int i = 0; i < 7; i++) { MyCircle myCircle = new MyCircle('Z', 1.0f*(i+1), 1.0f); iCircles[i] = new Shape3D(); iCircles[i].setGeometry(myCircle.Solid()); iCircles[i].setCapability(Shape3D.ALLOW_GEOMETRY_WRITE); iCircles[i].setAppearance(theShellAppearances[i]); iCircles[i].setCapability(Shape3D.ALLOW_APPEARANCE_READ); iCircles[i].setCapability(Shape3D.ALLOW_APPEARANCE_WRITE); groupICircles.addChild(iCircles[i]); } // end for statement groupICircles.setWhichChild(Switch.CHILD_MASK); groupICircles.setChildMask(getICirclesMask()); // // // Alpha Cluster Spheres // Scale all alphas Transform3D T3DASize = new Transform3D(); T3DASize.setScale(alphaRadius); AlphaTG = new TransformGroup(T3DASize); AlphaTG.setCapability(TransformGroup.ALLOW_TRANSFORM_WRITE); objRoot.addChild(AlphaTG); // Allow each alpha cluster sphere to be turned on and off groupAlphas = new Switch(); groupAlphas.setCapability(Switch.ALLOW_SWITCH_WRITE); AlphaTG.addChild(groupAlphas); for (int i = 0; i < numAlphas; i++) { // add a transform group to give location of alpha sphere float x = alphaCenter[i][0]; float y = alphaCenter[i][1]; float z = alphaCenter[i][2]; Transform3D T3DA = new Transform3D(); T3DA.setTranslation(new Vector3f(x, y, z)); TransformGroup TG = new TransformGroup(T3DA); groupAlphas.addChild(TG); TG.addChild(alphaSphere[i]); } // end for statement groupAlphas.setWhichChild(Switch.CHILD_MASK); groupAlphas.setChildMask(getAlphaMask()); // objRoot.compile(); return(objRoot); } // end of createSceneGraph method public void FCCcoordinates() { cntP = 0; cntN = 0; // generate all the (x, y, z) coordinates for the nucleons. int Shells = 6; int K = 0; for (int N = 0; N <= Shells; N++) { for (int L = N; L >=0; L--) { int JJ = (int)(2.0 * (double)L + 1.0); for (int M = (0-JJ); M<=JJ; M=M+2) { // for protons, i = -1 for (int i = -1; i<=1; i=i+2) { double x = Math.abs(M) * Math.pow(-1.0, ((double)M)/2.0 + 0.5); double y = ((double)(JJ) + 1.0 - Math.abs(x)) * Math.pow(-1.0, (double)(-i)/2.0+(double)(JJ)/2.0+(double)(M)/2.0+0.5); double z = (2.0*(double)(N) + 3.0 - Math.abs(x) - Math.abs(y)) * Math.pow(-1.0, (double)(-i)/2.0 + (double)(N) - (double)(JJ)/2.0 - 1.0); int f = (i + 1) / 2; FCC[K][0][f] = (int)x; FCC[K][1][f] = (int)y; FCC[K][2][f] = (int)z; if (i == -1) { // create a proton theProtons[cntP] = new MySphere(N, JJ, M, L, 1, i, (float)x, (float)y, (float)z); cntP++; } else { // create a neutron theNeutrons[cntN] = new MySphere(N, JJ, M, L, 1, i, (float)x, (float)y, (float)z); cntN++; } // end if else } // end for i K = K + 1; } // end for M statement } // end for L statement } // end for N statement } // end FCCcoordinates public void SCPcoordinates() { // called only after FCCcoordinates() has been called int j = -1; // for (int k = 0; k<=167; k++) for (int k = 0; k<=(cntP/2 - 1); k++) { j = j + 1; SCP[j][0][0] = FCC[k][0][0]; SCP[j][1][0] = FCC[k][1][0]; SCP[j][2][0] = FCC[k][2][0]; theProtons[j].scpX = FCC[k][0][0]; theProtons[j].scpY = FCC[k][1][0]; theProtons[j].scpZ = FCC[k][2][0]; SCP[j][0][1] = FCC[k][0][1]; SCP[j][1][1] = FCC[k][1][1]; SCP[j][2][1] = FCC[k][2][1]; theNeutrons[j].scpX = FCC[k][0][1]; theNeutrons[j].scpY = FCC[k][1][1]; theNeutrons[j].scpZ = FCC[k][2][1]; j = j + 1; SCP[j][0][0] = -FCC[k][0][0]; SCP[j][1][0] = FCC[k][1][0]; SCP[j][2][0] = FCC[k][2][0]; theProtons[j].scpX = -FCC[k][0][0]; theProtons[j].scpY = FCC[k][1][0]; theProtons[j].scpZ = FCC[k][2][0]; SCP[j][0][1] = FCC[k][0][1]; SCP[j][1][1] = -FCC[k][1][1]; SCP[j][2][1] = FCC[k][2][1]; theNeutrons[j].scpX = FCC[k][0][1]; theNeutrons[j].scpY = -FCC[k][1][1]; theNeutrons[j].scpZ = FCC[k][2][1]; } // end for k statement } // end SCPcoordinates public Appearance createAppearanceProton() { Appearance A = new Appearance(); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_MATERIAL_READ); A.setCapability(Appearance.ALLOW_MATERIAL_WRITE); RenderingAttributes RA = new RenderingAttributes(); RA.setDepthBufferEnable(true); A.setRenderingAttributes(RA); Material theMaterial = new Material(); theMaterial.setCapability(Material.ALLOW_COMPONENT_WRITE); // theMaterial.setAmbientColor(1.0f, 1.0f, 1.0f); theMaterial.setDiffuseColor(1.0f, 0.0f, 0.0f); // theMaterial.setEmissiveColor(1.0f, 1.0f, 1.0f); theMaterial.setLightingEnable(true); // theMaterial.setShininess(0.05f); // theMaterial.setSpecularColor(1.0f, 1.0f, 1.0f); A.setMaterial(theMaterial); A.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_FILL, PolygonAttributes.CULL_NONE, 0.01f, false)); TransparencyAttributes TA = new TransparencyAttributes(TransparencyAttributes.SCREEN_DOOR, 0.0f); TA.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE); A.setTransparencyAttributes(TA); return(A); } // end createAppearanceProton public Appearance createAppearanceNeutron() { Appearance A = new Appearance(); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_MATERIAL_READ); A.setCapability(Appearance.ALLOW_MATERIAL_WRITE); RenderingAttributes RA = new RenderingAttributes(); RA.setDepthBufferEnable(true); A.setRenderingAttributes(RA); Material theMaterial = new Material(); theMaterial.setCapability(Material.ALLOW_COMPONENT_WRITE); // theMaterial.setAmbientColor(1.0f, 1.0f, 1.0f); theMaterial.setDiffuseColor(0.0f, 0.0f, 1.0f); // theMaterial.setEmissiveColor(1.0f, 1.0f, 1.0f); theMaterial.setLightingEnable(true); // theMaterial.setShininess(0.05f); // theMaterial.setSpecularColor(1.0f, 1.0f, 1.0f); A.setMaterial(theMaterial); A.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_FILL, PolygonAttributes.CULL_NONE, 0.01f, false)); TransparencyAttributes TA = new TransparencyAttributes(TransparencyAttributes.SCREEN_DOOR, 0.0f); TA.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE); A.setTransparencyAttributes(TA); return(A); } // end createAppearanceNeutron public Appearance createAlphaWire() { Appearance A = new Appearance(); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_MATERIAL_READ); A.setCapability(Appearance.ALLOW_MATERIAL_WRITE); RenderingAttributes RA = new RenderingAttributes(); RA.setDepthBufferEnable(true); A.setRenderingAttributes(RA); Material theMaterial = new Material(); theMaterial.setCapability(Material.ALLOW_COMPONENT_WRITE); // theMaterial.setAmbientColor(1.0f, 1.0f, 1.0f); theMaterial.setDiffuseColor(0.50f, 0.70f, 1.0f); // theMaterial.setEmissiveColor(1.0f, 1.0f, 1.0f); theMaterial.setLightingEnable(true); // theMaterial.setShininess(0.05f); // theMaterial.setSpecularColor(1.0f, 1.0f, 1.0f); A.setMaterial(theMaterial); A.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_LINE, PolygonAttributes.CULL_NONE, 0.01f, false)); // TransparencyAttributes TA = new TransparencyAttributes(TransparencyAttributes.SCREEN_DOOR, 0.0f); // TA.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE); // A.setTransparencyAttributes(TA); return(A); } // end createAlphaWire public Appearance createAlphaSolid() { Appearance A = new Appearance(); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_MATERIAL_READ); A.setCapability(Appearance.ALLOW_MATERIAL_WRITE); RenderingAttributes RA = new RenderingAttributes(); RA.setDepthBufferEnable(true); A.setRenderingAttributes(RA); Material theMaterial = new Material(); theMaterial.setCapability(Material.ALLOW_COMPONENT_WRITE); // theMaterial.setAmbientColor(1.0f, 1.0f, 1.0f); theMaterial.setDiffuseColor(0.50f, 0.70f, 1.0f); // theMaterial.setEmissiveColor(1.0f, 1.0f, 1.0f); theMaterial.setLightingEnable(true); // theMaterial.setShininess(0.05f); // theMaterial.setSpecularColor(1.0f, 1.0f, 1.0f); A.setMaterial(theMaterial); A.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_FILL, PolygonAttributes.CULL_NONE, 0.01f, false)); TransparencyAttributes TA = new TransparencyAttributes(TransparencyAttributes.SCREEN_DOOR, 0.0f); TA.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE); A.setTransparencyAttributes(TA); return(A); } // end createAlphaSolid public Appearance createShellAppearance(float red, float green, float blue) { Appearance A = new Appearance(); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_READ); A.setCapability(Appearance.ALLOW_TRANSPARENCY_ATTRIBUTES_WRITE); // A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_READ); // A.setCapability(Appearance.ALLOW_LINE_ATTRIBUTES_WRITE); A.setCapability(Appearance.ALLOW_MATERIAL_READ); A.setCapability(Appearance.ALLOW_MATERIAL_WRITE); RenderingAttributes RA = new RenderingAttributes(); RA.setDepthBufferEnable(true); A.setRenderingAttributes(RA); Material theMaterial = new Material(); theMaterial.setCapability(Material.ALLOW_COMPONENT_READ); theMaterial.setCapability(Material.ALLOW_COMPONENT_WRITE); theMaterial.setAmbientColor(0.75f, 0.75f, 0.75f); theMaterial.setDiffuseColor(red, green, blue); // theMaterial.setLightingEnable(true); // theMaterial.setSpecularColor(0.05f, 0.05f, 0.05f); A.setMaterial(theMaterial); A.setPolygonAttributes(new PolygonAttributes(PolygonAttributes.POLYGON_FILL, PolygonAttributes.CULL_NONE, 0.01f, true)); TransparencyAttributes TA = new TransparencyAttributes(TransparencyAttributes.NICEST, SubStructureTransparency); // TA.setCapability(TransparencyAttributes.ALLOW_VALUE_WRITE); A.setTransparencyAttributes(TA); return(A); } // end createShellAppearance public BitSet getProtonMask() { BitSet mask = new BitSet(6); for (int i = 0; i < cntP; i++) { if (theProtons[i].currentlyDisplayed) { mask.set(i); } // end if sttaement } // end for statement return(mask); } // end getProtonsMask public BitSet getNeutronMask() { BitSet mask = new BitSet(6); for (int i = 0; i < cntN; i++) { if (theNeutrons[i].currentlyDisplayed) { mask.set(i); } // end if sttaement } // end for statement return(mask); } // end getNeutronMask public BitSet getAxesMask() { BitSet mask = new BitSet(6); if (xOn) { mask.set(0); } // end if sttaement if (yOn) { mask.set(1); } // end if sttaement if (zOn) { mask.set(2); } // end if sttaement if (xyOn) { mask.set(3); } // end if sttaement if (yzOn) { mask.set(4); } // end if sttaement if (xzOn) { mask.set(5); } // end if sttaement return(mask); } // end getAxesMask public BitSet getFCCBondMask() { cntFCCppBonds = 0; cntFCCnnBonds = 0; cntFCCpnBonds = 0; BitSet mask = new BitSet(12); // showBondType: 0=none, 1=PP, 2=NN, 3=PN, 4=PP&NN, 5=PP&PN, 6=NN&PN, 7=all if (showBondType == 0) return(mask); if (theApp.model != 'F') return(mask); for (int i = 0; i < numFCCBonds; i++) { switch (fccBonds[i].type) { case 1: if ((theProtons[fccBonds[i].p1].currentlyDisplayed) && (theProtons[fccBonds[i].p2].currentlyDisplayed) ) { if ((showBondType == 1) || (showBondType == 4) || (showBondType == 5) || (showBondType == 7)) { mask.set(i); cntFCCppBonds++; } // end if statement } // end if statement break; case 2: if ((theNeutrons[fccBonds[i].n1].currentlyDisplayed) && (theNeutrons[fccBonds[i].n2].currentlyDisplayed) ) { if ((showBondType == 2) || (showBondType == 4) || (showBondType == 6) || (showBondType == 7)) { mask.set(i); cntFCCnnBonds++; } } // end if statement break; case 3: if ((theProtons[fccBonds[i].p1].currentlyDisplayed) && (theNeutrons[fccBonds[i].n1].currentlyDisplayed) ) { if ((showBondType == 3) || (showBondType == 5) || (showBondType == 6) || (showBondType == 7)) { mask.set(i); cntFCCpnBonds++; } } // end if statement break; } // end switch } // end for statement return(mask); } // end getFCCBondMask public BitSet getSCPBondMask() { cntSCPppBonds = 0; cntSCPnnBonds = 0; cntSCPpnBonds = 0; BitSet mask = new BitSet(16); // showBondType: 0=none, 1=PP, 2=NN, 3=PN, 4=PP&NN, 5=PP&PN, 6=NN&PN, 7=all if (showBondType == 0) return(mask); if (theApp.model != 'S') return(mask); for (int i = 0; i < numSCPBonds; i++) { switch (scpBonds[i].type) { case 4: if ((theProtons[scpBonds[i].p1].currentlyDisplayed) && (theProtons[scpBonds[i].p2].currentlyDisplayed) ) { if ((showBondType == 1) || (showBondType == 4) || (showBondType == 5) || (showBondType == 7)) { mask.set(i); cntSCPppBonds++; } } // end if statement break; case 5: if ((theNeutrons[scpBonds[i].n1].currentlyDisplayed) && (theNeutrons[scpBonds[i].n2].currentlyDisplayed) ) { if ((showBondType == 2) || (showBondType == 4) || (showBondType == 6) || (showBondType == 7)) { mask.set(i); cntSCPnnBonds++; } } // end if statement break; case 6: if ((theProtons[scpBonds[i].p1].currentlyDisplayed) && (theNeutrons[scpBonds[i].n1].currentlyDisplayed) ) { if ((scpBonds[i].p1 == 3) && (scpBonds[i].n1 == 12)) { System.out.println("P3-N12 Checking for display: Bond #"+i); } if ((scpBonds[i].p1 == 12) && (scpBonds[i].n1 == 1)) { System.out.println("P12-N1 Checking for display: Bond #"+i); } if ((showBondType == 3) || (showBondType == 5) || (showBondType == 6) || (showBondType == 7)) { mask.set(i); cntSCPpnBonds++; System.out.println("To be displayed"); } // end if statement else { System.out.println("Not to be displayed"); } } // end if statement break; } // end switch } // end for statement return(mask); } // end getSCPBondMask public BitSet getFissionPlaneMask() { BitSet mask = new BitSet(6); if (whichFissionPlane < 0) return(mask); if ((model != 'S') && (model != 'F')) return(mask); if ((model == 'S') && (whichFissionPlane > 8)) { whichFissionPlane = -1; return(mask); } // end if statement mask.set(whichFissionPlane); // need to count intersecting bonds. cntFissionLeft = 0; cntFissionRight = 0; if (theApp.model == 'F') { cntFissionPP = 0; cntFissionNN = 0; cntFissionPN = 0; for (int i = 0; i < numFCCBonds; i++) { if ( (fccBonds[i].type == 1) && (theProtons[fccBonds[i].p1].currentlyDisplayed) && (theProtons[fccBonds[i].p2].currentlyDisplayed) && intersectsFP(theProtons[fccBonds[i].p1].fccX, theProtons[fccBonds[i].p1].fccY, theProtons[fccBonds[i].p1].fccZ, theProtons[fccBonds[i].p2].fccX, theProtons[fccBonds[i].p2].fccY, theProtons[fccBonds[i].p2].fccZ) ) { cntFissionPP++; } // end if statement if ( (fccBonds[i].type == 2) && (theNeutrons[fccBonds[i].n1].currentlyDisplayed) && (theNeutrons[fccBonds[i].n2].currentlyDisplayed) && intersectsFP(theNeutrons[fccBonds[i].n1].fccX, theNeutrons[fccBonds[i].n1].fccY, theNeutrons[fccBonds[i].n1].fccZ, theNeutrons[fccBonds[i].n2].fccX, theNeutrons[fccBonds[i].n2].fccY, theNeutrons[fccBonds[i].n2].fccZ) ) { cntFissionNN++; } // end if statement if ( (fccBonds[i].type == 3) && (theProtons[fccBonds[i].p1].currentlyDisplayed) && (theNeutrons[fccBonds[i].n1].currentlyDisplayed) && intersectsFP(theProtons[fccBonds[i].p1].fccX, theProtons[fccBonds[i].p1].fccY, theProtons[fccBonds[i].p1].fccZ, theNeutrons[fccBonds[i].n1].fccX, theNeutrons[fccBonds[i].n1].fccY, theNeutrons[fccBonds[i].n1].fccZ) ) { cntFissionPN++; } // end if statement } // end for statement } // end if statement // SCP bonds if (theApp.model == 'S') { cntFissionPP = 0; cntFissionNN = 0; cntFissionPN = 0; for (int i = 0; i < numSCPBonds; i++) { if ( (scpBonds[i].type == 4) && (theProtons[scpBonds[i].p1].currentlyDisplayed) && (theProtons[scpBonds[i].p2].currentlyDisplayed) && intersectsFP(theProtons[scpBonds[i].p1].scpX, theProtons[scpBonds[i].p1].scpY, theProtons[scpBonds[i].p1].scpZ, theProtons[scpBonds[i].p2].scpX, theProtons[scpBonds[i].p2].scpY, theProtons[scpBonds[i].p2].scpZ) ) { cntFissionPP++; } // end if statement if ( (scpBonds[i].type == 5) && (theNeutrons[scpBonds[i].n1].currentlyDisplayed) && (theNeutrons[scpBonds[i].n2].currentlyDisplayed) && intersectsFP(theNeutrons[scpBonds[i].n1].scpX, theNeutrons[scpBonds[i].n1].scpY, theNeutrons[scpBonds[i].n1].scpZ, theNeutrons[scpBonds[i].n2].scpX, theNeutrons[scpBonds[i].n2].scpY, theNeutrons[scpBonds[i].n2].scpZ) ) { cntFissionNN++; } // end if statement if ( (scpBonds[i].type == 6) && (theProtons[scpBonds[i].p1].currentlyDisplayed) && (theNeutrons[scpBonds[i].n1].currentlyDisplayed) && intersectsFP(theProtons[scpBonds[i].p1].scpX, theProtons[scpBonds[i].p1].scpY, theProtons[scpBonds[i].p1].scpZ, theNeutrons[scpBonds[i].n1].scpX, theNeutrons[scpBonds[i].n1].scpY, theNeutrons[scpBonds[i].n1].scpZ) ) { cntFissionPN++; } // end if statement } // end for statement } // end if statement countLeftRight(); return(mask); } // end getFissionPlaneMask public boolean intersectsFP(float x1, float y1, float z1, float x2, float y2, float z2) { float fA = fPlanes[whichFissionPlane].fissionNormA; float fB = fPlanes[whichFissionPlane].fissionNormB; float fC = fPlanes[whichFissionPlane].fissionNormC; float fD = fPlanes[whichFissionPlane].fissionNormD; // norm = (A, B, C) D = norm * (x1, y1, z1) // distance from a point (x, y, z) to plane defined by norm and (x1, y1, z1) // dist = abs(Ax + By + Cz - D) / sqrt(AA + BB + CC) // this is how we tell if fission plane cuts the bond. double hld1 = Math.abs(fA * x1 + fB * y1 + fC * z1 - fD); hld1 = hld1 / Math.sqrt(fA * fA + fB * fB + fC * fC); if (hld1 > 1.5) return (false); double hld2 = Math.abs(fA * x2 + fB * y2 + fC * z2 - fD); hld2 = hld2 / Math.sqrt(fA * fA + fB * fB + fC * fC); if (hld2 > 1.5) return (false); // Spheres are at right distance. // Check that they are on opposite sides of the fission plane // adjust the norm vector length double dx = fA * hld1; double dy = fB * hld1; double dz = fC * hld1; // now add norm to position double x3 = x1 + dx; double y3 = y1 + dy; double z3 = z1 + dz; double x4 = x2 + dx; double y4 = y2 + dy; double z4 = z2 + dz; // now put this point into equation for the plane double hld_d1 = fA * x3 + fB * y3 + fC * z3; double hld_d2 = fA * x4 + fB * y4 + fC * z4; if ( (Math.abs(fD - hld_d1) < 0.1) && (Math.abs(fD - hld_d2) < 0.1) ) return(false); if ( (Math.abs(fD - hld_d1) > 0.1) && (Math.abs(fD - hld_d2) > 0.1) ) return(false); return(true); } // end intersectsFP public void countLeftRight() { cntFissionLeft = 0; cntFissionRight = 0; float fA = fPlanes[whichFissionPlane].fissionNormA; float fB = fPlanes[whichFissionPlane].fissionNormB; float fC = fPlanes[whichFissionPlane].fissionNormC; float fD = fPlanes[whichFissionPlane].fissionNormD; double x1, y1, z1; for (int i = 0; i < cntP; i++) { if (!theProtons[i].currentlyDisplayed) break; if (model == 'F') { x1 = theProtons[i].fccX; y1 = theProtons[i].fccY; z1 = theProtons[i].fccZ; } // end if statement else { x1 = theProtons[i].scpX; y1 = theProtons[i].scpY; z1 = theProtons[i].scpZ; } // end else part // norm = (A, B, C) D = norm * (x1, y1, z1) // distance from a point (x, y, z) to plane defined by norm and (x1, y1, z1) // dist = abs(Ax + By + Cz - D) / sqrt(AA + BB + CC) // this is how we tell if fission plane cuts the bond. double hld1 = Math.abs(fA * x1 + fB * y1 + fC * z1 - fD); hld1 = hld1 / Math.sqrt(fA * fA + fB * fB + fC * fC); // adjust the norm vector length double dx = fA * hld1; double dy = fB * hld1; double dz = fC * hld1; // now add norm to position double x3 = x1 + dx; double y3 = y1 + dy; double z3 = z1 + dz; // now put this point into equation for the plane double hld_d1 = fA * x3 + fB * y3 + fC * z3; if (Math.abs(fD - hld_d1) < 0.1) { cntFissionLeft++; } else { cntFissionRight++; } // end else part } // end for statement for (int i = 0; i < cntN; i++) { if (!theNeutrons[i].currentlyDisplayed) break; if (model == 'F') { x1 = theNeutrons[i].fccX; y1 = theNeutrons[i].fccY; z1 = theNeutrons[i].fccZ; } // end if statement else { x1 = theNeutrons[i].scpX; y1 = theNeutrons[i].scpY; z1 = theNeutrons[i].scpZ; } // end else part // norm = (A, B, C) D = norm * (x1, y1, z1) // distance from a point (x, y, z) to plane defined by norm and (x1, y1, z1) // dist = abs(Ax + By + Cz - D) / sqrt(AA + BB + CC) // this is how we tell if fission plane cuts the bond. double hld1 = Math.abs(fA * x1 + fB * y1 + fC * z1 - fD); hld1 = hld1 / Math.sqrt(fA * fA + fB * fB + fC * fC); // adjust the norm vector length double dx = fA * hld1; double dy = fB * hld1; double dz = fC * hld1; // now add norm to position double x3 = x1 + dx; double y3 = y1 + dy; double z3 = z1 + dz; // now put this point into equation for the plane double hld_d1 = fA * x3 + fB * y3 + fC * z3; if (Math.abs(fD - hld_d1) < 0.2) { cntFissionLeft++; } else { cntFissionRight++; } // end else part } // end for statement } // end countLeftRight public BitSet getNSpheresMask() { // QNCOption: 0=none, 1=n, 2=j, 3=m, 4=l, 5=s, 6=i BitSet mask = new BitSet(6); if (!showSubstructure) return(mask); if (model != 'F') return(mask); if (QNCOption != 1) return(mask); // only display those structures for which there are // spheres displayed. // determine max n value displayed int maxN = -1; System.out.println("Counting N"); for (int i = 0; i < cntP; i++) { if (!theProtons[i].currentlyDisplayed) break; if (theProtons[i].n > maxN) maxN = theProtons[i].n; } // end for statement for (int i = 0; i < cntN; i++) { if (!theNeutrons[i].currentlyDisplayed) break; if (theNeutrons[i].n > maxN) maxN = theNeutrons[i].n; } // end for statement System.out.println("Max N"+maxN); for (int i = 0; i <= maxN; i++) { mask.set(i); } // end for statement return(mask); } // end getNSpheresMask public BitSet getJCylindersMask() { // QNCOption: 0=none, 1=n, 2=j, 3=m, 4=l, 5=s, 6=i BitSet mask = new BitSet(6); if (!showSubstructure) return(mask); if (model != 'F') return(mask); if (QNCOption != 2) return(mask); // only display those structures for which there are // spheres displayed. int maxJ = 0; float[] maxZ = new float[7]; for (int i = 0; i < cntP; i++) { if (!theProtons[i].currentlyDisplayed) break; if (theProtons[i].j > maxJ) maxJ = theProtons[i].j; int hldJ = (int)((float)theProtons[i].j / 2.0f); if (Math.abs(theProtons[i].fccZ) > maxZ[hldJ]) maxZ[hldJ] = Math.abs(theProtons[i].fccZ); } // end for statement for (int i = 0; i < cntN; i++) { if (!theNeutrons[i].currentlyDisplayed) break; if (theNeutrons[i].j > maxJ) maxJ = theNeutrons[i].j; int hldJ = (int)((float)theNeutrons[i].j / 2.0f); if (Math.abs(theNeutrons[i].fccZ) > maxZ[hldJ]) maxZ[hldJ] = Math.abs(theNeutrons[i].fccZ); } // end for statement maxJ = (int)((float)maxJ / 2.0f) + 2; for (int i = 0; i < maxJ-1; i++) { mask.set(i); MyCylinder myCyl = new MyCylinder(0.0f, 0.0f, -maxZ[i]-1, 0.0f, 0.0f, maxZ[i]+1, jRadius[i]); jCylinders[i].setGeometry(myCyl.Solid()); // The apperance is set and modified as needed in the menu // functions to change shell color and transparency. } // end for statement return(mask); } // end getJCylindersMask public BitSet getMConesMask() { // QNCOption: 0=none, 1=n, 2=j, 3=m, 4=l, 5=s, 6=i BitSet mask = new BitSet(6); if (!showSubstructure) return(mask); if (model != 'F') return(mask); if (QNCOption != 3) return(mask); // only display those structures for which there are // spheres displayed. int maxM = -1; int hldM = 0; float[] r = new float[7]; float[] height = new float[7]; float hldR; for (int i = 0; i < cntP; i++) { if (!theProtons[i].currentlyDisplayed) break; if (Math.abs(theProtons[i].m) > maxM) maxM = Math.abs(theProtons[i].m); hldM = Math.abs(theProtons[i].m) / 2; hldR = (float)Math.sqrt(theProtons[i].fccY * theProtons[i].fccY + theProtons[i].fccZ * theProtons[i].fccZ); if (hldR > r[hldM]) r[hldM] = hldR; if (Math.abs(theProtons[i].fccX) > height[hldM]) height[hldM] = Math.abs(theProtons[i].fccX); } // end for statement for (int i = 0; i < cntN; i++) { if (!theNeutrons[i].currentlyDisplayed) break; if (Math.abs(theNeutrons[i].m) > maxM) maxM = Math.abs(theNeutrons[i].m); hldM = Math.abs(theProtons[i].m) / 2; hldR = (float)Math.sqrt(theProtons[i].fccY * theProtons[i].fccY + theProtons[i].fccZ * theProtons[i].fccZ); if (hldR > r[hldM]) r[hldM] = hldR; if (Math.abs(theProtons[i].fccX) > height[hldM]) height[hldM] = Math.abs(theProtons[i].fccX); } // end for statement for (int i = 0; i < maxM; i++) { mask.set(i); MyCone myCone = new MyCone(height[i], r[i]); mCones[i].setGeometry(myCone.Solid()); // The apperance is set and modified as needed in the menu // functions to change shell color and transparency. } // end for statement return(mask); } // end getMConesMask public BitSet getSCirclesMask() { // QNCOption: 0=none, 1=n, 2=j, 3=m, 4=l, 5=s, 6=i BitSet mask = new BitSet(6); if (!showSubstructure) return(mask); if (model != 'F') return(mask); if (QNCOption != 5) return(mask); // only display those structures for which there are // spheres displayed. int maxPos = -1; int hldPos = 0; float[] r = new float[7]; float[] height = new float[7]; float hldR; for (int i = 0; i < cntP; i++) { if (!theProtons[i].currentlyDisplayed) break; if (Math.abs(theProtons[i].fccX) > maxPos) maxPos = (int)Math.abs(theProtons[i].fccX); System.out.println("X value: "+(int)Math.abs(theProtons[i].fccX)); hldPos = (int)Math.abs(theProtons[i].fccX) / 2; hldR = (float)Math.sqrt(theProtons[i].fccY * theProtons[i].fccY + theProtons[i].fccZ * theProtons[i].fccZ); if (hldR > r[hldPos]) r[hldPos] = hldR; if (Math.abs(theProtons[i].fccX) > height[hldPos]) height[hldPos] = Math.abs(theProtons[i].fccX); } // end for statement for (int i = 0; i < cntN; i++) { if (!theNeutrons[i].currentlyDisplayed) break; if (Math.abs(theNeutrons[i].fccX) > maxPos) maxPos = (int)Math.abs(theNeutrons[i].fccX); System.out.println("X value: "+(int)Math.abs(theNeutrons[i].fccX)); hldPos = (int)Math.abs(theNeutrons[i].fccX) / 2; hldR = (float)Math.sqrt(theNeutrons[i].fccY * theNeutrons[i].fccY + theNeutrons[i].fccZ * theNeutrons[i].fccZ); if (hldR > r[hldPos]) r[hldPos] = hldR; if (Math.abs(theNeutrons[i].fccX) > height[hldPos]) height[hldPos] = Math.abs(theNeutrons[i].fccX); } // end for statement for (int i = 1; i <= maxPos; i=i+2) { int index = i / 2; mask.set(index); MyCircle myCircle = new MyCircle('X', i, r[index]); sCircles[index].setGeometry(myCircle.Solid()); // The apperance is set and modified as needed in the menu // functions to change shell color and transparency. } // end for statement return(mask); } // end getSCirclesMask public BitSet getICirclesMask() { // QNCOption: 0=none, 1=n, 2=j, 3=m, 4=l, 5=s, 6=i BitSet mask = new BitSet(6); if (!showSubstructure) return(mask); if (model != 'F') return(mask); if (QNCOption != 6) return(mask); // only display those structures for which there are // spheres displayed. // only display those structures for which there are // spheres displayed. int maxPos = -1; int hldPos = 0; float[] r = new float[7]; float[] height = new float[7]; float hldR; for (int i = 0; i < cntP; i++) { if (!theProtons[i].currentlyDisplayed) break; if (Math.abs(theProtons[i].fccZ) > maxPos) maxPos = (int)Math.abs(theProtons[i].fccZ); System.out.println("Z value: "+(int)Math.abs(theProtons[i].fccZ)); hldPos = (int)Math.abs(theProtons[i].fccZ) / 2; hldR = (float)Math.sqrt(theProtons[i].fccX * theProtons[i].fccX + theProtons[i].fccY * theProtons[i].fccY); if (hldR > r[hldPos]) r[hldPos] = hldR; if (Math.abs(theProtons[i].fccZ) > height[hldPos]) height[hldPos] = Math.abs(theProtons[i].fccZ); } // end for statement for (int i = 0; i < cntN; i++) { if (!theNeutrons[i].currentlyDisplayed) break; if (Math.abs(theNeutrons[i].fccZ) > maxPos) maxPos = (int)Math.abs(theNeutrons[i].fccZ); System.out.println("Z value: "+(int)Math.abs(theNeutrons[i].fccZ)); hldPos = (int)Math.abs(theNeutrons[i].fccZ) / 2; hldR = (float)Math.sqrt(theNeutrons[i].fccX * theNeutrons[i].fccX + theNeutrons[i].fccY * theNeutrons[i].fccY); if (hldR > r[hldPos]) r[hldPos] = hldR; if (Math.abs(theNeutrons[i].fccZ) > height[hldPos]) height[hldPos] = Math.abs(theNeutrons[i].fccZ); } // end for statement for (int i = 1; i <= maxPos; i=i+2) { int index = i / 2; mask.set(index); MyCircle myCircle = new MyCircle('Z', i, r[index]); iCircles[index].setGeometry(myCircle.Solid()); // The apperance is set and modified as needed in the menu // functions to change shell color and transparency. } // end for statement return(mask); } // end getICirclesMask public BitSet getAlphaMask() { BitSet mask = new BitSet(6); if (model != 'A') return(mask); // only display those structures for which there are // spheres displayed. mask.set(0); mask.set(1); return(mask); } // end getAlphaMask } // end class NDCP