@Override

public void start(Stage primaryStage) {

primaryStage.setTitle("PolyStar 1.0 ");

GridPane grid = new GridPane();

//grid.setAlignment(Pos.CENTER);

grid.setHgap(6);

grid.setVgap(6);

grid.setPadding(new Insets(15, 15, 15, 15));

//grid.setAlignment(Pos.TOP_RIGHT);

Text scenetitle = new Text("PolyStar 1.0 (Hover for tool tips)");

scenetitle.setFont(Font.font("Tahoma", FontWeight.NORMAL, 16));

grid.add(scenetitle, 0, 0, 2, 1);

Label mainLbl = new Label("PolyStar polytropic stellar interior structure modeling");

mainLbl.setFont(Font.font("Tahoma", FontWeight.NORMAL, 11));

grid.add(mainLbl, 2, 0);

ImageView imageLogo;

imageLogo = new ImageView(

new Image(PolyStar.class.getResourceAsStream("graphics/SMULOGO2.png")));

grid.add(imageLogo, 4, 0, 2, 1);

// Model atmosphere parameters:

Label atmosLbl = new Label("Model star parameters:");

atmosLbl.setFont(Font.font("Tahoma", FontWeight.NORMAL, 12));

grid.add(atmosLbl, 0, 1);

Tooltip atmosTip = new Tooltip();

atmosTip.setText(

"Default parameters are for the Sun's central density, \r\n"

+ " rho_c = 162 g/cm^3, n=1.5"

);

atmosLbl.setTooltip(atmosTip);

//central density input - solar units

Label rhoCLbl = new Label("rho_c (0.1 - 10.0 x rho_C_Sun)");

grid.add(rhoCLbl, 0, 2);

Tooltip rhoCTip = new Tooltip();

rhoCTip.setText(

"Central mass density relative to that of Sun \r\n"

+ " rho_C_Sun = 162 g cm^-3"

);

rhoCLbl.setTooltip(rhoCTip);

TextField rhoCSolIn = new TextField("1.0");

grid.add(rhoCSolIn, 1, 2);

Label trialLbl = new Label(" ");

trialLbl.setFont(Font.font("Tahoma", FontWeight.NORMAL, 12));

grid.add(trialLbl, 2, 1);

//Polytropic index, n - dimensionless:

Label indexLbl = new Label("n (1.0 - 3.5)");

grid.add(indexLbl, 0, 3);

Tooltip indexTip = new Tooltip();

indexTip.setText(

"Dimensionless polytropic index. \r\n"

+ " = Adiabatic gamma = (n+1)/n \r\n"

+ " n=1.5 for ideal monatomic gas (best for Sun) \r\n"

+ " n=3.0 for photon gas - Eddington standard model"

);

indexLbl.setTooltip(indexTip);

TextField indexIn = new TextField("1.5");

grid.add(indexIn, 1, 3);

/*

// Radiation pressure fraction, beta:

Label betaLbl = new Label("Beta (0 - 1)");

grid.add(betaLbl, 0, 4);

Tooltip betaTip = new Tooltip();

betaTip.setText(

"Fractional contribution of gas pressure, P_Gas\r\n"

+ "to total pressure (ie. P_Gas = Beta * P = P - P_Rad)"

);

betaLbl.setTooltip(betaTip);

TextField betaIn = new TextField("0.0");

grid.add(betaIn, 1, 4);

*/

//He mass fraction (Y)

Label yFracLbl = new Label("He mass fraction, Y (0.2 - 0.5)");

grid.add(yFracLbl, 2, 2);

Tooltip yFracTip = new Tooltip();

yFracTip.setText(

"Helium mass fraction, Y (0.2 - 0.5)"

);

yFracLbl.setTooltip(yFracTip);

TextField yFracIn = new TextField("0.28");

grid.add(yFracIn, 3, 2);

//metal mass fraction (Z)

Label zFracLbl = new Label("Metal mass fraction, Z (0.0001 - 0.05)");

grid.add(zFracLbl, 2, 3);

Tooltip zFracTip = new Tooltip();

zFracTip.setText(

"Mass fraction of elements of z > 2, Z (0.0001 - 0.05)"

);

zFracLbl.setTooltip(zFracTip);

TextField zFracIn = new TextField("0.02");

grid.add(zFracIn, 3, 3);

//

//

Button btn = new Button("Model");

HBox hbBtn = new HBox(10);

hbBtn.setAlignment(Pos.BOTTOM_RIGHT);

hbBtn.getChildren().add(btn);

grid.add(hbBtn, 3, 5);

final Text actiontarget = new Text();

grid.add(actiontarget, 0, 8);

btn.setOnAction(new EventHandler<ActionEvent>() {

@Override

public void handle(ActionEvent event) {

actiontarget.setFill(Color.FIREBRICK);

//actiontarget.setText("Output here");

actiontarget.setFont(Font.font("Tahoma", FontWeight.NORMAL, 14));

String rhoCSolStr = rhoCSolIn.getText();

String indexStr = indexIn.getText();

//String betaStr = betaIn.getText();

String yFracStr = yFracIn.getText();

String zFracStr = zFracIn.getText();

// If *any* model atmosphere input string is empty, set rhoCSolStr to empty to simplify

// conditional logic below.

if (indexStr == null || indexStr.isEmpty()) {

rhoCSolStr = null;

}

//if (betaStr == null || betaStr.isEmpty()) {

// rhoCSolStr = null;

//}

if (yFracStr == null || yFracStr.isEmpty()) {

rhoCSolStr = null;

}

if (zFracStr == null || zFracStr.isEmpty()) {

rhoCSolStr = null;

}

if ((rhoCSolStr != null && !rhoCSolStr.isEmpty())) {

//Argument 1: Stellar mass, M, in solar masses

double rhoCSol = (Double.valueOf(rhoCSolStr)).doubleValue();

//Argument 2: He mass fraftion, Y

double yFrac = (Double.valueOf(yFracStr)).doubleValue();

//Argument 3: Metal mass fraftion, Z

double zFrac = (Double.valueOf(zFracStr)).doubleValue();

// Argument 4: Effective temperature, Teff, in K:

double index = (Double.valueOf(indexStr)).doubleValue();

//// Argument 5: Logarithmic surface gravity, g, in cm/s/s:

// double beta = (Double.valueOf(betaStr)).doubleValue();

// Sanity checks:

if (rhoCSol < 0.1) {

rhoCSol = 0.1;

rhoCSolStr = "0.1";

}

if (rhoCSol > 10.0) {

rhoCSol = 10.0;

rhoCSolStr = "10.0";

}

if (yFrac < 0.1) {

yFrac = 0.1;

yFracStr = "0.1";

}

if (yFrac > 0.5) {

yFrac = 0.5;

yFracStr = "0.5";

}

if (zFrac < 0.0002) {

zFrac = 0.0002;

zFracStr = "0.0002";

}

if (zFrac > 0.05) {

zFrac = 0.05;

zFracStr = "0.05";

}

if (index < 1.0) {

index = 1.0;

indexStr = "1.0";

}

if (index > 3.5) {

index = 3.5;

indexStr = "3.5";

}

//if (beta < 0.0) {

// beta = 0.0;

// betaStr = "0.0";

//}

//if (beta > 1.0) {

// beta = 1.0;

// betaStr = "1.0";

// }

// All code after this line

// Solar parameters:

double teffSun = 5778.0;

double log10gSun = 4.44;

double gravSun = Math.pow(10.0, log10gSun);

//Solar units:

double massSun = 1.0;

double radiusSun = 1.0;

double rhoCSun = 162.2; // g cm^-3

//double massStar = 1.0; //solar masses // test

//Composition by mass fraction - needed for opacity approximations

// and interior structure

double massXSun = 0.70; //Hydrogen

double massYSun = 0.28; //Helium

double massZSun = 0.02; // "metals"

// log_10 num density H in surface layer:

double log10NH = 17.0;

double log10E = Math.log10(Math.E); // convert log_e to log_10

double logE10 = Math.log(10.0); // convert log_10 to log_e

double xFrac = 1.0 - yFrac - zFrac;

double logXFrac = Math.log(xFrac);

double logYFrac = Math.log(yFrac);

double rhoC = rhoCSol * rhoCSun; //Sun's central mass density in cgs units

//Set up all the special Lane-Emden equation variables:

//Adiabatic gamma consistent with input polytropic index

double gammaPoly = (index + 1.0) / index;

//For convection criterion:

double gamThing = PhysData.gammaMono / (PhysData.gammaMono - 1.0);

//Initial Kay and lambda parameters from Lame-Embden equations:

/* Doesn't work

double Kay, KayTerm1, KayTerm2;

KayTerm1 = 3.0 * (1.0 - beta) / Useful.aStef();

KayTerm2 = Useful.k / beta / PhysData.muI(xFrac, yFrac, zFrac) / Useful.amu;

Kay = Math.pow(KayTerm1, 0.3333) * Math.pow(KayTerm2, 4.0 / 3.0);

*/

double Kay = 5.0e13; //hard wire to value at centre of Sun

double lambda, lamTerm, indxExp;

indxExp = (1.0 - index) / index;

lamTerm = (index + 1.0) * Kay * Math.pow(rhoC, indxExp) / 4.0 / Math.PI / Useful.GConst;

lambda = Math.pow(lamTerm, 0.5);

System.out.println("Kay " + Kay + " lambda " + lambda);

//Dimensionless Lane-Emden Equation variables, xi and D_n(xi)

//xi is the independenet variable

//y(xi) is a helper function to separate the 2nd order Lane-Emden equation

//into two coupled 1st order equations

int maxNumDeps = 1000;

double[] xi = new double[maxNumDeps];

double[] DFunc = new double[maxNumDeps];

double[] yFunc = new double[maxNumDeps];

double deltaXi, deltaDFunc, deltaY, deltaYMag;

//double logDeltaXi, logDeltaD, logDeltaY, logDeltaYMag;

//Physical variables:

double[] radShell = new double[maxNumDeps]; //shell radial width

double[] tempShell = new double[maxNumDeps]; //kinetic temperature

double[] pressShell = new double[maxNumDeps]; //total pressure

double[] pGasShell = new double[maxNumDeps]; //gas pressure

double[] pRadShell = new double[maxNumDeps]; //radiation pressure

double[] rhoShell = new double[maxNumDeps]; //total fluid density

double[] massShell = new double[maxNumDeps]; // shell mass

double[] lumShell = new double[maxNumDeps]; //shell luminosity

double[] lumPpShell = new double[maxNumDeps]; //shell luminosity

double[] lumCnoShell = new double[maxNumDeps]; //shell luminosity

double[] epsShell = new double[maxNumDeps]; //total nuclear energy generation rate

double[] epsPpShell = new double[maxNumDeps]; //nuclear p-p chain energy generation rate

double[] epsCnoShell = new double[maxNumDeps]; //nuclear cno cycle energy generation rate

double[] kapShell = new double[maxNumDeps]; //mean opacity

double[] kapBfShell = new double[maxNumDeps]; //mean b-f opacity

double[] kapFfShell = new double[maxNumDeps]; //mean f-f opacity

double[] kapEsShell = new double[maxNumDeps]; //mean e^- scattering opacity

double[] kapHminShell = new double[maxNumDeps]; //mean H^- opacity

//cumulative quantities

double[] radInt = new double[maxNumDeps]; //interior radius

//double[] logRadInt = new double[maxNumDeps];

double[] massInt = new double[maxNumDeps]; //interior mass

double[] lumInt = new double[maxNumDeps]; //interior luminosity

double[] lumPpInt = new double[maxNumDeps]; //interior luminosity

double[] lumCnoInt = new double[maxNumDeps]; //interior luminosity

double[] gravInt = new double[maxNumDeps]; //acceleration of gravity

//Convection:

double[] dLnPdLnT = new double[maxNumDeps];

boolean[] convFlag = new boolean[maxNumDeps];

double RHS, logRHS, logRHSMag; //, logLastXi;

double xiSquare; //useful

//Try uniform spacing for now...

// We know that at surface, xi >~ 3.0

//guess at a good spacing for now...

// Surface value of dimensionless xi parameter is in

// range 3 to 7 for polytropic index 1.5 to 3.0

deltaXi = 10.0 / maxNumDeps;

//deltaXi = 0.04; //debug mode

//logDeltaXi = Math.log(deltaXi);

//For Newton-Raphson temperature recovery:

double firstTemp = 0.0;

//central bounday (initial) values:

// NOTE: we cannot set xi=0 - singularity

// We know that at surface, xi >~ 3.0

//guess at a good initial abscissa and spacing for now...

int j = 0;

xi[j] = 0.001;

yFunc[j] = 0.0;

DFunc[j] = 1.0;

// The stuff that follows...

radInt[j] = lambda * xi[j];

radShell[j] = radInt[j];

rhoShell[j] = rhoC * Math.pow(DFunc[j], index);

pressShell[j] = Kay * Math.pow(rhoShell[j], gammaPoly);

tempShell[j] = NRtemp.getTemp(pressShell[j], rhoShell[j], xFrac, yFrac, zFrac, firstTemp);

//pGasShell[j] = beta * pressShell[j];

//pRadShell[j] = (1.0 - beta) * pressShell[j];

pGasShell[j] = Useful.k * rhoShell[j] * tempShell[j] / PhysData.muI(xFrac, yFrac, zFrac) / Useful.amu;

pRadShell[j] = Useful.aStef() * Math.pow(tempShell[j], 4.0) / 3.0;

//tempShell[i] = pressShell[i] * PhysData.muI(xFrac, yFrac, zFrac) * Useful.amu / Useful.k / rhoShell[i];

massInt[j] = rhoC * 4.0 * Math.PI * Math.pow(radInt[j], 3) / 3.0;

massShell[j] = massInt[j];

if (tempShell[j] >= PhysData.fusionPPTemp) {

epsPpShell[j] = Power.ppChain(tempShell[j], rhoShell[j], xFrac, zFrac); //H fusion p-p chain

epsCnoShell[j] = Power.cnoCycle(tempShell[j], rhoShell[j], xFrac, zFrac); //H fusion CNO cycle

epsShell[j] = epsPpShell[j] + epsCnoShell[j];

//lumInt[j] = rhoC * 4.0 * Math.PI * Math.pow(radInt[j], 3) * epsShell[j] / 3.0;

lumPpInt[j] = rhoC * 4.0 * Math.PI * Math.pow(radInt[j], 3) * epsPpShell[j] / 3.0;

lumCnoInt[j] = rhoC * 4.0 * Math.PI * Math.pow(radInt[j], 3) * epsCnoShell[j] / 3.0;

lumPpShell[j] = lumPpInt[j];

lumCnoShell[j] = lumCnoInt[j];

lumInt[j] = lumPpInt[j] + lumCnoInt[j];

lumShell[j] = lumPpShell[j] + lumCnoShell[j];

} else {

epsPpShell[j] = 0.0; //H fusion p-p chain

epsCnoShell[j] = 0.0; //H fusion CNO cycle

epsShell[j] = 0.0;

//lumInt[j] = rhoC * 4.0 * Math.PI * Math.pow(radInt[j], 3) * epsShell[j] / 3.0;

lumPpInt[j] = 0.0;

lumCnoInt[j] = 0.0;

lumPpShell[j] = 0.0;

lumCnoShell[j] = 0.0;

lumInt[j] = 0.0;

lumShell[j] = 0.0;

}

kapBfShell[j] = Kappa.kappaBfFn(tempShell[j], rhoShell[j], xFrac, zFrac); //b-f photo-ionization

kapFfShell[j] = Kappa.kappaFfFn(tempShell[j], rhoShell[j], xFrac, zFrac); //f-f Bremsstrahlung

kapEsShell[j] = Kappa.kappaEsFn(tempShell[j], rhoShell[j], xFrac, zFrac); //Thomson e^- scattering

kapHminShell[j] = Kappa.kappaHminFn(tempShell[j], rhoShell[j], xFrac, zFrac); //H^- b-f

kapShell[j] = kapBfShell[j] + kapFfShell[j] + kapEsShell[j] + kapHminShell[j];

gravInt[j] = Useful.GConst * massInt[j] / Math.pow(radInt[j], 2);

dLnPdLnT[j] = 0.0;

//4th order Runge-Kutta (RK4) helper variables

double k1y, k2y, k3y, k4y;

double k1D, k2D, k3D, k4D;

double hHalf = deltaXi / 2.0;

double yHalf, DHalf, xiHalf;

double yFull, DFull, xiFull;

//System.out.println(" i " + " radius " + " massIn " + " lumInt " + " temp " + " press "

// + " rh " + " kappa " + " epsilon " + " dLnPdLnT " + " gravInt " + " pGas/PTot "

// + " convection? ");

//System.out.println(" i " + " radius " + " press " + " rho ");

//Master numerical integration loop:

//Loop exits when surface is found

// Try Euler's method for now...

//System.out.println("i xi[i] yFunc[i] DFunc[i] ");

int iSurf = 0;

int iCore = 0;

for (int i = 1; i < maxNumDeps; i++) {

xi[i] = xi[i - 1] + deltaXi;

/* Logarithmic - difficult due to signs

logLastXi = Math.log(xi[i - 1]);

//Start by advanceing helper function, y(xi):

logRHSMag = index * Math.log(DFunc[i - 1]) + 2.0 * logLastXi;

//RHS = -1.0 * Math.exp(logRHSMag);

logDeltaYMag = logRHSMag + logDeltaXi;

deltaYMag = Math.exp(logDeltaYMag);

deltaY = -1.0 * deltaYMag;

yFunc[i] = yFunc[i - 1] + deltaY;

//Now use the updated value of y to update D_n

logRHS = Math.log(yFunc[i]) - 2.0 * logLastXi;

logDeltaD = logRHS + logDeltaXi;

deltaDFunc = Math.exp(logDeltaD);

DFunc[i] = DFunc[i - 1] + deltaDFunc;

*/

//

xiSquare = Math.pow(xi[i - 1], 2);

xiHalf = Math.pow((xi[i - 1] + hHalf), 2);

xiFull = Math.pow(xi[i], 2);

//

/*

//Euler's method

//Start by advanceing helper function, y(xi):

RHS = -1.0 * Math.pow(DFunc[i - 1], index) * xiSquare;

deltaY = RHS * deltaXi;

yFunc[i] = yFunc[i - 1] + deltaY;

//Now use the updated value of y to update D_n

RHS = yFunc[i] / xiSquare;

deltaDFunc = RHS * deltaXi;

DFunc[i] = DFunc[i - 1] + deltaDFunc;

System.out.format("Euler: %03d %15.10f %15.10f %15.10f%n", i, xi[i], yFunc[i], DFunc[i]);

*/

//4th order Runge-Kutta (RK4):

k1y = -1.0 * Math.pow(DFunc[i - 1], index) * xiSquare;

k1D = yFunc[i - 1] / xiSquare;

DHalf = DFunc[i - 1] + hHalf * k1D;

yHalf = yFunc[i - 1] + hHalf * k1y;

k2y = -1.0 * Math.pow(DHalf, index) * xiHalf;

k2D = yHalf / xiHalf;

DHalf = DFunc[i - 1] + hHalf * k2D;

yHalf = yFunc[i - 1] + hHalf * k2y;

k3y = -1.0 * Math.pow(DHalf, index) * xiHalf;

k3D = yHalf / xiHalf;

DFull = DFunc[i - 1] + deltaXi * k3D;

yFull = yFunc[i - 1] + deltaXi * k3y;

k4y = -1.0 * Math.pow(DFull, index) * xiFull;

k4D = yFull / xiFull;

deltaY = deltaXi * (k1y + 2.0 * k2y + 2.0 * k3y + k4y) / 6.0;

deltaDFunc = deltaXi * (k1D + 2.0 * k2D + 2.0 * k3D + k4D) / 6.0;

yFunc[i] = yFunc[i - 1] + deltaY;

DFunc[i] = DFunc[i - 1] + deltaDFunc;

//Are we there yet?

if ((DFunc[i] <= 0)

|| (Double.isNaN(DFunc[i]) == true)

|| (Double.isInfinite(DFunc[i]) == true)) {

break;

}

//System.out.format("RK4: %03d %15.10f %15.10f %15.10f%n", i, xi[i], yFunc[i], DFunc[i]);

radInt[i] = lambda * xi[i];

radShell[i] = radInt[i] - radInt[i - 1];

rhoShell[i] = rhoC * Math.pow(DFunc[i], index);

pressShell[i] = Kay * Math.pow(rhoShell[i], gammaPoly);

tempShell[i] = NRtemp.getTemp(pressShell[i], rhoShell[i], xFrac, yFrac, zFrac, tempShell[i - 1]);

//pGasShell[i] = beta * pressShell[i];

//pRadShell[i] = (1.0 - beta) * pressShell[i];

pGasShell[i] = Useful.k * rhoShell[i] * tempShell[i] / PhysData.muI(xFrac, yFrac, zFrac) / Useful.amu;

pRadShell[i] = Useful.aStef() * Math.pow(tempShell[i], 4.0) / 3.0;

//tempShell[i] = pressShell[i] * PhysData.muI(xFrac, yFrac, zFrac) * Useful.amu / Useful.k / rhoShell[i];

massShell[i] = 4.0 * Math.PI * Math.pow(radInt[i], 2) * rhoShell[i] * radShell[i];

massInt[i] = massInt[i - 1] + massShell[i];

//epsShell[i] = Power.nuclear(tempShell[i], rhoShell[i], xFrac, zFrac);

if (tempShell[i] >= PhysData.fusionPPTemp) {

iCore = i;

epsPpShell[i] = Power.ppChain(tempShell[i], rhoShell[i], xFrac, zFrac); //H fusion p-p chain

epsCnoShell[i] = Power.cnoCycle(tempShell[i], rhoShell[i], xFrac, zFrac); //H fusion CNO cycle

epsShell[i] = epsPpShell[i] + epsCnoShell[i];

//lumShell[i] = 4.0 * Math.PI * Math.pow(radInt[i], 2) * rhoShell[i] * epsShell[i] * radShell[i];

lumPpShell[i] = 4.0 * Math.PI * Math.pow(radInt[i], 2) * rhoShell[i] * epsPpShell[i] * radShell[i];

lumCnoShell[i] = 4.0 * Math.PI * Math.pow(radInt[i], 2) * rhoShell[i] * epsCnoShell[i] * radShell[i];

lumShell[i] = lumPpShell[i] + lumCnoShell[i];

lumPpInt[i] = lumPpInt[i - 1] + lumPpShell[i];

lumCnoInt[i] = lumCnoInt[i - 1] + lumCnoShell[i];

lumInt[i] = lumInt[i - 1] + lumShell[i];

} else {

epsPpShell[i] = 0.0; //H fusion p-p chain

epsCnoShell[i] = 0.0; //H fusion CNO cycle

epsShell[i] = 0.0;

//lumShell[i] = 4.0 * Math.PI * Math.pow(radInt[i], 2) * rhoShell[i] * epsShell[i] * radShell[i];

lumPpShell[i] = 0.0;

lumCnoShell[i] = 4.0 * Math.PI * Math.pow(radInt[i], 2) * rhoShell[i] * epsCnoShell[i] * radShell[i];

lumShell[i] = 0.0;

lumPpInt[i] = lumPpInt[i - 1];

lumCnoInt[i] = lumCnoInt[i - 1];

lumInt[i] = lumInt[i - 1];

}

//kapShell[i] = Kappa.kappaFn(tempShell[i], rhoShell[i], xFrac, zFrac);

kapBfShell[i] = Kappa.kappaBfFn(tempShell[i], rhoShell[i], xFrac, zFrac); //b-f photo-ionization

kapFfShell[i] = Kappa.kappaFfFn(tempShell[i], rhoShell[i], xFrac, zFrac); //f-f Bremsstrahlung

kapEsShell[i] = Kappa.kappaEsFn(tempShell[i], rhoShell[i], xFrac, zFrac); //Thomson e^- scattering

kapHminShell[i] = Kappa.kappaHminFn(tempShell[i], rhoShell[i], xFrac, zFrac); //H^- b-f

kapShell[i] = kapBfShell[i] + kapFfShell[i] + kapEsShell[i] + kapHminShell[i];

gravInt[i] = Useful.GConst * massInt[i] / Math.pow(radInt[i], 2);

dLnPdLnT[i] = (Math.log(pGasShell[i]) - Math.log(pGasShell[i - 1]))

/ (Math.log(tempShell[i]) - Math.log(tempShell[i - 1]));

if ((dLnPdLnT[i] >= gamThing)) {

//Radiative transport

convFlag[i] = false;

} else {

//Convective transport

convFlag[i] = true;

}

//Dynamically update Kay and lambda:

//Hmmm... these never seem to change, but let's update them anyway...

Kay = pressShell[i] / Math.pow(rhoShell[i], gammaPoly);

lamTerm = (index + 1.0) * Kay * Math.pow(rhoC, indxExp) / 4.0 / Math.PI / Useful.GConst;

lambda = Math.pow(lamTerm, 0.5);

//System.out.println("Kay " + Kay + " lambda " + lambda);

//System.out.println(" i " + " radius " + " massInt " + " lumInt " + " temp " + " press "

// + " rho " + " kappa " + " epsilon " + " dLnPdLnT " + " gravInt " + " pGas/PTot "

// + " convection? ");

//System.out.println(" i " + " radius " + " press " + " rho ");

//System.out.format("%03d %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f %10.6f %b%n",

// i, log10E * Math.log(radInt[i]), log10E * Math.log(massInt[i]), log10E * Math.log(lumInt[i]), log10E * Math.log(tempShell[i]),

// log10E * Math.log(pressShell[i]), log10E * Math.log(rhoShell[i]), kapShell[i], log10E * Math.log(epsShell[i]),

// dLnPdLnT[i], log10E * Math.log(gravInt[i]), pGasShell[i] / pressShell[i], convFlag[i]);

//System.out.format(" %03d %15.11f %15.11f %15.11f %15.11f %n",

// i, log10E * Math.log(radInt[i]), log10E * Math.log(pressShell[i]), log10E * Math.log(rhoShell[i]), log10E * Math.log(tempShell[i]));

//Surface boundary condition:

iSurf++;

}

int numDeps = iSurf;

System.out.println("Actual number of depths = " + numDeps);

//Independent total mass calculation:

//First derivative, dD_n/dXi at surface:

double dDFuncdXi = (DFunc[iSurf] - DFunc[iSurf - 1]) / (xi[iSurf] - xi[iSurf - 1]);

double totMass = -4.0 * Math.PI * Math.pow(lambda, 3.0) * rhoC * Math.pow(xi[iSurf], 2.0) * dDFuncdXi;

System.out.println("Total analytic mass " + totMass);

//Results:

//cgs units:

double mass = massInt[numDeps];

double radius = radInt[numDeps];

double luminosity = lumInt[numDeps];

double surfTemp = tempShell[numDeps];

//Compute the effective temperature of the model:

double teff4 = luminosity / 4.0 / Math.PI / Math.pow(radius, 2.0) / Useful.sigma;

double teff = Math.pow(teff4, 0.25);

//solar units:

double massSol = mass / Useful.mSun;

double radiusSol = radius / Useful.rSun;

double lumSol = luminosity / Useful.lSun;

//Run the loop inward to build the optical depth scasle, tauIn:

//// No!While we're at it - find the nuclear burning core

double[] tauIn = new double[numDeps];

tauIn[numDeps - 1] = 0.0;

//int iCore = numDeps - 1;

for (int i = numDeps - 2; i == 0; i--) {

tauIn[i] = tauIn[i - 1]

+ rhoShell[i] * kapShell[i] * radShell[i];

// if (lumInt[i] > 0.99 * luminosity) {

// iCore--;

// }

}

//Report:

System.out.println("cgs units:");

System.out.println("Radius: " + log10E * Math.log(radius) + " Mass: " + log10E * Math.log(mass) + " Bol Luminosity: " + log10E * Math.log(luminosity));

System.out.println("Teff: " + teff + " TSurf: " + surfTemp);

System.out.println("Solar units:");

System.out.println("Radius: " + radiusSol + " Mass: " + massSol + " Bol Luminosity: " + lumSol);

System.out.println("Nuclear burning core fractional radius: " + (radInt[iCore] / radius));

//Compute spectral energy distribution (SED):

//wavelength grid (cm):

double[] waveSetup = new double[3];

waveSetup[0] = 100.0 * 1.0e-7; // test Start wavelength, cm

waveSetup[1] = 2000.0 * 1.0e-7; // test End wavelength, cm

waveSetup[2] = 100; // test number of lambda

int numWaves = (int) waveSetup[2];

double[] SED = new double[numWaves];

double[] waveGrid = new double[numWaves];

double thisWave, thisLogWave, logWave0, logWave1;

logWave0 = Math.log(waveSetup[0]);

logWave1 = Math.log(waveSetup[1]);

double deltaLogWave = (logWave1 - logWave0) / numWaves;

for (int i = 0; i < numWaves; i++) {

thisLogWave = logWave0 + ((double) i) * deltaLogWave;

thisWave = Math.exp(thisLogWave);

waveGrid[i] = thisWave;

SED[i] = Planck.planck(teff, thisWave);

//System.out.println(" " + waveGrid[i] + " " + SED[i]);

}

//

//double colors[] = new double[5];

double colors[] = Photometry.UBVRI(waveGrid, SED);

// All code before this line

String patternCol = "0.00";

//String pattern = "#####.##";

DecimalFormat colFormatter = new DecimalFormat(patternCol);

// // String patternWl = "0.00";

// //String pattern = "#####.##";

// DecimalFormat WlFormatter = new DecimalFormat(patternWl);

actiontarget.setText("Photometric color indices: "

+ "U-B: " + colFormatter.format(colors[0])

+ " B-V: " + colFormatter.format(colors[1])

+ " V-R: " + colFormatter.format(colors[2])

+ " V-I: " + colFormatter.format(colors[3])

+ " R-I: " + colFormatter.format(colors[4]) + "\r\n"

);

// No! //grid.getChildren().add(r);

// Graphical output section:

/*

// Plot 1: T_Kin(radius):

LineChart<Number, Number> lineChartT2 = LineCharts.t2Plot(numDeps, radInt, tempShell);

grid.add(lineChartT2, 0, 9);

// Plot 2: log(P(radius):

LineChart<Number, Number> lineChartP = LineCharts.pressPlot(numDeps, radInt, pressShell, pGasShell, pRadShell);

grid.add(lineChartP, 2, 9);

// Plot 3: log rho:

LineChart<Number, Number> lineChartRho = LineCharts.rhoPlot(numDeps, radInt, rhoShell);

grid.add(lineChartRho, 2, 11);

// Plot 4: log cumulative L_Bol

LineChart<Number, Number> lineChartLum = LineCharts.lumPlot(numDeps, radInt, lumInt, lumPpInt, lumCnoInt);

grid.add(lineChartLum, 0, 10);

// Plot 5: log cumulative mass

LineChart<Number, Number> lineChartMass = LineCharts.massPlot(numDeps, radInt, massInt);

grid.add(lineChartMass, 2, 10);

// Plot 6: log epsilon (nuc power generation)

LineChart<Number, Number> lineChartEps = LineCharts.epsPlot(numDeps, radInt, epsShell, epsPpShell, epsCnoShell);

grid.add(lineChartEps, 0, 11);

// Plot 7: log kappa (mass extinction)

LineChart<Number, Number> lineChartKap = LineCharts.kapPlot(numDeps, radInt, kapShell, kapBfShell, kapFfShell, kapEsShell, kapHminShell);

grid.add(lineChartKap, 4, 10);

// Plot 8: log flux(lambda) (SED)

LineChart<Number, Number> lineChartSED = LineCharts.sedPlot(numWaves, waveGrid, SED);

grid.add(lineChartSED, 4, 11);

*/

// Graphical output section:

// Plot 1: T_Kin(radius):

LineChart<Number, Number> lineChartT2 = LineCharts.t2Plot(numDeps, radInt, tempShell);

grid.add(lineChartT2, 0, 9);

// Plot 2: log(P(radius):

LineChart<Number, Number> lineChartP = LineCharts.pressPlot(numDeps, radInt, pressShell, pGasShell, pRadShell);

grid.add(lineChartP, 2, 9);

// Plot 3: log rho:

LineChart<Number, Number> lineChartRho = LineCharts.rhoPlot(numDeps, radInt, rhoShell);

grid.add(lineChartRho, 2, 13);

// Plot 4: log cumulative L_Bol

LineChart<Number, Number> lineChartLum = LineCharts.lumPlot(numDeps, iCore, radInt, lumInt, lumPpInt, lumCnoInt);

grid.add(lineChartLum, 0, 11);

// Plot 5: log cumulative mass

LineChart<Number, Number> lineChartMass = LineCharts.massPlot(numDeps, radInt, massInt);

grid.add(lineChartMass, 2, 11);

// Plot 6: log epsilon (nuc power generation)

LineChart<Number, Number> lineChartEps = LineCharts.epsPlot(numDeps, radInt, epsShell, epsPpShell, epsCnoShell);

grid.add(lineChartEps, 0, 13);

// Plot 7: log kappa (mass extinction)

LineChart<Number, Number> lineChartKap = LineCharts.kapPlot(numDeps, radInt, kapShell, kapBfShell, kapFfShell, kapEsShell, kapHminShell);

grid.add(lineChartKap, 4, 11);

// Plot 8: log flux(lambda) (SED)

LineChart<Number, Number> lineChartSED = LineCharts.sedPlot(numWaves, waveGrid, SED);

grid.add(lineChartSED, 4, 13);

// LineChart<Number, Number> lineChartSpec = LineCharts.specPlot(numMaster, masterLams, cosTheta, masterIntens, masterFlux);

// grid.add(lineChartSpec, 2, 10);

////LineChart<Number, Number> lineChartLine = LineCharts.linePlot(numPoints, lineLambdas, cosTheta, lineProf, lam0);

// grid.add(lineChartLine, 4, 10);

//Debug versions of the function with parameters for plotting up quqntities used in line profile

// calculation:

//LineChart<Number, Number> lineChartLine = LineCharts.linePlot(numPoints, lineLambdas, cosTheta, logKappaL, lam0, kappa);

//grid.add(lineChartLine, 4, 10);

//LineChart<Number, Number> lineChartLine = LineCharts.linePlot(numPoints, lineLambdas, cosTheta, logTauL, lam0);

//grid.add(lineChartLine, 4, 10);

// Final scene / stage stuff:

//Scene scene = new Scene(grid, 1600, 900);

//scene.getStylesheets().add("../../GrayCascadeStyleSheet.css");

//

//primaryStage.setScene(scene);

//

//primaryStage.show();

} else {

actiontarget.setText("All fields must have values");

}

}

}

);

// Final scene / stage stuff:

Scene scene = new Scene(grid, 1600, 900);

//Stylesheet.css must go in /src/ directory

scene.getStylesheets()

.add("GrayCascadeStyleSheet.css");

primaryStage.setScene(scene);

primaryStage.show();

}

/**

* @param args the command line arguments

*/

public static void main(String[] args) {

launch(args);

}