package ppmrmn; import java.util.Observable; /***************************************************************************** * * * model MQMASpowderModel * * * *****************************************************************************/ public class MQMASpowderModel extends Observable { private int nbou, //number of increment of pulse duration matRow, //row and column of the selected mulitple- matColumn, //quantum coherence in the density matrix rowCT, //central-transition row in the density matrix maxAlpha, //for division of Euler angle alpha maxBeta, //for division of Euler angle beta maxGamma, //for division of Euler angle gamma progr, //for progressBar valueEkoAntieko, //0 if echo, 1 if antiecho valueSpin; //0 if spin 3/2 private char coherenceChoice; //for coherence generated by the 1st pulse private boolean stopRun; //for button Run private double coeff, //for signal normalisation use pop, //for signal normalisation use initialPulseDuration, //inital duration of the variable pulse initialPulseDuration1, //duration of the constant pulse-1 initialPulseDuration2, //duration of the constant pulse-2 pulseIncrement, //increment of the pulse duration finalPulseDuration, //final duration of the variable pulse asymmetryParameter, spinningSpeed, //rotor spinning speed in kHz unit omegaRFkHz, //RF field in kHz unit qcckHz; //quadrupole coupling constant in kHz unit private double[] amplitude; //FID intensity private Nmr myNmr; public MQMASpowderModel() { }//end of constructor //---------------------// // Setters and getters // //---------------------// public void setvalueEkoAntieko(int x) {valueEkoAntieko = x;} public void setvalueSpin(int x) {valueSpin = x;} public int getprogr() {return progr;} //for progressBar public void setMaxAlpha(int x) {maxAlpha = x;} public int getMaxAlpha() {return maxAlpha;} //for progressBar public void setMaxBeta(int x) {maxBeta = x;} public void setMaxGamma(int x) {maxGamma = x;} public void setnbou(int x) {nbou = x;} public int getnbou() {return nbou;} public void setcoherenceChoice(char x) {coherenceChoice = x;} public char getcoherenceChoice() {return coherenceChoice;} public void setstopRun(boolean x) {stopRun = x;} public boolean getstopRun() {return stopRun;} public void setcoeff(double x) {coeff = x;} public double getcoeff() {return coeff;} public void setpop(double x) {pop = x;} public double getpop() {return pop;} public void setinitialPulseDuration(double x) {initialPulseDuration = x;} public double getinitialPulseDuration() {return initialPulseDuration;} public void setinitialPulseDuration1(double x) {initialPulseDuration1 = x;} public double getinitialPulseDuration1() {return initialPulseDuration1;} public void setinitialPulseDuration2(double x) {initialPulseDuration2 = x;} public double getinitialPulseDuration2() {return initialPulseDuration2;} public void setpulseIncrement(double x) {pulseIncrement = x;} public double getpulseIncrement() {return pulseIncrement;} public void setfinalPulseDuration(double x) {finalPulseDuration = x;} public double getfinalPulseDuration() {return finalPulseDuration;} public void setasymmetryParameter(double x) {asymmetryParameter = x;} public void setspinningSpeed(double x) {spinningSpeed = x;} public void setomegaRFkHz(double x) {omegaRFkHz = x;} public double getomegaRFkHz() {return omegaRFkHz;} public void setqcckHz(double x) {qcckHz = x;} public double getqcckHz() {return qcckHz;} private void setamplitude(double[] x) {amplitude = x;} public double[] getamplitude() {return amplitude;} //-------------------// //normalisationSignal// //-------------------// private void normalisationSignal() { switch (valueEkoAntieko) { //echo case 0: switch (valueSpin) { case 0: ComplexMat.setMatrixSize(4); rowCT = 2; coeff = 5.0; pop = Math.sqrt(4); switch (coherenceChoice) { case '1': matRow = 1; matColumn = 2; break; case '3': matRow = 3; matColumn = 0; break; } myNmr = new Spin3Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; case 1: ComplexMat.setMatrixSize(6); rowCT = 3; coeff = 35.0/2.0; pop = Math.sqrt(9); switch (coherenceChoice) { case '1': matRow = 2; matColumn = 3; break; case '3': matRow = 1; matColumn = 4; break; case '5': matRow = 5; matColumn = 0; break; } myNmr = new Spin5Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; case 2: ComplexMat.setMatrixSize(8); rowCT = 4; coeff = 42.0; pop = Math.sqrt(16); switch (coherenceChoice) { case '1': matRow = 3; matColumn = 4; break; case '3': matRow = 2; matColumn = 5; break; case '5': matRow = 1; matColumn = 6; break; case '7': matRow = 7; matColumn = 0; break; } myNmr = new Spin7Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; case 3: ComplexMat.setMatrixSize(10); rowCT = 5; coeff = 165.0/2.0; pop = Math.sqrt(25); switch (coherenceChoice) { case '1': matRow = 4; matColumn = 5; break; case '3': matRow = 3; matColumn = 6; break; case '5': matRow = 2; matColumn = 7; break; case '7': matRow = 1; matColumn = 8; break; case '9': matRow = 9; matColumn = 0; break; } myNmr = new Spin9Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; }//end of switch case 0 break; //antiécho case 1: switch (valueSpin) { case 0: ComplexMat.setMatrixSize(4); rowCT = 2; coeff = 5.0; pop = Math.sqrt(4); switch (coherenceChoice) { case '1': matRow = 2; matColumn = 1; break; case '3': matRow = 0; matColumn = 3; break; } myNmr = new Spin3Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; case 1: ComplexMat.setMatrixSize(6); rowCT = 3; coeff = 35.0/2.0; pop = Math.sqrt(9); switch (coherenceChoice) { case '1': matRow = 3; matColumn = 2; break; case '3': matRow = 4; matColumn = 1; break; case '5': matRow = 0; matColumn = 5; break; } myNmr = new Spin5Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; case 2: ComplexMat.setMatrixSize(8); rowCT = 4; coeff = 42.0; pop = Math.sqrt(16); switch (coherenceChoice) { case '1': matRow = 4; matColumn = 3; break; case '3': matRow = 5; matColumn = 2; break; case '5': matRow = 6; matColumn = 1; break; case '7': matRow = 0; matColumn = 7; break; } myNmr = new Spin7Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; case 3: ComplexMat.setMatrixSize(10); rowCT = 5; coeff = 165.0/2.0; pop = Math.sqrt(25); switch (coherenceChoice) { case '1': matRow = 5; matColumn = 4; break; case '3': matRow = 6; matColumn = 3; break; case '5': matRow = 7; matColumn = 2; break; case '7': matRow = 8; matColumn = 1; break; case '9': matRow = 0; matColumn = 9; break; } myNmr = new Spin9Half(qcckHz, omegaRFkHz); //qcckHz and omegaRFkHz in kHz become //OmegaQ (= qcc) and omegaRF in rad/s break; }//end of switch case 1 break; }//end of switch choiceEkoAntieko }//end of normalisationSignal() //-----------------------------// // Sequences A(p1)B() and A(p1)// //-----------------------------// public void mqSequenceOne(int nCycle1, int nCycle2, int choiceSequence) { RealMat matHD, matR; ComplexMat matC4, matC10; double alpha, beta, gamma; double[] amp = new double[nbou + 1]; for (int i = 0; i <= nbou; i++) amp[i] = 0.0 ; //clear normalisationSignal(); double qcc = myNmr.getOmegaQ(), spin1 = myNmr.getSpin(), rap = 3.0*qcc/(8*spin1*(2*spin1 - 1)); for (int p1 = 0; p1 < maxAlpha; p1++) { if (stopRun == true) break; alpha = 2*Math.PI*p1/maxAlpha; for (int p2 = 1; p2 < maxBeta; p2++) { beta = Math.PI*p2/maxBeta; if (stopRun == true) break; for (int p3 = 0; p3 < maxGamma; p3++) { gamma = 2*Math.PI*p3/maxGamma; if (stopRun == true) break; matC4 = myNmr.matrixIz(); //one Iz matrix = one single crystal for (int i = 0; i < nCycle1; i++) { if (stopRun == true) break; double tp1 = i*pulseIncrement; double tmp2 = rap*myNmr.xtalmasQuadrupole(alpha, beta, gamma, spinningSpeed, asymmetryParameter, tp1); myNmr.setOmegaQ(tmp2); matHD = myNmr.hamiltonianEigenValue(); matR = myNmr.hamiltonianEigenVector(); matC4 = myNmr.excitationPulse(matC4, matHD, matR, pulseIncrement); if (choiceSequence == 2) //A(p1) amp[i+1] += Math.sin(Math.PI*p2/maxBeta) *matC4.im[matRow][matColumn]; //with amp[0] = 0, no pulse duration, no signal else { //A(p1)B() matC10 = myNmr.matSingleElement(matC4, matRow, matColumn); for (int j = 0; j < nCycle2; j++) { double tp2 = j*pulseIncrement; double tmp3 = rap*myNmr.xtalmasQuadrupole(alpha, beta, gamma, spinningSpeed, asymmetryParameter, tp1 + pulseIncrement + tp2); myNmr.setOmegaQ(tmp3); matHD = myNmr.hamiltonianEigenValue(); matR = myNmr.hamiltonianEigenVector(); matC10 = myNmr.conversionPulse(matC10, matHD, matR, pulseIncrement); }//end of for j amp[i+1] += Math.sin(Math.PI*p2/maxBeta) *matC10.im[rowCT][rowCT - 1]; }//end of else }//end of for i }//end of for p3 };//end of for p2 notifyAlphaIncrease(p1); };//end of for p1 setamplitude(amp); }//end of mqSequenceOne() //-------------------// // Sequences A()B(p2)// //-------------------// public void mqSequenceTwo(int nCycle1, int nCycle2, int choiceSequence) { RealMat matHD, matR; ComplexMat matC4, matC10; double alpha, beta, gamma; double[] amp = new double[nbou + 1]; for (int i = 0; i <= nbou; i++) amp[i] = 0.0 ; //clear normalisationSignal(); double qcc = myNmr.getOmegaQ(), spin1 = myNmr.getSpin(), rap = 3.0*qcc/(8*spin1*(2*spin1 - 1)), tp1 = 0; for (int p1 = 0; p1 < maxAlpha; p1++) { alpha = 2*Math.PI*p1/maxAlpha; if (stopRun == true) break; for (int p2 = 1; p2 < maxBeta; p2++) { beta = Math.PI*p2/maxBeta; if (stopRun == true) break; for (int p3 = 0; p3 < maxGamma; p3++) { gamma = 2*Math.PI*p3/maxGamma; if (stopRun == true) break; matC4 = myNmr.matrixIz(); //one Iz matrix = one single crystal for (int i = 0; i < nCycle1; i++) { if (stopRun == true) break; tp1 = i*pulseIncrement; double tmp2 = rap*myNmr.xtalmasQuadrupole(alpha, beta, gamma, spinningSpeed, asymmetryParameter, tp1); myNmr.setOmegaQ(tmp2); matHD = myNmr.hamiltonianEigenValue(); matR = myNmr.hamiltonianEigenVector(); matC4 = myNmr.excitationPulse(matC4, matHD, matR, pulseIncrement); }//end of for i double z1 = matC4.im[matRow][matColumn]; //antiecho && SQ coherence if ((choiceSequence == 1) && (coherenceChoice == '1')) amp[0] += Math.sin(Math.PI*p2/maxBeta)*z1; matC10 = myNmr.matSingleElement(matC4, matRow, matColumn); for (int j = 0; j < nCycle2; j++) { double tp2 = j*pulseIncrement; double tmp3 = rap*myNmr.xtalmasQuadrupole(alpha, beta, gamma, spinningSpeed, asymmetryParameter, tp1 + pulseIncrement + tp2); myNmr.setOmegaQ(tmp3); matHD = myNmr.hamiltonianEigenValue(); matR = myNmr.hamiltonianEigenVector(); matC10 = myNmr.conversionPulse(matC10, matHD, matR, pulseIncrement); amp[j+1] += Math.sin(Math.PI*p2/maxBeta) *matC10.im[rowCT][rowCT - 1]; }//end of for j }//end of for p3 };//end of for p2 notifyAlphaIncrease(p1); };//end of for p1 setamplitude(amp); }//end of mqSequenceTwo() private void notifyAlphaIncrease(int p) { progr = p; setChanged(); notifyObservers(this); //progressBarRun.setValue(p1 + 1); }//end of notifyAlphaIncrease }//end of class MQMASpowderModel