diff --git a/.gitignore b/.gitignore index 4690698155f882ea48222ac4d5d12944e408e93c..a667ac3c820150c212a66fa1d4a5cdd10cc5f8b2 100644 --- a/.gitignore +++ b/.gitignore @@ -8,3 +8,4 @@ reports/*.out reports/*.xml reports/*.snm reports/*.toc +powderAverage_inhBroadening*.mat diff --git a/images/stickSpectrum_zechThesis.png b/images/stickSpectrum_zechThesis.png new file mode 100755 index 0000000000000000000000000000000000000000..c759379753f02861a863ea9231ef4f5fcee52e9e Binary files /dev/null and b/images/stickSpectrum_zechThesis.png differ diff --git a/pathdef.m b/pathdef.m deleted file mode 100755 index a9fcf70989253fc97a2b75e7bba3891f5ce10dc6..0000000000000000000000000000000000000000 --- a/pathdef.m +++ /dev/null @@ -1,1954 +0,0 @@ -function p = pathdef -%PATHDEF Search path defaults. -% PATHDEF returns a string that can be used as input to MATLABPATH -% in order to set the path. - - -% Copyright 1984-2016 The MathWorks, Inc. - - -% DO NOT MODIFY THIS FILE. 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-if startsWith(computer, 'PC') % ispc and pathsep not available - separator = ';'; -else - separator = ':'; -end - -p = [userpath separator getenv('MATLABPATH') separator p]; diff --git a/reports/oop_ciss_trEPR_stickSpectra.pdf b/reports/oop_ciss_trEPR_stickSpectra.pdf new file mode 100644 index 0000000000000000000000000000000000000000..076350c7f8557f5537c17c1428b2e91bc4650025 Binary files /dev/null and b/reports/oop_ciss_trEPR_stickSpectra.pdf differ diff --git a/reports/oop_ciss_trEPR_stickSpectra.synctex.gz b/reports/oop_ciss_trEPR_stickSpectra.synctex.gz new file mode 100644 index 0000000000000000000000000000000000000000..3e691cb7e7c44e9e53cecd7d0f5ff3adc1d26505 Binary files /dev/null and b/reports/oop_ciss_trEPR_stickSpectra.synctex.gz differ diff --git a/reports/oop_ciss_trEPR_stickSpectra.tex b/reports/oop_ciss_trEPR_stickSpectra.tex new file mode 100644 index 0000000000000000000000000000000000000000..bd917db7884ff19280f596b4568286e9d0ffa9ab --- /dev/null +++ b/reports/oop_ciss_trEPR_stickSpectra.tex @@ -0,0 +1,109 @@ +\documentclass[a4paper]{report} + +\usepackage{import} +% Relative path to ~/files/soft/latex/latex-initial-commands-general.tex +\import{../../../soft/latex/}{latex-initial-commands-general.tex} + +\usepackage[nottoc,notlot,notlof]{tocbibind} +\usepackage{listings} + +\usepackage[style=numeric-comp, sorting=none, backend=biber]{biblatex} +\addbibresource{reportOopCissCalc.bib} + +\title{OOP-ESEEM trEPR stick spectra} +\author{Gianluca Marcozzi} +\date{August 2024} + +\begin{document} + \maketitle + + \chapter{Calculations of powder trEPR spectrum} + \section{Parameters} + We try to simulate the powder trEPR spectrum of PSI. The used parameters are:\\ + \begin{itemize} + \item g1 = [2.0030, 2.0026, 2.0023], g2 = [2.0062, 2.0051, 2.0022] for P700+ and A1- respectively; + \item Euler angles [-10, -128, -83] to transform from the reference frame of P700+ to the one of A1-; + \item dipolar interaction and exchange coupling dip = -0.177 mT and J = 0.001 mT (following the spin Hamiltonian convention used by Zech); + \item direction of the spin-spin interaction corresponding to the negative x-axis of the A1- frame of reference (hence Euler angles [0, 90, 0] to go from the dipolar frame of reference to the A1- frame of reference). + \end{itemize} + + \section{Transition frequencies and intensities} + To calculate the powder average, we keep our frame fixed with the frame of A1- and calculate the trEPR stick spectra for different orientations of the external magnetic field.\\ + As explained in Zech's thesis \cite{zechPulsedTransientElectron1998} chapter 4, the stick spectrum at a given orientation of the magnetic field is going to be similar to what shown in Fig. \ref{fig:stickSpectrum_zechThesis}. The position of the resonances is given by the values of J, dip and: + \begin{equation} + \omega_0 = \frac{ \mu_B B_0}{h}\frac{g1 - g2}{2} + \end{equation} + and: + \begin{equation} + \Omega = \sqrt{\Delta\omega^2 + (J + d/2)^2}, + \end{equation} + where: + \begin{equation} + \Delta\omega = \frac{ \mu_B B_0}{h}\frac{g1 - g2}{2}. + \end{equation} + The absolute value of the intensity is the same for all the transitions at a given orientation. In particular: + \begin{equation} + I_{12} = -I_{34} = I_{13} = -I_{24} \propto \frac{\Delta\omega^2}{\Omega^2} = \sin^2(2\alpha), + \end{equation} + where $\alpha$ is the mixing angle used in Zech's thesis, defined as: + \begin{equation} + \begin{aligned} + \sin(2\alpha) = \frac{\Delta\omega}{\Omega}, & + \cos(2\alpha) = \frac{J + d/2}{\Omega}, & + \tan(2\alpha) = \frac{\Delta\omega}{J + d/2}.\\ + \end{aligned} + \end{equation} + Note that $|\alpha| \rightarrow \pi/4$ for weakly interacting spin pair while $\alpha \rightarrow 0$ for strongly interacting spin pair.\\ + \begin{figure} + \centering + \includegraphics[width=\textwidth]{../images/stickSpectrum_zechThesis} + \caption{Stick spectrum for an orientation such that $\text{d} = \text{dip} \cdot (\cos(\theta_D) - 1/3) < 0$. Taken from \cite{zechPulsedTransientElectron1998}, Fig 4.2.} + \label{fig:stickSpectrum_zechThesis} + \end{figure} + + \section{Computational steps} + \begin{enumerate} + \item Calculate $d$ and effective g-values for each orientation in order to calculate $\omega_0$, $\Delta\omega$ and $\Omega$ + \item Find the transition frequencies and intensities + \item Apply a line broadening to the stick spectrum + \item Average over all orientations + \end{enumerate} + + \subsection{Calculate orientation-dependent parameters} + We define a grid of angles $\theta$ and $\phi$. These correspond to the polar and azimuthal angles of the external magnetic field with respect to the frame of reference of A1- (which we keep fixed).\\ + An example of the code where a step of 3 degree is used both for $\theta$ and for $\phi$: + \begin{lstlisting}[language=Octave] +% Theta and phi grid +thetas = (0:3:180)*pi/180; +nTheta = numel(thetas); +phis = (0:3:360)*pi/180; +nPhi = numel(phis); + \end{lstlisting} + In this case the array thetas will be thetas = [0, 3, 6, ..., 180]*pi/180 and the number of angles will be nTheta = 61.\\ + From here we can calculate the effective g-values at each orientations. First we calculate the versor $n$ indicating the direction of $B_0$: + \begin{lstlisting}[language=Octave] +% Direction of B0 +clear('nVers') +nVers(1, :, :) = sin(thetas')*cos(phis); +nVers(2, :, :) = sin(thetas')*sin(phis); +nVers(3, :, :) = cos(thetas')*ones(1, nPhi); + \end{lstlisting} + The matrix nVers will be a 3D matrix of dimensions 3 x nTheta x nPhi. For example, for the 61st value of the first dimension ($\theta = 180$ degrees) and the first value of the second dimension ($\phi = 0$ degrees), we will obtain nVers(:, 61, 1) = [0, 0, -1], as expected.\\ + Next step: calculate g2, that is the effective g-value of A1-. Since the g2 tensor is diagonal in this reference frame, for each orientation it will be: + \begin{equation} + g\textsubscript{eff} = \sqrt{(g_{xx}\cdot n_x)^2 + (g_{yy}\cdot n_y)^2 + (g_{zz}\cdot n_z)^2}. + \end{equation} + We basically want to multiply element-wise g2 by the value of nVers for each orientation and then take the square root of the sum of the squares of the projections. The code looks like: + \begin{lstlisting}[language=Octave] +% Effective g-values +g2 = squeeze(sqrt( sum( (Sys.g(2, :)'.*nVers).^2))); + \end{lstlisting} + First, the element-wise multiplication is carried out: Sys.g(2, :)' is the column vector 3 x 1 of [$g_{xx}, g_{yy}, g_{zz}$]. The operator .* does the element-wise multiplication at each fixed $\theta$ and $\phi$ value. As a consequence, the result of Sys.g(2, :)'.*nVers is still a 3 x nTheta x nPhi matrix. Afterwards these values are squared (also element wise), then they are summed along the first dimension and then the square root is calculated. At this point the result is a 1 x nTheta x nPhi matrix. The function squeeze() makes it a nTheta x nPhi matrix corresponding to the effective g-values for each orientation.\\ + For the P700+ radical the process to calculate the effective g-values is the same, but we first need to transform the g-tensor to the frame of A1-. The code is: + \begin{lstlisting}[language=Octave] +g1TensorInFrame2 = erot(eAngles)'*diag(Sys.g(1, :))*erot(eAngles); +g1 = squeeze(sqrt( sum( (pagemtimes(g1TensorInFrame2, nVers)).^2))); + \end{lstlisting} + Here erot(eAngles) is the rotation matrix with Euler angles [-10, -128, -83]. It is applied transposed on the left (' sign) and not transposed on the right side of the diagonal matrix (diag(Sys.g(1, :))). Afterwards we calculate the effective g-value multiplying the g-tensor by the nVers for each orientation. This is done by the function pagemtimes(), that enables multiplications of 3 x 3 matrices by 3 x 1 vectors for each value of $\theta$ and $\phi$. The rest is analogous to the A1- case.\\ + \printbibliography +\end{document} \ No newline at end of file diff --git a/zech_psiOopEseem_powderAverage_inhBroadening.asv b/zech_psiOopEseem_powderAverage_inhBroadening.asv deleted file mode 100755 index 798c79a92a6fe709ccabf424c29a6cbe2deda2fa..0000000000000000000000000000000000000000 --- a/zech_psiOopEseem_powderAverage_inhBroadening.asv +++ /dev/null @@ -1,685 +0,0 @@ -% -clearvars - -% Import -% cd('/net/storage/gianlum33/projects/oop_ciss_calculations/') -expName = 'data_extracted/zech_p46_oopEseem_expData.csv'; -fitName = 'data_extracted/zech_p46_oopEseem_fit.csv'; - -importedData = readtable(expName); -x = importedData{:, 1}*pi/180; -y = importedData{:, 2}; -importedData = readtable(fitName); -xx = importedData{:, 1}*pi/180; -yy = importedData{:, 2}; - -crystalEseem = @(p, beta) -( ... - 0.5*sin(2*beta) * sin(2*p)^4 + ... - sin(beta) * cos(2*p)^2 * sin(2*p)^2); % p = alpha - -p0Z = 31.5*pi/180; -p0Timmel = 41*pi/180; -initFit = rescaledata(crystalEseem(p0Z, xx), 'maxabs'); -expectFit = rescaledata(crystalEseem(p0Timmel, xx), 'maxabs'); - -crystalEseem = @(p, beta) -(... - 1/2 * sin(2*beta) .* cos(p).^4 + ... - 1/4 * sin(beta) .* sin(2*p).^2); % p = 2alpha - -p0B = pi/2 - 2*p0Z; % xi_Bittl = pi/2 - 2*alpha_Zech -initFit2 = rescaledata(crystalEseem(p0B, xx), 'maxabs'); - -clf -plot(x*180/pi, rescaledata(y, 'maxabs'), 'o-') -hold on -plot(xx*180/pi, rescaledata(yy, 'maxabs')) -plot(xx*180/pi, initFit) -plot(xx*180/pi, initFit2) -plot(xx*180/pi, expectFit) -% esfit() - -%% Dipolar interaction matrix, g1 and g2 - -% Dipolar interaction, p = [dip, theta, phi] -dipFunc = @(dip, theta, phi) dip*((sin(theta)*cos(phi)).^2 - 1/3); - -% Mixing angle, p = [dd, JJ, B0, g1, g2] in [MHz, MHz, T, adim, adim] -xiFunc = @(dd, JJ, B0, g1, g2) atan( (dd + JJ).*1e6 .* ... - planck./(2*pi*(bmagn*B0)) ./ (g1 - g2) ); - -% Parameters of the system -% Relative orientation of g_P700+ to g_A1- -eulerAnglesZech = [81, 126, 182]*pi/180; % Zech, 'A structural model ...' -% Same as used by Easyspin -% eulerAnglesZech1to2 = [-182, -126, -81]*pi/180; % Zech, 'A structural model ...' - -% Taken from Easyspin example -Sys.S = [1/2 1/2]; -Sys.g = [2.0030 2.0026 2.0023; ... % P700+ - 2.0062 2.0051 2.0022]; % A1- -Sys.gFrame = [-10 -128 -83; ... - 0 0 0]*pi/180; -Sys.eeFrame = [0 90 0]*pi/180; % zD direction is along -x of A1- -eulerAnglesEasyspin = Sys.gFrame(1, :); -% Sys.J = -unitconvert(1e-3,'mT->MHz'); % MHz -% Sys.dip = unitconvert(+0.177,'mT->MHz'); % MHz - -dip = unitconvert(0.177,'mT->MHz'); -JJ = unitconvert(-1e-3,'mT->MHz'); -mwFreq = 9.7e9; % Hz -B0 = 0.3459; % T, static magnetic field (max of trEPR spectrum) -% B0 = 0.3461; -tau = 0.; % us - -% Assume finite bandwidth of the excitation pulse -pulseBw = 0.5e-3; % T -gPulseBw = planck*mwFreq/bmagn*(pulseBw/B0/B0); -gPulsePosition = planck*mwFreq/bmagn/B0; -excitRange = [-1/2, +1/2]*gPulseBw + gPulsePosition; - -% Theta and phi grid -thetas = (0:0.5:180)*pi/180; -nTheta = numel(thetas); -phis = (0:0.5:360)*pi/180; -nPhi = numel(phis); - -tic - -clear('dd', 'nVers', 'nVersInFrame1', 'g1', 'g2', 'xiNoLw', 'xiNoLw3D', ... - 'signalNoLw', 'signalPowderNoLw') - -dd = dipFunc(dip, thetas', phis); -% B0 direction in frame 2 -nVers(1, :, :) = sin(thetas')*cos(phis); -nVers(2, :, :) = sin(thetas')*sin(phis); -nVers(3, :, :) = cos(thetas')*ones(1, nPhi); -g2 = squeeze(sqrt( sum( (Sys.g(2, :)'.*nVers).^2))); -% B0 direction in frame 1 -nVersInFrame1 = pagemtimes(erot(eulerAnglesZech), nVers); -g1 = squeeze(sqrt( sum( (Sys.g(1, :)'.*nVersInFrame1).^2))); - -% Mixing angles -xiNoLw = xiFunc(dd, JJ, B0, g1, g2); -% Signal -xiNoLw3D(1, :, :) = xiNoLw; -signalNoLw = crystalEseem(xiNoLw3D, xx); -% Average over all the solid angles with proper normalization -xiMeanNoLw = sum(sin(thetas').*abs(xiNoLw), 'all')/ ... - sum(sin(thetas')*ones(1, nPhi), 'all'); -signalNoLw = sin(thetas).*signalNoLw; -% Temporal prefactor sin(2*(dd - JJ)*tau) -if tau ~= 0 - timePrefac = sin(2*(dd - JJ)*tau); -else - timePrefac = ones(nTheta, nPhi); -end -signalNoLw = permute(signalNoLw, [2, 3, 1]); -signalNoLw = signalNoLw.*timePrefac; -signalNoLw = permute(signalNoLw, [3, 1, 2]); -% Sum every angular contribution to the signal -signalPowderNoLw = sum(squeeze(sum(signalNoLw, 3)), 2); - -toc - -%% - -% Fit to determine the best mixing angle if it were a crystal -fitModel = @(p) p(1)*crystalEseem(p(2), xx); -p0 = [2, 6.9*pi/180]; -vary = [2, 40*pi/180]; -FitOpt.x = xx; - -ydata = rescaledata(signalPowderNoLw, 'maxabs'); -Fit = esfit(ydata, fitModel, p0, vary, FitOpt); - -clf -plot(xx, ydata, xx, Fit.fit); -yline(0, '--') -yyaxis right -plot(xx, Fit.residuals) -yline(0, '--') - -Fit.pfit(2)*180/pi % Best fit crystal mixing angle - -%{ -%% - - -figure(6) -mySignal = rescaledata(signalPowderNoLw, 'maxabs'); -testManualFit = rescaledata(crystalEseem(6.18*pi/180, xx), 'maxabs'); -crystalMean = rescaledata(crystalEseem(xiNoLwMean, xx), 'maxabs'); - -clf -% tL = tiledlayout(2, 1, 'TileSpacing', 'compact', 'Padding', 'Compact'); -% nexttile -plot(x*180/pi, rescaledata(y, 'maxabs'), 'o-', 'DisplayName', 'Zech exp. data') -hold on -plot(xx*180/pi, rescaledata(yy, 'maxabs'), 'DisplayName', 'Zech Fit') -% plot(xx*180/pi, initFit) -% plot(xx*180/pi, initFit2) -plot(xx*180/pi, mySignal, 'DisplayName', 'Gianluca powder') -plot(xx*180/pi, expectFit, 'k', 'DisplayName', '8 degrees') -plot(xx*180/pi, testManualFit, 'r--', 'DisplayName', '6.18 deg test') -plot(xx*180/pi, crystalMean, 'DisplayName', 'X-tal of avg xi (4deg)') -xlim(setaxlim(xx*180/pi, 1)) - -% nexttile -% plot(xx*180/pi, mySignal - expectFit) -legend('Location', 'northwest') -labelaxesfig(gca, 'Flip angle beta', 'ESEEM intensity') - -% [temp01, temp1] = min(abs(expectFit(5:end - 1))); -% temp1 = 4 + temp1; -% xx(temp1)*180/pi -% mySignal(temp1) -%% - -% TODO maybe set same colorbar extremes for both -figure(1) -clf -tL = tiledlayout(1, 2); -nexttile -% imagesc(phis, thetas, g1) -imagesc(g1) -colorbar -title('g1') -nexttile -% imagesc(phis, thetas, g2) -imagesc(g2) -colorbar -labelaxesfig(tL, 'Phi', 'Theta') -title('g2') - -figure(2) -clf -% imagesc(dip*(valueOfCosThetaD.^2 - 1/3)) -% imagesc(thetas, phis, dd) -% imagesc(phis, thetas, dd) -imagesc(dd) -labelaxesfig(gca, 'Phi', 'Theta') -% imagesc(thetas, phis, xiNoLw) -cbar = colorbar; -% set(cbar, 'YDir', 'reverse'); -title('Dipolar interaction dd') - - -figure(3) -clf -% imagesc(phis, thetas, g1 - g2) -imagesc(g1 - g2) -labelaxesfig(gca, 'Phi', 'Theta') -cbar = colorbar; -title('g1 minus g2') - -figure(4) -clf -% imagesc(dip*(valueOfCosThetaD.^2 - 1/3)) -% imagesc(phis, thetas, xiNoLw) -imagesc(xiNoLw) -cbar = colorbar; -labelaxesfig(gca, 'Phi', 'Theta') -% set(cbar, 'YDir', 'reverse'); -title('xiNoLw') - -% -figure(5) -clf -plot(xx, signalNoLw_{22, 200}, 'DisplayName', string(xiNoLw(22, 200)*180/pi) + " deg") -hold on -plot(xx, signalNoLw_{45, 100}, 'DisplayName', string(xiNoLw(45, 100)*180/pi) + " deg") -plot(xx, signalNoLw_{46, 200}, 'DisplayName', string(xiNoLw(46, 200)*180/pi) + " deg") -plot(xx, signalNoLw_{43, 200}, 'DisplayName', string(xiNoLw(43, 200)*180/pi) + " deg") -plot(xx, signalNoLw_{335, 540}, 'DisplayName', string(xiNoLw(335, 540)*180/pi) + " deg") -legend() - -%} -%% Optimized for loop - -% Inhomogenous line broadening due to hfi (isotropic) -% Prisner et al., Time-resolved W-band..., 1995 -lw1 = 15e6; % Hz -lw2 = 15e6; % Hz -% The g-factor linewidth -glw1 = planck/bmagn/B0*lw1; -glw2 = planck/bmagn/B0*lw2; -% Spacing between g-values -dgax = 5e-5; -dgaxInterp = 1e-7; - -signal = zeros(numel(xx), nTheta, nPhi); -xi = zeros(nTheta, nPhi); - -computTimes = zeros(nTheta, 1); - -clear('xiPhi_', 'signalPhi_') -tic -for ith = 1:nTheta - tic - % Update waitbar and message - if ~exist('wbarTh', 'var') - wbarTh = waitbar(0, '1', 'Name', 'Theta'); - end - waitbar(ith/nTheta, wbarTh, sprintf('%d out of %d', ith, nTheta)) - - theta_ = thetas(ith); - % theta_ = theta_/multTheta; - % theta_ = theta_ * 10; - - signalPhi_ = zeros(numel(xx), nPhi); - xiPhi_ = zeros(1, nPhi); - ddPhi_ = dd(ith, :); - g1Phi_ = g1(ith, :); - g2Phi_ = g2(ith, :); - parfor iph = 1:nPhi - phi_ = phis(iph); - -% Finite pulse bandwidth: no signal from spins outside excitRange - %{ - if g1(ith, iph) < excitRange(1) || ... - g1(ith, iph) > excitRange(2) || ... - g2(ith, iph) < excitRange(1) || ... - g2(ith, iph) > excitRange(2) - continue - end - %} - - % Consider inhomogenous broadening - % Create g-axis in order to 'sample' the inh. broadened g-values - [gax, gInh1, gInh2] = ... - creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgax); - deltags = gax - gax(1); - % "Probability matrix" of a certain spin interacting with another - gaussianFactors = gInh1'*gInh2; - - % Calculate inh signal multiplicity using the fact that the signal - % is symmetric for xi -> -xi (hence sum the values of the - % non-central (meaning g1 - g2 != 0) multiplicity values) - xiMultiplicity = sum(spdiags(gaussianFactors), 1); - xiMultiplicity = xiMultiplicity(end/2 + 0.5:end) + ... - xiMultiplicity(end/2 + 0.5:-1:1); -% xiMultiplicity(1) = xiMultiplicity(1)/2; - - % Interpolate - [gaxInterp, ~, ~] = ... - creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgaxInterp); - deltagsInterp = gaxInterp - gaxInterp(1); -% xiMultiplicity(1) = xiMultiplicity(1)*2; - xiMultiplicityInterp = ... - interp1(deltags, xiMultiplicity, deltagsInterp, ... - 'linear', 'extrap'); - % xiMultiplicity2(1) = 1/2*xiMultiplicity2(1); - - % Mixing angles - xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... - planck/(2*pi*(bmagn*B0)) ./ deltagsInterp ); - % Average over inh. broadening - xiPhi_(iph) = sum(abs(xi_).*xiMultiplicityInterp)/... - sum(xiMultiplicityInterp); - % Signal - signalInh = crystalEseem(xi_, xx); - % Average over inh. broadening - signalPhi_(:, iph) = sum(signalInh.*xiMultiplicityInterp, 2)/ ... - sum(xiMultiplicityInterp); - - -% ngaxLarge = numel(gaxLarge); -% ngax = numel(gaussianFactors(1, :)); - -% gaxIdxs = round(ngaxLarge/2 - ngax/2):round(ngaxLarge/2 + ngax/2); -% gax = gaxLarge(gaxIdxs); -% gInh1 = gInh1Large(gaxIdxs); -% gInh2 = gInh2Large(gaxIdxs); -% xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... -% planck/(2*pi*(bmagn*B0)) ./ deltags ); - - - - end - % Store - signal(:, ith, :) = signalPhi_; - xi(ith, :) = xiPhi_; - computTimes(ith) = toc; -end -toc - -% Average over solid angle -xiMean = sum(sin(thetas').*abs(xi), 'all')/ ... - sum(sin(thetas')*ones(1, nPhi), 'all'); -signalPowder = sum(squeeze(sum(sin(thetas).*signal, 3)), 2)/ ... - sum(sin(thetas')*ones(1, nPhi), 'all'); - -save('powderAverage_inhBroadening_EasyspinAngles_20240812.mat', ... - 'xi', 'signal', 'xiMean', 'signalPowder') - -delete(wbarTh) -clear('wbarTh') - -% clf -% plot(xx, signal_{ith, iph}) -% hold on -% plot(xx, signalNoLw_{ith, iph}) - -% max(signal_{ith, iph}) -%% -ith = 342; -iph = 357; - signalPhi_ = zeros(numel(xx), nPhi); - xiPhi_ = zeros(1, nPhi); - ddPhi_ = dd(ith, :); - g1Phi_ = g1(ith, :); - g2Phi_ = g2(ith, :); - [gax, gInh1, gInh2] = ... - creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgax); - deltags = gax - gax(1); - % "Probability matrix" of a certain spin interacting with another - gaussianFactors = gInh1'*gInh2; - - % Calculate inh signal multiplicity using the fact that the signal - % is symmetric for xi -> -xi (hence sum the values of the - % non-central (meaning g1 - g2 != 0) multiplicity values) - xiMultiplicity = sum(spdiags(gaussianFactors), 1); - xiMultiplicity = xiMultiplicity(end/2 + 0.5:end) + ... - xiMultiplicity(end/2 + 0.5:-1:1); -% xiMultiplicity(1) = xiMultiplicity(1)/2; - - % Interpolate - [gaxInterp, ~, ~] = ... - creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgaxInterp); - deltagsInterp = gaxInterp - gaxInterp(1); -% xiMultiplicity(1) = xiMultiplicity(1)*2; - xiMultiplicityInterp = ... - interp1(deltags, xiMultiplicity, deltagsInterp, ... - 'linear', 'extrap'); - % xiMultiplicity2(1) = 1/2*xiMultiplicity2(1); - - % Mixing angles - xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... - planck/(2*pi*(bmagn*B0)) ./ deltagsInterp ); - % Average over inh. broadening - xiPhi_(iph) = sum(abs(xi_).*xiMultiplicityInterp)/... - sum(xiMultiplicityInterp); - xiPhi_(iph)*180/pi - % Signal - signalInh = crystalEseem(xi_, xx); - % Average over inh. broadening - signalPhi_(:, iph) = sum(signalInh.*xiMultiplicityInterp, 2)/ ... - sum(xiMultiplicityInterp); - -plot(deltags, gInh1, 'o-', deltags, gInh2, 'o-') -plot(deltags, xiMultiplicity, 'o', deltagsInterp, xiMultiplicityInterp) -yyaxis right -plot(deltagsInterp, xi_, 'o') - -%% -%{ -%% Test - -% tempInhMultiplicity = sum(spdiags(gaussianFactors), 1); -% InhMultiplicity = aa1(end/2 + 0.5:end) + aa1(end/2 + 0.5:-1:1); -clf -ngax = numel(gax); -plot(1:2*ngax - 1, xiMultiplicity, 1:ngax, xiMultiplicity) -hold on -plot(1:ngax, gInh1, 1:ngax, gInh2) -plot(1:2*ngax - 1, xiComplete_*1e-4) - -%% Test - -deltagDistr = linspace(0, 1e-4, 2*ngax - 1); -xiDistr = atan( (dd(30, 70) + 2*JJ)*1e6 * ... - planck/(2*pi*(bmagn*B0)) ./ deltagDistr ); -mean(xiDistr)*180/pi -atan( (dd(30, 70) + 2*JJ)*1e6 * ... - planck/(2*pi*(bmagn*B0)) ./ mean(deltagDistr))*180/pi - -%% Test - -ith = 30; -iph = 400; - -gax = creategaxis(g1(ith, iph), g2(ith, iph), glw1, glw2, dgax); -ngax = numel(gax); -% Inhomogeneously broadened gaussian distributions -gInh1 = gaussian(gax, g1(ith, iph), glw1); -gInh2 = gaussian(gax, g2(ith, iph), glw2); -% Normalization (?) -gInh1 = gInh1/sum(gInh1); -gInh2 = gInh2/sum(gInh2); - -diff = zeros(ngax, ngax); -for i1 = 1:ngax - for i2 = 1:ngax - diff(i1, i2) = gInh1(i1) - gInh2(i2); - end -end - -g1(ith, iph) - g2(ith, iph) -mean(abs(diff(:))) - - -clf -imagesc(diff) -colorbar -% clf -% plot(gax, gInh1, gax, gInh2) -% -% nStep = round(2*max(diff(:))/dgax); -% diffDistr = zeros(nStep, 1); -% for i1 = 1:ngax -% for i2 = 1:ngax -% aa = round(diff(i1, i2)/dgax); -% end -% end - -%% - -% size(crystalEseem(xi_(1:10)', xx)) - -%% Some plots - -ith = 1; -iph = 1; -fig = figure(6); -tiledlayout(2, 2, 'TileSpacing', 'compact', 'Padding', 'tight') -nexttile -%contour(xi{ith, iph}) -colorbar - -nexttile -% plot(1:numel(xi{ith, iph}(:, 100)), xi{ith, iph}(:, 100)) -% textStr = sprintf('Max = %.3f, Min = %.3f', ... -% max(xi{ith, iph}(:, 100)), min(xi{ith, iph}(:, 100))); -% text(10, -1.5, textStr) - -nexttile -%% -ith = 30; -iph = 59; -gax = creategaxis(g1(ith, iph), g2(ith, iph), glw1, glw2, dgax); -gInh1 = gaussian(gax, g1(ith, iph), glw1); -gInh2 = gaussian(gax, g2(ith, iph), glw2); -gInh1 = gInh1/sum(gInh1); -gInh2 = gInh2/sum(gInh2); -contour(gInh1'*gInh2) -colorbar - -clf -plot(gax, gInh1, '-o') -hold on -plot(gax, gInh2, '-o') -yyaxis right -plot(gax, gInh1.*gInh2, '-o') - -max(gInh1) -max(gInh2) -max(gInh1.*gInh2) -%{ -nexttile(5, [2, 2]) -plot(x*180/pi, rescaledata(y, 'maxabs'), 'o-') -hold on -plot(xx*180/pi, rescaledata(yy, 'maxabs')) -plot(xx*180/pi, initFit) -plot(xx*180/pi, initFit2) -plot(xx*180/pi, rescaledata(signalPowder, 'maxabs'), 'ko-') -textStr = sprintf('Max = %.3f, Min = %.3f', ... - max(rescaledata(signalPowder, 'maxabs')), ... - min(rescaledata(signalPowder, 'maxabs'))); -text(10, 0.5, textStr) - -textStr = "thetas = 0:0.5:180; phis = 0:0.5:360;" + newline + ... - "dgax = 0.00005; computational time 5.16 h"; -text(110, -0.5, textStr) -%} - -%% - -%{ -% [nTheta, nPhi] = size(xi); -signalPowder = zeros(numel(xx), 1); - -wbarTh = waitbar(0, '1', 'Name', 'signalPowder'); -% wbarPh = waitbar(0, '1', 'Name', 'In the for cycle (Phi)'); -% -for ith = 1:nTheta - % Update waitbar and message - waitbar(ith/nTheta, wbarTh, sprintf('%d out of %d', ith, nTheta)) - - for iph = 1:nPhi -% waitbar(iph/nPhi, wbarPh, sprintf('%d out of %d', iph, nPhi)) - xi_ = xi{ith, iph}; - [ngax, ~] = size(xi_); - signalSummed = zeros(numel(xx), ngax); - for ig1 = 1:ngax - for ig2 = 1:ngax - signalSummed(:, ig1) = signalSummed(:, ig1) + ... - crystalEseem(xi_(ig1, ig2), xx); - end - signal_{ith, iph} = sum(signalSummed, 2); - end - % Solid angle normalization -% theta_ = thetas(ith); -% signal_{ith, iph} = sum(signalSingleSumg2, 2)*sin(theta_); -% signalPowder = signalPowder + signal_{ith, iph}; - end - theta_ = thetas(ith); - signalPowder = signalPowder + signal_{ith, iph}*sin(theta_); -end - -delete(wbarTh) -% delete(wbarPh) -%} - -% signalPowder = zeros(numel(xx), 1); -% for ith = 1:nTheta -% theta_ = thetas(ith); -% for iph = 1:nPhi -% signalPowder = signalPowder + signal_{ith, iph}*sin(theta_); -% end -% end - - -% plot(xx*180/pi, -rescaledata(sin(2*xx), y)) - -%% -aa.signalPowder = zeros(numel(xx), 1); - -for ith = 1:nTheta - for iph = 1:nPhi - aa.signalPowder = aa.signalPowder + aa.signal_{ith, iph}; - end -end -%% Mean xi - -% for ith = 1:nTheta -% theta_ = thetas(ith); -% xitest(ith, :) = repmat(cos(theta_)^4, 1, nPhi); -% xitest(ith, :) = repmat(1, 1, nPhi); -% end - -for ith = 1:nTheta - theta_ = thetas(ith); - xiMean = xiMean + sum(xi(ith, :))*sin(theta_); -end -normTh = pi/2/nTheta; -normPh = 1/nPhi; -normTot = normPh*normTh; -xiMean = xiMean*normTot*180/pi % /nTheta*pi/2 -% xiMean = xiMean/normTh - -%% - -g1_ = g1(1, 1); -g2_ = g2(1, 1); -lw1 = 15e6; % Hz -lw2 = 15e6; % Hz -% The g-factor linewidth for each one is (delta_nu_i = lw_i): -% delta_g_i mu_B B0 = h delta_nu_i -glw1 = planck/bmagn/0.35*lw1; -glw2 = planck/bmagn/0.35*lw2; - -xx = creategaxis(g1_, g2_, glw1, glw2, 0.0001); -% xx = 1.995:0.0001:2.015; - -gd1 = gaussian(xx, g1_, glw1); -gd2 = gaussian(xx, g2_, glw2); - -figure() -plot(xx, gd1, xx, gd2) - -%% - -clf -aa = creategaxis(g1(140, 1), g2(140, 1), glw1, glw2, dgax); -plot(aa, gaussian(aa, g1(140, 1), glw1), ... - aa, gaussian(aa, g2(140, 1), glw2)) -yyaxis right -plot(aa, gaussian(aa, g1(140, 1), glw1) .* gaussian(aa, g2(140, 1), glw2)) - -%% - -%} - -function [gax, gInh1, gInh2] = creategaxis(g1, g2, glw1, glw2, dgax) - xxFactor = 1; - xmin = min([g1 - xxFactor*glw1, g2 - xxFactor*glw2]); - xmax = max([g1 + xxFactor*glw1, g2 + xxFactor*glw2]); - gax = xmin:dgax:xmax; - - % Inhomogeneously broadened gaussian distributions - gInh1 = gaussian(gax, g1, glw1); - gInh2 = gaussian(gax, g2, glw2); - % Normalization - gaxForNormaliz1 = ... - (gax(round(end/2)) - 5*glw1):dgax:(gax(round(end/2)) + 5*glw1); - gaxForNormaliz2 = ... - (gax(round(end/2)) - 5*glw2):dgax:(gax(round(end/2)) + 5*glw2); - normFactorgInh1 = sum(gaussian(gaxForNormaliz1, g1, glw1)); - normFactorgInh2 = sum(gaussian(gaxForNormaliz2, g2, glw2)); - gInh1 = gInh1/normFactorgInh1; - gInh2 = gInh2/normFactorgInh2; -end - -function centeredMatrix = createcenteredmatrix(gInh1, gInh2) - nPoints = numel(gInh1); - multipl = gInh1'*gInh2; - [~, idxMax1] = max(multipl(:, round(nPoints))); - [~, idxMax2] = max(multipl(round(nPoints), :)); - halfWidthFin = min([idxMax1, idxMax2]) - 2; - - centeredMatrix = ... - multipl(idxMax1 - halfWidthFin:idxMax1 + halfWidthFin, ... - idxMax2 - halfWidthFin:idxMax2 + halfWidthFin); -end - - - - - - - - - - - - diff --git a/zech_psiOopEseem_powderAverage_inhBroadening.m b/zech_psiOopEseem_powderAverage_inhBroadening.m index 9d565bfd152a45587bcc512f48cfda229547b10a..33da7e9f8de748c3dbd4d5e05db1403e4ea9840e 100755 --- a/zech_psiOopEseem_powderAverage_inhBroadening.m +++ b/zech_psiOopEseem_powderAverage_inhBroadening.m @@ -13,14 +13,14 @@ importedData = readtable(fitName); xx = importedData{:, 1}*pi/180; yy = importedData{:, 2}; -crystalEseem = @(p, beta) -( ... - 0.5*sin(2*beta) * sin(2*p)^4 + ... - sin(beta) * cos(2*p)^2 * sin(2*p)^2); % p = alpha +crystalEseemZech = @(p, beta) -( ... + 0.5*sin(2*beta) .* sin(2*p).^4 + ... + sin(beta) .* cos(2*p).^2 .* sin(2*p).^2); % p = alpha p0Z = 31.5*pi/180; p0Timmel = 41*pi/180; -initFit = rescaledata(crystalEseem(p0Z, xx), 'maxabs'); -expectFit = rescaledata(crystalEseem(p0Timmel, xx), 'maxabs'); +initFit = rescaledata(crystalEseemZech(p0Z, xx), 'maxabs'); +expectFit = rescaledata(crystalEseemZech(p0Timmel, xx), 'maxabs'); crystalEseem = @(p, beta) -(... 1/2 * sin(2*beta) .* cos(p).^4 + ... @@ -38,20 +38,29 @@ plot(xx*180/pi, initFit2) plot(xx*180/pi, expectFit) % esfit() +%% + +for ii = 1:4 + loadPath = append("powderAverage_inhBroadening_glw_0", string(ii), ".mat"); + sim{ii} = load(loadPath); +end + %% Dipolar interaction matrix, g1 and g2 % Dipolar interaction, p = [dip, theta, phi] dipFunc = @(dip, theta, phi) dip*((sin(theta)*cos(phi)).^2 - 1/3); % Mixing angle, p = [dd, JJ, B0, g1, g2] in [MHz, MHz, T, adim, adim] -xiFunc = @(dd, JJ, B0, g1, g2) atan( (dd + JJ).*1e6 .* ... - planck./(2*pi*(bmagn*B0)) ./ (g1 - g2) ); +xiFunc = @(dd, JJ, B0, g1, g2) atan( (dd + 2*JJ).*1e6 .* ... + planck./(bmagn*B0) ./ (g1 - g2) ); +alphaFunc = @(dd, JJ, B0, g1, g2) ... + 1/2*atan( (bmagn*B0)/planck.*(g1 - g2)/2 ./((JJ + dd/2)*1e6)); % Parameters of the system % Relative orientation of g_P700+ to g_A1- eulerAnglesZech = [81, 126, 182]*pi/180; % Zech, 'A structural model ...' % Same as used by Easyspin -% eulerAnglesZech1to2 = [-182, -126, -81]*pi/180; % Zech, 'A structural model ...' +% eulerAnglesZech = [-182, -126, -81]*pi/180; % Zech, 'A structural model ...' % Taken from Easyspin example Sys.S = [1/2 1/2]; @@ -64,8 +73,8 @@ eulerAnglesEasyspin = Sys.gFrame(1, :); % Sys.J = -unitconvert(1e-3,'mT->MHz'); % MHz % Sys.dip = unitconvert(+0.177,'mT->MHz'); % MHz -dip = unitconvert(0.177,'mT->MHz'); -JJ = unitconvert(-1e-3,'mT->MHz'); +dip = unitconvert(-0.177,'mT->MHz'); +JJ = unitconvert(1e-3,'mT->MHz'); mwFreq = 9.7e9; % Hz B0 = 0.3459; % T, static magnetic field (max of trEPR spectrum) % B0 = 0.3461; @@ -78,15 +87,16 @@ gPulsePosition = planck*mwFreq/bmagn/B0; excitRange = [-1/2, +1/2]*gPulseBw + gPulsePosition; % Theta and phi grid -thetas = (0:0.5:180)*pi/180; +thetas = (0:1:180)*pi/180; nTheta = numel(thetas); -phis = (0:0.5:360)*pi/180; +phis = (0:1:360)*pi/180; nPhi = numel(phis); tic clear('dd', 'nVers', 'nVersInFrame1', 'g1', 'g2', 'xiNoLw', 'xiNoLw3D', ... - 'signalNoLw', 'signalPowderNoLw') + 'alphaNoLw', 'alphaNoLw3D', .... + 'signalNoLw', 'signalPowderNoLw', 'asignalNoLw', 'asignalPowderNoLw') dd = dipFunc(dip, thetas', phis); % B0 direction in frame 2 @@ -99,13 +109,19 @@ nVersInFrame1 = pagemtimes(erot(eulerAnglesZech), nVers); g1 = squeeze(sqrt( sum( (Sys.g(1, :)'.*nVersInFrame1).^2))); % Mixing angles -xiNoLw = xiFunc(dd, JJ, B0, g1, g2); +alphaNoLw = alphaFunc(dd, JJ, B0, g1, g2); +xiNoLw = xiFunc(-dd, -JJ, B0, g1, g2); % Signal +alphaNoLw3D(1, :, :) = alphaNoLw; xiNoLw3D(1, :, :) = xiNoLw; +asignalNoLw = crystalEseemZech(alphaNoLw3D, xx); signalNoLw = crystalEseem(xiNoLw3D, xx); % Average over all the solid angles with proper normalization +alphaMeanNoLw = sum(sin(thetas').*abs(alphaNoLw), 'all')/ ... + sum(sin(thetas')*ones(1, nPhi), 'all'); xiMeanNoLw = sum(sin(thetas').*abs(xiNoLw), 'all')/ ... sum(sin(thetas')*ones(1, nPhi), 'all'); +asignalNoLw = sin(thetas).*asignalNoLw; signalNoLw = sin(thetas).*signalNoLw; % Temporal prefactor sin(2*(dd - JJ)*tau) if tau ~= 0 @@ -116,7 +132,11 @@ end signalNoLw = permute(signalNoLw, [2, 3, 1]); signalNoLw = signalNoLw.*timePrefac; signalNoLw = permute(signalNoLw, [3, 1, 2]); +asignalNoLw = permute(asignalNoLw, [2, 3, 1]); +asignalNoLw = asignalNoLw.*timePrefac; +asignalNoLw = permute(asignalNoLw, [3, 1, 2]); % Sum every angular contribution to the signal +asignalPowderNoLw = sum(squeeze(sum(asignalNoLw, 3)), 2); signalPowderNoLw = sum(squeeze(sum(signalNoLw, 3)), 2); toc @@ -239,123 +259,149 @@ legend() % Inhomogenous line broadening due to hfi (isotropic) % Prisner et al., Time-resolved W-band..., 1995 -% lwArray = logspace(-1, 2, 10); -lw1 = 15e6; % Hz -lw2 = 15e6; % Hz -% The g-factor linewidth -glw1 = planck/bmagn/B0*lw1; -glw2 = planck/bmagn/B0*lw2; -% Spacing between g-values -dgax = 5e-5; -dgaxInterp = 1e-7; +lwArray = logspace(-1, 2, 10); +% for ilw = 5:9 + lw1 = 15*1e6; % Hz + lw2 = 15*1e6; % Hz + % lw1 = 15e6; + % lw2 = 15e6; + % The g-factor linewidth + glw1 = planck/bmagn/B0*lw1; + glw2 = planck/bmagn/B0*lw2; + % Spacing between g-values + dgax = 1e-5; + dgaxInterp = 1e-7; + + signal = zeros(numel(xx), nTheta, nPhi); + asignal = zeros(numel(xx), nTheta, nPhi); + xi = zeros(nTheta, nPhi); + alpha = zeros(nTheta, nPhi); + + computTimes = zeros(nTheta, 1); + + clear('xiPhi_', 'signalPhi_', 'alphaPhi_', 'asignalPhi_') + % tic + for ith = 1:nTheta + tic + % Update waitbar and message + if ~exist('wbarTh', 'var') + wbarTh = waitbar(0, '1', 'Name', 'Theta'); + end + waitbar(ith/nTheta, wbarTh, sprintf('%d out of %d', ith, nTheta)) + + theta_ = thetas(ith); + % theta_ = theta_/multTheta; + % theta_ = theta_ * 10; + + signalPhi_ = zeros(numel(xx), nPhi); + asignalPhi_ = zeros(numel(xx), nPhi); + xiPhi_ = zeros(1, nPhi); + alphaPhi_ = zeros(1, nPhi); + ddPhi_ = dd(ith, :); + g1Phi_ = g1(ith, :); + g2Phi_ = g2(ith, :); + parfor iph = 1:nPhi + phi_ = phis(iph); + + % Finite pulse bandwidth: no signal from spins outside excitRange + %{ + if g1(ith, iph) < excitRange(1) || ... + g1(ith, iph) > excitRange(2) || ... + g2(ith, iph) < excitRange(1) || ... + g2(ith, iph) > excitRange(2) + continue + end + %} + + % Consider inhomogenous broadening + % Create g-axis in order to 'sample' the inh. broadened g-values + [gax, gInh1, gInh2] = ... + creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgax); + deltags = gax - gax(1); + % "Probability matrix" of a certain spin interacting with another + gaussianFactors = gInh1'*gInh2; + + % Calculate inh signal multiplicity using the fact that the signal + % is symmetric for xi -> -xi (hence sum the values of the + % non-central (meaning g1 - g2 != 0) multiplicity values) + diagsToExtract = -(numel(gInh1) - 1):(numel(gInh1) - 1); + % xiMultiplicity = spdiags(gaussianFactors, diagsToExtract); + xiMultiplicity = sum(spdiags(gaussianFactors, diagsToExtract), 1); + xiMultiplicity = xiMultiplicity(end/2 + 0.5:end) + ... + xiMultiplicity(end/2 + 0.5:-1:1); + % xiMultiplicity(1) = xiMultiplicity(1)/2; + + % Interpolate + [gaxInterp, ~, ~] = ... + creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgaxInterp); + deltagsInterp = gaxInterp - gaxInterp(1); + % xiMultiplicity(1) = xiMultiplicity(1)*2; + xiMultiplicityInterp = ... + interp1(deltags, xiMultiplicity, deltagsInterp, ... + 'linear', 'extrap'); + xiMultiplicityInterp = ... + xiMultiplicityInterp/sum(xiMultiplicityInterp); + % xiMultiplicity2(1) = 1/2*xiMultiplicity2(1); + + % Mixing angles + xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... + planck/(bmagn*B0) ./ deltagsInterp ); + alpha_ = 1/2*atan( (bmagn*B0)/planck.*(deltagsInterp)/2 ./ ... + ((JJ + ddPhi_(iph)/2)*1e6)); + % Average over inh. broadening + xiPhi_(iph) = sum(abs(xi_).*xiMultiplicityInterp)/... + sum(xiMultiplicityInterp); + alphaPhi_(iph) = sum(abs(alpha_).*xiMultiplicityInterp)/... + sum(xiMultiplicityInterp); + % Signal + signalInh = crystalEseem(xi_, xx); + asignalInh = crystalEseemZech(xi_, xx); + % Average over inh. broadening + signalPhi_(:, iph) = sum(signalInh.*xiMultiplicityInterp, 2)/ ... + sum(xiMultiplicityInterp); + asignalPhi_(:, iph) = sum(asignalInh.*xiMultiplicityInterp, 2)/ ... + sum(xiMultiplicityInterp); + + + % ngaxLarge = numel(gaxLarge); + % ngax = numel(gaussianFactors(1, :)); + + % gaxIdxs = round(ngaxLarge/2 - ngax/2):round(ngaxLarge/2 + ngax/2); + % gax = gaxLarge(gaxIdxs); + % gInh1 = gInh1Large(gaxIdxs); + % gInh2 = gInh2Large(gaxIdxs); + % xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... + % planck/(2*pi*(bmagn*B0)) ./ deltags ); -signal = zeros(numel(xx), nTheta, nPhi); -xi = zeros(nTheta, nPhi); -computTimes = zeros(nTheta, 1); -clear('xiPhi_', 'signalPhi_') -tic -for ith = 1:nTheta - tic - % Update waitbar and message - if ~exist('wbarTh', 'var') - wbarTh = waitbar(0, '1', 'Name', 'Theta'); - end - waitbar(ith/nTheta, wbarTh, sprintf('%d out of %d', ith, nTheta)) - - theta_ = thetas(ith); - % theta_ = theta_/multTheta; - % theta_ = theta_ * 10; - - signalPhi_ = zeros(numel(xx), nPhi); - xiPhi_ = zeros(1, nPhi); - ddPhi_ = dd(ith, :); - g1Phi_ = g1(ith, :); - g2Phi_ = g2(ith, :); - parfor iph = 1:nPhi - phi_ = phis(iph); - -% Finite pulse bandwidth: no signal from spins outside excitRange - %{ - if g1(ith, iph) < excitRange(1) || ... - g1(ith, iph) > excitRange(2) || ... - g2(ith, iph) < excitRange(1) || ... - g2(ith, iph) > excitRange(2) - continue end - %} - - % Consider inhomogenous broadening - % Create g-axis in order to 'sample' the inh. broadened g-values - [gax, gInh1, gInh2] = ... - creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgax); - deltags = gax - gax(1); - % "Probability matrix" of a certain spin interacting with another - gaussianFactors = gInh1'*gInh2; - - % Calculate inh signal multiplicity using the fact that the signal - % is symmetric for xi -> -xi (hence sum the values of the - % non-central (meaning g1 - g2 != 0) multiplicity values) - xiMultiplicity = sum(spdiags(gaussianFactors), 1); - xiMultiplicity = xiMultiplicity(end/2 + 0.5:end) + ... - xiMultiplicity(end/2 + 0.5:-1:1); -% xiMultiplicity(1) = xiMultiplicity(1)/2; - - % Interpolate - [gaxInterp, ~, ~] = ... - creategaxis(g1Phi_(iph), g2Phi_(iph), glw1, glw2, dgaxInterp); - deltagsInterp = gaxInterp - gaxInterp(1); -% xiMultiplicity(1) = xiMultiplicity(1)*2; - xiMultiplicityInterp = ... - interp1(deltags, xiMultiplicity, deltagsInterp, ... - 'linear', 'extrap'); - % xiMultiplicity2(1) = 1/2*xiMultiplicity2(1); - - % Mixing angles - xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... - planck/(2*pi*(bmagn*B0)) ./ deltagsInterp ); - % Average over inh. broadening - xiPhi_(iph) = sum(abs(xi_).*xiMultiplicityInterp)/... - sum(xiMultiplicityInterp); - % Signal - signalInh = crystalEseem(xi_, xx); - % Average over inh. broadening - signalPhi_(:, iph) = sum(signalInh.*xiMultiplicityInterp, 2)/ ... - sum(xiMultiplicityInterp); - - -% ngaxLarge = numel(gaxLarge); -% ngax = numel(gaussianFactors(1, :)); - -% gaxIdxs = round(ngaxLarge/2 - ngax/2):round(ngaxLarge/2 + ngax/2); -% gax = gaxLarge(gaxIdxs); -% gInh1 = gInh1Large(gaxIdxs); -% gInh2 = gInh2Large(gaxIdxs); -% xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... -% planck/(2*pi*(bmagn*B0)) ./ deltags ); - - - + % Store + signal(:, ith, :) = signalPhi_; + asignal(:, ith, :) = asignalPhi_; + xi(ith, :) = xiPhi_; + alpha(ith, :) = alphaPhi_; + computTimes(ith) = toc; +% computTimes(ith) end - % Store - signal(:, ith, :) = signalPhi_; - xi(ith, :) = xiPhi_; - computTimes(ith) = toc; -end -toc - -% Average over solid angle -xiMean = sum(sin(thetas').*abs(xi), 'all')/ ... - sum(sin(thetas')*ones(1, nPhi), 'all'); -signalPowder = sum(squeeze(sum(sin(thetas).*signal, 3)), 2)/ ... - sum(sin(thetas')*ones(1, nPhi), 'all'); - -save('powderAverage_inhBroadening_01.mat', ... - 'xi', 'signal', 'xiMean', 'signalPowder') - -delete(wbarTh) -clear('wbarTh') + % toc + + % Average over solid angle + xiMean = sum(sin(thetas').*abs(xi), 'all')/ ... + sum(sin(thetas')*ones(1, nPhi), 'all'); + signalPowder = sum(squeeze(sum(sin(thetas).*signal, 3)), 2)/ ... + sum(sin(thetas')*ones(1, nPhi), 'all'); + alphaMean = sum(sin(thetas').*abs(alpha), 'all')/ ... + sum(sin(thetas')*ones(1, nPhi), 'all'); + asignalPowder = sum(squeeze(sum(sin(thetas).*asignal, 3)), 2)/ ... + sum(sin(thetas')*ones(1, nPhi), 'all'); + +% savePath = append("powderAverage_inhBroadening_glw_0", string(ilw), ".mat"); +% save(savePath, 'xi', 'signal', 'xiMean', 'signalPowder') + + delete(wbarTh) + clear('wbarTh') +% end % clf % plot(xx, signal_{ith, iph}) @@ -364,9 +410,22 @@ clear('wbarTh') % max(signal_{ith, iph}) %% -ith = 342; -iph = 357; + +lwArrayTest = linspace(0.1, 50, 100); +ith = 15; +iph = 15; +% ith = 342; +% iph = 357; +% for ilw = 1:100 +% lw1 = lwArrayTest(ilw)*1e6; % Hz +% lw2 = lwArrayTest(ilw)*1e6; % Hz + lw1 = 5e6; + lw2 = 5e6; + glw1 = planck/bmagn/B0*lw1; + glw2 = planck/bmagn/B0*lw2; signalPhi_ = zeros(numel(xx), nPhi); + dgax = 1e-5; + dgaxInterp = 1e-7; xiPhi_ = zeros(1, nPhi); ddPhi_ = dd(ith, :); g1Phi_ = g1(ith, :); @@ -380,7 +439,9 @@ iph = 357; % Calculate inh signal multiplicity using the fact that the signal % is symmetric for xi -> -xi (hence sum the values of the % non-central (meaning g1 - g2 != 0) multiplicity values) - xiMultiplicity = sum(spdiags(gaussianFactors), 1); + diagsToExtract = -(numel(gInh1) - 1):(numel(gInh1) - 1); + % xiMultiplicity = spdiags(gaussianFactors, diagsToExtract); + xiMultiplicity = sum(spdiags(gaussianFactors, diagsToExtract), 1); xiMultiplicity = xiMultiplicity(end/2 + 0.5:end) + ... xiMultiplicity(end/2 + 0.5:-1:1); % xiMultiplicity(1) = xiMultiplicity(1)/2; @@ -397,17 +458,23 @@ iph = 357; % Mixing angles xi_ = atan( (ddPhi_(iph) + 2*JJ)*1e6 * ... - planck/(2*pi*(bmagn*B0)) ./ deltagsInterp ); + planck/(bmagn*B0) ./ deltagsInterp ); % Average over inh. broadening xiPhi_(iph) = sum(abs(xi_).*xiMultiplicityInterp)/... sum(xiMultiplicityInterp); - xiPhi_(iph)*180/pi + mixingAngle(ilw) = xiPhi_(iph)*180/pi; + [valMax, idxMax] = max(xiMultiplicityInterp); + positionMax(ilw) = deltagsInterp(idxMax); + [~, idxFwhm] = min(abs(valMax/2 - xiMultiplicityInterp)); + xiMultFwhm(ilw) = abs(deltagsInterp(idxFwhm) - positionMax(ilw)); % Signal signalInh = crystalEseem(xi_, xx); % Average over inh. broadening signalPhi_(:, iph) = sum(signalInh.*xiMultiplicityInterp, 2)/ ... sum(xiMultiplicityInterp); +% end +clf plot(deltags, gInh1, 'o-', deltags, gInh2, 'o-') plot(deltags, xiMultiplicity, 'o', deltagsInterp, xiMultiplicityInterp) yyaxis right @@ -652,14 +719,14 @@ function [gax, gInh1, gInh2] = creategaxis(g1, g2, glw1, glw2, dgax) gInh1 = gaussian(gax, g1, glw1); gInh2 = gaussian(gax, g2, glw2); % Normalization - gaxForNormaliz1 = ... - (gax(round(end/2)) - 5*glw1):dgax:(gax(round(end/2)) + 5*glw1); - gaxForNormaliz2 = ... - (gax(round(end/2)) - 5*glw2):dgax:(gax(round(end/2)) + 5*glw2); - normFactorgInh1 = sum(gaussian(gaxForNormaliz1, g1, glw1)); - normFactorgInh2 = sum(gaussian(gaxForNormaliz2, g2, glw2)); - gInh1 = gInh1/normFactorgInh1; - gInh2 = gInh2/normFactorgInh2; +% gaxForNormaliz1 = ... +% (gax(round(end/2)) - 5*glw1):dgax:(gax(round(end/2)) + 5*glw1); +% gaxForNormaliz2 = ... +% (gax(round(end/2)) - 5*glw2):dgax:(gax(round(end/2)) + 5*glw2); +% normFactorgInh1 = sum(gaussian(gaxForNormaliz1, g1, glw1)); +% normFactorgInh2 = sum(gaussian(gaxForNormaliz2, g2, glw2)); +% gInh1 = gInh1/normFactorgInh1; +% gInh2 = gInh2/normFactorgInh2; end % function centeredMatrix = createcenteredmatrix(gInh1, gInh2) diff --git a/zech_psiOopEseem_trEPRstickSpectra.m b/zech_psiOopEseem_trEPRstickSpectra.m new file mode 100755 index 0000000000000000000000000000000000000000..f67fdf4feaad102af2f2869ac432f9d7de757a97 --- /dev/null +++ b/zech_psiOopEseem_trEPRstickSpectra.m @@ -0,0 +1,363 @@ +% +clearvars + +%% Easyspin simulation + +% Taken from Easyspin example +clear('Sys', 'Exp', 'Vary', 'VaryExp') + +Sys.S = [1/2 1/2]; +Sys.g = [2.0030 2.0026 2.0023; ... % P700+ + 2.0062 2.0051 2.0022]; % A1- +Sys.gFrame = [-10 -128 -83; ... + 0 0 0]*pi/180; +Sys.eeFrame = [0 90 0]*pi/180; % zD direction is along -x of A1- + +Sys.J = unitconvert(-1e-3,'mT->MHz'); % MHz +Sys.dip = unitconvert(+0.177,'mT->MHz'); % MHz +Sys.lw = 10; % MHz +Sys.initState = 'singlet'; +% Vary.dip = 1; +% Vary.J = 0.1; +% Vary.lw = 5; +% VaryExp.mwCenterSweep = [0.1, 0]; + +B0 = 345.9; % mT +mwFreq = 9.7; +xxSim = linspace(9.65, 9.75, 2048); % GHz +xxSim1 = mhz2mt(xxSim*1e3); % mT + +% Frequency sweep +Exp.mwCenterSweep = [mean(xxSim), max(xxSim) - min(xxSim)]; +Exp.Field = B0; + +% Magnetic field sweep +% Exp.CenterSweep = [mean(xxSim1), max(xxSim1) - min(xxSim1)]; % mT +% Exp.mwFreq = mwFreq; % GHz + +Exp.nPoints = numel(xxSim1); +Exp.Harmonic = 0; + +% Opt.GridSize = 10; +FitOpt.Verbosity = 0; + +ySim = pepper(Sys, Exp); + +hold on +clf +plot(xxSim, ySim/max(ySim), xxSim, trSignalPowder/max(trSignalPowder)) +legend('Easyspin', 'Gianluca') + +Ham = ham(Sys, [0, 0, B0]); +[Ham0, mux, muy, muz] = ham(Sys); + +%% + +esfit(trSignalPowder, @pepper, {Sys, Exp}, {Vary}, FitOpt) + +%% My powder average + +% For some reason I need to multiply by these random factors in order to +% have a good match with the spectrum simulated using Easyspin +dip = - Sys.dip*1.4; % MHz +JJ = - Sys.J/2.4; % MHz +% Ahfi = [9, 9, 12.8]; % MHz, only for A1- radical +eAngles = Sys.gFrame(1, :); + +% Expected input: B0 in mT +% Output: frequency nu in GHz +g2wFunc = @(B0, g) bmagn*B0/planck*g*1e-12; +% Expected input: deltaw in GHz, J in MHz, d in MHz +% Output: Omega in GHz +OmegaFunc = @(deltaw, J, d) sqrt(deltaw.^2 + (J*1e-3 + d/2*1e-3).^2); +% Dipolar interaction +% Makes use of the fact that cos(thetaD) = dotProduct(B0, zD) +% Expected input: +% dip: 1 x 1 +% nVers: 3 x nTheta x nPhi +% zD: 3 x 1 +dipFunc = @(dip, nVers, zD) dip*((sum(nVers.*zD)).^2 - 1/3); + +% Theta, phi grid +thetas = (0:3:180)*pi/180; +nTheta = numel(thetas); +phis = (0:3:360)*pi/180; +nPhi = numel(phis); + +% Direction of B0 +clear('nVers') +nVers(1, :, :) = sin(thetas')*cos(phis); +nVers(2, :, :) = sin(thetas')*sin(phis); +nVers(3, :, :) = cos(thetas')*ones(1, nPhi); +% Effective g-values +g2 = squeeze(sqrt( sum( (Sys.g(2, :)'.*nVers).^2))); +% nVersInFrame1 = pagemtimes(erot(eAngles), nVers); +% g1 = squeeze(sqrt( sum( (Sys.g(1, :)'.*nVersInFrame1).^2))); +g1TensorInFrame2 = erot(eAngles)'*diag(Sys.g(1, :))*erot(eAngles); +g1 = squeeze(sqrt( sum( (pagemtimes(g1TensorInFrame2, nVers)).^2))); +% Dipolar interaction +zD = erot(Sys.eeFrame)*[0, 0, 1]'; +dd = squeeze(dipFunc(dip, nVers, zD)); +% Atensor = squeeze(sqrt( sum( (Ahfi'.*nVers).^2))); + +w0 = g2wFunc(B0, (g1 + g2)/2); % GHz +deltaw = g2wFunc(B0, (g1 - g2)/2); % GHz +Omega = OmegaFunc(deltaw, JJ, dd); % GHz + +clear('wReson', 'intensityOfLine', 'intensityReson4D') + +wReson(1, :, :) = w0 - (JJ - dd)*1e-3 - (Omega); % w12 +wReson(2, :, :) = w0 + (JJ - dd)*1e-3 - (Omega); % w34 +wReson(3, :, :) = w0 - (JJ - dd)*1e-3 + (Omega); % w13 +wReson(4, :, :) = w0 + (JJ - dd)*1e-3 + (Omega); % w24 +% BReson = ... +% unitconvert(wReson*1e-6, 'MHz->mT', ... +% permute(repmat((g1 + g2)/2, [1, 1, 4]), [3, 1, 2])); + + +intensityOfLine = 1/8*(deltaw.^2)./(Omega.^2); +intensityReson = repmat([1; -1; 1; -1], [1, nTheta, nPhi]); +% This is correct only if the lw is isotropic (not dependent on angles) +intensityReson = ... + intensityReson.*reshape(intensityOfLine, [1, nTheta, nPhi]); + +lw1 = repmat(Sys.lw*1e-3, [4, nTheta, nPhi]); +%lwHfi = repmat(Atensor*1e-3, [4, 1, 1]); +trSignal = gaussiantransitions(xxSim', wReson, lw1, "fwhm"); + +trSignal = trSignal.*reshape(intensityReson, [1, size(intensityReson)]); +trSignalSum = squeeze(sum(trSignal, 2)); % Sum over transitions + +solidAngleWeight = sin(thetas)/sum(sin(thetas')*ones(1, nPhi), 'all'); +trSignalPowder = sum(squeeze(sum(trSignalSum.*solidAngleWeight, 3)), 2); + +hold on +% clf +plot(xxSim, trSignalPowder/max(trSignalPowder)) + +%% + +%{ +yA = gaussiantransitions(xxSim', wReson, ... + repmat(Sys.lw*1e-3, [4, nTheta, nPhi]), "fwhm"); +yB = gaussiantransitions(xxSim', wReson, ... + repmat(reshape(Atensor*1e-3, [1, nTheta, nPhi]), [4, 1, 1]), "fwhm"); + +yC = gaussiantransitionshfi(xxSim', wReson, ... + repmat(Sys.lw*1e-3, [4, nTheta, nPhi]), ... + repmat(reshape(Atensor*1e-3, [1, nTheta, nPhi]), [4, 1, 1]), "fwhm"); + +ith = 1; +iph = 1; +yplot1 = yA(:, itrans, ith, iph); +yplot1 = yplot1/max(yplot1); +yplot2 = yB(:, itrans, ith, iph); +yplot2 = yplot2/max(yplot2); +yplot3 = yC(:, itrans, ith, iph); +yplot3 = yplot3/max(yplot3); +clf +itrans = 1; +plot(xxSim, yplot1) +hold on +plot(xxSim, yplot2) + +convSpectrum = conv(yplot1, yplot2, 'same'); +plot(xxSim, convSpectrum/max(convSpectrum)) +plot(xxSim - 0.0051, yplot3) +yline(0.5) + +%% Reproduce experimental data + +load('S:\projects\zech_psi\data\processed\ZePSI-E-007015.mat'); +% clf +% h = ScrollableAxes(); +% plot(h, x{2}, x{1}, y'); +xdata = x{2}/10; % mT +ydata = y(815, :); +ydata = ydata/max(ydata); + +% Taken from Easyspin example +clear('Sys', 'Exp', 'Vary', 'VaryExp') +Sys.S = [1/2 1/2]; +Sys.g = [2.0030 2.0026 2.0023; ... % P700+ + 2.0062 2.0051 2.0022]; % A1- +Sys.gFrame = [-10 -128 -83; ... + 0 0 0]*pi/180; +Sys.eeFrame = [0 90 0]*pi/180; % zD direction is along -x of A1- + +Sys.J = unitconvert(-1e-3,'mT->MHz'); % MHz +Sys.dip = unitconvert(0.177,'mT->MHz'); % MHz +Sys.lw = 0.3; +Sys.Nucs = 'H'; +Sys.A = [0, 0, 0, 9, 9, 13]; + +Sys.initState = 'singlet'; + +% Vary.g = [0.001, 0.001, 0.001; 0.001, 0.001, 0.001]; +Vary.lw = 5; +Vary.dip = 1; +Vary.J = 0.1; +Vary.A = [0, 0, 0, 9, 9, 13]; + + +Exp.CenterSweep = [mean(xdata) + 2, max(xdata) - min(xdata)]; +Exp.mwFreq = 9.6; +Exp.nPoints = numel(xdata); +Exp.Harmonic = 0; +VaryExp.CenterSweep = [3, 0]; + +% Opt.GridSize = 10; +FitOpt.Verbosity = 0; + + +clf +plot(xdata, ydata, xdata, pepper(Sys, Exp)/max(pepper(Sys, Exp))) + +%% + +esfit(ydata, @pepper, {Sys, Exp}, {Vary, VaryExp}) + +%% + +figure(4) +s = surf(X, Y, Z, g2, 'EdgeColor', 'none'); +axis equal +viridis = viridis(); +colormap(viridis) +colorbar +xlabel('X') +title('g2') + +figure(6) +s = surf(X, Y, Z, gSys, 'EdgeColor', 'none'); +axis equal +viridis = viridis(); +colormap(viridis) +colorbar +xlabel('X') +title('g1Sys') + +figure(7) +s = surf(X, Y, Z, g11, 'EdgeColor', 'none'); +axis equal +viridis = viridis(); +colormap(viridis) +colorbar +xlabel('X') +title('g11') + +figure(8) +s = surf(X, Y, Z, g12, 'EdgeColor', 'none'); +axis equal +viridis = viridis(); +colormap(viridis) +colorbar +xlabel('X') +title('g12') + +nVersInFrame1 = pagemtimes(erot([81 126 50]*pi/180), nVers); +% nVersInFrame1 = nVers; +g1 = squeeze(sqrt( sum( (Sys.g(1, :)'.*nVersInFrame1).^2))); + +figure(9) +s = surf(X, Y, Z, g1, 'EdgeColor', 'none'); +axis equal +viridis = viridis(); +colormap(viridis) +colorbar +xlabel('X') +title('g1') + +%% + +trxx1 = planck*trxx/bmagn/gfree; +ith = 10; +iph = 300; +ith = 62; +iph = 185; +ith = 1; +iph = 1; +clf +for ith = 1:nTheta + for iph = 1:nPhi +for itrans = 1:4 + plot(xxSim, trSignal(:, itrans, ith, iph)) + hold on +end + end +end +plot(xxSim, trSignal(:, 1, 30, 60)) +xlim([-1, 1]*(Omega(ith, iph) + JJ - dd(ith, iph) + 2*trlw)) +xline(0) +title(string(dd(ith, iph))) + +%} + +%% + +function y1 = gaussiantransitions(xx, x0, c, mode) + % Output: + % y1: nAx x 4 x nTheta x nPhi + arguments + xx (:, 1) double % nA x 1 equally spaced values + x0 (4, :, :) double % 4 x nTheta x nPhi + c (4, :, :) double % 4 x nTheta x nPhi + mode string = "var" + end + + if strcmp(mode, "fwhm") + % If the input is fwhm, multiply the input parameters to have var + c = c/(2*sqrt(2*log(2))); + end + + nAx = numel(xx); + xx = repmat(xx, [1, size(x0)]); + x0 = repmat( ... + reshape(x0, [1, size(x0)]), ... + [nAx, 1, 1, 1]); + c = repmat( ... + reshape(c, [1, size(c)]), ... + [nAx, 1, 1, 1]); + y1 = exp(-1/2 * (xx - x0).^2 ./ c.^2); + % Normalization over a range equal to 10*fwhm such that the area is + % equal to 1 +% dxx = xx(2) - xx(1); +% xxNorm = -5*max(fwhm(:)):dxx:5*max(fwhm(:)); +% xxNorm = repmat(xxNorm', size(x04D)); +% xxNorm = xxNorm + x04D; +% y2 = exp(-4*log(2)*(xxNorm - x04D).^2 ./ fwhm4D.^2); +% norm = sum(y2, 1)*dxx; +% y1 = y1 ./ norm; + +end + +function [y1, yc, yhfi] = gaussiantransitionshfi(xx, x0, c, hfi, mode) + % Output: + % y1: nAx x 4 x nTheta x nPhi + arguments + xx (:, 1) double % nA x 1 equally spaced values + x0 (4, :, :) double % 4 x nTheta x nPhi + c (4, :, :) double % 4 x nTheta x nPhi + hfi (4, :, :) double % 4 x nTheta x nPhi + mode string = "var" + end + + if strcmp(mode, "fwhm") + % If the input is fwhm, multiply the input parameters to have var + c = c/(2*sqrt(2*log(2))); + hfi = hfi/(2*sqrt(2*log(2))); + end + + % Convolution of N_sigma1 and N_sigma2 is N_(sqrt(sigma1^2 + sigma2^2)) + y1 = gaussiantransitions(xx, x0, sqrt(c.^2 + hfi.^2), "var"); + yc = gaussiantransitions(xx, x0, c, "var"); + yhfi = gaussiantransitions(xx, x0, hfi, "var"); +end + + + + + + + +