diff --git a/data_extracted/zech_p46_oopEseem_expData.csv b/data/extracted/zech_p46_oopEseem_expData.csv
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rename from data_extracted/zech_p46_oopEseem_expData.csv
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diff --git a/data_extracted/zech_p46_oopEseem_fit.csv b/data/extracted/zech_p46_oopEseem_fit.csv
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rename from data_extracted/zech_p46_oopEseem_fit.csv
rename to data/extracted/zech_p46_oopEseem_fit.csv
diff --git a/signalPowder.mat b/data/generated/signalPowder.mat
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rename from signalPowder.mat
rename to data/generated/signalPowder.mat
diff --git a/images/zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison.pdf b/images/zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison.pdf
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rename to images/zech_psiOopEseem_trEPRstickSpectra_easyspinComparison.pdf
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diff --git a/reports/oop_ciss_trEPR_stickSpectra.pdf b/reports/oop_ciss_trEPR_stickSpectra.pdf
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diff --git a/reports/oop_ciss_trEPR_stickSpectra.synctex.gz b/reports/oop_ciss_trEPR_stickSpectra.synctex.gz
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diff --git a/reports/oop_ciss_trEPR_stickSpectra.tex b/reports/oop_ciss_trEPR_stickSpectra.tex
index f954898e69029991e452b205e7980c2559bd5655..43f7002b0efe82349710e92dd2bad61698238969 100644
--- a/reports/oop_ciss_trEPR_stickSpectra.tex
+++ b/reports/oop_ciss_trEPR_stickSpectra.tex
@@ -207,11 +207,10 @@ wReson(4, :, :, :) = w0 + dipInteraction + (Omega) ; % w24
At this point we calculate the lines for each of these transitions:
\begin{lstlisting}[language=Octave]
% Lineshapes for each transition
-trlw = trlw*1e-3; % GHz
trSignal = ...
gaussiantransitions(xxSim', wReson, trlw, "fwhm");
\end{lstlisting}
- where guassiantransitions returns the gaussian lineshapes in the range xxSim centered at wReson with FWHM equal to trlw (which in our case would be around 12 MHz).\\
+ where guassiantransitions returns the gaussian lineshapes in the range xxSim centered at wReson with FWHM equal to trlw. In our case, trlw is around [0.7, 0.7, 0.35, 0.35] mT, that means that the transitions of P700+ have larger linewidth than the ones of A1-.\\
The intensity of each of these lines is determined by Eq. \ref{eq:formula_for_intensity_resonances}:
\begin{lstlisting}[language=Octave]
intensityReson = 1/8*(deltaw.^2)./(Omega.^2);
@@ -246,23 +245,27 @@ trSignalPowder = sum(squeeze(sum(trSignalSum.*solidAngleWeight, 3)), 2);
\section{Comparison with Easyspin}
We calculate the spectrum using our code with parameters:
\begin{itemize}
- \item dip = -0.177 mT = -4.9 MHz and JJ = 0.001 mT = 0.028 MHz;
- \item linewidth trlw = 0.42 mT = 12 MHz;
+ \item linewidth trlw = 0.42 mT = 12 MHz, same for all the transitions;
\item all the other parameters as specified at the beginning of this document.
\end{itemize}
We compare it with a simulation obtained using Easyspinusing the same parameters (changing the sign of the dipolar coupling and dividing it by 1.5 due to a different definition of the spin Hamiltonian). The comparison is in Fig. \ref{fig:zech_psiOopEseem_trEPRstickSpectra_EasyspinComparison}.
\begin{figure}
\centering
- \includegraphics[width=.9\textwidth]{../images/zech_psiOopEseem_trEPRstickSpectra_EasyspinComparison}
+ \includegraphics[width=.9\textwidth]{../images/zech_psiOopEseem_trEPRstickSpectra_easyspinComparison}
\caption{Comparison between Easyspin and our spectrum.}
\label{fig:zech_psiOopEseem_trEPRstickSpectra_EasyspinComparison}
\end{figure}
\section{Comparison with experimental data}
- The calculation from our code is compared to experimental data in Fig. \ref{fig:zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison} (the spectrum is flipped and the axis is transformed to magnetic field axis). The high field part of the spectrum is not well reproduced. In \cite{kamlowskiRadicalPairState} Fig. 5, the spectrum is fitting better the high field part. There they used different linewidths: the one for P700+ equal to 0.7 mT and the one for A1- equal to 0.335 mT. In our code we used the same value of 0.42 mT for both.
+ We calculate the spectrum using our code with parameters:
+ \begin{itemize}
+ \item linewidth trlw = [0.84, 0.84, 0.42, 0.42] mT = [];
+ \item all the other parameters as specified at the beginning of this document.
+ \end{itemize}
+ The calculation from our code is compared to experimental data in Fig. \ref{fig:zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison} (the spectrum is flipped and the axis is transformed to magnetic field axis). The high field part of the spectrum is not well reproduced. Nevertheless, the simulation is in agreement with the simulation reported in \cite{kamlowskiRadicalPairState} Fig. 5, where the used linewidths were [0.7, 0.7, 0.35, 0.35] mT.
\begin{figure}
\centering
- \includegraphics[width=.9\textwidth]{../images/zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison}
+ \includegraphics[width=.9\textwidth]{../images/zech_psiOopEseem_trEPRstickSpectra_experimentComparison}
\caption{Comparison between experimental data and our spectrum.}
\label{fig:zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison}
\end{figure}
diff --git a/zech_psiOopEseem_trEPRstickSpectra.m b/zech_psiOopEseem_trEPRstickSpectra.m
index 8082b7a3f2234baa27d996ad96c7595eead38830..30c57bb79492636e87d0062e315c03dd7e4bb29d 100755
--- a/zech_psiOopEseem_trEPRstickSpectra.m
+++ b/zech_psiOopEseem_trEPRstickSpectra.m
@@ -17,7 +17,7 @@ Sys.eeFrame = [0 90 0]*pi/180; % zD direction is along -x of A1-
% Factor 1/1.5 coming from different definition of spin Hamiltonian?
Sys.J = unitconvert(-1e-3,'mT->MHz')/1.5; % MHz
Sys.dip = unitconvert(+0.177,'mT->MHz')/1.5; % MHz
-Sys.lw = 12; % MHz
+Sys.lw = mt2mhz(0.35); % MHz
% Sys.lw = mhz2mt(11); % MHz
Sys.initState = 'singlet';
@@ -86,7 +86,9 @@ else
nNuc = 0;
end
nHfiLine = nNuc + 1;
-trlw = Sys.lw; % ONLY gaussian lw implemented for now
+% ONLY gaussian lw implemented for now
+% One linewidth for each transition (w12, w34, w13, w24)
+trlw = [Sys.lw*2*42/35, Sys.lw*2*42/35, Sys.lw*42/35, Sys.lw*42/35]*1e-3; % GHz, 0.7 and 0.35 mT
if isfield(Exp, 'mwFreq')
trlw = mt2mhz(trlw);
end
@@ -189,7 +191,6 @@ wReson(4, :, :, :) = w0 + dipInteraction + (Omega) ; % w24
% permute(repmat((g1 + g2)/2, [1, 1, 4]), [3, 1, 2]));
% Lineshapes for each transition
-trlw = trlw*1e-3; % GHz
trSignal = ...
gaussiantransitions(xxSim', wReson, trlw, "fwhm");
@@ -208,9 +209,10 @@ solidAngleWeight = sin(thetas)/sum(sin(thetas')*ones(1, nPhi), 'all');
trSignalPowder = sum(squeeze(sum(trSignalSum.*solidAngleWeight, 3)), 2);
% hold on
-clf
+% clf
% plot(xxSim1, ySim/max(ySim), xxSim1 - 0.21, flip(trSignalPowder/max(trSignalPowder)))
plot(xxSim, ySim/max(ySim), xxSim, trSignalPowder/max(trSignalPowder))
+% plot(xxSim, trSignalPowder/max(trSignalPowder))
toc
%% Plot
@@ -252,8 +254,8 @@ legend('Exp. data', 'Gianluca')
% Using Sys.dip = unitconvert(+0.177,'mT->MHz')/1.5; % MHz
figPath = "/net/storage/gianlum33/projects/oop_ciss_calculations/images/";
-figPath = figPath + "zech_psiOopEseem_trEPRstickSpectra_ExperimentComparison";
-% exportgraphics(gcf, append(figPath, '.pdf'))
+figPath = figPath + "zech_psiOopEseem_trEPRstickSpectra_experimentComparison";
+exportgraphics(gcf, append(figPath, '.pdf'))
%%
@@ -486,9 +488,9 @@ function y1 = gaussiantransitions(xx, x0, c, mode)
% Output:
% y1:
arguments
- xx % [nA, 1] equally spaced values
+ xx % [nAx, 1] equally spaced values
x0 % [4, nHfiLine, nTheta, nPhi]
- c (1, 1) double
+ c
mode string = "fwhm"
end
@@ -497,7 +499,7 @@ function y1 = gaussiantransitions(xx, x0, c, mode)
c = c/(2*sqrt(2*log(2)));
end
- % Adjust dimensions of xx
+ % Adjust dimensions of xx if needed
[nAx, dim2] = size(xx);
if nAx < dim2
xx = xx';
@@ -515,7 +517,7 @@ function y1 = gaussiantransitions(xx, x0, c, mode)
reshape(x0_, [1, size(x0_)]), ...
[nAx, ones(1, numel(size(x0_)))]);
xx_ = xx - x0_;
- y1(:, :, iNuc, :, :) = exp(-1/2 * (xx_).^2 ./ c^2);
+ y1(:, :, iNuc, :, :) = exp(-1/2 * (xx_).^2 ./ c.^2);
end
% y1 = exp(-1/2 * (xx - x0).^2 ./ c.^2);
% Normalization over a range equal to 10*fwhm such that the area is