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index 1c645c2e1f2e1e57e313c9502d82e8660a18e545..47073fe7d31a4af8cadf8305525aa50624ff8d02 100644
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 \bibcite{Tungsten_evap}{{10}{}{{}}{{}}}
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 \bibcite{sputter_damage}{{13}{}{{}}{{}}}
 \bibcite{florian_forster}{{14}{}{{}}{{}}}
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 \bibcite{arduino_cpu_datasheet}{{25}{}{{}}{{}}}
 \bibcite{switch_datasheet}{{26}{}{{}}{{}}}
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diff --git a/chap04.tex b/chap04.tex
index a8f31d32d69f56af0215b2dfc343932bd81225dc..9dcf33355dc88f7ebc5baa91139784fa33085c45 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -227,9 +227,9 @@ In order to prevent the longer cables of the front plates of Z1 and Z3 from inte
 \todo{Maybe image}
 
 \subsection{Small capacitance stack}
-During the investigation into the problems with the driving of the Z3 motor, the capacitance values for the piezo stacks of the Z3 motors were determined. Since the cables had to be re-soldered, they could be measured separately. The motor that was re-glued in Section \ref{sec:piezo_reglue} has a lower capacitance value than the surrounding piezo stacks. The value of $1.05$ nF is lower by approximately the amount a single piezo has of $0.4$ nF from the expected $1.6 \pm 0.4$ nF (the range is not a measurement uncertainty, but due to variance in temperature). The different capacitances measured for all the piezo stacks can be seen in Figure \ref{fig:Z3_weaker_stack}. The piezo stacks both showing $1.62$ nF were only measured together since they were always wired in parallel, when measurements were taken. The plate stacks were also only measured together. Measurements were taken by measuring capacitance of the entire motor Z3 with the piezos detached from the circuit. \\
+During the investigation of the Z3 motor, the capacitance values for the piezo stacks of the Z3 motors were measured. The motor that was re-glued in Section \ref{sec:piezo_reglue} has a lower capacitance value than the surrounding piezo stacks. The value of $1.05$ nF is lower by approximately the amount a single piezo has of $0.4$ nF from the expected $1.6 \pm 0.4$ nF. The different capacitances measured for all the piezo stacks can be seen in Figure \ref{fig:Z3_weaker_stack}. The piezo stacks both showing $1.62$ nF were only measured together since they were always wired in parallel. The plate stacks were also only measured together. \\
 
-The deviation of the upper left piezo stack would imply that one of the piezo layers has depolarized and is no longer functioning, this could lead to a slight deviance in the driving behavior of Z3 at low screw firmness, but was determined to not be an issue. It should however be mentioned in case of future problems with the Z3 motor, so it can be determined if it can be a source of the issue.
+This indicates, that one of the piezo layers depolarized. This could cause the deviance in the driving behavior of Z3 at low screw firmness. It should be born in mind since it might cause problems with Z3 in the future. It might also be the reason Z3 is more prone to failures.
 
 \begin{figure}[H]
     \centering
@@ -239,8 +239,7 @@ The deviation of the upper left piezo stack would imply that one of the piezo la
 \end{figure}
 
 \section{Feed through cabling optimizations}
-A last step of optimization that was performed was on the feedthroughts that lead the signal coming from the capacitance sensors on the mask to the outside of the Mask Aligner flange, so the signal can be finally read out with the Lock-in Amplifier. The cables for the capacitance signals are coaxial cables with a shielding to prevent stray influences from the system affecting the readout. These cables were noticed to be overly long and only one of the cables shielding was grounded on the feedthrough side, instead the shielding of the other cables was grounded on the Mask Stage side, to the Mask Aligner Body. The shielding was also stripped from a large part of the cable near the feedthrough exposing the cable near the metal body of the feedthrough flange.
-
+A last step of optimization that was performed was on the feedthrought cables. The cables for the capacitance signals are coaxial cables with a shielding to prevent stray capacitances. These cables were very and only one of the cables shieldings was grounded on the feedthrough side. The length also made insertion into UHV more difficult since the cable could easily be caught behind the copper gaskets. The shielding was instead ground on the Mask Stage side to the Mask Aligner Body. The shielding was also stripped from a large part of the cable near the feedthrough exposing the cable near the metal body of the feedthrough flange.
 
 \begin{figure}[H]
     \centering
@@ -258,7 +257,7 @@ A last step of optimization that was performed was on the feedthroughts that lea
     \label{fig:Feedthrough_Repairs}
 \end{figure}
 
-In order to reduce possible interference to the signal, the cables were shortened and were properly grounded on the feedthroughs. In order to connect the feedthroughs to the body of the feedthroughs, a gold pin was soldered to the inside of the feedthrough and the male end was soldered to the coaxial cable shielding with a short copper cable. This is easier than soldering the shielding to the body directly, since a large solder amount of solder is required to properly stick to the smooth steel surface. Only the small part near the gold pins, that connect the coaxial cable to the feedthrough is now without shielding.\\
+In order to reduce possible interference to the signal, the cables were shortened and were properly ground on the feedthroughs. In order to connect to the body of the feedthroughs, a female gold pin was soldered to the inside of the feedthrough. The male end was soldered to the coaxial cable shielding with a short copper cable. This is easier than soldering the shielding to the body directly. A large solder amount of solder is required to properly stick to the smooth steel surface. Only the small section near the gold pins is now without shielding.\\
 
 \begin{table}[H]
 \centering
@@ -270,11 +269,11 @@ Mask 1 before & $7.11 \pm 0.02$      & $3.20 \pm 0.12$       & $0.19 \pm
 Mask 1 after  & $7.11 \pm 0.03$      & $3.37 \pm 0.14$       & $0.06 \pm
 0.08$        \\ \hline
 \end{tabular}
-\caption{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma$ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}
+\caption{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}
 \label{tab:cross_cap_after_repair}
 \end{table}
 
-Afterward, changes in stray capacitance were measured and it compared to measurements taken before. As can be seen in Table \ref{tab:cross_cap_after_repair} the change in cabling did not seem to have any effect on capacitance values as the differences between them are well within the measurement uncertainty. Regardless, this change does provide an improvement in cable management and possibly reduces the amount of points of failure for the system.  
+Afterward, changes in stray capacitance were measured and compared to measurements taken before. As can be seen in Table \ref{tab:cross_cap_after_repair} the change in cabling did not affect the capacitance values as the differences between them are well within the uncertainty. Regardless, this change does provide an improvement in cable management and possibly reduces the amount of points of failure for the system.  
 
 \section{Final test}
 In order to determine the proper screw setup and to test the function of the changes made to the Mask Aligner, a calibration was performed. 
@@ -286,5 +285,5 @@ In order to determine the proper screw setup and to test the function of the cha
     \label{fig:calibration_after_repair}
 \end{figure}
 
-This calibration shows similarity of performance between the 3 motors in the approach regime, as seen in Figure \ref{fig:calibration_after_repair}. In approach direction the 3 motors deviate by about $3$ nm/step, which is at least within $2$ $\sigma$ of each other, when comparing Z1 to Z2 and Z2 to Z3. Z3 and Z1 however can deviate by up to $6$ nm/step, which is within $6$$\sigma$ of each other. Assuming a difference of $6 nm$, as the worst case, the data would give an angular tilt per step of $\approx (5.73 \times 10^{-6})^\circ$ or a difference in height on the sample of $\approx 0.5$ nm/step. This in turn would give a difference in penumbra of $1.2$ nm for every $100$ steps.\\
-In the retract regime, the difference between motors is within the margin of error for Z2 and Z1, but Z3 deviates by about $4 \sigma$ from the others. Since alignment happens with approach mostly and retract is only used to move the mask back from the sample after an evaporation, this is of lesser importance than a deviation in approach behavior. After each evaporation, the mask is retracted to about $50$ $\mu$m to ensure movement of the x piezo does not damage the sample. Within these, a difference of $1.2$ $\mu$m would appear from side to side of the evaporation field, which corresponds to an angle of $\approx 0.004^\circ$. This difference should result in a deviation of $\approx 38$ nm in penumbra for the evaporation, however by driving the Z1 and Z2 motors $100$ steps up after the retraction this can be compensated almost fully and should result in an error of at most $\approx 6$ nm of additional penumbra induced by tilt. \\
+This calibration shows similarity of performance between the 3 motors in the approach regime, as shown in Figure \ref{fig:calibration_after_repair}. In approach direction the 3 motors deviate by about $3$ nm/step, which is at least within $2$ $\sigma$ of each other, when comparing Z1 to Z2 and Z2 to Z3. Z3 and Z1 however can deviate by up to $6$ nm/step, which is within $6$$\sigma$ of each other. Assuming a difference of $6 nm$, as the worst case, the data gives an angular tilt per step of $\approx (5.73 \times 10^{-6})^\circ$. This is a difference in height on the sample of $\approx 0.5$ nm/step. In turn this would give a difference in penumbra of $1.2$ nm for every $100$ steps.\\
+In the retract regime, the difference between motors is within the margin of error for Z2 and Z1, but Z3 deviates by about $4 \sigma$ from the others. Since the mask is aligned during approach, deviations in retract affect alignment less. After each evaporation, the mask is retracted to about $50$ $\mu$m. This ensures movement of the x piezo does not damage the sample. Within these, a difference of $1.2$ $\mu$m would appear from side to side of the evaporation field, which corresponds to an angle of $\approx 0.004^\circ$. This difference results in a deviation of $\approx 38$ nm in penumbra. By driving the Z1 and Z2 motors $100$ steps up after the retraction this can be compensated almost fully and should result in an error of at most $\approx 6$ nm of additional penumbra induced by tilt. \\
diff --git a/chap05.aux b/chap05.aux
index 0e980f1095347b0b95078fc392045943b709819b..1078b253e1a2d9805e04d55f574f0af6a8c20d67 100644
--- a/chap05.aux
+++ b/chap05.aux
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+\newlabel{fig:evaporation_SEM_sample}{{5.9a}{76}{\relax }{figure.caption.90}{}}
+\newlabel{sub@fig:evaporation_SEM_sample}{{a}{76}{\relax }{figure.caption.90}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces SEM images of field 2 on the sample (\subref  {fig:evaporation_SEM_sample}) and the mask (\subref  {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects.}}{76}{figure.caption.90}\protected@file@percent }
+\newlabel{fig:evaporation_SEM}{{5.9}{76}{SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects}{figure.caption.90}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog}{{5.10a}{77}{\relax }{figure.caption.91}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{77}{\relax }{figure.caption.91}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces An example of the clogging noticed on $4$ of the mask holes (\subref  {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{77}{figure.caption.91}\protected@file@percent }
+\newlabel{fig:evaporation_SEM_analysis}{{5.10}{77}{An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields}{figure.caption.91}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {5.5}Simulation}{77}{section.5.5}\protected@file@percent }
+\newlabel{sec:simulation}{{5.5}{77}{Simulation}{section.5.5}{}}
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+\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{79}{\relax }{figure.caption.92}{}}
+\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.11b}{79}{\relax }{figure.caption.92}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces (a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image. }}{79}{figure.caption.92}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare}{{5.11}{79}{(a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image}{figure.caption.92}{}}
 \citation{Bhaskar}
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-\newlabel{fig:evaporation_simulation_overlap}{{5.12}{81}{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask}{figure.caption.92}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref  {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ (\subref  {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{82}{figure.caption.93}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness}{{5.13}{82}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.93}{}}
-\newlabel{fig:evaporation_simulation_rejection_prev}{{5.14a}{83}{\relax }{figure.caption.94}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{83}{\relax }{figure.caption.94}{}}
-\newlabel{fig:evaporation_simulation_rejection_after}{{5.14b}{83}{\relax }{figure.caption.94}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{83}{\relax }{figure.caption.94}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Simulated evaporation dots without (\subref  {fig:evaporation_simulation_rejection_prev}) and with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) shows the AFM image from which the parameters for the simulation were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{83}{figure.caption.94}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_rejection}{{5.14}{83}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image from which the parameters for the simulation were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.94}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.15}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$. The image is very grainy due to a low amount of rays cast.}}{84}{figure.caption.95}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_progression}{{5.15}{84}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$. The image is very grainy due to a low amount of rays cast}{figure.caption.95}{}}
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-\@writefile{toc}{\contentsline {subsection}{\numberline {5.5.4}Final Remark}{85}{subsection.5.5.4}\protected@file@percent }
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+\newlabel{fig:evaporation_simulation_overlap}{{5.12}{80}{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask}{figure.caption.93}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.13a}{81}{\relax }{figure.caption.94}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{81}{\relax }{figure.caption.94}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.13b}{81}{\relax }{figure.caption.94}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{81}{\relax }{figure.caption.94}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.13c}{81}{\relax }{figure.caption.94}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{81}{\relax }{figure.caption.94}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref  {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ (\subref  {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{81}{figure.caption.94}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness}{{5.13}{81}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.94}{}}
+\newlabel{fig:evaporation_simulation_rejection_prev}{{5.14a}{82}{\relax }{figure.caption.95}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{82}{\relax }{figure.caption.95}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{5.14b}{82}{\relax }{figure.caption.95}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{82}{\relax }{figure.caption.95}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.14c}{82}{\relax }{figure.caption.95}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{82}{\relax }{figure.caption.95}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Simulated evaporation dots without (\subref  {fig:evaporation_simulation_rejection_prev}) and with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) shows the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{82}{figure.caption.95}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{5.14}{82}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.95}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.15}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$. The image is very grainy due to a low amount of rays cast.}}{83}{figure.caption.96}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_progression}{{5.15}{83}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$. The image is very grainy due to a low amount of rays cast}{figure.caption.96}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.5.3}Software improvements}{83}{subsection.5.5.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {5.5.4}Final Remark}{84}{subsection.5.5.4}\protected@file@percent }
 \@setckpt{chap05}{
-\setcounter{page}{86}
+\setcounter{page}{85}
 \setcounter{equation}{1}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -124,7 +124,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{8}
+\setcounter{@todonotes@numberoftodonotes}{9}
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diff --git a/chap05.tex b/chap05.tex
index 809d1c464d7d4df2b5dd4588ca97bf7bf02b89be..e84de6d9c388deb626acaa655b205a8e931fd89e 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -2,23 +2,23 @@
 \chapter{Evaporations and measurement}
 \section{Evaporation configuration}
 
-As a test for positioning and to optimize the growth of \ce{Pb} islands on a \ce{Si} sample, while minimizing the shadow obtained from mask sample alignment, evaporations were performed on a \ce{Si} sample. The \ce{Si}(111) sample was prepared and cleaned using the process described in Section \ref{sec:sample_prep}. Cleanliness of the sample and mask were confirmed optically before insertion into the Load Lock.
+As a test for positioning and to optimize the penumbra of \ce{Pb} islands on a \ce{Si} sample, evaporations were performed on a \ce{Si} sample. The \ce{Si}(111) sample was prepared and cleaned using the process described in Section \ref{sec:sample_prep}. The Cleanliness of the sample and mask was confirmed optically before insertion into the Load Lock.
 
 \begin{figure}[H]
     \centering
     \includegraphics[width=\linewidth]{img/Evaporation/Approach_Curve_Field01.pdf}
-    \caption{The approach curve measured for Field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference of the current to the last step, C1 was used for alignment primarily.}
+    \caption{The approach curve measured for field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference, C1 was used for alignment primarily.}
     \label{fig:evaporation_approach_curve}
 \end{figure}
 
-Five subsequent evaporations were performed at different lateral positions on the sample. Each evaporation consists of a field of $9 \times 9$ $3$ $\mu$m \ce{Pb} circles, as seen previously in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}. Each field was evaporated at different mask sample distances, as described by the approach curve. The approach curve to full contact of this particular sample is shown in Figure \ref{fig:evaporation_approach_curve} \\  
+Five subsequent evaporations were performed at different lateral positions on the sample. Each evaporation consists of a field of $9 \times 9$ $3$ $\mu$m \ce{Pb} circles, as seen previously in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}. Each field was evaporated at different mask sample distances, as described by the approach curve. The approach curve to full contact of this particular sample is shown in Figure \ref{fig:evaporation_approach_curve} for field 1.\\  
 
 \begin{itemize}
-	\item Field 1: Full contact
-	\item Field 2: First Contact
-	\item Field 3: Shortly before first contact at stop condition $0.12$ pF
-	\item Field 4: Second Contact
-	\item Field 5: Full Contact
+	\item Field 1: $1$ $\mu$m distance to sample (Full contact )
+	\item Field 2: $16$ $\mu$m distance to sample (First Contact)
+	\item Field 3: $16$ $\mu$m (Shortly before first contact at stop condition $0.12$ pF)
+	\item Field 4: $1$ $\mu$m (Second Contact)
+	\item Field 5: $1$ $\mu$m (Full Contact)
 \end{itemize}
 
 The evaporation parameters are shown in Table \ref{tab:evaporation_settings}.
@@ -44,7 +44,7 @@ The evaporation parameters are shown in Table \ref{tab:evaporation_settings}.
     \label{fig:evaporation_chamber_status}
 \end{figure}
 
-Figure \ref{fig:evaporation_chamber_status} shows the vacuum chamber status when the evaporation was performed. The turbomolecular pump was not turned off. The gold evaporator attached to the system was in use during the evaporations, requiring the system to be vented and pumped multiple times in the $2$ days, during which the 5 fields were evaporated. These two factors could have affected the evaporation performance.
+Figure \ref{fig:evaporation_chamber_status} shows the vacuum chamber status when the evaporation was performed. The turbomolecular pump was not turned off. 
 
 The pressure of the main chamber before each of the evaporations was $4.5 \times 10^{-10}$ mbar. The pressure during each evaporation was recorded, except for evaporation 4, where the software crashed during saving, corrupting the file. In this case, only the highest pressure value was recorded.
 
@@ -70,7 +70,7 @@ The pressure of the main chamber before each of the evaporations was $4.5 \times
 Figure \ref{fig:Evaporation_diagramm_sample_img} shows the positions of the evaporated fields in regard to the sample edges and each other. The fields angle was measured to be about $10^\circ$ with regard to the sample edge. This comes from a slight misalignment of the mask on the mask holder, as seen in Figure \ref{fig:Evaporation_diagramm_mask_img}.
 
 \section{Contamination}
-The entire sample's surface is contaminated with small particles, which are about $\approx 50$ nm in height and of a diameter on the order of $ 10$ nm. The contaminants are not visible in an optical microscope. After cleaning, the sample was only checked optically, which is why it is unknown if they were present after cleaning or were deposited afterwards. 
+The entire sample's surface is contaminated with small particles, which are about $\approx 50$ nm in height with a diameter on the order of $ 10$ nm. The contaminants are not visible in an optical microscope. After cleaning, the sample was only checked optically, which is why it is unknown if they were present after cleaning or were deposited afterward. 
 
 \begin{figure}[H]
     \centering
@@ -90,14 +90,14 @@ The entire sample's surface is contaminated with small particles, which are abou
     \label{fig:evaporation_contamination}
 \end{figure}
 
-The data in Figure \ref{fig:evaporation_contamination} shows that the particles are up to $\approx 40$ nm in height and with an average height of $20 \pm 10$ nm. The particle's average width is $40 \pm 10$. Height and width were obtained by fitting flattened Gaussian functions to the particles line cuts and extracting $2\sigma$ as well as the height of the peak. The distribution of particles across the sample surface appears approximately isotropic.
+The data in Figure \ref{fig:evaporation_contamination} shows that the particles are up to $\approx 40$ nm in height and with an average height of $24 \pm 10$ nm. The particle's average width is $40 \pm 10$. Height and width were obtained by fitting flattened Gaussian functions to the particles line cuts and extracting $2\sigma$ as well as the height of the peak. The distribution of particles across the sample surface appears approximately isotropic.
 
-In addition, the sample was contaminated with larger particles possibly from long exposure at atmospheric conditions as well as being inside the Mask Aligner Chamber during vacuum bakeout, where the system is heated to $>100$°C on $2$ separate occasions. The size of these larger particles was determined to be in the order of $\mathcal{O}(100 \text{nm})$ using SEM and on the order of $\mathit{O}(10)$ $\mu$m in diameter. \\
-Since the sample was checked only optically before insertion into UHV the small particle contamination might have been overlooked. It is suggested that in future before the sample is inserted into UHV possible contamination should be quantified in an AFM measurement and if necessary more cleaning steps performed.
+In addition, the sample was contaminated with larger particles possibly from long exposure at atmospheric conditions as well as being inside the Mask Aligner Chamber during vacuum bakeout, where the system was heated to $>100$°C on $2$ separate occasions. The size of these larger particles was determined to be in the order of $\mathcal{O}(100 \text{nm})$ using SEM and on the order of $\mathit{O}(10)$ $\mu$m in diameter. \\
+Since the sample was checked only optically before insertion into UHV the small particle contamination might have been overlooked. Therefore, to check the for contamination of the sample with an AFM measurement, before it is inserted into UHV.
 
 \section{Penumbra}
 
-To analyze the penumbra, different penumbras are analyzed, since the evaporated \ce{Pb} dots are not entirely circular (see Figure \ref{fig:penumbra_explanation_tilt}). Due to the elliptical abberation visible on the dots two different penumbra widths are analyzed. These are labeled $\sigma_s$ and $\sigma_l$. Both are defined along the major axis of the elliptical abberation. Additionally, the angle of tilt and the semi major and semi minor axis of the ellipse were measured. An example of how this would look can be seen in Figure \ref{fig:penumbra_tilt_sigmas} \\
+In AFM measurements it becomes clear, that the dots are not entirely circular (Fig. \ref{fig:penumbra_tilt_sigmas}). This can potentially come from a tilted mask (see Figure \ref{fig:penumbra_explanation_tilt}). Due to the elliptical abberation visible on the dots two different penumbra widths were analyzed. These are named $\sigma_s$ and $\sigma_l$. Both are defined along the major axis of the elliptical abberation. Additionally, the angle of tilt and the semi major and semi minor axis of the ellipse were measured. An example of how this would look can be seen in Figure \ref{fig:penumbra_tilt_sigmas} \\
 
 \begin{figure}[H]
     \centering
@@ -112,13 +112,14 @@ To analyze the penumbra, different penumbras are analyzed, since the evaporated
 	\label{fig:Evaporation_diagramm_field}
 	\end{subfigure}
     
-    \caption{AFM image of evaporated \ce{Pb} dot (\subref{fig:penumbra_tilt_sigmas}) illustrating the penumbral widths used for evaporation analysis $\sigma_s$ and $\sigma_l$, depicted in \textcolor{tab_red}{red}, and the major axis of the tilt \textcolor{tab_green}{(green)}.  $\sigma_s$ is drawn larger than actually measured, since the measured value would be hardly visible. The \textcolor{tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data stems from Evaporation 5 In Chapter 5. (\subref{fig:Evaporation_diagramm_field}) shows an AFM image of the top right part of the evaporated field labeled $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field.}
+    \caption{AFM image of evaporated \ce{Pb} dot (\subref{fig:penumbra_tilt_sigmas}) illustrating the penumbral widths used for evaporation analysis $\sigma_s$ and $\sigma_l$, depicted in \textcolor{tab_red}{red}, and the major axis of the tilt \textcolor{tab_green}{(green)}.  $\sigma_s$ is drawn larger than actually measured, to aid visibility. The \textcolor{tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data is from Evaporation 5. (\subref{fig:Evaporation_diagramm_field}) shows an AFM image of the top right part of field $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field.}
     \label{fig:penumbra_tilt_sigmas_and_field_show}
 \end{figure}
 
-In order to obtain the width of the penumbra, as well as other characteristics of the performed evaporation, AFM measurements were taken. For all fields, at least one measurement was taken of the $4$ cardinal direction by first measuring a low resolution image of the top right of the field and selecting $3$ dots to take higher resolution images of. One on the top, one on the right and one near the center. An example of this is shown in Figure \ref{fig:Evaporation_diagramm_field}. The dot visualized on the left of the image is near the center of the whole field, as the image shows only a partial field. The same process is repeated for the lower left of the field. The center dot is not recorded again in the lower left image. With this high resolution, images of dots in all 4 cardinal directions as well as the center are obtained. These are not necessarily the ones in the middle of the $4$ cardinal directions, and can be different dots across the 5 different fields. Dots were not picked for direct correspondence to the cardinal direction, but for low amount of artifacts in the AFM image.\\
-First, the data is cleaned by masking the contamination of the \ce{Si} sample. This works very well since the evaporated dots are of a height of $\approx 3$ nm, while the contamination particles are of the much greater height $\approx 50$ nm. The area under the mask is now interpolated in order to erase most of the particles. \\
-The width of the penumbra was then obtained by getting line cuts close to the line along which the tilt of the dots points and by fitting a Gaussian fall of to the slopes of the resulting line cut. The fit function is:
+In order to obtain the width of the penumbra, and other characteristics of the performed evaporation, AFM measurements were performed. For all fields, at least one measurement was taken of the $4$ cardinal directions by first measuring a low resolution image of the top right of the field and then selecting $3$ dots to take higher resolution images of. One on the top, one on the right and one near the center. An example of this is shown in Figure \ref{fig:Evaporation_diagramm_field}. The dot visualized on the left of the image is near the center of the whole field, as the image shows only a partial field. The same process is repeated for the lower left of the field. The center dot is not recorded again. The chosen dots are not necessarily the ones in the middle of the $4$ cardinal directions. They are also different dots across the 5 different fields. The criterion for choice of dot was minimal amount of contamination and AFM artifacts rather than direct correspondence to direction. \\
+
+The data is cleaned by masking the contamination of the \ce{Si} sample. This worked very well since the dots' height is $\approx 3$ nm, while the contamination particles are much taller ($\approx 50$ nm). The area under the mask is interpolated in order to remove most of the particles. \\
+The width of the penumbra was then obtained by getting line cuts close to the line along which the tilt of the dots points and by fitting a Gaussian falloff to the slopes of the resulting line cut. The fit function is:
 
 \begin{equation}
  f(x, b, h, \mu, \sigma_s, \sigma_l, r) = \begin{cases} 
@@ -128,10 +129,9 @@ The width of the penumbra was then obtained by getting line cuts close to the li
    \end{cases}
 \end{equation}
 
-where $r$ is the radius of the dot, $b$ is an offset from $0$, $\mu$ is the midpoint of the dot, $h$ is the height of the dot and $\sigma_s$ and $\sigma_l$ are the two different penumbras. This fit function allows the determination of the height, radius and penumbra of each dot 
+where $r$ is the radius of the dot, $b$ is an offset from $0$, $\mu$ is the midpoint of the dot, $h$ is the height of the dot and $\sigma_s$ and $\sigma_l$ are the two different penumbras. This fit function allows the determination of the height, radius and penumbra of each dot.
 
-An example is shown in Figure \ref{fig:evaporation_analysis}. In the example, the "Half Moon" shape of the dot, induced by a tilt, can be easily seen in both image and line cut. This results in $2$ extreme penumbra widths that were separately fitted.
-Also obtained by this method are the height and the diameter of each dot.
+An example is shown in Figure \ref{fig:evaporation_analysis}. In the example, the elliptical shape of the dot, induced by a tilt, can be easily seen in both image and line cut. This results in $2$ extreme penumbra widths.
  
 \begin{figure}[H]
     \centering
@@ -150,11 +150,11 @@ Also obtained by this method are the height and the diameter of each dot.
     	\includegraphics[width=0.95\linewidth]{img/Evaporation/TopField5Fit.pdf}
     	\caption{}
 	\end{subfigure}
-	\caption{Example of the analysis performed on each of the recorded dots for a single line cut. (a) shows the raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) shows the cleaned image, as well as the line cut \textcolor{tab_green}{(green)} from which the line cut data (c) was obtained. The black lines in (b) show how multiple line cuts were obtained on a single image to obtain values for $\sigma_s$ and $\sigma_l$. The fit parameters are the two different penumbra widths induced by the tilt $\sigma_s$ and $\sigma_l$ for a single line cut.}
+	\caption{Example of the analysis conducted on each of the recorded dots for a single line cut. (a) shows the raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) shows the cleaned image, as well as the line cut \textcolor{tab_green}{(green)} from which the line cut data (\textcolor{tab_blue}{(blue)}) in (c) was obtained. The black lines in (b) show how multiple line cuts were obtained on a single image to obtain values for $\sigma_s$ and $\sigma_l$. The fit parameters are the two different penumbra widths induced by the tilt $\sigma_s$ and $\sigma_l$ for a single line cut.}
     \label{fig:evaporation_analysis}
 \end{figure}
 
-This process was performed for every recorded dot and with multiple line cuts near the line in which the tilt is pointing, as well as for both trace and retrace images. This gives multiple data points for each image for both $\sigma_s$ and $\sigma_l$. The final values for each dot were then obtained by taking the mean and standard deviation for all the line cuts. When drawing line cuts, contamination grains were avoided whenever possible as these might affect fit accuracy.
+This process was performed for every recorded dot and with multiple line cuts near the tilt line, for both trace and retrace images. This gives multiple data points for each image for $\sigma_s$ and $\sigma_l$. The final values for each dot were then obtained by taking the mean and standard deviation for all line cuts. Contamination grains were avoided when drawing line cuts to increase data accuracy.
 
 \begin{figure}[H]
     \centering
@@ -178,21 +178,24 @@ This process was performed for every recorded dot and with multiple line cuts ne
     	\caption{}
 		\label{fig:evaporation_measured_penumbra_circle_r}
 	\end{subfigure}
-	\caption{Data obtained from the previously described method for each of the 5 evaporations, from evaporated dot each from the center of the field, the left, the right, the bottom and the top. The dot chosen depended on measurement condition such as contamination and phase characteristics of the dot. The data shows the smaller penumbra $\sigma_s$ (\subref{fig:evaporation_measured_penumbra_sigs}) the larger penumbra $\sigma_l$ (\subref{fig:evaporation_measured_penumbra_sigl}), the height of the dot (\subref{fig:evaporation_measured_penumbra_height}) and the diameter of the circle (\subref{fig:evaporation_measured_penumbra_circle_r}).}
+	\caption{Data obtained from the previously described method for each of the 5 evaporations, one dot each from the center, the left, the right, the bottom and the top. (\subref{fig:evaporation_measured_penumbra_sigs}) shows the smaller penumbra $\sigma_s$  (\subref{fig:evaporation_measured_penumbra_sigl}) the larger penumbra $\sigma_l$, (\subref{fig:evaporation_measured_penumbra_height}) the height of the dot and (\subref{fig:evaporation_measured_penumbra_circle_r}) the diameter of the circle .}
     \label{fig:evaporation_measured_penumbra}
 \end{figure}
-Figure \ref{fig:evaporation_measured_penumbra} shows the values obtained from analysis of exemplary \ce{Pb} dots of each field. For each field one dot on the top of the field, one on the bottom, one near the center and on each on the left and the right were chosen to analyze. The dots were chosen based on how contaminated the data looked in an AFM image of the top right and bottom left of the field, and if the phase showed line artifacts. \\
-The data in Figure \ref{fig:evaporation_measured_penumbra_sigs} shows that for the smaller penumbra values of well below the threshold of $100$ nm can be found, with most of the fields lying near $50$ nm. Showing that the evaporation gave very sharp interfaces. From the evaporation conditions it would be expected, that field $1$ and field $5$ should be very similar and both should show smaller penumbra than the other fields, but this does not appear to be the case. While field $5$ shows some of the smallest penumbras, its behavior seems to be more akin to field $3$ than $1$. Field $4$ also has the largest penumbras, which is unexpected since it was evaporated at the point of second contact and should thus perform better than both field $3$ and field $2$. Both field $2$ and $4$ have the largest uncertainties, due to more noisy data, which could explain this discrepancy. The differences between top, bottom, right, left and center are within measurement uncertainty and thus no conclusive statements can be made about it.\\
+Figure \ref{fig:evaporation_measured_penumbra} shows the values obtained from analysis of \ce{Pb} dots of each field. 
+For $\sigma_s$ most data is below the $100$ nm threshold. Most of the fields have near $50$ nm penumbra. This shows that very sharp interfaces are possible. It would be expected, that field $1$ and field $5$ should be very similar. Both should show smaller penumbra than the rest since they were performed at lowest distance. This does not appear to be the case. Field $5$ shows some of the smallest penumbras, however they are more like field $3$ rather than $1$. Field $4$ also has the largest penumbras, which is unexpected since it was evaporated at the point of second contact. Both field $2$ and $4$ have the largest uncertainties, due to more noisy data. This noise most likely comes from the AFM tip age. It failed shortly afterward, when someone else was using the AFM. New measurements could not be performed in time. The differences between top, bottom, right, left and center are within measurement uncertainty. Which implies no difference across the field. \\
 
+The height of the dots (Figure \ref{fig:evaporation_measured_penumbra_height}) is spread around a mean value of $2.6 \pm 0.3$ nm and shows deviation from the expected $5$ nm expected from flux. \\
 
-The height of the dots (Figure \ref{fig:evaporation_measured_penumbra_height}) is spread around a mean value of $2.6 \pm 0.3$ nm and shows strong deviation from the expected $5$ nm, obtained from calibration measurements for the particle flux that was used in the evaporation. This seems to suggest a large amount of \ce{Pb} particles never reaches the mask, even though they are expected to by the setup conditions. \\
+The diameter of the \ce{Pb} dots is expected to decrease with subsequent evaporation due to clogging of the mask. This trend is mirrored in the data. The average diameter of evaporation decreases from $3.02 \pm 0.04$ $\mu$m for field $1$ to $2.947 \pm 0.008$ $\mu$m for field $5$. From a linear regression a decrease in diameter of $0.017 \pm 0.004$ $\mu$m per evaporation is determined. \\
 
-The diameter of the \ce{Pb} dots would be expected to decrease with subsequent evaporation due to clogging of the mask. This trend is mirrored in the data as the average diameter of evaporation decreases from $3.02 \pm 0.04$ $\mu$m for field $1$ to $2.947 \pm 0.008$ $\mu$m for field $4$ with a linear fit to the average values giving a decrease in diameter of $0.017 \pm 0.004$ $\mu$m per evaporation. The eccentricity of the dot's outer shape was determined by measuring the diameter of multiple line cuts on the circle via fit and comparing measurements of perpendicular line cuts. The resulting eccentricity was as in the weighted mean $0.2 \pm 0.1$, which suggest that the dots are circular within measurement accuracy. This means the outer dot shape is not affected by the tilting effects.\\
+The eccentricity of the dot's outer shape was determined by measuring the diameter of multiple line cuts on the circle via fit and comparing measurements of perpendicular line cuts. The resulting eccentricity was as in the weighted mean $0.2 \pm 0.1$, which suggest that the dots are circular within measurement accuracy. This means the outer dot shape is not affected by the tilting effects.\\
 
-The larger penumbra data (Figure \ref{fig:evaporation_measured_penumbra_sigl}) indicates no pattern within each field and only possibly a reduction in penumbra for the bottom and center dots. This might be due to different dots being chosen for each analysis, some of which are not completely at the top or bottom (or left and right), but one row below or above. In the following, the penumbra and direction of tilt will be treated more thoroughly. \\
+The larger penumbra data (Figure \ref{fig:evaporation_measured_penumbra_sigl}) indicates no clear pattern within each field, except for possibly a reduction in penumbra for the bottom and center dots. This might be explained by different dots being chosen for each analysis. In the following, the penumbra and direction of tilt will be treated more thoroughly. \\
 
 \section{Tilt and deformation}
 
+All evaporated dots, showed signs of a tilt between mask hole and sample, even when the capacitance signal was within the full contact regime. If this was due to misalignment between the entire mask and the sample, one would expect the direction of the tilt to be uniform. The size of $\sigma_l$ would also diminish along the direction of the tilt. To determine if this was the case the direction of the angle of the major axis was measured (example Fig. \ref{fig:evaporation_tilts_example}) and recorded for all fields (Fig. \ref{fig:evaporation_tilts_all}). As shown in Figure \ref{fig:evaporation_tilts_all} the direction of the tilt is not uniform and instead seems to point outwards for dots on the edge. This suggests the mask itself is slightly bent towards the edges, resulting in an alignment error. \\
+
 \begin{figure}[H]
     \centering
 	\begin{subfigure}{0.495\linewidth}
@@ -205,15 +208,11 @@ The larger penumbra data (Figure \ref{fig:evaporation_measured_penumbra_sigl}) i
     	\caption{}
 		\label{fig:evaporation_tilts_all}
 	\end{subfigure}
-	\caption{Image of the reconstruction of the tilt angle for Field 3 as an example (\subref{fig:evaporation_tilts_example}) and the data given by all fields (\subref{fig:evaporation_tilts_all}). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}
+	\caption{(\subref{fig:evaporation_tilts_example}) image of the reconstruction of the tilt angle for Field 3. (\subref{fig:evaporation_tilts_all}) the same for all fields. For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn in this case are the high resolution AFM scans of single dots.}
     \label{fig:evaporation_tilts}
 \end{figure}
 
-All evaporated dots, even when the capacitance signal was within the full contact regime, showed signs of a tilt between mask hole and sample in the form of a half moon shaped second penumbra. If this was due to a misalignment between the entire mask and the sample, one would expect the direction of the tilt to be the same for the entire evaporated field and the size of the second penumbra to diminish along the direction of the tilt. But as seen in Figure \ref{fig:evaporation_tilts} the direction of the tilt is not uniform and instead seems to point outwards for the dots on the edge. This suggests the mask itself is slightly bent towards the edges, resulting in an alignment error. \\
-
-The smallest minor that was found in the AFM data was $2.15 \pm 0.08$ $\mu$m against the $3.01\pm 0.05$ $\mu$m of the evaporated circle. This would imply a tilt from one side of the dot on the mask to the other of $44 \pm 9 ^\circ$, which implies a difference in mask sample distance from one side of the hole in the mask to the other side of $2.08 \pm 0.31$ $\mu$m. Even with a mask sample distance average of $1$ $\mu$m this is still possible since one side can be retracted from the mask by $2.08 \pm 0.31$ $\mu$m rather than the other being closer, but this still implies a significant deformation of the mask membrane.
-
-The different angles the tilt takes can be seen in Figure \ref{fig:evaporation_tilts}. All the lead dots show a tilt and displacement as defined in Figure \ref{fig:penumbra_tilt_sigmas}, but noticeably the inner dots show lower tilt and displacement, than the ones on the outside of the field. The lead dots on the outer edge of the field point outwards from the field center, which could suggest an upwards bending of the mask towards the center of the field. \\
+The smallest minor axis found in the AFM data was $2.15 \pm 0.08$ $\mu$m compared to the $3.01\pm 0.05$ $\mu$m of the evaporated circle. This would imply a tilt from one side of the dot on the mask to the other of $44 \pm 9 ^\circ$. This corresponds to a difference in mask sample distance of $2.08 \pm 0.31$ $\mu$m. This tilt and distance are too large to be plausible. Another effect is likely at play in addition to some bending. \\
 
 \begin{figure}[H]
     \centering
@@ -233,8 +232,8 @@ The different angles the tilt takes can be seen in Figure \ref{fig:evaporation_t
     \label{fig:evaporation_SEM}
 \end{figure}
 
-To confirm the Mask was undamaged during the evaporation, SEM images were taken of the mask as well as the sample. The resulting images can be seen in Figure \ref{fig:evaporation_SEM}. The evaporation of field $2$ shown in Figure \ref{fig:evaporation_SEM_sample} shows the elliptical tilt also visible in the AFM images. The elliptical part of the evaporation shows different value in the SEM image, which is an indicator, that the conductivity is different from the part of the dot. \\
-The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to the mask. The white areas are charging artifacts and were not stable in multiple images. The mask looks to be bending, but this is most likely due to charging artifacts and an inherent fish-eye effect of SEM images at high magnifications. Furthermore, some clogging from the underside of the mask is visible in the SEM images in Figure \ref{fig:evaporation_SEM_mask}.
+To check whether the Mask was undamaged during the evaporation, SEM images were taken of the mask as well as the sample. The resulting images can be seen in Figure \ref{fig:evaporation_SEM}. The evaporation of field $2$ shown in Figure \ref{fig:evaporation_SEM_sample} shows the elliptical tilt also visible in the AFM images. The elliptical part of the dot shows different value in the SEM image, which is an indicator, that the conductivity is different for that part of the dot. \\
+The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to the mask. The white areas are charging artifacts and were not stable in multiple images. The mask looks to be bending, but this is most likely due to charging artifacts and an inherent fish-eye effect of SEM images at high magnification. Furthermore, some clogging from the underside of the mask is visible in the SEM images in Figure \ref{fig:evaporation_SEM_mask}.
 
 \begin{figure}[H]
     \centering
@@ -255,27 +254,30 @@ The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to
 \end{figure}
 
 An example of this clogging in the SEM image is shown in Figure \ref{fig:evaporation_SEM_analysis_clog}
-To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. It also mostly points outwards. For a lot of points the clogging is not clearly visible in the image however, so that no strong conclusion can be drawn from the SEM image alone.
+To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. It also points outwards. For a lot of points the clogging is not clearly visible in the image however, so that no strong conclusion can be drawn from the SEM image alone. \\
+
+This data suggests multiple possible hypothesis for this elliptical pattern. It could be that the mask deformed during evaporation or is permanently deformed. Additionally, a displacement of the mask due to vibration could cause elliptical artifacts.
+
 
 \section{Simulation} \label{sec:simulation}
 \subsection{Overview and principle}
 In order to gain more information about the different hypotheses for the tilted evaporation dots, a simple evaporation simulation program was written. The simulation is based on ray tracing and is written in the open source Godot game engine, since game engines support checking of rays against collision natively and thus a ray tracing simulation could be implemented quickly. \\
 
+Objects in the Godot game engine are moved, rotated and scaled with a $3 \times 4$ matrix called a "transform" matrix. This matrix performs rotations via their quaternion representation, which is a way to represent $3$-dimensional rotations as a $4$ component complex number. Modifying the transform matrix directly is possible, but would be very unintuitive and cumbersome, so the engine allows modification of the component's displacement and scale via $3$D vectors. The components of the displacement vector will be called x, y and z. The rotation can be modified via Euler angles. Internally the Euler angles are called x, y and z as well, based on the axis they rotate around. To avoid confusion the angles will be called $\alpha$, $\beta$ and $\gamma$, where $\alpha$ rotates around the x-axis, $\beta$ around the y-axis and $\gamma$ around the z-axis.
+
 The simulation works as follows:
-At a time $0$ at a distance $L$ from the sample a random point inside the circle is generated, and from it a ray is cast to a point behind the sample. The point behind the mask is chosen such that the ray casts in a cone with opening angle $\phi$. The ray is then checked against collision with a mask hole, which is represented by a cylinder collider with very small height. When collision with the mask "hole" is determined, the ray is cast again and the position at which the sample would be hit is determined. This position is then recorded as a hit in an array, that is structured like an image, spanning a user defined area around the middle of the sample and with user specified resolution. For each element in the array, the amount of hits the "pixel" has received is stored. This step is repeated many times in a single time step.\\
+At a time $0$ and at a distance $L$ from the sample a random point inside a circle is generated. This represents the aperture of the crucible. From it a ray is cast to a point behind the sample. The point behind the mask is chosen such that the ray casts in a cone with opening angle $\phi$. The ray is then checked for collision with a mask hole, which is represented by a cylinder with very small height. If collision with the mask hole is determined, the position at which the sample is hit is determined. Otherwise the ray is discarded. This position is then recorded in an array. It is structured like an image, spanning a user defined area around the middle of the sample with user specified resolution in pixels. For each element in the array, the amount of hits it has received is stored. This step is repeated many times in a single time step. \\
 
 %\begin{figure}[H]
 %    \centering
 %	\includegraphics[width=0.6\linewidth]{img/Evaporation/Sim/GodotCoordinate.png}
 %	\caption{Diagram depicting the coordinate system Godot uses. The order of rotation for the Euler angles is $\alpha$, $\beta$ and $\gamma$.}
 %    \label{fig:evaporation_simulation_godotcoords}
-%\end{figure}
-
-Objects in the Godot game engine are moved, rotated and scaled with a $3 \times 4$ matrix called a "transform" matrix. This matrix performs rotations via their quaternion representation, which is a way to represent $3$-dimensional rotations as a $4$ component complex number. Modifying the transform matrix directly is possible, but would be very unintuitive and cumbersome, so the engine allows modification of the component's displacement and scale via $3$D vectors. The components of the displacement vector will be called x, y and z. The rotation can be modified via Euler angles. Internally the Euler angles are called x, y and z as well, based on the axis they rotate around. To avoid confusion the angles will be called $\alpha$, $\beta$ and $\gamma$, where $\alpha$ rotates around the x-axis, $\beta$ around the y-axis and $\gamma$ around the z-axis.
+%\end{figure
 
-In order to simulate vibration effects, the cylinder collider for the mask can be moved and rotated in a periodic manner. The rotation, position and oscillation period are parameters defined by the user. And after each time step the collider is moved and in the next iteration the new collider position and rotation is checked against. The position of the current time step is obtained by linear interpolation between the start position and rotation and the end position and rotation. The interpolation parameter is determined with the function $|\sin(\frac{t}{T})|$, where $T$ is the period of the oscillation in time steps and $t$ is the current time step. This allows the simulation of $3$D vibrations in the resulting image. It does not take into account possible bending of the mask, since the colliders are stiff rigid bodies, but using rotation, bending can be locally approximated. \\
+In order to simulate vibration effects, the cylinder collider for the mask can be moved and rotated in a periodic manner. The rotation, position and oscillation period are parameters given by the user. After each time step the collider is moved. The position of the current time step is obtained by linear interpolation between the start position and rotation and the end position and rotation. The interpolation parameter is determined with the function $|\sin(\frac{t}{T})|$, where $T$ is the period of the oscillation in time steps and $t$ is the current time step. This allows the simulation of $3$D vibrations. It does not take into account possible bending of the mask, since the colliders are stiff rigid bodies, but using rotation, bending can be locally approximated. \\
 
-After a user specified time has passed, the amount of hits on each pixel is saved into a file and the image can then be displayed using a python script. For a more detailed look at the different parameters the script provides, see the Appendix \ref{sec:appendix_raycast}.\\
+After a user specified time has passed, the amount of hits on each pixel is saved into a file and the image can then be displayed using a python script. For a more detailed look at the different parameters the simulation provides see the Appendix \ref{sec:appendix_raycast}.\\
 
 \subsection{Results}
 
@@ -291,13 +293,13 @@ After a user specified time has passed, the amount of hits on each pixel is save
     	\caption{}
 		\label{fig:evaporation_simulation_first_compare_SIM}
 	\end{subfigure}
-	\caption{Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce{Pb}-\ce{Si} and \ce{Pb}-\ce{Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu$m in x and $-0.358$ $\mu$m in z direction and a tilt of $-41.12^\circ$ in $\alpha$, $10^\circ$ in $\beta$ and $31^\circ$ in $\gamma$.}
+	\caption{(a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image. }
     \label{fig:evaporation_simulation_first_compare}
 \end{figure}
 
-An image of a simple simulation for an oscillating mask dot with parameters obtained from the AFM measurement can be seen in Figure \ref{fig:evaporation_simulation_first_compare_SIM}. The parameters for the amplitude of the oscillation were extracted from the AFM image shown in Figure \ref{fig:evaporation_simulation_first_compare_AFM}. The values were $0.143$ $\mu$m in x and $-0.358$ $\mu$m in z direction and a tilt of $-41.12^\circ$ in $\alpha$ and $31^\circ$ in $\gamma$. \\
+An image of a simple simulation for an oscillating mask dot with parameters obtained from the AFM measurement can be seen in Figure \ref{fig:evaporation_simulation_first_compare_SIM}. The parameters for the amplitude of the oscillation were extracted from the AFM image shown in Figure \ref{fig:evaporation_simulation_first_compare_AFM}. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce{Pb}-\ce{Si} and \ce{Pb}-\ce{Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu$m in x and $-0.358$ $\mu$m in z direction and a tilt of $-41.12^\circ$ in $\alpha$, $10^\circ$ in $\beta$ and $31^\circ$ in $\gamma$. \\
 
-The mask being deformed by nearly $45^\circ$ at a single hole site locally would induce large strain upon the mask. The visible tilt is most likely an outcome of both an x-y displacement and a bending of the mask. If there was just a displacement due to the vibration, the mask would shift between 2 lateral positions with a certain frequency. If there is strong overlap, the $2$ extreme positions would have a certain overlap, which is elliptical. If there is now an additional displacement component in the z direction, this causes a smaller circle on top of the flat mask position. It is likely that the effect on the edge is an overlap of both a bending of the mask giving the mask some angle and an additional contribution from the displacement in both x-y and z direction. A simulation of this is shown in Figure \ref{fig:evaporation_simulation_overlap}
+A local deformation of nearly $45^\circ$ at a single hole site would lead to large strain on the mask. The visible tilt is most likely an outcome of both an x-y displacement and a bending of the mask. If there would be caused by vibrations only, the mask would shift between 2 lateral positions with a certain frequency. The $2$ extreme positions would have overlap, which is elliptical. If there is now an additional displacement component in the z direction, a smaller circle on top of the flat mask position would form. It is likely that the effect on the edge is an overlap of both a bending of the mask giving the mask some angle and an additional contribution from the displacement in both x-y and z direction. A simulation of this is shown in Figure \ref{fig:evaporation_simulation_overlap}
 
 \begin{figure}[H]
     \centering
@@ -306,9 +308,9 @@ The mask being deformed by nearly $45^\circ$ at a single hole site locally would
     \label{fig:evaporation_simulation_overlap}
 \end{figure}
 
-The amplitude of displacement in the example in Figure \ref{fig:evaporation_simulation_first_compare_SIM} is $\approx 0.4$ $\mu$m, this is in line with the peak to peak amplitude of an active turbomolecular pump given by $1$ $\mu$m, obtained in the PhD thesis of Priyamvada Bhaskar~\cite{Bhaskar}. Some features of the AFM measurement are mirrored in the simulation, however it does not match the simulated image in a number of characteristics. The "half moon" shaped penumbra (\textcolor{tab_red}{red} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) in the AFM image is very rough, but on average of equal height, while in the simulation the penumbra gradually lowers from the highest part. The lower edge of the elliptical shape visible in the AFM dot below the circle (\textcolor{tab_cyan}{cyan} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) is so faint as to be invisible in the AFM image, while it is very pronounced in the simulated image and the lower edge is sharp in the AFM image $61 \pm 9$ nm while it is smeared out in the simulated image. \\
+The amplitude of displacement in the example in Figure \ref{fig:evaporation_simulation_first_compare_SIM} is $\approx 0.4$ $\mu$m, this is in line with the peak to peak amplitude of an active turbomolecular pump given by $1$ $\mu$m, obtained in the PhD thesis of Priyamvada Bhaskar~\cite{Bhaskar}. Some features of the AFM measurement are mirrored in the simulation, however it does not match the simulated image in a number of characteristics. For example the elliptical penumbra (\textcolor{tab_red}{red} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) is very rough in the AFM image, but on average of equal height, while in the simulation the penumbra gradually lowers. Furthermore, the lower edge of the elliptical shape visible in the AFM dot below the circle (\textcolor{tab_cyan}{cyan} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) is so faint as to be invisible in the AFM image, while it is very pronounced in the simulated image. The lower edge is sharp in the AFM image $61 \pm 9$ nm while it is smeared out in the simulated image. \\
 
-The different roughness from circle and ellipse might suggest different possible reasons. First it could be a chronological effect where the circle is deposited first, and the ellipse is deposited second. Another possibility is that the vibration cause the displacement and bending of the mask in a pattern that is anharmonic, which causes the extreme points of the oscillation to be preferred. In order to investigate possible sources of this effect, the simulation was amended. \\
+The different roughness of circle and ellipse might suggest different possible reasons. First it could be a chronological effect where the circle is deposited first, and the ellipse is deposited second. Another possibility is that the vibration causes the displacement and bending of the mask in a pattern that is anharmonic, which causes the extreme points of the oscillation to be preferred. In order to investigate possible sources of this effect, the simulation was amended. \\
 
 \begin{figure}[H]
     \centering
@@ -331,11 +333,11 @@ The different roughness from circle and ellipse might suggest different possible
     \label{fig:evaporation_simulation_sharpness}
 \end{figure}
 
-The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_initial} compared with the simpler model (Figure \ref{fig:evaporation_simulation_sharpness_stick_simple}) this gives an image more similar to the AFM measurement. Another possibility is an oscillation, which is not harmonic. For this instead of choosing the oscillation as $\sin(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\sin(\frac{t}{T} + \phi)^p$ with $p$ being the oscillation power. The resulting image can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_power}. The effect of this is very similar to the initial circular shape. The vibrations causing the deformation and tilt are unlikely to be very anharmonic, but due to growth of thin films happening near grains, the actual growth of \ce{Pb} on the \ce{Si} is concentrated at the extreme positions of the oscillation.
+The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_initial}. Compared with the simpler model (Figure \ref{fig:evaporation_simulation_sharpness_stick_simple}) this is more similar to the AFM measurement. Another possibility is an oscillation, which is not harmonic. For this instead of choosing the oscillation as $\sin(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\sin(\frac{t}{T} + \phi)^p$ with $p$ being the oscillation power. The resulting image can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_power}. The effect of this is very similar to the initial circular shape. The vibrations causing the deformation and tilt are unlikely to be very anharmonic, but due to growth of thin films happening near grains, the actual growth of \ce{Pb} on the \ce{Si} is concentrated at the extreme positions of the oscillation.
 
-When looking at the measured AFM image, it is very noticeable, that the surface of the "half moon" is rougher than the surface of the inner circle. On average, the roughness is $1.7 \pm 0.4$ times higher. This could be due to the \ce{Pb} preferring already established particle sites to diffuse and grow near another possible reason is a chronology of events where the growth happens first on the outer circle and then on the elliptical shape, as previously looked at.\\
+When looking at the measured AFM image, it is very noticeable, that the surface of the "half moon" is rougher than the surface of the inner circle. On average, the roughness is $1.7 \pm 0.4$ times higher. The \ce{Pb} can more easily grow at already established sites. This causes the growth to be in grains. With larger layer height this effect typically decreases. Another possible reason is a chronology of events where the growth happens first on the outer circle and then on the elliptical shape, as previously discussed. \\
 
-Lead or in general any deposited material deposits more easily, when there is already some of the same material deposited. This nucleation effect can be relatively simply be modeled in the simulation by penalizing deposition for pixels, where no material has been deposited previously. The probability to deposit on an empty surface is a user controlled parameter called "first\_layer\_depo\_prob". It controls the probability with which a particle hitting the sample is deposited, when no material has previously been deposited on the relevant pixel. \\
+The grain growth can be be modeled in the simulation by penalizing deposition for pixels, where no material has been deposited previously. The probability to deposit on an empty surface is a user controlled parameter called "first\_layer\_depo\_prob". It specifies the probability with which a particle hitting the sample is deposited, when no material has previously been deposited on the relevant pixel. \\
 
 \begin{figure}[H]
     \centering
@@ -354,13 +356,15 @@ Lead or in general any deposited material deposits more easily, when there is al
     	\caption{}
 		\label{fig:evaporation_simulation_rejection_comparison}
 	\end{subfigure}
-	\caption{Simulated evaporation dots without (\subref{fig:evaporation_simulation_rejection_prev}) and with (\subref{fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref{fig:evaporation_simulation_rejection_comparison}) shows the AFM image from which the parameters for the simulation were obtained. The parameters of the ellipse are the same as in Figure \ref{fig:evaporation_simulation_first_compare}.}
+	\caption{Simulated evaporation dots without (\subref{fig:evaporation_simulation_rejection_prev}) and with (\subref{fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref{fig:evaporation_simulation_rejection_comparison}) shows the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref{fig:evaporation_simulation_first_compare}.}
     \label{fig:evaporation_simulation_rejection}
 \end{figure}
 
-The results of adding this penalty for initial deposition are shown in Figure \ref{fig:evaporation_simulation_rejection_after}. As compared to the previous simulation step in Figure \ref{fig:evaporation_simulation_rejection_prev} the dot appears more rough and the height has decreases. The outer tail of the ellipse disappears nearly completely, these parameters match the deposition in the actual AFM image more closely, but crucially the decreased roughness of the elliptical part of the dot is not mirrored in the simulation, where the dot also appears rough. Typically, growth prefers to occur at grains, since these function as nucleation sites. Particles impinging on the surface will diffuse to a nearby large nucleation site. The simulation does not take this effect into account at all. But it could be implemented, by having each pixel interact with neighboring pixels. \\
+The results of adding this penalty for initial deposition are shown in Figure \ref{fig:evaporation_simulation_rejection_after}. Compared to the previous simulation step in Figure \ref{fig:evaporation_simulation_rejection_prev} the dot appears more rough and the height has decreased. The outer tail of the ellipse disappears nearly completely. This version matches the deposition in the actual AFM image more closely, but crucially the decreased roughness of the elliptical part of the dot is not mirrored in the simulation. \\
+
+Particles impinging on the surface will typically diffuse to a nearby large nucleation site. The simulation does not take this effect into account at all. This could be implemented by having pixels interact with neighboring ones.\\
 
-The simulation image matches the one given by the AFM measurement pretty well, which shows that vibrations bending the hole pattern of the mask induced by the vibrations of the turbomolecular pump are a plausible explanation for the abberant penumbra of the measured dots. Particularly it shows that a mixture of deformation on the mask edge and lateral vibrations can cause the artifacts seen in the AFM images.
+Apart from this the simulation image matches the one given by the AFM measurement pretty well. This shows that vibrations bending the hole pattern of the mask in combination with a displacement are a plausible explanation for the abberant penumbra of the measured dots. \\
 
 \begin{figure}[H]
     \centering
@@ -369,14 +373,17 @@ The simulation image matches the one given by the AFM measurement pretty well, w
     \label{fig:evaporation_simulation_progression}
 \end{figure}
 
-The simulation allows for taking in progress images at specified time intervals, with this a progression of the evaporation can be created. An example for the previously discussed case can be seen in Figure \ref{fig:evaporation_simulation_progression}. With this, the chronology of events can be made visible more easily and visualizations could easily be created. \\
+The simulation software allows for taking in progress images at specified time intervals. An example for the previously discussed case can be seen in Figure \ref{fig:evaporation_simulation_progression}. With this, the chronology of events can be made visible more easily and visualizations could be created. \\
 
 \subsection{Software improvements}
-The simulation is accurate in geometrical configuration of the Mask Aligner setup, but it assumes each particle hitting the surface either sticks to it or is rejected with a certain probability, which is a reasonable approximation as it follows the linear behavior from the Knudsen equation (Eq. \ref{eq:hertz_knudsen}), but it does not currently take into account grain size and diffusion of particles, which makes the graininess of the image resolution dependent.\\
+The simulation is accurate with respect to geometrical configuration of the Mask Aligner setup, but it assumes each particle hitting the surface either sticks to it or is rejected. This is a reasonable approximation as it follows the linear behavior from the Knudsen equation (Eq. \ref{eq:hertz_knudsen}), but it currently does not take into account grain size and diffusion of particles. \\
+
 The current way of implementing the simulation using Godot allowed for very quick implementation and bug fixing, but lacks in performance. Each ray is cast sequentially on the CPU and significant overhead is caused by the game engine computing things necessary for games, but unnecessary for the purposes of this simple simulation. This causes the render time of each image to be in the minute to hour range for images of higher resolutions. \\
-In order to improve performance, a dedicated ray tracing engine with support for threading and maybe even parallel deployment on the \textbf{G}raphics \textbf{P}rocessing \textbf{U}nit (GPU) using \textbf{A}pplication \textbf{P}rogramming \textbf{I}nterfaces (APIs) like for example CUDA or OpenCL could give significant performance improvements since many thousands of rays could be cast in parallel this way. This would most likely shorten generation times by several orders of magnitude. \\
-Since Godot uses its own units for length measurement, which are stored as $32$-bit floating point numbers, this also causes unit conversion from real world units to Godot's units to be time-consuming and can potentially cause floating point rounding issues. With a dedicated ray casting engine, real world units could be used and accuracy of the simulation could be improved by using higher precision floating point numbers. \\
+
+In order to improve performance, a dedicated ray tracing engine with support for threading could give significant performance improvements. Parallel deployment on the \textbf{G}raphics \textbf{P}rocessing \textbf{U}nit (GPU) using \textbf{A}pplication \textbf{P}rogramming \textbf{I}nterfaces (APIs) like for example CUDA or OpenCL could improve this further. This would most likely shorten generation times by several orders of magnitude. \\
+
+Godot uses its own units for length measurement, which are stored as $32$-bit floating point numbers. For this reason the numbers had to be converted manually from real world units. This was time-consuming and it can potentially cause floating point rounding issues. With a dedicated ray casting engine, real world units could be used and the accuracy of the simulation could be improved by using higher precision floating point numbers. \\
 
 \subsection{Final Remark}
 
-The results of the simulation show that a x-y-z vibration with a component of "bending" simulated as a strong tilt can explain the shape of the penumbra obtained in the AFM, and that its peak to peak amplitude is within the expected range for this system. This also shows that the sharper penumbra edge, which for this evaporation was measured to be $\approx 60$ nm is the penumbra that would likely be obtained had there been no vibrational influence on the experiment. This shows that the Mask Aligner is capable of creating sharp interfaces, that fall within a superconductor's coherence length. \\
\ No newline at end of file
+The results of the simulation show that a x-y-z vibration with a component of "bending" simulated as a strong tilt can explain the shape of the penumbra obtained in the AFM, and that its peak to peak amplitude is within the expected range for this system. It shows that the sharper penumbra edge ($\approx 60$ nm) is the penumbra that one would obtained had there been no vibrational influence on the experiment. This shows that the Mask Aligner is capable of creating sharp interfaces. \\
\ No newline at end of file
diff --git a/conclusion.aux b/conclusion.aux
index a2b8029206bc59cee0c9d6e8c5ffec84322166da..2762cc8abf34009be33234b83877a63e11866a7e 100644
--- a/conclusion.aux
+++ b/conclusion.aux
@@ -1,9 +1,9 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{86}{chapter*.96}\protected@file@percent }
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diff --git a/conclusion.tex b/conclusion.tex
index d9509d881e50b7473466053cf930a84b0d9f858d..72d25540eaaeef89dbe4ac3c898c4da74a4c1b39 100644
--- a/conclusion.tex
+++ b/conclusion.tex
@@ -4,19 +4,19 @@ In this thesis, the function of a mask aligner operating in UHV was optimized an
 
 Mask Aligner functionality was restored and measures were taken to prevent further failure. 
 Maintenance procedures for certain potential faults of the Mask Aligner system were established and applied to the Mask Aligner.
-Potential sources of cross capacitances on the Mask Aligner were investigated and likely candidates for sources of cross capacitance were found on the Mask holders/shuttles, with the Mask Aligner itself found to be negligible in the creation of cross capacitance. \\
+Potential sources of cross capacitances on the Mask Aligner were investigated. Likely candidates for sources of cross capacitance were found on the Mask holders/shuttles. The Mask Aligner itself found to be negligible in the creation of cross capacitance. \\
 
-Further research will have to be done on the prevention of faults in the mask preparation procedure, as issues with leakage currents created in the process of mask bonding were found to be the likely reason for large correlations in the capacitance sensors of the Mask Aligner. \\
+Further research is needed on the prevention of faults in the mask preparation procedure, as issues with leakage currents, created in the process of mask bonding, were found to be the likely reason for large correlations in the capacitance signals. \\
 
 A new controller for the Mask Aligner was created by the electronics workshop. Programming of the new electronic was done, and initial performance tests showed favorable results over the old driver electronics. The new controller, however, still suffers from hardware issues, which is why tests under load could not be performed. A final performance test with calibration is still pending. \\
 
-The new controller will have to be tested under load for its driving behavior in comparison to the old driver and hardware instability issues will have to be resolved before larger scale evaporation, can be performed.
-In order to adapt voltage output per channel, during approach, a control script with the Mask Aligner will also have to be created and a new calibration as a function of voltage will have to be recorded. \\
+The new controller will have to be tested under load for its driving behavior in comparison to the old driver and hardware instability issues will have to be resolved before larger scale evaporation can be performed.
+In order to adapt voltage output per channel, during approach, a control script for the Mask Aligner will also have to be developed and a new calibration as a function of voltage will have to be recorded. \\
 
 It was shown that sharp interfaces on the sub-$60$ nm scale can be created using the Mask Aligner and that under good conditions sharp pristine interfaces can be created using the previously established alignment procedure. Ellipsoidal artifacts on the resulting evaporation could be explained using a simulation approach as a result of vibrations that created bending and x-y shifting of the mask with regard to the sample. \\
 
-In future the Mask Aligner will be first used to test evaporation properties of \ce{Pb} on \ce{Au}. With this it will be established if \ce{Pb} is a good candidate for a superconductor/topological insulator interface and if the previously established alignment process transfers to other types of sample. 
-Characterization of these new samples using a low temperature STM to record a superconducting gap is also a subject of future research. The determination of properties, such as appearance of a wetting layer is another important factor that will be done in STM analysis, as the appearance of a wetting layer across the sample's surface would make \ce{Pb} a bad candidate for Majorana Zero Mode research.\\
+In future the Mask Aligner will be first used to test evaporation properties of \ce{Pb} on \ce{Au}. With this it will be established if \ce{Pb} is a good candidate for a superconductor/topological insulator interface and if the previously established alignment process can be used for other samples. 
+Characterization of these new samples using a low temperature STM to record a superconducting gap is also a subject of future research. The determination of properties, such as appearance of a wetting layer is another important factor that will be determined in STM analysis.\\
 
 Another possible candidate for evaporation on a topological insulator seems to be \ce{Pd}. As recent papers have shown it to have interesting self epitaxial growth properties when evaporated on the topological insulator \ce{(Bi_{1-x}Sb_{x})2Te3}~\cite{self_epitaxy}. This could be a good candidate for further research. The current evaporator attached is unable to perform palladium evaporation. If \ce{Pd} would be chosen over \ce{Pb} a new evaporator would need to be connected to the Mask Aligner system.
 
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