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\bibcite{arduino_datasheet}{{20}{}{{}}{{}}}
\bibcite{arduino_cpu_datasheet}{{21}{}{{}}{{}}}
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diff --git a/bibliography.bib b/bibliography.bib
index 166834b4d5b87da5fc6cfab8f7c641cfaeb4e5d2..9558cb618d4dc7e38cc1ed2c155a21d7b31a769f 100644
--- a/bibliography.bib
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@@ -317,4 +317,18 @@ title = {An Atomic Force Microscopy Study of Single-Layer FeSe Superconductor},
volume = {6},
journal = {Applied Physics Express},
doi = {10.7567/APEX.6.113101}
-}
\ No newline at end of file
+}
+
+@article{grain_growth,
+url = {https://doi.org/10.1524/zkri.1958.110.16.372},
+title = {Phänomenologische Theorie der Kristallabscheidung an Oberflächen. I},
+title = {},
+author = {ERNST BAUER},
+pages = {372--394},
+volume = {110},
+number = {1-6},
+journal = {Zeitschrift für Kristallographie - Crystalline Materials},
+doi = {doi:10.1524/zkri.1958.110.16.372},
+year = {1958},
+lastchecked = {2024-10-01}
+}
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@@ -56,73 +56,50 @@
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\newlabel{fig:camera_alignment_example}{{2.11}{26}{Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment}{figure.caption.25}{}}
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+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.4}Capacitive distance measurements}{27}{subsection.2.3.4}\protected@file@percent }
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces (\subref {fig:mask_aligner_nomenclature_capacitances_motors}) shows a cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor {tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref {fig:mask_aligner_nomenclature_capacitances_mask}) shows a diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is used to create patterns. Below is a cross section of the materials used.}}{27}{figure.caption.27}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven.}}{28}{figure.caption.28}\protected@file@percent }
+\newlabel{fig:diagram_MA_circ}{{2.14}{28}{Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven}{figure.caption.28}{}}
+\newlabel{eq:plate_capacitor}{{2.1}{28}{Capacitive distance measurements}{equation.2.3.1}{}}
+\newlabel{fig:approach_curve_example_cap}{{2.15a}{29}{\relax }{figure.caption.29}{}}
+\newlabel{sub@fig:approach_curve_example_cap}{{a}{29}{\relax }{figure.caption.29}{}}
+\newlabel{fig:approach_curve_example_cap_diff}{{2.15b}{29}{\relax }{figure.caption.29}{}}
+\newlabel{sub@fig:approach_curve_example_cap_diff}{{b}{29}{\relax }{figure.caption.29}{}}
+\newlabel{fig:approach_curve_example_first}{{2.15c}{29}{\relax }{figure.caption.29}{}}
+\newlabel{sub@fig:approach_curve_example_first}{{c}{29}{\relax }{figure.caption.29}{}}
+\newlabel{fig:approach_curve_example_second}{{2.15d}{29}{\relax }{figure.caption.29}{}}
+\newlabel{sub@fig:approach_curve_example_second}{{d}{29}{\relax }{figure.caption.29}{}}
+\newlabel{fig:approach_curve_example_full}{{2.15e}{29}{\relax }{figure.caption.29}{}}
+\newlabel{sub@fig:approach_curve_example_full}{{e}{29}{\relax }{figure.caption.29}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces (a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample.}}{29}{figure.caption.29}\protected@file@percent }
+\newlabel{fig:approach_curve_example}{{2.15}{29}{(a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample}{figure.caption.29}{}}
\citation{Beeker}
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-\newlabel{sub@fig:approach_replicability_cap}{{a}{31}{\relax }{figure.caption.32}{}}
-\newlabel{fig:approach_replicability_cap_diff}{{2.16b}{31}{\relax }{figure.caption.32}{}}
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-\newlabel{fig:approach_replicability}{{2.16}{31}{(\subref {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.32}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces Diagram showing a cross section of the mask at a gold pad location. A small tear in the \ce {SiO2} layer removes insulation between the gold wire and the Si of the mask. Parallel black lines depict plate capacitors illustratively. Larger plate shows larger capacitance. }}{34}{figure.caption.35}\protected@file@percent }
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-\newlabel{fig:cross_cap_diagramm}{{2.20}{37}{Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger}{figure.caption.38}{}}
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+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.30}\protected@file@percent }
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+\newlabel{sub@fig:approach_replicability_cap}{{a}{30}{\relax }{figure.caption.31}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.16b}{30}{\relax }{figure.caption.31}{}}
+\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{30}{\relax }{figure.caption.31}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces (\subref {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier.}}{30}{figure.caption.31}\protected@file@percent }
+\newlabel{fig:approach_replicability}{{2.16}{30}{(\subref {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.31}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {2.4}Mask Aligner operation}{31}{section.2.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{31}{subsection.2.4.1}\protected@file@percent }
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\@setckpt{chap02}{
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diff --git a/chap02.tex b/chap02.tex
index 4c0bb0d1aae51e628213690bc99d4fced364a06e..73c9d46199108b0793b9273cf7c211679f40c00b 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -112,7 +112,25 @@ control of the camera angle. \\
The procedure for step size calibration is very simple: $2000$, $4000$,
$6000$, $8000$ and $10000$ steps are driven and after each set of steps the distance
-the prism has traveled in the image of the camera is measured. This is done with the Bresser MicroCam II software. In the software a line is drawn at the initial position, from a remarkable point on the motor. After driving another line is drawn at the end position. The distance between these are measured using the software. An example for motor Z1 and Z2 can be seen in Figure \ref{fig:calibration_uhv_example_driving} for a $1000$ step measurement. If changes to the motors have been performed a calibration has to be performed outside of UHV before reinsertion into UHV. Afterwards the motors have to be calibrated in UHV. \\
+the prism has traveled in the image of the camera is measured. This is done with the Bresser MicroCam II software. In the software a line is drawn at the initial position, from a remarkable point on the motor (Fig. \ref{fig:calibration_uhv_points_of_interest}). After driving another line is drawn at the end position. The distance between these are measured using the software. An example for motor Z1 and Z2 is shown in Figure \ref{fig:calibration_uhv_example_driving} for a $1000$ step measurement. If changes to the motors have been performed a calibration has to be performed outside of UHV before reinsertion into UHV. Afterwards the motors have to be calibrated in UHV. \\
+
+\begin{figure}[H]
+ \centering
+ \begin{subfigure}{0.42\textwidth}
+ \includegraphics[width=\linewidth]{img/CalibrationUHV_Z1.pdf}
+ \caption{}
+ \label{fig:calibration_uhv_points_of_interest_z1}
+ \end{subfigure}
+ \begin{subfigure}{0.42\textwidth}
+ \includegraphics[width=\linewidth]{img/CalibrationUHV_Z2_Z3.pdf}
+ \caption{}
+ \label{fig:calibration_uhv_points_of_interest_z2z3}
+ \end{subfigure}
+ \caption{Points of interest for the calibration of the step size of the 3 piezo motors in
+ UHV. (a) motor Z1, \textcolor{tab_red}{red:} top of sapphire prism, \textcolor{tab_green}{green:} end of top plate used for step size determination (b)
+ motors Z2/Z3, \textcolor{tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor{tab_green}{green:} lines used for step size determination.}
+ \label{fig:calibration_uhv_points_of_interest}
+\end{figure}
\begin{figure}[H]
\centering
@@ -128,18 +146,17 @@ the prism has traveled in the image of the camera is measured. This is done with
\caption{}
\label{fig:calibration_uhv_example_driving_z2}
\end{subfigure}
- \caption{Comparison of photographs recorded prior and after $1000$ steps were driven. (\subref{fig:calibration_uhv_example_driving_z1}) shows the top of motor Z1, inset shows a zoom in of the top plate with the image after driving $1000$ approach steps superimposed. \textcolor{tab_red}{Red} lines show the top edge difference and resulting travel length. (\subref{fig:calibration_uhv_example_driving_z2}) shows the same as (\subref{fig:calibration_uhv_example_driving_z1}) for the screw used to determine step size for motor Z2. Inset shows both approach and retract for $1000$ steps.}
+ \caption{Comparison of photographs recorded prior and after $1000$ steps were driven. (\subref{fig:calibration_uhv_example_driving_z1}) top of motor Z1, inset shows a zoom in of the top plate. The image after driving $1000$ approach steps superimposed. \textcolor{tab_red}{Red} lines show the top edge difference and resulting travel length. (\subref{fig:calibration_uhv_example_driving_z2}) shows the same as (\subref{fig:calibration_uhv_example_driving_z1}) for the screw used to determine step size for motor Z2. Inset shows both approach and retract for $1000$ steps.}
\label{fig:calibration_uhv_example_driving}
\end{figure}
%Outside UHV the best points are small scratches on the prisms
%\ce{Al2O3} plate, since these are already in a focal plane with the motors.
-The distance measurement using the camera is calibrated by using an object of known size in the focal plane. One example that can be used are the \ce{Nd} magnets ($5$ mm diameter).
-
-Inside UHV the process is more complicated, the motors Z2 and Z3 cannot be directly observed. Instead, the 2
-screws very close to the motors are (seen in Figure
+The distance measurement using the camera is calibrated by using an object of known size in the focal plane. One example that can be used are the \ce{Nd} magnets ($5$ mm diameter). \\
+The motors Z2 and Z3 cannot be directly observed in the Mask Aligner chamber. Instead, the 2
+screws very close to the motors (seen in Figure
\ref{fig:calibration_uhv_points_of_interest}
-\subref{fig:calibration_uhv_points_of_interest_z2z3}) observed. For camera calibration their diameter is chosen as this is also known to be $3$ mm.
+\subref{fig:calibration_uhv_points_of_interest_z2z3}) are observed. For camera calibration their diameter is chosen as this is also known to be $3$ mm.
The screws are a little closer to the camera than the motors themselves, this is accounted for by using a simple trigonometric model seen in Figure \ref{fig:calibration_screw_diff_explain}.
With this one gets that for each unit of distance the motor moves, the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. \\
@@ -150,34 +167,15 @@ With this one gets that for each unit of distance the motor moves, the screws mo
\label{fig:calibration_screw_diff_explain}
\end{figure}
-
\begin{figure}[H]
- \centering
- \begin{subfigure}{0.45\textwidth}
- \includegraphics[width=\linewidth]{img/CalibrationUHV_Z1.pdf}
- \caption{}
- \label{fig:calibration_uhv_points_of_interest_z1}
- \end{subfigure}
- \begin{subfigure}{0.45\textwidth}
- \includegraphics[width=\linewidth]{img/CalibrationUHV_Z2_Z3.pdf}
- \caption{}
- \label{fig:calibration_uhv_points_of_interest_z2z3}
- \end{subfigure}
- \caption{Points of interest for the calibration of the step size of the 3 piezo motors in
-UHV. (a) motor Z1, \textcolor{tab_red}{red:} top of sapphire prism, \textcolor{tab_green}{green:} end of top plate used for step size determination (b)
-motors Z2/Z3, \textcolor{tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor{tab_green}{green:} lines used for step size determination.}
- \label{fig:calibration_uhv_points_of_interest}
+ \centering
+ \includegraphics[width=0.8\linewidth]{img/Plots/Calibrations/80V.pdf}
+ \caption{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref{fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}
+ \label{fig:calibration_example}
\end{figure}
A linear fit is performed for the given data. The slope gives the step size. Results are shown in Figure \ref{fig:calibration_example}. After each set of steps it has to be ensured, that the mask frame is not tilted. Excessive tilt will affect the step size. It should also be taken care that the movement range of the piezos is not exceeded. The \ce{Nd} magnets should not detach from the frame. Moreover, the sapphire prism can fall out of the motor if it is driven too far down. The measurement has to be done for both driving directions separately, since the step sizes will be different. Indeed, in Fig. \ref{fig:calibration_example} shows that the positive retract direction has consistently larger step sizes. The Z3 motor also shows a larger difference in step size for approach and retract than the other $2$ motors.
-\begin{figure}[H]
- \centering
- \includegraphics[width=0.8\linewidth]{img/Plots/Calibrations/80V.pdf}
- \caption{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref{fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}
- \label{fig:calibration_example}
-\end{figure}
-
This calibration has been performed for various voltage amplitudes. This can be
seen in Figure \ref{fig:calibration_voltage}
@@ -228,7 +226,7 @@ can see the surface of the sample holder. Additionally, the side of the sample i
placed or angled too low, (b) too high and (c) placed in good alignment. }
\label{fig:camera_alignment_example}
\end{figure}
-\todo{Fix}
+
When the camera is aligned with the sample, the mask can be moved close to
the sample. A visible gap must remain between sample and mask (Fig. \ref{fig:optical_approach_a}). Then the mask is moved toward the sample until only a five pixel gap remains (Fig. \ref{fig:optical_approach}\subref{fig:optical_approach_b}, \subref{fig:optical_approach_c}). The length of the gap can
@@ -343,7 +341,7 @@ least once. \\
\caption{}
\label{fig:approach_curve_example_full}
\end{subfigure}
- \caption{(a) A capacitance (approach) curve. (b) the difference of each capacitance value.
+ \caption{(a) capacitance (approach) curve. (b) difference of each capacitance value.
Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac{1}{r}$ curve changes. Below are images of the geometry between mask and
sample at First (c), Second (d) and Full contact (e). Red lines or points indicate
where the mask is touching the sample.}
@@ -422,172 +420,176 @@ One question concerning reproducibility is whether the approach curve is strongl
\label{fig:approach_replicability}
\end{figure}
-Reinserting the mask, the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}. The process of moving the mask out and back in to the mask frame might induce enough perturbation to the mask holder to move it slightly in the mask. This fault could potentially be fixed by better gold pin design, when designing newer mask discussed further in \ref{subsec:cross_cap}\\
+Reinserting the mask, the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}. The process of moving the mask out and back in to the mask frame might induce enough perturbation to the mask holder to move it slightly in the mask. This fault could potentially be fixed by better gold pin design.
Another reason might be small movement of the mask frame on the \ce{Nd} magnets tilting the mask. This problem cannot be fixed without a complete redesign of the Mask Aligner. \\
Reinserting the sample also induced a difference in approach curves, but this difference is much smaller as can be seen in Figure \ref{fig:approach_replicability} (\textcolor{tab_blue}{blue} and \textcolor{tab_green}{green}). The trend of the curve remains the same, but the absolute value changes slightly. However, the peak in $dC$ changed significantly. A stop condition determined on the \textcolor{tab_green}{green} curve (for example $0.04$ pF) would overshoot the point of first contact on the \textcolor{tab_blue}{blue} curve. This means that after switching a conservative stop condition has to be chosen. \\
-
-\subsection{Capacitance correlations} \label{subsec:cross_cap}
-The biggest alignment problem with the current set of masks is heavy correlation
-between mask sensors, \todo{Replace with approach curve} $C_i$ see Figure \ref{fig:cross_cap_approach}~\subref{fig:cross_cap_approach_difference}-\subref{fig:cross_cap_approach_difference_2}. If the
-alignment were perfect, these curves should indeed appear to be very similar
-since moving any of the motors affects all capacitance sensors. If the distances from the \ce{Si} is different for each sensor, their approach curves should be distinct. A simulated approach curve for a difference of $440$ nm between $C_1$ and $C_2$ and $560$ nm between $C_1$ and $C_3$ is shown in Figure \ref{fig:cross_cap_approach_sim}. The model assumes no capacitance between the 3 capacitance sensors and to the environment. Additionally, the model assumes all motors drive exactly the same. It also assumes the mask first makes contact with the sample at the corner that is aligned with $C_1$ such that the motor aligned with $C_1$ stops moving. After that, the same happens for $C_2$.
-
-\begin{figure}[H]
- \centering
- \begin{subfigure}{0.32\textwidth}
- \centering
- \includegraphics[width=\linewidth]{img/Diagram/cross_example_1.pdf}
- \caption{}
- \label{fig:cross_cap_approach_difference}
- \end{subfigure}
- \begin{subfigure}{0.32\textwidth}
- \centering
- \includegraphics[width=\linewidth]{img/Diagram/cross_example_2.pdf}
- \caption{}
- \label{fig:cross_cap_approach_difference_2}
- \end{subfigure}
- \begin{subfigure}{0.32\textwidth}
- \centering
- \includegraphics[width=\linewidth]{img/Diagram/ExplanationCurveDifference.pdf}
- \caption{}
- \label{fig:cross_cap_approach_sim}
- \end{subfigure}
- \caption{(\subref{fig:cross_cap_approach_difference}, \subref{fig:cross_cap_approach_difference_2}) approach curves of two example measurements of 2 different masks normalized to ensure the same scale. (\subref{fig:cross_cap_approach_sim}) shows a simple simulation of the approach with tilted sample.}
- \label{fig:cross_cap_approach}
-\end{figure}
-
-For the gold pads, this would result in a capacitance of $\approx 0.40$ fF, at a distance of $\approx 50$ micron (measured optically). The capacitance values of the curve $C_1$ was $\approx 2.4$
-pF, which deviates by $4$ orders of magnitude. This corresponds more closely to the
-value expected for capacitance from the \ce{Si} of the mask to the \ce{Si} of
-the sample. The expected value for a plate capacitor would be $\approx
-1.44$ pF. The deviation in this case can be explained by the oversimplification
-of the model. It does not take into account any stray capacitances the system
-might have. \\
-
-The model in Figure \ref{fig:cross_cap_approach_sim} assumes a distance between the sensors on the z-axis of $440$ nm for C1-C2 and $220$ nm for C2-C3. A distance that is well within the optical accuracy of $\approx 5$ $\mu$m for maximum zoom and resolution. Even for such a small difference, the deviation between the curves, is easily visible. \\
-
-However, measured capacitances show a deviation in behavior from the model (Fig. \ref{fig:cross_cap_approach_difference}). The different capacitances vary by $1$-$2$ order of magnitude. The largest capacitance was measured to $19.12$ pF. The curves (Fig. \ref{fig:cross_cap_approach_difference}) start with large deviation and converge near full contact. This is the opposite to the expected behavior (Fig. \ref{fig:cross_cap_approach_sim}). The general shape of the curves is identical for all $3$, while it is expected that the first contact affects the $3$ capacitances differently. \\
-
-Another mask (Figure \ref{fig:cross_cap_approach_difference_2}) shows behavior more close to the expected, with a difference for the $3$ capacitances at first contact. However, $C_2$ and $C_3$ behave identically again. The largest capacitance was measured to be $19.78$ pF and $C_2$ and $C_3$ varied by $2$ orders of magnitude from $C_1$. \\
-
+%
+%\subsection{Capacitance correlations} \label{subsec:cross_cap}
+%
+%%\begin{figure}[H]
+%% \centering
+%% \begin{subfigure}{0.32\textwidth}
+%% \centering
+%% \includegraphics[width=\linewidth]{img/Diagram/cross_example_1.pdf}
+%% \caption{}
+%% \label{fig:cross_cap_approach_difference}
+%% \end{subfigure}
+%% \begin{subfigure}{0.32\textwidth}
+%% \centering
+%% \includegraphics[width=\linewidth]{img/Diagram/cross_example_2.pdf}
+%% \caption{}
+%% \label{fig:cross_cap_approach_difference_2}
+%% \end{subfigure}
+%% \begin{subfigure}{0.32\textwidth}
+%% \centering
+%% \includegraphics[width=\linewidth]{img/Diagram/ExplanationCurveDifference.pdf}
+%% \caption{}
+%% \label{fig:cross_cap_approach_sim}
+%% \end{subfigure}
+%% \caption{(\subref{fig:cross_cap_approach_difference}, \subref{fig:cross_cap_approach_difference_2}) approach curves of two example measurements of 2 different masks normalized to ensure the same scale. (\subref{fig:cross_cap_approach_sim}) shows a simple simulation of the approach with tilted sample.}
+%% \label{fig:cross_cap_approach}
+%%\end{figure}
+%
+%%For the gold pads, this would result in a capacitance of $\approx 0.40$ fF, at a distance of $\approx 50$ micron (measured optically). The capacitance values of the curve $C_1$ was $\approx 2.4$
+%%pF, which deviates by $4$ orders of magnitude. This corresponds more closely to the
+%%value expected for capacitance from the \ce{Si} of the mask to the \ce{Si} of
+%%the sample. The expected value for a plate capacitor would be $\approx
+%%1.44$ pF. The deviation in this case can be explained by the oversimplification
+%%of the model. It does not take into account any stray capacitances the system
+%%might have. \\
+%%
+%%The model in Figure \ref{fig:cross_cap_approach_sim} assumes a distance between the sensors on the z-axis of $440$ nm for C1-C2 and $220$ nm for C2-C3. A distance that is well within the optical accuracy of $\approx 5$ $\mu$m for maximum zoom and resolution. Even for such a small difference, the deviation between the curves, is easily visible. \\
+%%
+%%However, measured capacitances show a deviation in behavior from the model (Fig. \ref{fig:cross_cap_approach_difference}). The different capacitances vary by $1$-$2$ order of magnitude. The largest capacitance was measured to $19.12$ pF. The curves (Fig. \ref{fig:cross_cap_approach_difference}) start with large deviation and converge near full contact. This is the opposite to the expected behavior (Fig. \ref{fig:cross_cap_approach_sim}). The general shape of the curves is identical for all $3$, while it is expected that the first contact affects the $3$ capacitances differently. \\
+%%
+%%Another mask (Figure \ref{fig:cross_cap_approach_difference_2}) shows behavior more close to the expected, with a difference for the $3$ capacitances at first contact. However, $C_2$ and $C_3$ behave identically again. The largest capacitance was measured to be $19.78$ pF and $C_2$ and $C_3$ varied by $2$ orders of magnitude from $C_1$. \\
+%
+%%\begin{figure}[H]
+%% \centering
+%% \includegraphics[width=0.9\linewidth]{img/SimilarityApproach.pdf}
+%% \caption{}
+%% \label{fig:cross_cap_approach_sim}
+%%\end{figure}
+%%\todo{Plot of heavily correlated approach curves}
+%
+%The masks used for approach and subsequent evaporation are in theory supposed to have $3$ independent capacitance sensors that together give a measurement of the distance and tilt of the mask. However, the masks show strong correlation between the $3$ sensors(Fig. \ref{fig:example_correlation_capacitances}). This prohibits precise control of the alignment. \\
+%In his master thesis Jonas Beeker looked at the possibility of capacitances between the $3$ sensors as a possible reason for this strong correlation. It was determined that for a cross capacitance of more than $150$ fF the capacitance curves cannot be distinguished anymore\cite{Beeker}.
+%
+%\begin{figure}[H]
+% \centering
+% \includegraphics[width=0.9\linewidth]{img/MA/CorrelationExample.pdf}
+% \caption{3 capacitance curves of a mask scaled to be
+% within the same range. The lower plots show deviations from comparison curve.}
+% \label{fig:example_correlation_capacitances}
+%\end{figure}
+%
+%
+%
+%\begin{table}[H]
+% \centering
+% \begin{tabular}{|l|l|l|l|}
+% \hline & C C1-C2 (pF) & C C1-C3 (pF) & C C2-C3 (pF) \\
+% \hline \hline
+% Mask 1 & $7.11 \pm 0.02$ & $3.20 \pm 0.12$ & $0.19 \pm
+% 0.06$ \\ \hline
+% Mask 2 & $0.64 \pm 0.06$ & $0.64 \pm 0.06$ & $0.85 \pm
+% 0.02$ \\ \hline
+% Mask 3 & $3.33 \pm 0.04$ & $3.94 \pm 0.07$ & $0.86 \pm
+% 0.02$ \\ \hline
+% Mask old & $0.50 \pm 0.02$ & $0.29 \pm 0.09$ & $0.35 \pm
+% 0.14$ \\ \hline \hline
+% Mask shuttle 1 & $0.24 \pm 0.02$ & $0.25 \pm 0.02$ & $0.041 \pm
+% 0.004$ \\ \hline
+% Mask shuttle 2 & $0.30 \pm 0.04$ & $0.29 \pm 0.03$ & $0.041 \pm 0.004$
+% \\ \hline
+% Mask shuttle 3 & $0.23 \pm 0.02$ & $0.25 \pm 0.02$ & $0.049 \pm
+% 0.004$ \\ \hline \hline
+% Shuttles average & $0.26 \pm 0.03$ & $0.26 \pm 0.02$ & $0.043 \pm 0.004$
+% \\ \hline
+% \end{tabular}
+% \caption{Table of cross capacitance measurement results. }
+% \label{tab:cross_cap}
+%\end{table}
+%
+%The reason for this large deviation is a leakage current from the cable connecting
+%the gold pads to the Si of the Mask. This most likely happens
+%due to accidental piercing of the insulating \ce{SiO2} layer during assembly of the gold cable. This is depicted in Figure \ref{fig:leakage_current}. The capacitance measured is in this case dominated by the leakage capacitance from \ce{Si$_\text{Sample}$} to \ce{Si$_\text{Mask}$} (Figure \ref{fig:leakage_current}).
+%
+%
%\begin{figure}[H]
% \centering
-% \includegraphics[width=0.9\linewidth]{img/SimilarityApproach.pdf}
-% \caption{}
-% \label{fig:cross_cap_approach_sim}
+% \includegraphics[width=0.5\linewidth]{img/LeakageCurrent.pdf}
+% \caption{Diagram showing a cross section of the mask at a gold pad location. A small tear in the \ce{SiO2} layer removes insulation between the gold wire and the Si of the mask. Parallel black lines depict plate capacitors illustratively. Larger plate shows larger capacitance.
+%}
+% \label{fig:leakage_current}
%\end{figure}
-%\todo{Plot of heavily correlated approach curves}
-
-The reason for this large deviation is most likely a leakage current from the cable connecting
-the gold pads to the Si of the Mask. This most likely happens
-due to accidental piercing of the insulating \ce{SiO2} layer during assembly of the gold cable. This is depicted in Figure \ref{fig:leakage_current}. The capacitance measured is in this case dominated by the leakage capacitance from \ce{Si$_\text{Sample}$} to \ce{Si$_\text{Mask}$} (Figure \ref{fig:leakage_current}).
-\begin{figure}[H]
- \centering
- \includegraphics[width=0.5\linewidth]{img/LeakageCurrent.pdf}
- \caption{Diagram showing a cross section of the mask at a gold pad location. A small tear in the \ce{SiO2} layer removes insulation between the gold wire and the Si of the mask. Parallel black lines depict plate capacitors illustratively. Larger plate shows larger capacitance.
-}
- \label{fig:leakage_current}
-\end{figure}
-
-\newpage
-
-Another reason for the correlation of capacitances are cross capacitances between the gold pad sensors. \\
-
-\begin{table}[H]
-\centering
-\begin{tabular}{|l|l|l|l|}
- \hline & C Ch1-Ch2 (pF) & C Ch1-Ch3 (pF) & C Ch2-Ch3 (pF) \\
-\hline \hline
-Mask 1 & $7.11 \pm 0.02$ & $3.20 \pm 0.12$ & $0.19 \pm
-0.06$ \\ \hline
-Mask 2 & $0.64 \pm 0.06$ & $0.64 \pm 0.06$ & $0.85 \pm
-0.02$ \\ \hline
-Mask 3 & $3.33 \pm 0.04$ & $3.94 \pm 0.07$ & $0.86 \pm
-0.02$ \\ \hline
-Mask old & $0.50 \pm 0.02$ & $0.29 \pm 0.09$ & $0.35 \pm
-0.14$ \\ \hline \hline
-Mask shuttle 1 & $0.24 \pm 0.02$ & $0.25 \pm 0.02$ & $0.041 \pm
-0.004$ \\ \hline
-Mask shuttle 2 & $0.30 \pm 0.04$ & $0.29 \pm 0.03$ & $0.041 \pm 0.004$
- \\ \hline
-Mask shuttle 3 & $0.23 \pm 0.02$ & $0.25 \pm 0.02$ & $0.049 \pm
-0.004$ \\ \hline \hline
-Shuttles average & $0.26 \pm 0.03$ & $0.26 \pm 0.02$ & $0.043 \pm 0.004$
- \\ \hline
-\end{tabular}
-\caption{Table of cross capacitance measurement results. }
-\label{tab:cross_cap}
-\end{table}
-
-In order to quantify the effect of this source, cross capacitances were measured directly between $3$ masks holders inside mask shuttles, as well as
-3 empty shuttles. For the measurement Input and output of the Lock-in were connected to two of the capacitance sensors of the mask. Measurements were performed inside the Mask Aligner with a sample inserted. Additionally, mask shuttles without any mask inserted were tested for cross capacitance. The results are shown in Table \ref{tab:cross_cap} \\
-
-The shuttles themselves have large cross capacitance values. It is of the same order of magnitude as the capacitance expected from gold pad to sample. When adding the mask
-the cross capacitances increase, often by an order of magnitude. \\
-
-To check if this is also the dominant cause of correlation, the mask labeled "old" is looked at more closely. The cross capacitance values for this mask were small compared with the other masks (Table \ref{tab:cross_cap}). The approach curve of this mask however, shows the heaviest correlation of all masks tested. This indicates that in this case a leakage current from gold to mask \ce{Si} is the main cause. \\
-
-To confirm the similarity between the different capacitance sensors signals, the data of each was overlaid over one another. The data was normalized to allow for comparison. Then an offset was fitted. The result of this can be seen in Figure \ref{fig:mask_old_correl}. The $3$ different capacitance sensors give the same signal. Systematic deviations in the residuals are only visible near the jump in capacitance signal, which is of unknown cause. The deviations are within $0.1$~\%, which is on the same order as the expected measurement error for the given LockIn parameters.
-
+%
+%\begin{figure}[H]
+% \centering
+% \includegraphics[width=0.75\linewidth]{img/CrossCapacitances.pdf}
+% \caption{Circuit diagram of the measurement setup with the cross
+% capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to
+% the main capacitances that are used for mask alignment. $C_{ij}$ refers to a
+% cross capacitance between capacitance sensor $i$ and sensor $j$.
+% $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the
+% Si of the Sample, usually this should not be measured since the Si of the Mask
+% is separated from the gold pads with a SiN layer, but should that layer be
+% pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$
+% are small enough) this will be measured instead of $C_i$, since it is an order
+% of magnitude larger.}
+% \label{fig:cross_cap_diagramm}
+%\end{figure}
+%
+%
+%\newpage
+%
+%Another reason for the correlation of capacitances are cross capacitances between the gold pad sensors. \\
+%
+%%In order to quantify the effect of this source, cross capacitances were measured directly between $3$ masks holders inside mask shuttles, as well as
+%%3 empty shuttles. For the measurement Input and output of the Lock-in were connected to two of the capacitance sensors of the mask. Measurements were performed inside the Mask Aligner with a sample inserted. Additionally, mask shuttles without any mask inserted were tested for cross capacitance. The results are shown in Table \ref{tab:cross_cap} \\
+%%
+%%The shuttles themselves have large cross capacitance values. It is of the same order of magnitude as the capacitance expected from gold pad to sample. When adding the mask
+%%the cross capacitances increase, often by an order of magnitude. \\
+%%
+%%To check if this is also the dominant cause of correlation, the mask labeled "old" is looked at more closely. The cross capacitance values for this mask were small compared with the other masks (Table \ref{tab:cross_cap}). The approach curve of this mask however, shows the heaviest correlation of all masks tested. This indicates that in this case a leakage current from gold to mask \ce{Si} is the main cause. \\
+%%
+%%To confirm the similarity between the different capacitance sensors signals, the data of each was overlaid over one another. The data was normalized to allow for comparison. Then an offset was fitted. The result of this can be seen in Figure \ref{fig:mask_old_correl}. The $3$ different capacitance sensors give the same signal. Systematic deviations in the residuals are only visible near the jump in capacitance signal, which is of unknown cause. The deviations are within $0.1$~\%, which is on the same order as the expected measurement error for the given LockIn parameters.
+%
%\begin{figure}[H]
% \centering
% \includegraphics[width=0.9\linewidth]{img/Plots/Mask_Old_Caps.pdf}
% \caption{The 3 capacitance curves of the Mask labeled "old". Of note is the difference in scale of the capacitance signal.}
% \label{fig:mask_old_caps}
%\end{figure}
-
-\begin{figure}[H]
- \centering
- \includegraphics[width=0.95\linewidth]{img/Plots/Mask_Old_Correl.pdf}
- \caption{The 3 capacitance curves of the Mask labeled "old" scaled to be
-within the same range. The lower plots show deviations from comparison curve. }
- \label{fig:mask_old_correl}
-\end{figure}
-
-
-This leads to the conclusion that while the cross capacitances have a strong influence on
-the correlation, they are not the dominating
-factor. Both leakage currents and cross capacitances have to be considered and their sources minimized. \\
-
-Figure \ref{fig:cross_cap_diagramm} shows a circuit diagram for the known sources of capacitance correlation.
-
-\begin{figure}[H]
- \centering
- \includegraphics[width=0.75\linewidth]{img/CrossCapacitances.pdf}
- \caption{Circuit diagram of the measurement setup with the cross
-capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to
-the main capacitances that are used for mask alignment. $C_{ij}$ refers to a
-cross capacitance between capacitance sensor $i$ and sensor $j$.
-$C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the
-Si of the Sample, usually this should not be measured since the Si of the Mask
-is separated from the gold pads with a SiN layer, but should that layer be
-pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$
-are small enough) this will be measured instead of $C_i$, since it is an order
-of magnitude larger.}
- \label{fig:cross_cap_diagramm}
-\end{figure}
-
-In order to decrease the correlation between the sensors the following methods are proposed:
-
-\paragraph{Leakage current}
-The leakage current between the Si of the Mask and the Si of the sample seems,
-for many of the current masks, to be the main source of correlation. In order to
-ensure no leakage current, a better mask preparation method has to be found that
-ensures no piercing of the \ce{SiNi} layer. This however goes beyond the scope of
-this thesis.
-
-\paragraph{Improved gold pin fitting}
-The gold pins for the current set of masks were cut to correct size by hand.
-This causes a problem with the fit between male and female side of the gold pins.
-The mask stage can move inside the holder slightly. This changes both distance to sample and gives a loose contact.
-Instead, they should be machined with precision by a workshop. The stability of the fit should be tested after assembly.
-
-\todo{Image of gold pins}
-
-The cross capacitances of the mask holders should also be reduced. No proposal is made in this thesis about how to accomplish this, because the cause is undetermined. The other $2$ factors play a larger role and should be improved first.
+%
+%\begin{figure}[H]
+% \centering
+% \includegraphics[width=0.95\linewidth]{img/Plots/Mask_Old_Correl.pdf}
+% \caption{3 capacitance curves of the Mask labeled "old" scaled to be
+%within the same range. The lower plots show deviations from comparison curve. }
+% \label{fig:mask_old_correl}
+%\end{figure}
+%
+%
+%This leads to the conclusion that while the cross capacitances have a strong influence on
+%the correlation, they are not the dominating
+%factor. Both leakage currents and cross capacitances have to be considered and their sources minimized. \\
+%
+%Figure \ref{fig:cross_cap_diagramm} shows a circuit diagram for the known sources of capacitance correlation.
+%
+%In order to decrease the correlation between the sensors the following methods are proposed:
+%
+%\paragraph{Leakage current}
+%The leakage current between the Si of the Mask and the Si of the sample seems to be the main source of correlation. A better mask preparation method has to be found that ensures no piercing of the \ce{SiNi} layer. This will be investigated in the near future in a Bachelor thesis.
+%
+%\paragraph{Improved gold pin fitting}
+%The gold pins for the current set of masks were cut to size by hand.
+%%This causes a problem with the fit between male and female side of the gold pins.
+%%The mask stage can move inside the holder slightly. This changes both distance to sample and gives a loose contact.
+%Instead, they should be machined with precision by a workshop. The stability of the fit should be tested after assembly.
%\subsection{Stop Conditions}
%During recording of a calibration approach curve two different scenarios can arise:
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index a5347210ac1e327a18a3e7bc82c1c381737ce918..ec242969e5dc837dce35691f018702a757161e5d 100644
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index 502d911888b0627a7d9a202d5492f6908dce8a96..8ca43f2712966e549240a20595c7cbe67e2324ce 100644
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\@setckpt{chap04}{
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+\setcounter{page}{55}
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@@ -101,7 +101,7 @@
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diff --git a/chap04.tex b/chap04.tex
index 83523af38e96c4a77f7f003c1648b13969994538..70036c40c68a9e561adb0b349f75c57e571f2198 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -261,14 +261,14 @@ In order to reduce capacitance noise, the cables were shortened and were grounde
\begin{table}[H]
\centering
\begin{tabular}{|l|l|l|l|}
- \hline & C Ch1-Ch2 (pF) & C Ch1-Ch3 (pF) & C Ch2-Ch3 (pF) \\
+ \hline & C C1-C2 (pF) & C C1-C3 (pF) & C C2-C3 (pF) \\
\hline \hline
Mask 1 before & $7.11 \pm 0.02$ & $3.20 \pm 0.12$ & $0.19 \pm
0.06$ \\ \hline
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. 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}
@@ -284,5 +284,5 @@ 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 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$$\sigma$ of each other. Assuming a difference of $6 nm$, as the worst case, the data gives an angular tilt per step of $\approx (5.73 \times 10^{-6})^\circ$. This is a difference in height on the sample of $\approx 0.5$ nm/step. In turn this would give a difference in penumbra of $1.2$ nm for every $100$ steps.\\
-In the retract regime, the difference between motors is within the margin of error for Z2 and Z1, but Z3 deviates by about $4 \sigma$ from the others. Since the mask is aligned during approach, deviations in retract affect alignment less. After each evaporation, the mask is retracted to about $50$ $\mu$m. This ensures movement of the x piezo does not damage the sample. Within these, a difference of $1.2$ $\mu$m would appear from side to side of the evaporation field, which corresponds to an angle of $\approx 0.004^\circ$. This difference results in a deviation of $\approx 38$ nm in penumbra. By driving the Z1 and Z2 motors $100$ steps up after the retraction this can be compensated almost fully and should result in an error of at most $\approx 6$ nm of additional penumbra induced by tilt. \\
+This calibration shows similarity of performance between the 3 motors in the approach direction, as shown in Figure \ref{fig:calibration_after_repair}. In approach direction the deviation between Z2 and the other motors is within $2$$\sigma$. Between Z3 and Z1 it deviates 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 direction, 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. Therefore, a tilt of $1.2$ $\mu$m would appear over 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 09af83cf32786340d97ab5c95bdfff5df9593fcc..67933c7e84ae2a8f0049707e029972749be79ba0 100644
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+++ b/chap05.aux
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+\@writefile{lof}{\contentsline {figure}{\numberline {5.5}{\ignorespaces Example of the analysis conducted on each of the recorded dots for a single line cut. (a) raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) cleaned image. 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. (c) line cut data from one line as an example. This line cut was obtained from \textcolor {tab_green}{(green)} line in (b). }}{61}{figure.caption.74}\protected@file@percent }
+\newlabel{fig:evaporation_analysis}{{5.5}{61}{Example of the analysis conducted on each of the recorded dots for a single line cut. (a) raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) cleaned image. 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. (c) line cut data from one line as an example. This line cut was obtained from \textcolor {tab_green}{(green)} line in (b)}{figure.caption.74}{}}
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+\newlabel{sub@fig:evaporation_SEM_sample}{{a}{65}{\relax }{figure.caption.77}{}}
+\newlabel{fig:evaporation_SEM_mask}{{5.8b}{65}{\relax }{figure.caption.77}{}}
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+\newlabel{fig:evaporation_SEM}{{5.8}{65}{(\subref {fig:evaporation_SEM_sample}) SEM images of field 2 on the sample. (\subref {fig:evaporation_SEM_mask}) SEM image of the 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.77}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog}{{5.9a}{66}{\relax }{figure.caption.78}{}}
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+\newlabel{fig:evaporation_SEM_analysis}{{5.9}{66}{(\subref {fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes. \subref {fig:evaporation_SEM_analysis_clog_overlay} 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.78}{}}
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\citation{Bhaskar}
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-\newlabel{fig:evaporation_simulation_rejection}{{5.13}{77}{(\subref {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref {fig:evaporation_simulation_rejection_prev}) 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}) 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.93}{}}
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+\newlabel{fig:evaporation_simulation_overlap}{{5.11}{69}{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.80}{}}
+\citation{grain_growth}
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+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{70}{\relax }{figure.caption.81}{}}
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+\newlabel{fig:evaporation_simulation_sharpness}{{5.12}{70}{(\subref {fig:evaporation_simulation_sharpness_stick_simple}) Comparison of the evaporation with harmonic oscillation. (\subref {fig:evaporation_simulation_sharpness_stick_initial}) initial phase with no elliptical oscillation and then drift to the elliptical shape. (\subref {fig:evaporation_simulation_sharpness_stick_power})an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ . The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.81}{}}
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\@setckpt{chap05}{
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diff --git a/chap05.tex b/chap05.tex
index 6a69e7490e1945da7b3ab287fbbdaf7df4930033..b8da8df561ede9fdb82ee48f0f7142aa66a97847 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -10,7 +10,6 @@ As a test for positioning and to optimize the penumbra of \ce{Pb} islands on a \
\caption{The approach curve measured for field 1 until full contact.}
\label{fig:evaporation_approach_curve}
\end{figure}
-\todo{steps wrong}
The 3 capacitance sensors appear heavily correlated (Fig. \ref{fig:evaporation_approach_curve}) and the uncertainty on C2 and C3 is an order of magnitude larger than the step in $dC$. For this reason C1 was primarily used for alignment. C2 and C3 were recorded but went unused.
@@ -338,7 +337,8 @@ The different roughness of circle and ellipse might suggest different possible r
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. Instead the oscillation is 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.
-In the AFM image 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. \\
+In the AFM image the surface of the outer 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 particles first forming larger grains, which is common for PVD~\cite{grain_growth}. With larger layer height this effect typically becomes less visible. \\
+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. \\
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. \\
diff --git a/conclusion.aux b/conclusion.aux
index d1713dc6729ef746d49db09ba0abfd1259926e50..0c9ca67559cd8f54f9a58c8da7b261f419a9f415 100644
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diff --git a/img/CalibrationUHV_Z1.pdf b/img/CalibrationUHV_Z1.pdf
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diff --git a/thesis.bbl b/thesis.bbl
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--- a/thesis.bbl
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@@ -164,4 +164,12 @@ Atmel. The {A}tmel | {SMART} {SAM3X/A} series datasheet. Online; accessed
\bibitem{switch_datasheet}
\emph{IC SWITCH SPDTX2 1.8OHM 16TSSOP}, Analog Devices Inc., 2016, rev. B.
+\bibitem{grain_growth}
+\BIBentryALTinterwordspacing
+E.~BAUER, ``Phänomenologische theorie der kristallabscheidung an oberflächen.
+ i,'' \emph{Zeitschrift für Kristallographie - Crystalline Materials}, vol.
+ 110, no. 1-6, pp. 372--394, 1958. [Online]. Available:
+ \url{https://doi.org/10.1524/zkri.1958.110.16.372}
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diff --git a/thesis.pdf b/thesis.pdf
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diff --git a/thesis.synctex.gz b/thesis.synctex.gz
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diff --git a/thesis.toc b/thesis.toc
index 479979b6b7a2a77f603b2d3ca0487c0a554660bd..7b9650f284441d2a7d8a37d02be81ad97b3a974d 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -18,99 +18,96 @@
\contentsline {section}{\numberline {2.3}Shadow mask alignment}{20}{section.2.3}%
\contentsline {subsection}{\numberline {2.3.1}Motor screw configuration}{20}{subsection.2.3.1}%
\contentsline {subsection}{\numberline {2.3.2}Motor calibration}{21}{subsection.2.3.2}%
-\contentsline {subsection}{\numberline {2.3.3}Optical alignment}{26}{subsection.2.3.3}%
-\contentsline {subsection}{\numberline {2.3.4}Capacitive distance measurements}{28}{subsection.2.3.4}%
-\contentsline {subsection}{\numberline {2.3.5}Reproducibility}{31}{subsection.2.3.5}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{31}{section*.31}%
-\contentsline {subsection}{\numberline {2.3.6}Capacitance correlations}{32}{subsection.2.3.6}%
-\contentsline {paragraph}{Leakage current}{37}{section*.39}%
-\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.40}%
-\contentsline {section}{\numberline {2.4}Mask Aligner operation}{38}{section.2.4}%
-\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{38}{subsection.2.4.1}%
-\contentsline {chapter}{\numberline {3}Electronics}{39}{chapter.3}%
-\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{39}{section.3.1}%
-\contentsline {subsection}{\numberline {3.1.1}Overview}{39}{subsection.3.1.1}%
-\contentsline {paragraph}{amplitude}{39}{section*.42}%
-\contentsline {paragraph}{sweep period}{39}{section*.43}%
-\contentsline {paragraph}{time between sweeps}{39}{section*.44}%
-\contentsline {subsection}{\numberline {3.1.2}Pulse shape}{39}{subsection.3.1.2}%
-\contentsline {section}{\numberline {3.2}KIM001}{40}{section.3.2}%
-\contentsline {subsection}{\numberline {3.2.1}Overview}{40}{subsection.3.2.1}%
-\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{40}{subsection.3.2.2}%
-\contentsline {subsection}{\numberline {3.2.3}Voltage behavior}{41}{subsection.3.2.3}%
-\contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{42}{section.3.3}%
-\contentsline {subsection}{\numberline {3.3.1}Overview}{42}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Signal generation}{42}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Fast flank}{43}{subsection.3.3.3}%
-\contentsline {subsection}{\numberline {3.3.4}Amplification}{44}{subsection.3.3.4}%
-\contentsline {subsection}{\numberline {3.3.5}Programming}{45}{subsection.3.3.5}%
-\contentsline {subsubsection}{Parameters}{45}{section*.55}%
-\contentsline {paragraph}{Amplitude (amp)}{45}{section*.56}%
-\contentsline {paragraph}{Voltage (volt)}{45}{section*.57}%
-\contentsline {paragraph}{Channel}{45}{section*.58}%
-\contentsline {paragraph}{Max Step}{45}{section*.59}%
-\contentsline {paragraph}{Polarity}{45}{section*.60}%
-\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{45}{subsection.3.3.6}%
-\contentsline {subsection}{\numberline {3.3.7}Operation with the Mask Aligner}{47}{subsection.3.3.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{49}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{49}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{50}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}UHV compatible Soldering}{50}{subsection.4.2.1}%
-\contentsline {section}{\numberline {4.3}Soldering anchors}{50}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo regluing}{53}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 motor}{54}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{55}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{57}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{58}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final test}{59}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{61}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{61}{section.5.1}%
-\contentsline {section}{\numberline {5.2}Contamination}{63}{section.5.2}%
-\contentsline {section}{\numberline {5.3}Penumbra}{64}{section.5.3}%
-\contentsline {section}{\numberline {5.4}Tilt and deformation}{69}{section.5.4}%
-\contentsline {section}{\numberline {5.5}Simulation}{72}{section.5.5}%
-\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{72}{subsection.5.5.1}%
-\contentsline {subsection}{\numberline {5.5.2}Results}{74}{subsection.5.5.2}%
-\contentsline {subsection}{\numberline {5.5.3}Software improvements}{77}{subsection.5.5.3}%
-\contentsline {subsection}{\numberline {5.5.4}Final Remark}{78}{subsection.5.5.4}%
-\contentsline {chapter}{Conclusions and Outlook}{79}{chapter*.94}%
-\contentsline {chapter}{Bibliography}{80}{chapter*.95}%
-\contentsline {chapter}{List of Abbreviations}{82}{chapter*.96}%
-\contentsline {chapter}{Appendix}{i}{chapter*.97}%
+\contentsline {subsection}{\numberline {2.3.3}Optical alignment}{25}{subsection.2.3.3}%
+\contentsline {subsection}{\numberline {2.3.4}Capacitive distance measurements}{27}{subsection.2.3.4}%
+\contentsline {subsection}{\numberline {2.3.5}Reproducibility}{30}{subsection.2.3.5}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.30}%
+\contentsline {section}{\numberline {2.4}Mask Aligner operation}{31}{section.2.4}%
+\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{31}{subsection.2.4.1}%
+\contentsline {chapter}{\numberline {3}Electronics}{33}{chapter.3}%
+\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{33}{section.3.1}%
+\contentsline {subsection}{\numberline {3.1.1}Overview}{33}{subsection.3.1.1}%
+\contentsline {paragraph}{amplitude}{33}{section*.32}%
+\contentsline {paragraph}{sweep period}{33}{section*.33}%
+\contentsline {paragraph}{time between sweeps}{33}{section*.34}%
+\contentsline {subsection}{\numberline {3.1.2}Pulse shape}{33}{subsection.3.1.2}%
+\contentsline {section}{\numberline {3.2}KIM001}{34}{section.3.2}%
+\contentsline {subsection}{\numberline {3.2.1}Overview}{34}{subsection.3.2.1}%
+\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{34}{subsection.3.2.2}%
+\contentsline {subsection}{\numberline {3.2.3}Voltage behavior}{35}{subsection.3.2.3}%
+\contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{36}{section.3.3}%
+\contentsline {subsection}{\numberline {3.3.1}Overview}{36}{subsection.3.3.1}%
+\contentsline {subsection}{\numberline {3.3.2}Signal generation}{36}{subsection.3.3.2}%
+\contentsline {subsection}{\numberline {3.3.3}Fast flank}{37}{subsection.3.3.3}%
+\contentsline {subsection}{\numberline {3.3.4}Amplification}{38}{subsection.3.3.4}%
+\contentsline {subsection}{\numberline {3.3.5}Programming}{39}{subsection.3.3.5}%
+\contentsline {subsubsection}{Parameters}{39}{section*.45}%
+\contentsline {paragraph}{Amplitude (amp)}{39}{section*.46}%
+\contentsline {paragraph}{Voltage (volt)}{39}{section*.47}%
+\contentsline {paragraph}{Channel}{39}{section*.48}%
+\contentsline {paragraph}{Max Step}{39}{section*.49}%
+\contentsline {paragraph}{Polarity}{39}{section*.50}%
+\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{39}{subsection.3.3.6}%
+\contentsline {subsection}{\numberline {3.3.7}Operation with the Mask Aligner}{41}{subsection.3.3.7}%
+\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{43}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Overview}{43}{section.4.1}%
+\contentsline {section}{\numberline {4.2}General UHV device preparation}{44}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}UHV compatible Soldering}{44}{subsection.4.2.1}%
+\contentsline {section}{\numberline {4.3}Soldering anchors}{44}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo regluing}{47}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 motor}{48}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{49}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{51}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{52}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final test}{53}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{55}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{55}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Contamination}{57}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Penumbra}{58}{section.5.3}%
+\contentsline {section}{\numberline {5.4}Tilt and deformation}{63}{section.5.4}%
+\contentsline {section}{\numberline {5.5}Simulation}{66}{section.5.5}%
+\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{66}{subsection.5.5.1}%
+\contentsline {subsection}{\numberline {5.5.2}Results}{68}{subsection.5.5.2}%
+\contentsline {subsection}{\numberline {5.5.3}Software improvements}{71}{subsection.5.5.3}%
+\contentsline {subsection}{\numberline {5.5.4}Final Remark}{72}{subsection.5.5.4}%
+\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.83}%
+\contentsline {chapter}{Bibliography}{74}{chapter*.84}%
+\contentsline {chapter}{List of Abbreviations}{76}{chapter*.85}%
+\contentsline {chapter}{Appendix}{i}{chapter*.86}%
\contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
\contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
\contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}%
\contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}%
-\contentsline {paragraph}{pulse?}{vi}{section*.100}%
-\contentsline {paragraph}{pol x}{vi}{section*.101}%
-\contentsline {paragraph}{amp x}{vi}{section*.102}%
-\contentsline {paragraph}{volt x}{vi}{section*.103}%
-\contentsline {paragraph}{channel x}{vi}{section*.104}%
-\contentsline {paragraph}{maxmstep x}{vi}{section*.105}%
-\contentsline {paragraph}{step x}{vi}{section*.106}%
-\contentsline {paragraph}{mstep x}{vi}{section*.107}%
-\contentsline {paragraph}{cancel}{vii}{section*.108}%
-\contentsline {paragraph}{help}{vii}{section*.109}%
+\contentsline {paragraph}{pulse?}{vi}{section*.89}%
+\contentsline {paragraph}{pol x}{vi}{section*.90}%
+\contentsline {paragraph}{amp x}{vi}{section*.91}%
+\contentsline {paragraph}{volt x}{vi}{section*.92}%
+\contentsline {paragraph}{channel x}{vi}{section*.93}%
+\contentsline {paragraph}{maxmstep x}{vi}{section*.94}%
+\contentsline {paragraph}{step x}{vi}{section*.95}%
+\contentsline {paragraph}{mstep x}{vi}{section*.96}%
+\contentsline {paragraph}{cancel}{vii}{section*.97}%
+\contentsline {paragraph}{help}{vii}{section*.98}%
\contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
-\contentsline {paragraph}{radius\_1}{vii}{section*.110}%
-\contentsline {paragraph}{angle}{vii}{section*.111}%
-\contentsline {paragraph}{radius\_mask}{vii}{section*.112}%
-\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.113}%
-\contentsline {paragraph}{distance\_sample}{vii}{section*.114}%
-\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.115}%
-\contentsline {paragraph}{running\_time}{vii}{section*.116}%
-\contentsline {paragraph}{deposition\_gain}{vii}{section*.117}%
-\contentsline {paragraph}{penalize\_deposition}{vii}{section*.118}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.119}%
-\contentsline {paragraph}{oscillation\_period}{vii}{section*.120}%
-\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.121}%
-\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.122}%
-\contentsline {paragraph}{save\_intervall}{viii}{section*.123}%
-\contentsline {paragraph}{oscillation\_dir}{viii}{section*.124}%
-\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.125}%
-\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.126}%
-\contentsline {paragraph}{random\_seed}{viii}{section*.127}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.128}%
-\contentsline {paragraph}{resolution}{viii}{section*.129}%
-\contentsline {paragraph}{path}{viii}{section*.130}%
-\contentsline {chapter}{Acknowledgments}{ix}{chapter*.131}%
+\contentsline {paragraph}{radius\_1}{vii}{section*.99}%
+\contentsline {paragraph}{angle}{vii}{section*.100}%
+\contentsline {paragraph}{radius\_mask}{vii}{section*.101}%
+\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.102}%
+\contentsline {paragraph}{distance\_sample}{vii}{section*.103}%
+\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.104}%
+\contentsline {paragraph}{running\_time}{vii}{section*.105}%
+\contentsline {paragraph}{deposition\_gain}{vii}{section*.106}%
+\contentsline {paragraph}{penalize\_deposition}{vii}{section*.107}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.108}%
+\contentsline {paragraph}{oscillation\_period}{vii}{section*.109}%
+\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.110}%
+\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.111}%
+\contentsline {paragraph}{save\_intervall}{viii}{section*.112}%
+\contentsline {paragraph}{oscillation\_dir}{viii}{section*.113}%
+\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.114}%
+\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.115}%
+\contentsline {paragraph}{random\_seed}{viii}{section*.116}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.117}%
+\contentsline {paragraph}{resolution}{viii}{section*.118}%
+\contentsline {paragraph}{path}{viii}{section*.119}%
+\contentsline {chapter}{Acknowledgments}{ix}{chapter*.120}%