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 \bibcite{afm_bio}{{12}{}{{}}{{}}}
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 \bibcite{SEM_image_01}{{13}{}{{}}{{}}}
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diff --git a/chap02.tex b/chap02.tex
index e8d5f48d9614eb57f294f3a92d3d2b2ae6aab1b5..4c0bb0d1aae51e628213690bc99d4fced364a06e 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -429,9 +429,9 @@ Another reason might be small movement of the mask frame on the \ce{Nd} magnets
 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{Cross capacitances} \label{subsec:cross_cap}
+\subsection{Capacitance correlations} \label{subsec:cross_cap}
 The biggest alignment problem with the current set of masks is heavy correlation
-between mask sensors, $C_i$ see Figure \ref{fig:cross_cap_approach}~\subref{fig:cross_cap_approach_difference}-\subref{fig:cross_cap_approach_difference_2}. If the
+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 $C_2$.
 
@@ -467,7 +467,7 @@ the sample. The expected value for a plate capacitor would be $\approx
 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 deviance between the curves, is easily visible. \\
+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. \\
 
diff --git a/chap03.aux b/chap03.aux
index f44240800214395da169a2b78aa1a22806b35578..a5347210ac1e327a18a3e7bc82c1c381737ce918 100644
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diff --git a/chap04.aux b/chap04.aux
index fd18b78dce3d8e163b967c79a895ac8ed4442e8e..502d911888b0627a7d9a202d5492f6908dce8a96 100644
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 \citation{Olschewski}
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+\newlabel{fig:Z3_reglue_process}{{4.4}{53}{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing}{figure.caption.69}{}}
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+\newlabel{fig:Z3_after reglue}{{4.5}{54}{The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $}{figure.caption.70}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{54}{section.4.5}\protected@file@percent }
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+\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after.}}{55}{figure.caption.71}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot}{{4.6}{55}{Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after}{figure.caption.71}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{55}{subsection.4.5.1}\protected@file@percent }
 \citation{Olschewski}
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+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{57}{\relax }{figure.caption.73}{}}
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 \@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{58}{section.4.6}\protected@file@percent }
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+\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{59}{\relax }{figure.caption.75}{}}
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+\newlabel{fig:Feedthrough_Repairs}{{4.10}{59}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.75}{}}
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+\newlabel{tab:cross_cap_after_repair}{{4.1}{59}{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}{table.caption.77}{}}
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-\newlabel{fig:calibration_after_repair}{{4.11}{60}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.77}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.11}{\ignorespaces The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions.}}{60}{figure.caption.78}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{60}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.78}{}}
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diff --git a/chap05.aux b/chap05.aux
index b072c57724b175573604db58c6485b1b483b6488..09af83cf32786340d97ab5c95bdfff5df9593fcc 100644
--- a/chap05.aux
+++ b/chap05.aux
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-\newlabel{tab:evaporation_settings}{{5.1}{62}{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}{table.caption.79}{}}
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@@ -120,7 +121,7 @@
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diff --git a/chap05.tex b/chap05.tex
index bd1881d9b5f6bd57619237dea3a103e8a6bd4ebf..6a69e7490e1945da7b3ab287fbbdaf7df4930033 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -10,16 +10,17 @@ 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.
 
 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: $1$ $\mu$m distance to sample (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 4: $4$ $\mu$m (Second Contact)
 	\item Field 5: $1$ $\mu$m (Full Contact)
 \end{itemize}
 
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diff --git a/preface.tex b/preface.tex
index 0aacb13ac32978eec3a88911ff8cfd2610117f3b..9de7de1474e9edb2a37c101a2d160c49d0689957 100644
--- a/preface.tex
+++ b/preface.tex
@@ -1,9 +1,10 @@
 \chapter*{Introduction}
 \addcontentsline{toc}{chapter}{Introduction}
-In condensed matter physics, precise fabrication of nanostructures with sharp patterns is paramount for research in various fields like electronics, photonics and quantum computing. One problem, that is highly sought after in quantum computing, is the creation of Majorana Zero Modes, as these could potentially provide a stable and controllable way to encode information. \textbf{M}ajorana \textbf{Z}ero \textbf{M}odes (MZM) are quasi particles that behave like Majorana fermions with non-Abelian statistics. MZMs are predicted to emerge at the core of vortices at superconductor/topological insulator interfaces~\cite{majorana_zero_modes}. These interfaces require pristine conditions and at the same time patterns, smaller than the coherence length ($<100$ nm) of the superconductor.\\
+In condensed matter physics, precise fabrication of nanostructures with sharp patterns is paramount for research in various fields like electronics, photonics and quantum computing. One problem, that is highly sought after in quantum computing, is the creation of Majorana Zero Modes, as these could potentially provide a stable and controllable way to encode information. \textbf{M}ajorana \textbf{Z}ero \textbf{M}odes (MZM) are quasi particles that behave like Majorana fermions with non-Abelian statistics. MZMs are predicted to emerge at the core of vortices at superconductor/topological insulator interfaces~\cite{majorana_zero_modes}. These interfaces require pristine conditions and at the same time patterns, smaller than the coherence length ($<100$ nm) of the superconductor. \\
+
 Atmospheric conditions typically deteriorate surface properties of the required samples. Due to this \textbf{U}ltra \textbf{H}igh \textbf{V}accuum (UHV) conditions are required for the sample. This often limits the pattern creation process, as exposure to ambient conditions or other chemicals are required. \\
 
-Many methods like \textbf{E}lectron \textbf{B}eam \textbf{L}ithography (EBL) or \textbf{E}xtreme \textbf{U}ltra\textbf{V}iolet \textbf{L}ithography (EUVL or EUV) give the required precision for patterning at the sub $100$ nm scale,~\cite{euv} but require resists, which typically are deposited with the help of solvents. These leave residues after the patterning process, which damage the pristine condition of the substrate. Typically, these methods can also not be performed under UHV conditions. \\
+Many methods like \textbf{E}lectron \textbf{B}eam \textbf{L}ithography (EBL) or \textbf{E}xtreme \textbf{U}ltra\textbf{V}iolet \\ \textbf{L}ithography (EUVL or EUV) give the required precision for patterning at the sub $100$ nm scale,~\cite{euv} but require resists, which typically are deposited with the help of solvents. These leave residues after the patterning process, which damage the pristine condition of the substrate. Typically, these methods can also not be performed under UHV conditions. \\
 
 Other methods of patterning superconductors on topological insulators have been proposed, but many have shortcomings that make their use impractical. There are for example scanning probe approaches,~\cite{afm_pattern} which can directly manipulate single atoms on surfaces, but require 
 long timescales and expensive equipment. Additionally, many Scanning Probe approaches still require resists, leading to the same issues as previously mentioned.\\
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 Chapter 3.
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diff --git a/thesis.pdf b/thesis.pdf
index b81ec1958a51ec25486c8b72ddaf9082a92a7546..fd2e3d8abbeb1088d3cbfe837ab4b5f1becc43df 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index 3d8396dddb14244a08a01800ecc716473495d726..ac069d1ad8de29b2361ddf0f6c87b15a1c1ea0b7 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.toc b/thesis.toc
index 8bda8d7d1b35bec58b6924ef697faa0a57c58533..479979b6b7a2a77f603b2d3ca0487c0a554660bd 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -22,17 +22,17 @@
 \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}Cross capacitances}{32}{subsection.2.3.6}%
-\contentsline {paragraph}{Leakage current}{37}{section*.38}%
-\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.39}%
+\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*.41}%
-\contentsline {paragraph}{sweep period}{39}{section*.42}%
-\contentsline {paragraph}{time between sweeps}{39}{section*.43}%
+\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}%
@@ -44,12 +44,12 @@
 \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*.54}%
-\contentsline {paragraph}{Amplitude (amp)}{45}{section*.55}%
-\contentsline {paragraph}{Voltage (volt)}{45}{section*.56}%
-\contentsline {paragraph}{Channel}{45}{section*.57}%
-\contentsline {paragraph}{Max Step}{45}{section*.58}%
-\contentsline {paragraph}{Polarity}{45}{section*.59}%
+\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}%
@@ -73,44 +73,44 @@
 \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*.92}%
-\contentsline {chapter}{Bibliography}{80}{chapter*.93}%
-\contentsline {chapter}{List of Abbreviations}{82}{chapter*.94}%
-\contentsline {chapter}{Appendix}{i}{chapter*.95}%
+\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 {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*.98}%
-\contentsline {paragraph}{pol x}{vi}{section*.99}%
-\contentsline {paragraph}{amp x}{vi}{section*.100}%
-\contentsline {paragraph}{volt x}{vi}{section*.101}%
-\contentsline {paragraph}{channel x}{vi}{section*.102}%
-\contentsline {paragraph}{maxmstep x}{vi}{section*.103}%
-\contentsline {paragraph}{step x}{vi}{section*.104}%
-\contentsline {paragraph}{mstep x}{vi}{section*.105}%
-\contentsline {paragraph}{cancel}{vii}{section*.106}%
-\contentsline {paragraph}{help}{vii}{section*.107}%
+\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 {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
-\contentsline {paragraph}{radius\_1}{vii}{section*.108}%
-\contentsline {paragraph}{angle}{vii}{section*.109}%
-\contentsline {paragraph}{radius\_mask}{vii}{section*.110}%
-\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.111}%
-\contentsline {paragraph}{distance\_sample}{vii}{section*.112}%
-\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.113}%
-\contentsline {paragraph}{running\_time}{vii}{section*.114}%
-\contentsline {paragraph}{deposition\_gain}{vii}{section*.115}%
-\contentsline {paragraph}{penalize\_deposition}{vii}{section*.116}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.117}%
-\contentsline {paragraph}{oscillation\_period}{vii}{section*.118}%
-\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.119}%
-\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.120}%
-\contentsline {paragraph}{save\_intervall}{viii}{section*.121}%
-\contentsline {paragraph}{oscillation\_dir}{viii}{section*.122}%
-\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.123}%
-\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.124}%
-\contentsline {paragraph}{random\_seed}{viii}{section*.125}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.126}%
-\contentsline {paragraph}{resolution}{viii}{section*.127}%
-\contentsline {paragraph}{path}{viii}{section*.128}%
-\contentsline {chapter}{Acknowledgments}{ix}{chapter*.129}%
+\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}%