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diff --git a/acknowledgments.tex b/acknowledgments.tex
index 3d8de2f7e0bd75be92ae8aed00d37dea37d9e151..0e6fc47e148dea87c9016a796bba5564f4acf398 100644
--- a/acknowledgments.tex
+++ b/acknowledgments.tex
@@ -1,9 +1,11 @@
 \chapter*{Acknowledgments}
 \addcontentsline{toc}{chapter}{Acknowledgments}
 
-I want to thank Florian Muckel for teaching me all the techniques I needed for the repairs on the mask aligner, as well as general aid in the first months of my thesis.
+I want to thank Florian Muckel for teaching me all the techniques I needed for the repairs on the mask aligner, as well as general aid in the first half of my thesis.
+
+For help with writing the software for the Walker and explanations of the existing Walker code, I want to thank Jonas Duffhaus. 
+For the building of the mask aligner controller and patience with debugging of the Walker software, I want to thank both Paul Dinslage and Uwe Wichmann.
 
-For help with writing the software for the mask aligner controller, I want to thank Jonas Duffhaus. For the building of the mask aligner controller, I want to thank both Paul Dinslage and Uwe Wichmann.
 
 \todo{Thank Florian Muckel}
 \todo{Thank Jonas Beeker and Priya}
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diff --git a/appendix.tex b/appendix.tex
index f2f73c4f8c95a24970237ed8e3854ccacdecb967..6cb16dddf3234ebf6dd063ab53a840056db8471f 100644
--- a/appendix.tex
+++ b/appendix.tex
@@ -1,10 +1,37 @@
-\chapter{Appendix}
+\chapter*{Appendix}
+\addcontentsline{toc}{chapter}{Appendix}
 \pagenumbering{roman}
 %\sectionnumbering{roman} 
 \setcounter{section}{0}
 \renewcommand{\thesection}{\Alph{section}}
 
-\section{LockIn amplifier settings}\label{sec:appendix_lockIn}
+\section{LockIn amplifier settings}\label{sec:app_lock_in}
+
+\begin{table}[H]
+\centering
+\begin{tabular}{|l|l|}
+\hline
+Setting                             & Value \\ \hline
+Frequency                           & 2 mV                                \\ \hline
+Phase Shift                         & 0                                   \\ \hline
+Harmonic                            & 1                                   \\ \hline
+Trigger                             & sine                                \\ \hline
+Sensitivity                         & variable*                            \\ \hline
+\multicolumn{1}{|l|}{Time constant} & 300 ms                              \\ \hline
+\multicolumn{1}{|l|}{Input}         & Current 10\textasciicircum{}6       \\ \hline
+\multicolumn{1}{|l|}{Couple}        & AC                                  \\ \hline
+\end{tabular}
+\caption{Settings used for the Lock-in amplifier in the experiment. Sensitivity is increased a step at a time until the Lock-in is no longer in overload. Source is chosen as internal. Ground is set to grounded.}
+\label{fig:app_lock_in}
+\end{table}
+
+\section{Walker principle diagram}\label{app:walker_diagram}
+\begin{figure}[H]
+    \centering
+    \includegraphics[width=\linewidth, angle=90]{img/ElectronicsDiagramm.pdf}
+    \caption{Overview of the entire signal generation and amplification process of the new Mask Aligner controller.}
+    \label{fig:electronics_diagramm}
+\end{figure}
 
 \section{Walker circuit diagrams}\label{app:circuit_electronics}
 \includepdf[pages=-,pagecommand={},width=\textwidth,angle=90]{img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf}
diff --git a/bibliography.aux b/bibliography.aux
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-\bibcite{knudsen}{{4}{}{{}}{{}}}
-\bibcite{Tungsten_evap}{{5}{}{{}}{{}}}
-\bibcite{tungsten_evaporation}{{6}{}{{}}{{}}}
-\bibcite{Vapor_depo_princ}{{7}{}{{}}{{}}}
-\bibcite{sputter_damage}{{8}{}{{}}{{}}}
-\bibcite{florian_forster}{{9}{}{{}}{{}}}
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-\bibcite{Beeker}{{16}{}{{}}{{}}}
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-\bibcite{arduino_cpu_datasheet}{{18}{}{{}}{{}}}
-\bibcite{switch_datasheet}{{19}{}{{}}{{}}}
-\bibcite{olschewski}{{20}{}{{}}{{}}}
+\bibcite{majorana_zero_modes}{{1}{}{{}}{{}}}
+\bibcite{euv}{{2}{}{{}}{{}}}
+\bibcite{afm_pattern}{{3}{}{{}}{{}}}
+\bibcite{stencil_resolution}{{4}{}{{}}{{}}}
+\bibcite{Olschewski}{{5}{}{{}}{{}}}
+\bibcite{Bhaskar}{{6}{}{{}}{{}}}
+\bibcite{Tungsten_melt}{{7}{}{{}}{{}}}
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+\bibcite{SEM_image_01}{{17}{}{{}}{{}}}
+\bibcite{SEM_image_02}{{18}{}{{}}{{}}}
+\bibcite{SEM_book}{{19}{}{{}}{{}}}
+\bibcite{self_epitaxy}{{20}{}{{}}{{}}}
+\bibcite{Mask_Aligner}{{21}{}{{}}{{}}}
+\bibcite{SiN_dielectric}{{22}{}{{}}{{}}}
+\bibcite{Beeker}{{23}{}{{}}{{}}}
+\bibcite{arduino_datasheet}{{24}{}{{}}{{}}}
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diff --git a/bibliography.bib b/bibliography.bib
index 20940699991cd5888a24af0f736e4b93ef9f31da..166834b4d5b87da5fc6cfab8f7c641cfaeb4e5d2 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -206,7 +206,7 @@ keywords = {sputtering, buffer layers, optoelectronic devices, perovskite/organi
 }
 
 @article{self_epitaxy,
-   title={Novel self-epitaxy for inducing superconductivity in the topological insulator \ce{(Bi{1-x}Sb{x})2Te3}},
+   title={Novel self-epitaxy for inducing superconductivity in the topological insulator \ce{(Bi_{1-x}Sb_{x})2Te3}},
    volume={4},
    ISSN={2475-9953},
    url={http://dx.doi.org/10.1103/PhysRevMaterials.4.094801},
@@ -216,7 +216,8 @@ keywords = {sputtering, buffer layers, optoelectronic devices, perovskite/organi
    publisher={American Physical Society (APS)},
    author={Bai, Mengmeng and Yang, Fan and Luysberg, Martina and Feng, Junya and Bliesener, Andrea and Lippertz, Gertjan and Taskin, A. A. and Mayer, Joachim and Ando, Yoichi},
    year={2020},
-   month=sep }
+   month=sep 
+}
 
 @article{sputter_damage,
 author = {Kanda, Hiroyuki and Uzum, Abdullah and Baranwal, Ajay and Peiris, T. A. Nirmal and Umeyama, Tomokazu and Imahori, Hiroshi and Segawa, Hiroshi and Miyasaka, Tsutomu and Ito, Seigo},
@@ -244,3 +245,76 @@ date = {21-08-2024},
 url = {https://ww1.microchip.com/downloads/en/DeviceDoc/Atmel-11057-32-bit-Cortex-M3-Microcontroller-SAM3X-SAM3A_Datasheet.pdf},
 note = {Online; accessed 10-August-2024}
 }
+
+@article{majorana_zero_modes,
+   title={Superconducting Proximity Effect and Majorana Fermions at the Surface of a Topological Insulator},
+   volume={100},
+   ISSN={1079-7114},
+   url={http://dx.doi.org/10.1103/PhysRevLett.100.096407},
+   DOI={10.1103/physrevlett.100.096407},
+   number={9},
+   journal={Physical Review Letters},
+   publisher={American Physical Society (APS)},
+   author={Fu, Liang and Kane, C. L.},
+   year={2008},
+   month=mar }
+
+@article{euv,
+author = {Fu, Nan and Liu, Yanxiang and Ma, Xiaolong and Chen, Zhanfeng},
+year = {2019},
+month = {06},
+pages = {1-6},
+title = {EUV Lithography: State-of-the-Art Review},
+volume = {2},
+journal = {Journal of Microelectronic Manufacturing},
+doi = {10.33079/jomm.19020202}
+}
+
+@article{afm_pattern,
+author = {Custance, Oscar and Pérez, Rubén and Morita, Seizo},
+year = {2009},
+month = {12},
+pages = {803-10},
+title = {Atomic force microscopy as a tool for atom manipulation},
+volume = {4},
+journal = {Nature nanotechnology},
+doi = {10.1038/nnano.2009.347}
+}
+
+@article{stencil_resolution,
+title = {Fabrication of nanoscale stencils through focused ion beam milling and dry transfer of silicon-on-nothing membrane with perforations},
+journal = {Microelectronic Engineering},
+volume = {289},
+pages = {112172},
+year = {2024},
+issn = {0167-9317},
+doi = {https://doi.org/10.1016/j.mee.2024.112172},
+url = {https://www.sciencedirect.com/science/article/pii/S0167931724000418},
+author = {Taeyeong Kim and Jungchul Lee},
+keywords = {Stencil lithography, Silicon-on-nothing, Nanofabrication, High temperature annealing},
+}
+
+@article{afm_bio,
+title = {Measurement of nanomechanical properties of biomolecules using atomic force microscopy},
+journal = {Micron},
+volume = {43},
+number = {2},
+pages = {116-128},
+year = {2012},
+issn = {0968-4328},
+doi = {https://doi.org/10.1016/j.micron.2011.07.017},
+url = {https://www.sciencedirect.com/science/article/pii/S0968432811001375},
+author = {Nicholas E. Kurland and Zouheir Drira and Vamsi K. Yadavalli},
+keywords = {Atomic force microscopy, Nanoindentation, Protein, Biomolecule, Young's modulus},
+}
+
+@article{afm_physics,
+author = {Li, Na and Li, Zhi and Ding, Hao and Ji, Shuaihua and Chen, Xi and Xue, Qi-Kun},
+year = {2013},
+month = {11},
+pages = {113101},
+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
diff --git a/bibliography.log b/bibliography.log
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diff --git a/chap01.tex b/chap01.tex
index 5362f90b0010b71c296247eed721fd2065208b27..b4004251114fb419fd620b6b130515e7c1495683 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -3,19 +3,19 @@
 The Mask Aligner and its Molecular Beam Evaporation chamber are used to create thin films on samples with high accuracy. This chapter will introduce the required background behind the evaporation of thin films on sample surface as well as explain the basic evaporation and alignment setup the Mask Aligner uses.
 
 \section{Electron beam evaporation}
-Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{p}hysical \textbf{v}apor \textbf{d}eposition (EBPVD) is a \textbf{p}hysical \textbf{v}apor \textbf{d}eposition (PVD) technique used in vacuum and \textbf{U}ltra \textbf{h}igh \textbf{v}acuum (UHV) conditions, to deposit material onto a substrates surface. 
+Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique used in vacuum and \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) conditions, to deposit material onto a substrates surface. 
 
 \begin{figure}[H]
     \centering
-    \includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
-    \caption{Schematic diagram of a general E-beam evaporation chamber.}
+y    \includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
+    \caption{Schematic diagram of a general E-beam evaporation chamber. The B-field is used to focus the beam onto the source. Alternatively one can use a filament nearby and put the crucible under positive potential, which will attract the emitted electrons from the filament. The shutter is used to control when the beam can interact with the sample. The funnel is used to focus the vapor beam. }
     \label{fig:e-beam_evap}
-\end{figure}\todo{Label things for text and Current}
+\end{figure}
  
-The general setup of an electron beam evaporator is seen in Figure \ref{fig:e-beam_evap}. The source material is placed inside a crucible as pellets of ultra pure (>$99$ \%) material.
+The general setup of an electron beam evaporator is seen in Figure \ref{fig:e-beam_evap}. The source material is placed inside a crucible as pellets of ultra pure ($>99$ \%) material.
 The crucible is also heated during the evaporation process, in order to prevent the crucible itself from being damaged a material with high melting point has to be chosen. Tungsten with a melting point of 3695 K \cite{Tungsten_melt} is usually chosen. Additionally, the crucible usually has to be water cooled to prevent damaging the system.
 
-In order to heat the source material locally beyond its boiling point it is hit with a high current electron beam ($\mathcal{O}$(1 kV)), emitted by either an electron gun or a filament, this beam usually has to be focused using magnetic fields to hit the source material. The highly energetic electrons interact with the atomic nuclei and the atomic electrons of the source material and transfer energy. This energy transfer heats the hit atoms locally and eventually causes the system to reach its melting and then its boiling point, if enough current is applied to give the required heating power. \\
+In order to heat the source material locally beyond its boiling point it is hit with a high current electron beam ($\mathcal{O}$($1$ kV)), emitted by either an electron gun or a filament, this beam usually has to be focused using magnetic fields to hit the source material. The highly energetic electrons interact with the atomic nuclei and the atomic electrons of the source material and transfer energy. This energy transfer heats the hit atoms locally and eventually causes the system to reach its melting and then its boiling point, if enough current is applied to give the required heating power. \\
 
 The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)\cite{CASINO} so the heating occurs only very near to the source materials surface. This allows for less energy loss and more controlled evaporation as the crucible and the rest of the system is not heated by the electron beam directly, but only by the radiant heat emitted by the source material.\\
 
@@ -39,8 +39,16 @@ E-beam evaporation offers more control over deposition rate than thermal evapora
 In order to control the duration of the evaporation precisely a shutter is usually included in the evaporation chamber which can be closed or opened to control when the sample is exposed to the vapor beam. This is also needed for improved deposition rate accuracy since the source material needs to initially heat up when the electron beam is started, which leads to unstable flux at the start of the evaporation. By closing the shutter this can be avoided.
 
 \subsection{Mask Aligner lead evaporator}
-The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in 2009.\cite{florian_forster} The crucible of this evaporator is made from tungsten. The evaporator uses a filament placed near the crucible to bombard the material placed inside the crucible with highly energetic electrons. To accomplish this a high current (up to $1$ kV) is applied between filament and crucible to emit electrons from the filament to the crucible. In addition, the system can be heated with radiative heat from the filament. This is also used to degas the evaporator and to prevent contaminants from settling on the filament, when no evaporation is taking place. The heating element and crucible are surrounded by a copper cylinder, that functions as a heat sink for the system. The heat sink needs to be water cooled to prevent damage to the evaporator. In order to prevent cooling failure, a thermal sensor measures the temperature of the copper cylinder. \\
-In order to control the molecular flow, one can change the current applied to the filament or the voltage accelerating the electron beam towards the source. Additionally, the crucible can be shifted on the z-axis closer to or further away from the filament, controlling the amount of heating that is received by the source material. This method of temperature control was unused in this thesis, as the distance was previously optimized already. In order to determine if the applied controls have the desired effect, the current of $\text{Pb}^+$ ions leaving the crucible is measured by a flux monitor positioned at the top of the evaporator, below the shutter, which can be used to open the molecular flow to the mask aligner chamber. \\
+The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in $2009$.\cite{florian_forster} The crucible of this evaporator is made from tungsten. The evaporator uses a filament placed near the crucible to bombard the material placed inside the crucible with highly energetic electrons. To accomplish this a high current (up to $1$ kV) is applied between filament and crucible to emit electrons from the filament to the crucible. In addition, the system can be heated with radiative heat from the filament. This is also used to degas the evaporator and to prevent contaminants from settling on the filament, when no evaporation is taking place. The heating element and crucible are surrounded by a copper cylinder, that functions as a heat sink for the system. The heat sink needs to be water cooled to prevent damage to the evaporator. In order to prevent cooling failure, a thermal sensor measures the temperature of the copper cylinder. \\
+
+\begin{figure}[H]
+    \centering
+    \includegraphics[width=0.8\linewidth]{img/MA/Evaporator.pdf}
+    \caption{Solidworks diagram of the evaporator used on the Mask Aligner.}
+    \label{fig:ma_evap}
+\end{figure}
+
+In order to control the molecular flow, one can change the current applied to the filament or the voltage accelerating the electron beam towards the source. Additionally, the crucible can be shifted on the z-axis closer to or further away from the filament, controlling the amount of heating that is received by the source material. This method of temperature control was unused in this thesis, as the distance was previously optimized already. In order to determine if the applied controls have the desired effect, the current of $\text{Pb}^+$ ions leaving the crucible is measured by a flux monitor positioned at the top of the evaporator, below the shutter, which can be used to open the molecular flow to the mask aligner chamber. An schematic of the evaporator can be seen in Figure \ref{fig:ma_evap}\\
 
 \section{Stencil lithography}
 Stencil lithography is a method of depositing patterned structures on a nanometer scale on substrates (sample) using a stencil. The stencil is made of a membrane of \ce{SiN} that is patterned with a lithography process such as electron beam lithography. Using e-beam lithography masks can be produced at sub micrometer scales \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) processes are used to deposit material on the substrates surface, while the mask is placed on top of the sample. The mask protects the substrate from the molecular beam, except in the places where the pattern has been cut into the mask. In this way the pattern is transferred from the mask to the sample. \\
@@ -135,8 +143,8 @@ Tapping mode is a hybrid of both contact and non-contact modes. It is also somet
 
 There are more ways to get useful sample information from an AFM, the tip can for example be coated in a magnetic coating in order to perform Magnetic Force Microscopy, but for the purposes of this thesis other uses will be neglected.
 
-AFMs provide high resolution topographical images at the nanometer scale and allow for accurate estimation of surface properties of a samples surface. 
-\todo{Maybe write cool things AFMs have accomplished}
+AFMs provide high resolution topographical images at the nanometer scale and allow for accurate estimation of surface properties of a samples surface. Atomic force microscopy is a commonly used tool to characterize nano-lithography samples and has been extensively used in physics, material science and biology among others.\cite{afm_physics, afm_bio}
+
 
 \subsection{Scanning Electron Microscopy} 
 A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope (SEM) is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this a sample is hit by a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample the electron can undergo various interactions with the sample.
@@ -165,6 +173,3 @@ SEMs give high contrast large area images with good spatial resolution and were
 On insulating or semiconducting samples the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focusing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference, and thus they are not sufficient for sample characterization. \\
 
 SEM images and in particular the related technologies of \textbf{T}ransmission \textbf{E}lectron \\ \textbf{M}icroscopy and \textbf{S}canning \textbf{Tunneling} \textbf{E}lectron \textbf{M}icroscopy have been used to characterize properties of thin films and characterize interfaces down to the single atomic scale.\cite{self_epitaxy}\\
-
-%\subsection{Energy-dispersive X-ray spectroscopy}
-%\textbf{E}nergy \textbf{d}ispersive \textbf{X}-ray spectroscopy (EDX)
\ No newline at end of file
diff --git a/chap02.aux b/chap02.aux
index 0233b20f4dbd429a29d7af320f1209da221a807d..4cd01de9bb2f098fa463cc0f98abe80e21229664 100644
--- a/chap02.aux
+++ b/chap02.aux
@@ -1,116 +1,111 @@
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 \citation{SiN_dielectric}
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\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 $C_i$ in order. The RHK relay controls, which motor is currently driven.}}{29}{figure.caption.27}\protected@file@percent }
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+\newlabel{eq:plate_capacitor}{{2.1}{29}{Approach curves}{equation.2.2.1}{}}
+\newlabel{fig:approach_curve_example_cap}{{2.13a}{30}{\relax }{figure.caption.28}{}}
+\newlabel{sub@fig:approach_curve_example_cap}{{a}{30}{\relax }{figure.caption.28}{}}
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+\newlabel{fig:approach_curve_example_full}{{2.13e}{30}{\relax }{figure.caption.28}{}}
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+\newlabel{fig:approach_curve_example}{{2.13}{30}{A capacitance (approach) curve, for one of the capacitive sensors, as an example (a) and the difference of each capacitance value to the last (b). Only one sensor is pictured. Marked are the important point where the slope of the $\frac {1}{r}$ curve changes. These points, where the geometry of the alignment process changes are marked labeled First, Second and Full contact. Before each of these points the difference goes to a local maximum. These are marked with blue dashed lines. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points mark where the mask is touching the sample}{figure.caption.28}{}}
 \citation{Beeker}
-\newlabel{eq:cap_slope_change}{{2.3}{29}{Approach curves}{equation.2.2.3}{}}
+\newlabel{eq:cap_slope_change}{{2.3}{31}{Approach curves}{equation.2.2.3}{}}
 \citation{Beeker}
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+\newlabel{fig:approach_replicability_cap_diff}{{2.15b}{33}{\relax }{figure.caption.31}{}}
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+\newlabel{subsec:cross_cap}{{2.2.5}{34}{Cross capacitances}{subsection.2.2.5}{}}
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+\newlabel{sub@fig:cross_cap_approach_difference}{{a}{34}{\relax }{figure.caption.32}{}}
+\newlabel{fig:cross_cap_approach_difference_2}{{2.16b}{34}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:cross_cap_approach_difference_2}{{b}{34}{\relax }{figure.caption.32}{}}
+\newlabel{fig:cross_cap_approach_sim}{{2.16c}{34}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:cross_cap_approach_sim}{{c}{34}{\relax }{figure.caption.32}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref  {fig:cross_cap_approach_difference}, \subref  {fig:cross_cap_approach_difference_2}). (\subref  {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case.}}{34}{figure.caption.32}\protected@file@percent }
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+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{36}{table.caption.34}\protected@file@percent }
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty.}}{37}{figure.caption.35}\protected@file@percent }
+\newlabel{fig:mask_old_caps}{{2.18}{37}{The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty}{figure.caption.35}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{38}{figure.caption.36}\protected@file@percent }
+\newlabel{fig:mask_old_correl}{{2.19}{38}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.36}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces 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.}}{39}{figure.caption.37}\protected@file@percent }
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+\newlabel{sec:sample_prep}{{2.3.1}{40}{Sample preparation}{subsection.2.3.1}{}}
 \@setckpt{chap02}{
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diff --git a/chap02.tex b/chap02.tex
index b17f2f14b1777ac129be18d0642140bd5cd975bd..52c8ecff2f5836ba97784090c2ec0f836d2b1c04 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -55,7 +55,7 @@ path from the \ce{Pb} evaporator.}
 
 The Mask Aligner vacuum system consists of three distinct vacuum chambers that can be separated with vacuum gate valves.\cite{Mask_Aligner} The first part is the \textbf{M}ain \textbf{C}hamber (MC), in which the Mask Aligner is located and the evaporator chamber used to create a molecular beam into the main chamber, secondly the \textbf{L}oad \textbf{L}ock (LL), which is a vacuum suitcase that is used to insert new samples and masks into the system and thirdly a Turbomolecular pump loop used to pump the system down to UHV vacuum pressures. The main chamber is equipped with an Ion Getter Pump, due to this the system can be separated from the main pumping loop of the Turbo molecular pump, without loss of vacuum pressure. The system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV), one located directly on the main chamber and one separating the evaporator from the Turbomolecular pump loop. Additionally, the Load Lock and the main chamber are separated using a Gate Valve. In order to detect leaks in the vacuum system a mass spectrometer is also attached to the main chamber. \\
 The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV pressures for extended periods of time, even while separated from the main pump loop. A garage with spaces for up to $10$ samples and $4$ additional spaces for Omicron samples is part of the Load Lock. This allows insertion of multiple samples and masks, that can then be later inserted into the main chamber. For insertion and removal of masks and sample a wobble stick is attached to the Load Lock chamber. The sample/mask insertion path of the wobblestick can be seen in \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. The Load Lock is designed to be a detachable vacuum suitcase, allowing samples to be stored in the garage and then transported with the suitcase to another vacuum system without intermediate exposure to ambient conditions.\\
-The main pump loop consists of a rotary vane prepump and a turbomolecular pump \todo{Look up exact model}. Between prepump and turbo molecular pump is a pressure sensor to determine if the prepump is providing suitable backing pressure and a valve, which can be opened to a Nitrogen bottle to allow the system to be vented to atmospheric pressure with an inert gas. \\
+The main pump loop consists of a rotary vane prepump and a turbomolecular pump. Between prepump and turbo molecular pump is a pressure sensor to determine if the prepump is providing suitable backing pressure and a valve, which can be opened to a Nitrogen bottle to allow the system to be vented to atmospheric pressure with an inert gas. \\
 The 3 parts are seen as distinct, as the 3 components can be decoupled safely once the entire system is pumped to UHV without risk of losing vacuum pressure since no part of the system is not pumped. \\ 
 Another device, unrelated to this thesis, a gold evaporator, is connected to the vacuum system of the Mask Aligner, but it can be currently run fully separately, as it has its own Turbomolecular pump with attached prepump. As such the system is completely independent and only needs to be opened to the Mask Aligner system to check its pressure, since it currently is not equipped with any pressure sensor of its own. The pressure sensor is however not needed, since in testing the turbomolecular pump can pump the system down to the necessary pressures in very short time. Opening to the Mask Aligner system would only be needed in case there is a suspected leak. \\
 
@@ -121,7 +121,7 @@ little closer to the camera than the motors themselves, if one neglects the smal
     \includegraphics[width=0.6\linewidth]{img/Plots/Calibrations/screw_diff_explain.pdf}
     \caption{Diagram explaining how to derive the deviation of measured step size on the screws near the Z2 and Z3 motors from the actual step size of the motors.}
     \label{fig:calibration_screw_diff_explain}
-\end{figure} \todo{Maybe leave out or put tranparent image of motor below}
+\end{figure}
 
 With this one gets that for each unit of distance the motor moves the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. With this the actual movement on the motor can be obtained. \\
 
@@ -176,8 +176,6 @@ obtained is shown in Figure \ref{fig:calibration_example}. In this image it can
 be seen, that the positive direction has larger step sizes and that steps size
 is on the order of $10$ nm/step.
 
-
-
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.8\linewidth]{img/Plots/Calibrations/80V.pdf}
@@ -224,7 +222,7 @@ To do this a Bresser MicroCam II camera with a resolution of $20$ megapixel is
 mounted on a stand in front of the window of the mask aligner chamber. The
 mounting of it can be controlled via 3 micrometer screws in x, y and z
 direction. Additionally, the camera can be rotated on $2$ axes allowing full
-control of the camera angle.\todo{Maybe image} No optical adjustment can be done
+control of the camera angle. No optical adjustment can be done
 in the axis, in which the camera is pointed as depth information is difficult to
 obtain. For this reason the sample has to be aligned so that its surface normal
 is perpendicular to the cameras view direction i.e. no sample surface can be
@@ -268,7 +266,6 @@ can be for example chosen since its edge is known to be $5940 \pm 20 $ $\mu$m.
 In camera view direction the mask and sample should now be aligned within
 achievable optical accuracy. The progression of this can be seen in Figure \ref{fig:optical_approach}
  
-
 \begin{figure}[H]
     \centering
 	\begin{subfigure}{0.3\textwidth}
@@ -287,11 +284,10 @@ achievable optical accuracy. The progression of this can be seen in Figure \ref{
     \label{fig:optical_approach}
 \end{figure}
 
-
+\newpage
 
 \subsection{Approach curves}
 
-
 After optical alignment the final step towards an aligned sample comes via
 capacitive measurement to obtain the distance to the sample surface. The 3
 capacitive sensors on the mask are aligned with the 3 motors of the Mask Aligner
@@ -313,6 +309,15 @@ and are labeled as seen in Figure \ref{fig:mask_aligner_nomenclature_capacitance
 	\caption{(\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 an diagram of the masks dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is actually used to create patterns.}
 \end{figure}
 
+The readout of the capacitance sensors is performed with a Lock-in amplifier and the movement of the piezo motor stacks is done with the RHK piezo motor controller. Communication with both the RHK and the Lock-in amplifier is done with a Matlab script. The communication with the RHK is done via a network interface while the Lock-in uses a serial interface. Figure \ref{fig:diagram_MA_circ} shows a diagram of the communication circuit. Settings of the Lock-in amplifier are available in Appendix \ref{app:lock_in}.
+
+\begin{figure}[H]
+    \centering
+    \includegraphics[width=0.75\linewidth]{img/MA/SchaltDiagramRHK.pdf}
+    \caption{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 $C_i$ in order. The RHK relay controls, which motor is currently driven.}
+    \label{fig:diagram_MA_circ}
+\end{figure}
+
 Note that this diagram is not true for all masks, since some were assembled with
 the capacitance sensors pointed in the wrong direction. 
 The capacitance of each of the $3$ sensors can be approximated using a simple
@@ -450,14 +455,14 @@ capacitance is used and the stop condition is used to determine good alignement
 \begin{figure}[H]
     \centering
    
-\includegraphics[width=0.9\linewidth]{img/MA/SubsequentApproachDeviation.pdf}
+\includegraphics[width=0.95\linewidth]{img/MA/SubsequentApproachDeviation.pdf}
     \caption{Plot of data of approach curves recorded on two different days. The
 second curve was recorded after retraction and subsequent approach. The 2 curves
 do not start at the same distance away from sample, which is why they are not
 aligned on the x-axis. A clear drop in capacitance can be observed from one
 measurement to the other regardless.}
     \label{fig:approach_subsequent}
-\end{figure}\todo{Plot too smol}
+\end{figure}
 
 \subsection{Reproducibility}
 One of the questions about the efficacy of Mask Aligner as an alignment tool is
@@ -468,25 +473,25 @@ and a comparison before and after evaporation was discussed.\cite{Beeker}
 
 \subsubsection{Reproducibility when removing sample/mask}
 
-One reproducibility question is whether the approach curve is strongly affected by the exchange of mask or sample or even just the reinsertion of mask or sample. This is important since an exchange of sample to perform a new evaporation is a common operation in the creation of patterned samples. The process could be accelerated and be made less probable to damage the sample, when any approach curve made with the same mask can be used and no additional calibration approach to full contact has to be done for each sample. \todo{If you do not have data for this maybe scratch line, me!}
+One question concerning reproducibility is whether the approach curve is strongly affected by the exchange of mask or sample or even just the reinsertion of mask or sample. This is important since an exchange of sample to perform a new evaporation is a common operation in the creation of patterned samples. 
 
 \begin{figure}[H]
     \centering
-	\begin{subfigure}{0.45\textwidth}
+	\begin{subfigure}{0.495\textwidth}
     \includegraphics[width=\linewidth]{img/MA/InsertionReproducibility.pdf}
     \caption{}
 	\label{fig:approach_replicability_cap}
 	\end{subfigure}
-	\begin{subfigure}{0.45\textwidth}
+	\begin{subfigure}{0.495\textwidth}
     \includegraphics[width=\linewidth]{img/MA/InsertionReproducibility_diff.pdf}
     \caption{}
 	\label{fig:approach_replicability_cap_diff}
 	\end{subfigure}
 	\caption{3 subsequent approach curves \subref{fig:approach_replicability_cap} and differences in capacitance for each step \subref{fig:approach_replicability_cap_diff} recorded. \textcolor{tab_green}{Green} is initial curve. \textcolor{tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \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.}
     \label{fig:approach_replicability}
-\end{figure} \todo{Plot needs labels and bigger}
+\end{figure} 
 
-The reproducibility between exchanging just the mask and sample and reinserting it is looked at. When 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}. This might be feature of the particular batch of masks this thesis worked with as the gold pins connecting the mask holder and mask stage do not have fully stable contact between the male and female side and allow for a certain level of movement. 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 with better gold pin design, when designing newer mask mentioned further in \ref{subsec:cross_cap}\\
+The reproducibility when exchanging just the mask and sample and reinserting it is looked at. When 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}. This might be feature of the particular batch of masks this thesis worked with as the gold pins connecting the mask holder and mask stage do not have fully stable contact between the male and female side and allow for a certain level of movement. 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 with better gold pin design, when designing newer mask mentioned further in \ref{subsec:cross_cap}\\
 
 Another reason might be small movement of the mask frame on the \ce{Nd} magnets tilting the mask, when reinserting the mask. This problem cannot be fixed without a complete redesign of the Mask Aligner. \\
 
@@ -562,7 +567,7 @@ more closely, suggesting this is the cause.
 
 \begin{figure}[H]
     \centering
-    \includegraphics[width=0.75\linewidth]{img/LeakageCurrent.pdf}
+    \includegraphics[width=0.65\linewidth]{img/LeakageCurrent.pdf}
     \caption{Diagram showing one possible explanation for the large correlation
 in Capacitance readings. A small Tear in the \ce{SiNi} layer removes insulation
 between the gold wire and the Si of the Mask allowing current to travel through.
@@ -631,7 +636,7 @@ mask often determine the shape.
 
 \begin{figure}[H]
     \centering
-    \includegraphics[width=0.9\linewidth]{img/Plots/Mask_Old_Correl.pdf}
+    \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 same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit
 to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars
@@ -692,7 +697,6 @@ alignment and subsequent approach.
 The stop condition in this case is a single peak in the derivative of the
 capacitance curve. This peak in the capacitance curve happens right before first
 contact, and by stopping slightly before it, decent alignment can be achieved. 
-\todo{Plot stop condition}
 
 \paragraph{Low correlation between capacitance curves}
 When all 3 capacitance curves are mostly uncorrelated, information of the mask sample can be gathered directly from the value of each
diff --git a/chap03.aux b/chap03.aux
index f4ab96cd0bf60ec2107ac9205676233be08d07c0..eb6e158f7602ff4dbd142b8d0bb900dda15d446c 100644
--- a/chap03.aux
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 \citation{switch_datasheet}
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-\@writefile{toc}{\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{50}{subsection.3.4.7}\protected@file@percent }
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+\newlabel{fig:bessel_filter_filter}{{3.6b}{48}{\relax }{figure.caption.50}{}}
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+\newlabel{fig:bessel_filter}{{3.6}{48}{Plots showing both an aliased signal (a) and the same signal, but smoothed out with an 8th order Bessel filter (b). The amount of aliasing is not representative of the Walker electronics and is simply for illustration purposes. After filtering, the signal appears very smooth and without sharp steps}{figure.caption.50}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.4.3}Fast flank}{48}{subsection.3.4.3}\protected@file@percent }
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+\newlabel{fig:signal_switch_switched}{{3.7b}{49}{\relax }{figure.caption.51}{}}
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+\newlabel{fig:walker_pulse_shape_slow}{{3.8}{51}{Plots showing both an approach step (a) and a retract step (b) for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly}{figure.caption.57}{}}
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+\newlabel{fig:walker_pulse_shape_fast}{{3.9}{52}{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both approach (a) and retract (b), for a nominal voltage of 80 V (without load)}{figure.caption.58}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{52}{subsection.3.4.7}\protected@file@percent }
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+\newlabel{fig:diagram_MA_circ_walker}{{3.10}{53}{Diagram showing how communication with the Walker 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 $C_i$ in order}{figure.caption.59}{}}
 \@setckpt{chap03}{
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diff --git a/chap03.tex b/chap03.tex
index 84916c5330d07068bd18ef997d62220dd1bc7882..f46e33825a949b6e17dc1a516336ba4ebfab4af4 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -6,7 +6,7 @@ In order to control the movement of the mask stage using the mask aligner, 3 mot
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.9\linewidth]{img/SlipStickGrafix.pdf}
-    \caption{Image showing the slip-stick principle.}
+    \caption{Image showing the slip-stick principle. The plot on the right is only an example. Different functions are possible.}
     \label{fig:slip_stick_diagram}
 \end{figure}
 
@@ -95,14 +95,7 @@ Due to the aforementioned behaviors of the KIM001 device, the device was found t
 
 \section{Mask Aligner controller "Walker"}
 \subsection{Overview}
-In order to find a suitable replacement for the RHK Piezo Motor controller, a new device to drive control pulses to the piezo stacks in the mask aligner was built. The PCB is heavily based around the piezo Walker electronics designed to control the piezo walker for the \todo{}. Due to this the device is often referred to as the "Mask Aligner Walker", even though it is not a walker or stepper motor controller. Adaptations were made to adjust it to the desired slip-stick behavior needed for application in the mask aligner. The Controller takes a serial input command and then drives sinusoidal steps with a sharp fast flank in the middle of them. Controllable are the amplitude of the signal and the number of steps. A simplified overview of the entire signal generation process is shown in Figure \ref{fig:electronics_diagramm}. The following section will look at each part of the process depicted in detail.
-
-\begin{figure}[H]
-    \centering
-    \includegraphics[width=\linewidth]{img/ElectronicsDiagramm.pdf}
-    \caption{Overview of the entire signal generation and amplification process of the new Mask Aligner controller.}
-    \label{fig:electronics_diagramm}
-\end{figure}\todo{Fix Plot}
+In order to find a suitable replacement for the RHK Piezo Motor controller, a new device to drive control pulses to the piezo stacks in the mask aligner was built. The PCB is heavily based around the piezo Walker electronics designed to control the piezo Walker used for SEM control. Due to this the device is often referred to as the "Mask Aligner Walker", even though it is not a walker or stepper motor controller. Adaptations were made to adjust it to the desired slip-stick behavior needed for application in the mask aligner. The Controller takes a serial input command and then drives sinusoidal steps with a sharp fast flank in the middle of them. Controllable are the amplitude of the signal and the number of steps. A simplified overview of the entire signal generation process is shown in Appendix \ref{app:walker_diagram}. The following section will look at each part of the process depicted in detail.
 
 \subsection{Signal generation}
 The core of the Mask aligner controller is an Arduino DUE.~\cite{arduino_datasheet} The  \textbf{C}entral to \textbf{P}rocessing \textbf{U}nit CPU of the Arduino DUE the "Atmel SAM3X8E ARM Cortex-M3 CPU" is a $32$-Bit ARM-Core microcontroller. Intgrated into the CPU is a $12$-Bit \textbf{D}igital to \textbf{A}nalog \textbf{C}onverter (DAC).~\cite{arduino_cpu_datasheet} The DAC comes with two output channels that can be controlled to output a signal simultaneously. The Arduino CPU is responsible for the generation of the original signal shape in software. The Arduino generates a signal internally with a sampling rate of $404$ kHz with the shape given by:
@@ -110,8 +103,6 @@ The core of the Mask aligner controller is an Arduino DUE.~\cite{arduino_datashe
      S = 4095 * \frac{A}{2 \pi} * \sin(2 \pi * t/P) + t/P
 \end{equation}
 
-\todo{Maybe add Arduino Pin out}
-
 Where $A$ is an amplitude parameter given by the user, that controls the voltage given at the output. $t$ is the time elapsed since the start of the current step, and $P$ is the period of a single step. The value $4095$ is chosen to use the full range of the $12$-Bit accuracy the Arduino DUE DAC provides. This gives a sinus-like shape of the pulse depicted in Figure \ref{fig:bessel_filter_unfiltered}, that closely matches the pulse shape given by the RHK. Due to this similar behavior is expected. This signal is then output on the DAC 0 pin of the Arduino. Since the Arduino can only output one polarity of voltage, but our final signal is intended to be bipolar, another signal is generated on DAC 1 with $1 - S$ as the given function. If one now subtracts the signals as depicted in Figure \ref{fig:bessel_filter_unfiltered} gets a bipolar signal following the desired sinusoidal shape. This is done via a hardware subtractor. \\
 The Signal given by the Arduino contains aliasing artifacts from the digital to analog conversion. Aliasing leads to sharp very short steps in the signal, this could potentially put the piezo movement into the slip rather than the stick regime. In order to prevent that, the aliasing steps in the signal have to be smoothed out. This is done by applying an 8th order Bessel filter to the signal. The effect of this can be seen in Figure \ref{fig:bessel_filter_filter}.
 
@@ -208,5 +199,14 @@ The slow flank was also measured for both the RHK and the Walker, again in an un
 
 
 \subsection{Driving the Mask Aligner}
+The communication diagram with the Walker looks slightly different from the one in Figure \ref{fig:diagram_MA_circ}, since the RHK relay is no longer needed since the Walker can take over its function. The new diagram can be seen in Figure \ref{fig:diagram_MA_circ_walker}
+
+\begin{figure}[H]
+    \centering
+    \includegraphics[width=0.75\linewidth]{img/MA/SchaltDiagramWalker.pdf}
+    \caption{Diagram showing how communication with the Walker 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 $C_i$ in order. }
+    \label{fig:diagram_MA_circ_walker}
+\end{figure}
+
 Due to hardware issues with the Walker, no final test with the Mask Aligner attached as a load could not be performed and the driving performance could not be tested. Some hardware failure caused the positive polarity to no longer reach full $120$ V peak and with a load attached it could no longer reach beyond $0$ V giving a unipolar piezo driving signal in approach direction and no slip stick driving signal in retract.
 
diff --git a/chap04.aux b/chap04.aux
index 60a31139b383f0ebd18c423dfcd64710a86835f8..0b17fb588b79126c1e7245c31ac1f60a2c89e92d 100644
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+\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref  {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref  {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref  {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref  {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref  {fig:solder_anchors_diagram_SmallerDot}-\subref  {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref  {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably. }}{56}{figure.caption.63}\protected@file@percent }
+\newlabel{fig:solder_anchors_diagram}{{4.2}{56}{Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref {fig:solder_anchors_diagram_SmallerDot}-\subref {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably}{figure.caption.63}{}}
+\newlabel{fig:solder_anchors_examples_glue_bottom}{{4.3a}{57}{\relax }{figure.caption.64}{}}
+\newlabel{sub@fig:solder_anchors_examples_glue_bottom}{{a}{57}{\relax }{figure.caption.64}{}}
+\newlabel{fig:solder_anchors_examples_AlO}{{4.3b}{57}{\relax }{figure.caption.64}{}}
+\newlabel{sub@fig:solder_anchors_examples_AlO}{{b}{57}{\relax }{figure.caption.64}{}}
+\newlabel{fig:solder_anchors_examples_shear_01}{{4.3c}{57}{\relax }{figure.caption.64}{}}
+\newlabel{sub@fig:solder_anchors_examples_shear_01}{{c}{57}{\relax }{figure.caption.64}{}}
+\newlabel{fig:solder_anchors_examples_shear_02}{{4.3d}{57}{\relax }{figure.caption.64}{}}
+\newlabel{sub@fig:solder_anchors_examples_shear_02}{{d}{57}{\relax }{figure.caption.64}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.3}{\ignorespaces Examples for the different approaches taken to solve the issues with the solder anchor points. (\subref  {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref  {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref  {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref  {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely.}}{57}{figure.caption.64}\protected@file@percent }
+\newlabel{fig:solder_anchors_examples}{{4.3}{57}{Examples for the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely}{figure.caption.64}{}}
 \citation{olschewski}
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-\newlabel{fig:Z3_after reglue}{{4.5}{57}{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.76}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{57}{section.4.5}\protected@file@percent }
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-\newlabel{fig:Front_plate_repair_tool}{{4.8a}{60}{\relax }{figure.caption.79}{}}
-\newlabel{sub@fig:Front_plate_repair_tool}{{a}{60}{\relax }{figure.caption.79}{}}
-\newlabel{fig:Front_plate_repair_plate}{{4.8b}{60}{\relax }{figure.caption.79}{}}
-\newlabel{sub@fig:Front_plate_repair_plate}{{b}{60}{\relax }{figure.caption.79}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref  {fig:Front_plate_repair_tool}). (\subref  {fig:Front_plate_repair_plate}) shows final front plate assembled.}}{60}{figure.caption.79}\protected@file@percent }
-\newlabel{fig:Front_plate_repair}{{4.8}{60}{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled}{figure.caption.79}{}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{61}{subsection.4.5.2}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezos stacks of the motor Z3. }}{61}{figure.caption.80}\protected@file@percent }
-\newlabel{fig:Z3_weaker_stack}{{4.9}{61}{The measured capacitance values for the piezos stacks of the motor Z3}{figure.caption.80}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{62}{section.4.6}\protected@file@percent }
-\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{62}{\relax }{figure.caption.81}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{62}{\relax }{figure.caption.81}{}}
-\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{62}{\relax }{figure.caption.81}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{62}{\relax }{figure.caption.81}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces 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.}}{62}{figure.caption.81}\protected@file@percent }
-\newlabel{fig:Feedthrough_Repairs}{{4.10}{62}{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.81}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{63}{table.caption.82}\protected@file@percent }
-\newlabel{tab:cross_cap_after_repair}{{4.1}{63}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.82}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{63}{section.4.7}\protected@file@percent }
-\@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.}}{63}{figure.caption.83}\protected@file@percent }
-\newlabel{fig:calibration_after_repair}{{4.11}{63}{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.83}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.4}Piezo re-gluing}{58}{section.4.4}\protected@file@percent }
+\newlabel{sec:piezo_reglue}{{4.4}{58}{Piezo re-gluing}{section.4.4}{}}
+\newlabel{fig:Z3_reglue_process_off}{{4.4a}{59}{\relax }{figure.caption.65}{}}
+\newlabel{sub@fig:Z3_reglue_process_off}{{a}{59}{\relax }{figure.caption.65}{}}
+\newlabel{fig:Z3_reglue_process_scratched}{{4.4b}{59}{\relax }{figure.caption.65}{}}
+\newlabel{sub@fig:Z3_reglue_process_scratched}{{b}{59}{\relax }{figure.caption.65}{}}
+\newlabel{fig:Z3_reglue_process_dot}{{4.4c}{59}{\relax }{figure.caption.65}{}}
+\newlabel{sub@fig:Z3_reglue_process_dot}{{c}{59}{\relax }{figure.caption.65}{}}
+\newlabel{fig:Z3_reglue_process_down}{{4.4d}{59}{\relax }{figure.caption.65}{}}
+\newlabel{sub@fig:Z3_reglue_process_down}{{d}{59}{\relax }{figure.caption.65}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move.}}{59}{figure.caption.65}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{4.4}{59}{The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move}{figure.caption.65}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces 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 $.}}{60}{figure.caption.66}\protected@file@percent }
+\newlabel{fig:Z3_after reglue}{{4.5}{60}{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.66}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{60}{section.4.5}\protected@file@percent }
+\@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.}}{61}{figure.caption.67}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot}{{4.6}{61}{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.67}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{61}{subsection.4.5.1}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces Screw rotation calibration data for Z2 and Z3 after front plate repairs.}}{62}{figure.caption.68}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{62}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.68}{}}
+\newlabel{fig:Front_plate_repair_tool}{{4.8a}{63}{\relax }{figure.caption.69}{}}
+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{63}{\relax }{figure.caption.69}{}}
+\newlabel{fig:Front_plate_repair_plate}{{4.8b}{63}{\relax }{figure.caption.69}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{63}{\relax }{figure.caption.69}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref  {fig:Front_plate_repair_tool}). (\subref  {fig:Front_plate_repair_plate}) shows final front plate assembled.}}{63}{figure.caption.69}\protected@file@percent }
+\newlabel{fig:Front_plate_repair}{{4.8}{63}{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled}{figure.caption.69}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{64}{subsection.4.5.2}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezos stacks of the motor Z3. }}{64}{figure.caption.70}\protected@file@percent }
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+\@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{65}{section.4.6}\protected@file@percent }
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+\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{65}{\relax }{figure.caption.71}{}}
+\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{65}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{65}{\relax }{figure.caption.71}{}}
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+\newlabel{fig:Feedthrough_Repairs}{{4.10}{65}{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.71}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{66}{table.caption.72}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{66}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.72}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{66}{section.4.7}\protected@file@percent }
+\@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.}}{66}{figure.caption.73}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{66}{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.73}{}}
 \@setckpt{chap04}{
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diff --git a/chap05.aux b/chap05.aux
index 95b411d5ea5861aebe22c28a5d04c6ff22ca1acb..25566d2f88d06e6614bf15586cc895a6f325e35f 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -1,98 +1,98 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{\numberline {5}Evaporations and measurement}{65}{chapter.5}\protected@file@percent }
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 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
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-\newlabel{fig:evaporation_approach_curve}{{5.1}{65}{The approach curve measured for Field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference of the current to the last step, C1 was used for alignment primarily}{figure.caption.84}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces 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 $450-520$}}{66}{table.caption.85}\protected@file@percent }
-\newlabel{tab:evaporation_settings}{{5.1}{66}{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.85}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {5.1}{\ignorespaces The approach curve measured for Field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference of the current to the last step, C1 was used for alignment primarily.}}{68}{figure.caption.74}\protected@file@percent }
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+\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces 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 $450-520$}}{69}{table.caption.75}\protected@file@percent }
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+\newlabel{fig:evaporation_contamination}{{5.4}{71}{(\subref {fig:evaporation_contamination_img}) shows an AFM image of field $3$ without any grain removal applied. Data was obtained on multiple different spots on the sample. \textcolor {tab_red}{Red} and \textcolor {tab_green}{green} lines show the average height and width of the contamination particles obtained from peak fits. (\subref {fig:evaporation_contamination_anal}) shows line cuts obtained from contamination particles}{figure.caption.78}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {5.5}{\ignorespaces AFM image of evaporated \ce {Pb} dot (\subref  {fig:penumbra_tilt_sigmas}) illustrating the penumbral widths used for evaporation analysis $\sigma _s$ and $\sigma _l$, depicted in \textcolor {tab_red}{red}, and the major axis of the tilt \textcolor {tab_green}{(green)}. $\sigma _s$ is drawn larger than actually measured, since the measured value would be hardly visible. The \textcolor {tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data stems from Evaporation 5 In Chapter 5. (\subref  {fig:Evaporation_diagramm_field}) shows an AFM image of the top right part of the evaporated field labeled $3$. Grains were reduced using post processing. Black circles show the dots chosen for further examination on this particular field.}}{72}{figure.caption.79}\protected@file@percent }
+\newlabel{fig:penumbra_tilt_sigmas_and_field_show}{{5.5}{72}{AFM image of evaporated \ce {Pb} dot (\subref {fig:penumbra_tilt_sigmas}) illustrating the penumbral widths used for evaporation analysis $\sigma _s$ and $\sigma _l$, depicted in \textcolor {tab_red}{red}, and the major axis of the tilt \textcolor {tab_green}{(green)}. $\sigma _s$ is drawn larger than actually measured, since the measured value would be hardly visible. The \textcolor {tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data stems from Evaporation 5 In Chapter 5. (\subref {fig:Evaporation_diagramm_field}) shows an AFM image of the top right part of the evaporated field labeled $3$. Grains were reduced using post processing. Black circles show the dots chosen for further examination on this particular field}{figure.caption.79}{}}
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+\newlabel{fig:evaporation_SEM}{{5.9}{78}{SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects}{figure.caption.83}{}}
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+\newlabel{fig:evaporation_SEM_analysis}{{5.10}{79}{An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields}{figure.caption.84}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {5.5}Simulation}{79}{section.5.5}\protected@file@percent }
+\newlabel{sec:simulation}{{5.5}{79}{Simulation}{section.5.5}{}}
+\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.11a}{81}{\relax }{figure.caption.85}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{81}{\relax }{figure.caption.85}{}}
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+\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{81}{\relax }{figure.caption.85}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $.}}{81}{figure.caption.85}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare}{{5.11}{81}{Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $}{figure.caption.85}{}}
 \citation{Bhaskar}
-\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.11a}{78}{\relax }{figure.caption.97}{}}
-\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{78}{\relax }{figure.caption.97}{}}
-\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.11b}{78}{\relax }{figure.caption.97}{}}
-\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{78}{\relax }{figure.caption.97}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $.}}{78}{figure.caption.97}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_first_compare}{{5.11}{78}{Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $}{figure.caption.97}{}}
-\@writefile{tdo}{\contentsline {todo}{you use tilt and deformation of mask very interchangably. Please distinguish tilt as a stiff mask with an angle to the mask. Deformation/bending in the mask is not same as tilt. If you want to talk about local angle on the deformed mask, that is a separate third thing}{78}{section*.98}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.12a}{79}{\relax }{figure.caption.99}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{79}{\relax }{figure.caption.99}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.12b}{79}{\relax }{figure.caption.99}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{79}{\relax }{figure.caption.99}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.12c}{79}{\relax }{figure.caption.99}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{79}{\relax }{figure.caption.99}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref  {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ (\subref  {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{79}{figure.caption.99}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness}{{5.12}{79}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.99}{}}
-\newlabel{fig:evaporation_simulation_rejection_prev}{{5.13a}{80}{\relax }{figure.caption.100}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{80}{\relax }{figure.caption.100}{}}
-\newlabel{fig:evaporation_simulation_rejection_after}{{5.13b}{80}{\relax }{figure.caption.100}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{80}{\relax }{figure.caption.100}{}}
-\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.13c}{80}{\relax }{figure.caption.100}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{80}{\relax }{figure.caption.100}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Simulated evaporation dots without (\subref  {fig:evaporation_simulation_rejection_prev}) and with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{80}{figure.caption.100}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_rejection}{{5.13}{80}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.100}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$.}}{81}{figure.caption.101}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_progression}{{5.14}{81}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$}{figure.caption.101}{}}
-\@writefile{toc}{\contentsline {paragraph}{Software improvements}{81}{section*.102}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask. }}{82}{figure.caption.86}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_overlap}{{5.12}{82}{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.86}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.13a}{82}{\relax }{figure.caption.87}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{82}{\relax }{figure.caption.87}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.13b}{82}{\relax }{figure.caption.87}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{82}{\relax }{figure.caption.87}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.13c}{82}{\relax }{figure.caption.87}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{82}{\relax }{figure.caption.87}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref  {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ (\subref  {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{82}{figure.caption.87}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness}{{5.13}{82}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.87}{}}
+\newlabel{fig:evaporation_simulation_rejection_prev}{{5.14a}{83}{\relax }{figure.caption.88}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{83}{\relax }{figure.caption.88}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{5.14b}{83}{\relax }{figure.caption.88}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{83}{\relax }{figure.caption.88}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.14c}{83}{\relax }{figure.caption.88}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{83}{\relax }{figure.caption.88}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Simulated evaporation dots without (\subref  {fig:evaporation_simulation_rejection_prev}) and with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{83}{figure.caption.88}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{5.14}{83}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.88}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.15}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$.}}{84}{figure.caption.89}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_progression}{{5.15}{84}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$}{figure.caption.89}{}}
+\@writefile{toc}{\contentsline {paragraph}{Software improvements}{84}{section*.90}\protected@file@percent }
 \@setckpt{chap05}{
-\setcounter{page}{83}
+\setcounter{page}{86}
 \setcounter{equation}{1}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -107,7 +107,7 @@
 \setcounter{subsubsection}{0}
 \setcounter{paragraph}{0}
 \setcounter{subparagraph}{0}
-\setcounter{figure}{14}
+\setcounter{figure}{15}
 \setcounter{table}{1}
 \setcounter{section@level}{4}
 \setcounter{Item}{18}
@@ -121,7 +121,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{17}
+\setcounter{@todonotes@numberoftodonotes}{2}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap05.tex b/chap05.tex
index 17159e73d120230f427f2d6cf44307b19c2915fc..694ff01163085182e5eed82db579051ca129ea6f 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -11,7 +11,7 @@ As a test for positioning and as a test for the Mask Aligners capabilities after
     \label{fig:evaporation_approach_curve}
 \end{figure}
 
-Five subsequent evaporations were performed at different lateral positions on the sample. 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} \\  
+Five subsequent evaporations were performed at different lateral positions on the sample. 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} \\  
 
 \begin{itemize}
 	\item Field 1: Full contact
@@ -181,7 +181,6 @@ This process was performed for every recorded dot and with multiple line cuts ne
 	\caption{Data obtained from the previously described method for each of the 5 evaporations, from evaporated dot each from the center of the field, the left, the right, the bottom and the top. The dot chosen depended on measurement condition such as contamination and phase characteristics of the dot. The data shows the smaller penumbra $\sigma_s$ (\subref{fig:evaporation_measured_penumbra_sigs}) the larger penumbra $\sigma_l$ (\subref{fig:evaporation_measured_penumbra_sigl}), the height of the dot (\subref{fig:evaporation_measured_penumbra_height}) and the diameter of the circle (\subref{fig:evaporation_measured_penumbra_circle_r}).}
     \label{fig:evaporation_measured_penumbra}
 \end{figure}
-\todo{Check if script can fit negative penumbra}
 Figure \ref{fig:evaporation_measured_penumbra} shows the values obtained from analysis of exemplary \ce{Pb} dots of each field. For each field a dot on the top of the field, one on the bottom, one near the center and on each on the left and the right were chosen to analyze. The dots were chosen based on how contaminated the data looked in an AFM image of the top right and bottom left of the field, and if the phase showed line artifacts. \\
 The data in Figure \ref{fig:evaporation_measured_penumbra_sigs} shows that for the smaller penumbra values of well below the threshold of $100$ nm can be found, with most of the fields lying near $50$ nm. From the evaporation conditions it would be expected, that field $1$ and field $5$ should be very similar and both should show smaller penumbra than the other fields, but this does not appear to be the case. While field $5$ shows some of the smallest penumbras, its behavior seems to be more akin to field $3$ than $1$. Field $4$ also has the largest penumbras, which is unexpected since it was evaporated at the point of second contact and should thus perform better than both field $3$ and field $2$. Both field $2$ and $4$ have the largest uncertainties, due to more noisy data, which could explain this discrepancy. The difference between top, bottom, right, left and center seems to be within measurement uncertainty and thus no conclusive statements can be made about it.\\
 
@@ -219,22 +218,22 @@ The different angles the tilt takes can be seen in Figure \ref{fig:evaporation_t
     \centering
 	\begin{subfigure}{0.49\linewidth}
 		\centering
-    	\includegraphics[width=0.9\linewidth]{img/Evaporation/SEM/SEM_Probe_01_cropped.png}
+    	\includegraphics[width=0.95\linewidth]{img/Evaporation/SEM/SEM_Probe_01_cropped.png}
     	\caption{}
 		\label{fig:evaporation_SEM_sample}
 	\end{subfigure}
 	\begin{subfigure}{0.49\linewidth}
 		\centering
-    	\includegraphics[width=0.9\linewidth]{img/Evaporation/SEM/SEM_Mask_cropped.pdf}
+    	\includegraphics[width=0.95\linewidth]{img/Evaporation/SEM/SEM_Mask_cropped.pdf}
     	\caption{}
 		\label{fig:evaporation_SEM_mask}
 	\end{subfigure}
-	\caption{SEM images of field 2 on the sample (\subref{fig:evaporation_SEM_sample}) and the mask (\subref{fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. The \textcolor{tab_red}{red} lines show a line drawn approximately through the center of the holes. The outer red line shows curvature, while the inner one is completely straight. This shows some deformation due to bending.}
+	\caption{SEM images of field 2 on the sample (\subref{fig:evaporation_SEM_sample}) and the mask (\subref{fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects.}
     \label{fig:evaporation_SEM}
 \end{figure}
 
 To confirm the Mask was undamaged during the evaporation, SEM images were taken of the mask as well as the sample. The resulting images can be seen in Figure \ref{fig:evaporation_SEM}. The evaporation of field $2$ shown in Figure \ref{fig:evaporation_SEM_sample} shows the elliptical tilt also visible in the AFM images. The elliptical part of the evaporation shows different color in the SEM image, which is an indicator, that the conductivity is different from the part of the dot. \\
-The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to the mask, but the mask seems to be bending upward. The white areas were not stable due to charging effects, but the bending is visible in multiple images (see inset of Figure \ref{fig:evaporation_SEM_mask}). Furthermore, some clogging from the underside of the mask is visible in the SEM images in Figure \ref{fig:evaporation_SEM_mask}.
+The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to the mask. The white areas are charging artifacts and were not stable in multiple images. The mask looks to be bending, but this is most likely due to charging artifacts and an inherent fish-eye effect of SEM images at high magnifications. Furthermore, some clogging from the underside of the mask is visible in the SEM images in Figure \ref{fig:evaporation_SEM_mask}.
 
 \begin{figure}[H]
     \centering
@@ -255,15 +254,20 @@ The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to
 \end{figure}
 
 An example of this clogging in the SEM image is shown in Figure \ref{fig:evaporation_SEM_analysis_clog}
-To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. They also all point in the direction of bending
+To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. It also mostly points outwards. For a lot of points the clogging is not clearly visible in the image however so no strong conclusion can be made from the SEM image alone.
 
-\section{Simulation}
+\section{Simulation} \label{sec:simulation}
 In order to gain more information about the different hypothesis for the tilted evaporation dots, a simple evaporation simulation was written. The simulation is based on ray tracing and is written in the open source Godot game engine, since game engines support checking of rays against collision natively and thus a ray tracing simulation could be implemented quickly. \\
 
 The simulation works as follows:
 At a time $0$ at a distance $L$ from the sample a random point inside the circle is generated, and from it a ray is cast to a point behind the sample. The point behind the mask is chosen such that the ray casts in a cone with opening angle $\phi$. The ray is then checked against collision with a mask hole, which is represented by a cylinder collider with very small height. When collision with the mask "hole" is determined, the ray is cast again and the position at which the sample would be hit is determined. This position is then recorded as a hit in an array, that is structured like an image, spanning a user defined area around the middle of the sample and with user specified resolution. For each element in the array, the amount of hits the "pixel" has received is stored. This step is repeated many times in a single time step.\\
 
-\todo{place image of Godot transform thing here}
+%\begin{figure}[H]
+%    \centering
+%	\includegraphics[width=0.6\linewidth]{img/Evaporation/Sim/GodotCoordinate.png}
+%	\caption{Diagram depicting the coordinate system Godot uses. The order of rotation for the Euler angles is $\alpha$, $\beta$ and $\gamma$.}
+%    \label{fig:evaporation_simulation_godotcoords}
+%\end{figure}
 
 Objects in the Godot game engine are moved, rotated and scaled with a $3 \times 4$ matrix called a transform matrix. This matrix performs rotations via their quaternion representation, which is a way to represent $3$-dimensional rotations as a $4$ component complex number. Modifying the transform matrix directly is possible, but would be very unintuitive and cumbersome, so the engine allows modification of the component's displacement and scale via $3$D vectors. The components of the displacement vector will be called x, y and z. The rotation can be modified via Euler angles. Internally the Euler angles are called, based on the axis they rotate around,  x, y and z as well. To avoid confusion the angles will be called $\alpha$, $\beta$ and $\gamma$, where $\alpha$ rotates around the x-axis, $\beta$ around the y-axis and $\gamma$ around the z-axis.
 
@@ -288,8 +292,20 @@ After a user specified time has passed, the amount of hits on each pixel is save
     \label{fig:evaporation_simulation_first_compare}
 \end{figure}
 
-An image of a simple simulation for an oscillating mask dot with parameters obtained from the AFM measurement can be seen in Figure \ref{fig:evaporation_simulation_first_compare_SIM}. The parameters for the amplitude of the oscillation were extracted from the AFM image shown in Figure \ref{fig:evaporation_simulation_first_compare_AFM}. The values were $0.143$ $\mu$m in x and $-0.358$ $\mu$m in z direction and a tilt of $-41.12^\circ$ in $\alpha$ and $31^\circ$ in $\gamma$. The amplitude of displacement in this case is $\approx 0.4$ $\mu$m, this is in line with the peak to peak amplitude of an active turbomolecular pump given by $1$ $\mu$m, obtained in the PhD thesis of Priyamvada Bhaskar.~\cite{Bhaskar} Some features of the AFM measurement are mirrored in the simulation, however it does not match the simulated image in a decent number of characteristics. The "half moon" shaped penumbra (\textcolor{tab_red}{red} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) in the AFM image is very rough, but on average of equal height, while in the simulation the penumbra gradually lowers from the highest part. The lower edge of the elliptical shape visible in the AFM dot below the circle (\textcolor{tab_cyan}{cyan} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) is so faint as to be invisible in the AFM image, while it is very pronounced in the simulated image and the lower edge is sharp in the AFM image $61 \pm 9$ nm while it is smeared out in the simulated image. \\
-The greater circle in the AFM has an average height for all dots of about $2.6 \pm 0.3$ nm, while the part of the ellipse exceeding the circle is of such low height, that it is not possible to estimate the height as it is within the surface roughness of the sample. This suggests that during the evaporation, the mask was for a majority of the time in the configuration without tilting. Either the mask started in the untilted state and then drifted slowly into the tilted state, or the vibration causing the tilt is non-regular in nature. In order to investigate this further, an initial period, where the oscillation is turned off, was implemented. \todo{you use tilt and deformation of mask very interchangably. Please distinguish tilt as a stiff mask with an angle to the mask. Deformation/bending in the mask is not same as tilt. If you want to talk about local angle on the deformed mask, that is a separate third thing}
+An image of a simple simulation for an oscillating mask dot with parameters obtained from the AFM measurement can be seen in Figure \ref{fig:evaporation_simulation_first_compare_SIM}. The parameters for the amplitude of the oscillation were extracted from the AFM image shown in Figure \ref{fig:evaporation_simulation_first_compare_AFM}. The values were $0.143$ $\mu$m in x and $-0.358$ $\mu$m in z direction and a tilt of $-41.12^\circ$ in $\alpha$ and $31^\circ$ in $\gamma$. \\
+
+The mask being deformed by nearly $45^\circ$ at a single hole site locally would induce large strain upon the mask. The visible tilt is most likely an outcome of both an x-y displacement and a bending of the mask. If there was just a displacement due to the vibration the mask would shift between 2 lateral positions with a certain frequency. If there is strong overlap the $2$ extreme positions would have a certain overlap, which is elliptical. If there is now an additional displacement component in the z direction this causes a smaller circle on top of the flat mask position. It is likely that the effect on the edge is an overlap of both a bending of the mask giving the mask some angle and an additional contribution from the displacement in both x-y and z direction.
+
+\begin{figure}[H]
+    \centering
+	\includegraphics[width=0.45\linewidth]{img/Evaporation/Sim/OverlapCircles.pdf}
+	\caption{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask. }
+    \label{fig:evaporation_simulation_overlap}
+\end{figure}
+
+
+The amplitude of displacement in the case in Figure \ref{fig:evaporation_simulation_first_compare_SIM} is $\approx 0.4$ $\mu$m, this is in line with the peak to peak amplitude of an active turbomolecular pump given by $1$ $\mu$m, obtained in the PhD thesis of Priyamvada Bhaskar.~\cite{Bhaskar} Some features of the AFM measurement are mirrored in the simulation, however it does not match the simulated image in a decent number of characteristics. The "half moon" shaped penumbra (\textcolor{tab_red}{red} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) in the AFM image is very rough, but on average of equal height, while in the simulation the penumbra gradually lowers from the highest part. The lower edge of the elliptical shape visible in the AFM dot below the circle (\textcolor{tab_cyan}{cyan} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) is so faint as to be invisible in the AFM image, while it is very pronounced in the simulated image and the lower edge is sharp in the AFM image $61 \pm 9$ nm while it is smeared out in the simulated image. \\
+
 
 \begin{figure}[H]
     \centering
@@ -312,7 +328,7 @@ The greater circle in the AFM has an average height for all dots of about $2.6 \
     \label{fig:evaporation_simulation_sharpness}
 \end{figure}
 
-The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_initial} compared with the simpler model Figure \ref{fig:evaporation_simulation_sharpness_stick_simple}) this gives an image more simple to the AFM measurement. Another possibility is an oscillation, which is not harmonic and is near the initial stage of the oscillation for a longer period of time. For this instead of choosing the oscillation as $\sin(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\sin(\frac{t}{T} + \phi)^p$ with $p$ being the oscillation power. The resulting image can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_power}. The effect of this is very similar to the initial circular shape. 
+The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_initial} compared with the simpler model Figure \ref{fig:evaporation_simulation_sharpness_stick_simple}) this gives an image more simple to the AFM measurement. Another possibility is an oscillation, which is not harmonic. For this instead of choosing the oscillation as $\sin(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\sin(\frac{t}{T} + \phi)^p$ with $p$ being the oscillation power. The resulting image can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_power}. The effect of this is very similar to the initial circular shape. 
 
 When looking at the measured AFM image, it is very noticeable, that the surface of the "half moon" is rougher than the surface of the inner circle. On average, the roughness is $1.7 \pm 0.4$ times higher. This might be due to the reduced height the outer circle has, or due to being deposited at a different time. \\
 
@@ -350,7 +366,7 @@ The simulation image matches the one given by the AFM measurement pretty well, w
     \label{fig:evaporation_simulation_progression}
 \end{figure}
 
-The simulation allows for taking in progress images at specified time intervals, with this a progression of the evaporation can be created. An example for the previously discussed example can be seen in Figure \ref{fig:evaporation_simulation_progression}. With this the chronology of events can be made visible more easily and animations could be created, as visualizations.
+The simulation allows for taking in progress images at specified time intervals, with this a progression of the evaporation can be created. An example for the previously discussed example can be seen in Figure \ref{fig:evaporation_simulation_progression}. With this the chronology of events can be made visible more easily and visualizations could easily be created.
 
 \paragraph{Software improvements}
 The simulation is accurate in geometrical configuration of the Mask Aligner setup, but it assumes each particle hitting the surface either sticks to it or is rejected with a certain probability, which is a reasonable approximation as it follows the linear behavior from the Knudsen equation (Eq. \ref{eq:hertz_knudsen}), but it does not currently take into account grain size and diffusion of particles, which makes the graininess of the image resolution dependent.\\
diff --git a/conclusion.aux b/conclusion.aux
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+++ b/conclusion.aux
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+\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{86}{chapter*.91}\protected@file@percent }
+\citation{self_epitaxy}
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diff --git a/conclusion.tex b/conclusion.tex
index e73e81cddaad7a71041a8f4f450114f27d203fa7..d1931a818a991cb65e2bb1c779d46551ab4a66b7 100644
--- a/conclusion.tex
+++ b/conclusion.tex
@@ -1,2 +1,21 @@
 \chapter*{Conclusions and Outlook}
 \addcontentsline{toc}{chapter}{Conclusions and Outlook}
+In this thesis, the function of a mask aligner operating in UHV was optimized and its capabilities were analyzed. 
+
+Mask Aligner functionality was restored and measures were taken to prevent further failure in the future. 
+Maintenance procedures for certain potential faults of the Mask Aligner system were established and applied to the Mask Aligner. With this, the initially failing performance of the Mask Aligner was restored. 
+Potential sources of cross capacitances on the Mask Aligner were investigated and likely candidates for sources of cross capacitance were found on the Mask holders/shuttles, with the Mask Aligner itself found to be negligible in the creation of cross capacitance. \\
+
+Further research will have to be done on the prevention of faults in the mask preparation procedure, as issues with leakage currents created in the process of mask bonding were found to be the likely reason for large correlations in the capacitance sensors of the Mask Aligner. \\
+
+A new controller for the Mask Aligner was created by the electronics workshop. Programming of the new electronic was done, and initial performance tests showed favorable results over the old driver electronics. The new controller, however, still suffers from hardware issues, which is why tests under load could not be performed. A final performance test with calibration is still outstanding. \\
+
+The new controller will have to be tested under load for its driving behavior in comparison to the old driver and hardware instability issues will have to be resolved before larger scale evaporation, can be performed.
+In order to adapt voltage output per channel, during approach, a control script with the Mask Aligner will also have to be created and a new calibration as a function of voltage will have to be recorded. \\
+
+It was shown that sharp interfaces on the sub-$60$ nm scale can be created using the Mask Aligner and that under good conditions sharp pristine interfaces can be created using the previously established alignment procedure. Ellipsoidal artifacts on the resulting evaporation could be explained using a simulation approach as a result of vibrations that created bending and x-y shifting of the mask with regard to the sample. \\
+
+In future the Mask Aligner will be first used to test evaporation properties of \ce{Pb} on \ce{Au} with this it will be established if \ce{Pb} is a good candidate for a superconductor/topological insulator interface and if the previously established alignment process transfers to other types of sample. 
+Characterization of these new samples using a low temperature STM to record a superconducting gap is also a subject of future research. The determination of properties, such as appearance of a wetting layer is another important factor that will be done in STM analysis, as the appearance of a wetting layer across the sample's surface would make \ce{Pb} a bad candidate for Majorana Zero Mode research.\\
+
+Another possible candidate for evaporation on a topological insulator seems to be \ce{Pd}. As recent papers have shown it to have interesting self epitaxial growth properties when evaporated on the topological insulator \ce{(Bi_{1-x}Sb_{x})2Te3}.\cite{self_epitaxy} This could be a good candidate for further research. The current evaporator attached is unable to perform palladium evaporation. If \ce{Pd} were chosen over \ce{Pb} a new evaporator need to be connected to the Mask Aligner system.
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diff --git a/img/SlipStickGrafix.pdf b/img/SlipStickGrafix.pdf
index 00cd6df0d39c35217f4fdbbe8fc537768d4015a9..5550e1d45262c1dac19d9ce84b4f0bbee297059c 100644
Binary files a/img/SlipStickGrafix.pdf and b/img/SlipStickGrafix.pdf differ
diff --git a/pdfa.xmpi b/pdfa.xmpi
index 788c8fa863af74e9ee0c3b4b273643bac5ead18f..7355215b10638b95e8e75720b7abeb5c2029a519 100644
--- a/pdfa.xmpi
+++ b/pdfa.xmpi
@@ -73,15 +73,15 @@
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   <rdf:Description rdf:about="" xmlns:xmp="http://ns.adobe.com/xap/1.0/"> 
    <xmp:CreatorTool>LaTeX with hyperref</xmp:CreatorTool> 
-   <xmp:ModifyDate>2024-08-26T01:20:49+02:00</xmp:ModifyDate> 
-   <xmp:CreateDate>2024-08-26T01:20:49+02:00</xmp:CreateDate> 
-   <xmp:MetadataDate>2024-08-26T01:20:49+02:00</xmp:MetadataDate> 
+   <xmp:ModifyDate>2024-08-28T03:49:03+02:00</xmp:ModifyDate> 
+   <xmp:CreateDate>2024-08-28T03:49:03+02:00</xmp:CreateDate> 
+   <xmp:MetadataDate>2024-08-28T03:49:03+02:00</xmp:MetadataDate> 
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   <rdf:Description rdf:about="" xmlns:xmpRights = "http://ns.adobe.com/xap/1.0/rights/"> 
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    <xmpMM:DocumentID>uuid:C8CFC28F-88E1-7995-E9AD-F6D12EAD346B</xmpMM:DocumentID> 
-   <xmpMM:InstanceID>uuid:1265422A-18EF-CB5A-AE1D-362AB8C0EDC3</xmpMM:InstanceID> 
+   <xmpMM:InstanceID>uuid:B9F32601-3301-D571-D499-EBACA36C0ACF</xmpMM:InstanceID> 
   </rdf:Description> 
  </rdf:RDF> 
 </x:xmpmeta> 
diff --git a/preface.aux b/preface.aux
index 912283b57c369b3326f3f07e038580523a6f58b1..f1dadcfbac4290733fdf91a89eaf9d74395a9581 100644
--- a/preface.aux
+++ b/preface.aux
@@ -1,9 +1,13 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\citation{bhaskar}
+\citation{majorana_zero_modes}
+\citation{euv}
+\citation{afm_pattern}
+\citation{stencil_resolution}
+\citation{Olschewski,Bhaskar}
 \@writefile{toc}{\contentsline {chapter}{Introduction}{3}{chapter*.2}\protected@file@percent }
 \@setckpt{preface}{
-\setcounter{page}{4}
+\setcounter{page}{5}
 \setcounter{equation}{0}
 \setcounter{enumi}{0}
 \setcounter{enumii}{0}
diff --git a/preface.tex b/preface.tex
index 66f53f6d9124090c23043a7e773304aa1949cfd3..31bd55813a667b55b47b9e7f0197222ca47727eb 100644
--- a/preface.tex
+++ b/preface.tex
@@ -1,5 +1,10 @@
 \chapter*{Introduction}
 \addcontentsline{toc}{chapter}{Introduction}
-The Mask Aligner is designed to study superconductor / topological insulator interfaces, specifically the creation of Majorana zero modes via superconducting vortices. \cite{bhaskar}
-The study of such interfaces is limited by the difficulty of creating patterned structures on the surfaces of topological insulators without damaging or contaminating the surface in the process. Ideally the creation, as well as analysis of such interfaces would be performed under \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) conditions, in order to preserve a pristine sample surface and avoid chemical reactions such as sample oxidisation. \\
-Commonly used fabrication processes often use solvent based resists, which contaminate the surface with residues and are difficult to perform in situ under UHV conditions. Some methods of 
\ No newline at end of file
+In condensed matter physics, precise fabrication of nanostructures with sharp patterns is paramount for research in various fields like electronics, photonics and quantum computing among others. 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 the small patterns, that are smaller than the coherence length ($<100$ nm) of the superconductor, required to create the vortices need high accuracy. \\
+Atmospheric conditions typically damage 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 often required. \\
+Many substrate patterning methods like \textbf{E}lectron \textbf{B}eam \textbf{L}ithography or \textbf{E}xtreme \linebreak \textbf{U}ltra\textbf{V}iolet \textbf{L}ithography (EUVL) or sometimes (EUV) give the required precision needed for patterning sample at the sub $100$ nm scale,\cite{euv} but require resists, which typically contain 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 and thus may damage the sample further. \\
+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 that require 
+long timescales and expensive equipment. Additionally, many Scanning Probe approaches still require resists and development, leading to the same issues as previously mentioned lithography methods.\\
+A simple and inexpensive approach is given by stencil lithography and \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD), where a stencil (mask) is used to mask off a section of the sample. When the sample is hit with a molecular vapor beam, the masked off areas are protected from the impinging material and stay pristine, while the ones not protected by the stencil built patterned structures. In this method, no resist is required, and the procedure is required to be performed at UHV conditions. Resolutions of sub-$50$ nm have been achieved using stencil lithography.\cite{stencil_resolution} \\
+Stencil lithography however has its own downside. In order to get very high resolution, the mask and the sample have to be very close together as otherwise the aperture of the mask creates a "penumbra", which can affect the final resolution of the pattern on the sample negatively. The simple and often used approach is to simply bring mask and sample into direct contact, ensuring minimal distance. This however is for the case of the creation of many interfaces not possible, since the damage the sample sustains when brought into contact with the mask would damage the condition of the sample. \\
+For this reason the Mask Aligner, the subject of this work, was designed.\cite{Olschewski, Bhaskar} The Mask Aligner is a tool to use capacitive measurement to ensure minimal mask sample distance during PVD, while avoiding full contact with the sample, thus preserving the samples condition. This work concerns the optimization, improvement and analysis of the Mask Aligner and its capabilities, as well as work on the creation of additional electronics and software to drive the Mask Aligners operation. 
\ No newline at end of file
diff --git a/thesis.aux b/thesis.aux
index 4e441c13269f6be57a026596cebd5b16393cd271..a608a837b80ea21c75c7cb88b0c4d3416a259ffc 100644
--- a/thesis.aux
+++ b/thesis.aux
@@ -6,74 +6,29 @@
 \@input{title.aux}
 \@input{preface.aux}
 \@input{chap01.aux}
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+\pgfsyspdfmark {pgfid6}{30232596}{32349237}
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 \@input{chap05.aux}
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 \@input{conclusion.aux}
 \@input{bibliography.aux}
-\@writefile{toc}{\contentsline {chapter}{List of Abbreviations}{86}{chapter*.105}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{List of Abbreviations}{91}{chapter*.93}\protected@file@percent }
 \@input{appendix.aux}
 \@input{acknowledgments.aux}
-\pgfsyspdfmark {pgfid86}{4736286}{43689156}
-\pgfsyspdfmark {pgfid89}{37433768}{43709930}
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-\pgfsyspdfmark {pgfid100}{39282063}{34415180}
+\pgfsyspdfmark {pgfid11}{4736286}{42738884}
+\pgfsyspdfmark {pgfid14}{37433768}{42759658}
+\pgfsyspdfmark {pgfid15}{39282063}{42484932}
+\pgfsyspdfmark {pgfid16}{4736286}{42738884}
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+\pgfsyspdfmark {pgfid21}{4736286}{42738884}
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 \providecommand\NAT@force@numbers{}\NAT@force@numbers
-\gdef \@abspage@last{95}
+\gdef \@abspage@last{101}
diff --git a/thesis.bbl b/thesis.bbl
index 4132a43602ae485e8bd9aed4995b8422e9190a08..5a54c852ceedee4b2eff47d40c1c12689ec4113a 100644
--- a/thesis.bbl
+++ b/thesis.bbl
@@ -21,7 +21,39 @@
 \providecommand{\BIBdecl}{\relax}
 \BIBdecl
 
-\bibitem{bhaskar}
+\bibitem{majorana_zero_modes}
+\BIBentryALTinterwordspacing
+L.~Fu and C.~L. Kane, ``Superconducting proximity effect and majorana fermions
+  at the surface of a topological insulator,'' \emph{Physical Review Letters},
+  vol. 100, no.~9, Mar. 2008. [Online]. Available:
+  \url{http://dx.doi.org/10.1103/PhysRevLett.100.096407}
+\BIBentrySTDinterwordspacing
+
+\bibitem{euv}
+N.~Fu, Y.~Liu, X.~Ma, and Z.~Chen, ``Euv lithography: State-of-the-art
+  review,'' \emph{Journal of Microelectronic Manufacturing}, vol.~2, pp. 1--6,
+  06 2019.
+
+\bibitem{afm_pattern}
+O.~Custance, R.~Pérez, and S.~Morita, ``Atomic force microscopy as a tool for
+  atom manipulation,'' \emph{Nature nanotechnology}, vol.~4, pp. 803--10, 12
+  2009.
+
+\bibitem{stencil_resolution}
+\BIBentryALTinterwordspacing
+T.~Kim and J.~Lee, ``Fabrication of nanoscale stencils through focused ion beam
+  milling and dry transfer of silicon-on-nothing membrane with perforations,''
+  \emph{Microelectronic Engineering}, vol. 289, p. 112172, 2024. [Online].
+  Available:
+  \url{https://www.sciencedirect.com/science/article/pii/S0167931724000418}
+\BIBentrySTDinterwordspacing
+
+\bibitem{Olschewski}
+T.~Olschewski, ``{K}onstruktion und {A}ufbau eines {M}ask {A}ligners für
+  {U}ltrahochvakuum,'' Aachen, 2015, unpublished, but viewable on the Server of
+  the 2nd institute of physics B.
+
+\bibitem{Bhaskar}
 \BIBentryALTinterwordspacing
 P.~Bhaskar, ``{F}abrication and investigation of ultrahigh vacuum compatible
   interfaces of topological insulators and superconductors,'' Aachen, pp. 1
@@ -81,6 +113,19 @@ F.~Forster, ``Aufbau und {T}est eines {M}olekularstrahlverdampfers,'' Aachen,
   2009, unpublished, but viewable on the Server of the 2nd institute of physics
   B.
 
+\bibitem{afm_physics}
+N.~Li, Z.~Li, H.~Ding, S.~Ji, X.~Chen, and Q.-K. Xue, ``An atomic force
+  microscopy study of single-layer fese superconductor,'' \emph{Applied Physics
+  Express}, vol.~6, p. 113101, 11 2013.
+
+\bibitem{afm_bio}
+\BIBentryALTinterwordspacing
+N.~E. Kurland, Z.~Drira, and V.~K. Yadavalli, ``Measurement of nanomechanical
+  properties of biomolecules using atomic force microscopy,'' \emph{Micron},
+  vol.~43, no.~2, pp. 116--128, 2012. [Online]. Available:
+  \url{https://www.sciencedirect.com/science/article/pii/S0968432811001375}
+\BIBentrySTDinterwordspacing
+
 \bibitem{SEM_image_01}
 \BIBentryALTinterwordspacing
 N.~Gleichmann. (2024) {SEM} vs {TEM}. Online; accessed 10-August-2024.
@@ -103,7 +148,7 @@ W.~Zhou and Z.~Wang, \emph{Scanning Microscopy for Nanotechnology. Techniques
 \BIBentryALTinterwordspacing
 M.~Bai, F.~Yang, M.~Luysberg, J.~Feng, A.~Bliesener, G.~Lippertz, A.~A. Taskin,
   J.~Mayer, and Y.~Ando, ``Novel self-epitaxy for inducing superconductivity in
-  the topological insulator \ce{(Bi{1-x}Sb{x})2Te3},'' \emph{Physical Review
+  the topological insulator \ce{(Bi_{1-x}Sb_{x})2Te3},'' \emph{Physical Review
   Materials}, vol.~4, no.~9, Sep. 2020. [Online]. Available:
   \url{http://dx.doi.org/10.1103/PhysRevMaterials.4.094801}
 \BIBentrySTDinterwordspacing
@@ -148,9 +193,4 @@ 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{olschewski}
-T.~Olschewski, ``{K}onstruktion und {A}ufbau eines {M}ask {A}ligners für
-  {U}ltrahochvakuum,'' Aachen, 2015, unpublished, but viewable on the Server of
-  the 2nd institute of physics B.
-
 \end{thebibliography}
diff --git a/thesis.blg b/thesis.blg
index 87d9ff6bd206112215e2be9934d1c07d61bea17f..c715a9b63a8170c7e22419d8a7c637e5c2591cc5 100644
--- a/thesis.blg
+++ b/thesis.blg
@@ -9,19 +9,24 @@ Reallocating 'name_of_file' (item size: 1) to 12 items.
 A level-1 auxiliary file: preface.aux
 Reallocating 'name_of_file' (item size: 1) to 11 items.
 A level-1 auxiliary file: chap01.aux
+Case mismatch error between cite keys bhaskar and Bhaskar
+---line 27 of file chap01.aux
+ : \citation{bhaskar
+ :                  }
+I'm skipping whatever remains of this command
 Reallocating 'name_of_file' (item size: 1) to 11 items.
 A level-1 auxiliary file: chap02.aux
 Reallocating 'name_of_file' (item size: 1) to 11 items.
 A level-1 auxiliary file: chap03.aux
 Reallocating 'name_of_file' (item size: 1) to 11 items.
 A level-1 auxiliary file: chap04.aux
+Case mismatch error between cite keys olschewski and Olschewski
+---line 35 of file chap04.aux
+ : \citation{olschewski
+ :                     }
+I'm skipping whatever remains of this command
 Reallocating 'name_of_file' (item size: 1) to 11 items.
 A level-1 auxiliary file: chap05.aux
-Case mismatch error between cite keys Bhaskar and bhaskar
----line 67 of file chap05.aux
- : \citation{Bhaskar
- :                  }
-I'm skipping whatever remains of this command
 Reallocating 'name_of_file' (item size: 1) to 15 items.
 A level-1 auxiliary file: conclusion.aux
 Reallocating 'name_of_file' (item size: 1) to 17 items.
@@ -56,45 +61,45 @@ Warning--missing publisher in Tungsten_melt
 Warning--missing publisher in SEM_book
 
 Done.
-You've used 20 entries,
+You've used 26 entries,
             4087 wiz_defined-function locations,
-            969 strings with 11579 characters,
-and the built_in function-call counts, 12177 in all, are:
-= -- 979
-> -- 265
-< -- 80
-+ -- 114
-- -- 48
-* -- 560
-:= -- 2013
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diff --git a/thesis.synctex.gz b/thesis.synctex.gz
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diff --git a/thesis.tex b/thesis.tex
index 6508ee79aaaf9fe09b62f610d015e992ef819d7c..959d1805500cd9882dcf4cd5743098631645ef15 100644
--- a/thesis.tex
+++ b/thesis.tex
@@ -158,7 +158,8 @@ FEEG = \textbf{F}ield \textbf{E}mission \textbf{E}lectron \textbf{G}uns\\
 GPU = \textbf{G}raphics \textbf{P}rocessing \textbf{U}nit \\
 LL = \textbf{L}oad \textbf{L}ock \\
 MC = \textbf{M}ain \textbf{C}hamber \\
-Opamp = \textbf{O}perational \textbf{A}mplifier \\
+MZM = \textbf{M}ajorana \textbf{Z}ero \textbf{M}odes \\
+Opamp = \textbf{Op}erational \textbf{Amp}lifier \\
 PMT = \textbf{P}hoto\textbf{m}ultiplier \textbf{T}ube \\
 PVD = \textbf{P}hysical \textbf{V}apor \textbf{D}eposition \\
 RIE = \textbf{R}eactive \textbf{I}on \textbf{E}tching \\
@@ -168,20 +169,6 @@ STM = \textbf{S}canning \textbf{T}unneling \textbf{M}icroscope \\
 UHV = \textbf{U}ltra \textbf{H}igh \textbf{V}accuum \\
 VdW forces = \textbf{V}an \textbf{d}er \textbf{W}aals forces \\
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
 \include{appendix}
 \include{acknowledgments}
 
diff --git a/thesis.toc b/thesis.toc
index 103978ec2cdc67379fdd8597ade50237526facfa..4e092df0a866434edc666feddf241ebc86052d2e 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -1,114 +1,115 @@
 \contentsline {chapter}{Introduction}{3}{chapter*.2}%
-\contentsline {chapter}{\numberline {1}Mask Aligner background}{4}{chapter.1}%
-\contentsline {section}{\numberline {1.1}Electron beam evaporation}{4}{section.1.1}%
-\contentsline {subsection}{\numberline {1.1.1}Mask Aligner lead evaporator}{6}{subsection.1.1.1}%
-\contentsline {section}{\numberline {1.2}Stencil lithography}{7}{section.1.2}%
-\contentsline {subsubsection}{Penumbra}{7}{section*.5}%
-\contentsline {subsubsection}{Tilt induced penumbra}{9}{section*.7}%
-\contentsline {section}{\numberline {1.3}Measurement techniques}{10}{section.1.3}%
-\contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{10}{subsection.1.3.1}%
-\contentsline {subsubsection}{Modes}{11}{section*.10}%
-\contentsline {paragraph}{Contact}{11}{section*.11}%
-\contentsline {paragraph}{Non-Contact}{11}{section*.12}%
-\contentsline {paragraph}{Tapping}{12}{section*.13}%
-\contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{13}{subsection.1.3.2}%
-\contentsline {chapter}{\numberline {2}Mask Aligner}{16}{chapter.2}%
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-\contentsline {subsection}{\numberline {2.2.2}Optical alignment}{25}{subsection.2.2.2}%
-\contentsline {subsection}{\numberline {2.2.3}Approach curves}{26}{subsection.2.2.3}%
-\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{30}{subsection.2.2.4}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.34}%
-\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{32}{subsection.2.2.5}%
-\contentsline {paragraph}{Leakage current}{37}{section*.44}%
-\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.45}%
-\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{37}{subsection.2.2.6}%
-\contentsline {paragraph}{High correlation between capacitance curves}{38}{section*.46}%
-\contentsline {paragraph}{Low correlation between capacitance curves}{38}{section*.48}%
-\contentsline {section}{\numberline {2.3}Mask Aligner operation}{38}{section.2.3}%
-\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{38}{subsection.2.3.1}%
-\contentsline {chapter}{\numberline {3}Electronics}{40}{chapter.3}%
-\contentsline {section}{\numberline {3.1}Slip stick principle}{40}{section.3.1}%
-\contentsline {section}{\numberline {3.2}RHK}{41}{section.3.2}%
-\contentsline {subsection}{\numberline {3.2.1}Overview}{41}{subsection.3.2.1}%
-\contentsline {paragraph}{amplitude}{41}{section*.50}%
-\contentsline {paragraph}{sweep period}{41}{section*.51}%
-\contentsline {paragraph}{time between sweeps}{41}{section*.52}%
-\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{41}{subsection.3.2.2}%
-\contentsline {section}{\numberline {3.3}KIM001}{42}{section.3.3}%
-\contentsline {subsection}{\numberline {3.3.1}Overview}{42}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Pulse shape}{42}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{43}{subsection.3.3.3}%
-\contentsline {section}{\numberline {3.4}Mask Aligner controller "Walker"}{44}{section.3.4}%
-\contentsline {subsection}{\numberline {3.4.1}Overview}{44}{subsection.3.4.1}%
-\contentsline {subsection}{\numberline {3.4.2}Signal generation}{45}{subsection.3.4.2}%
-\contentsline {subsection}{\numberline {3.4.3}Fast flank}{46}{subsection.3.4.3}%
-\contentsline {subsection}{\numberline {3.4.4}Amplification}{47}{subsection.3.4.4}%
-\contentsline {subsection}{\numberline {3.4.5}Parameters}{47}{subsection.3.4.5}%
-\contentsline {paragraph}{Amplitude (amp)}{47}{section*.63}%
-\contentsline {paragraph}{Voltage (volt)}{48}{section*.64}%
-\contentsline {paragraph}{Channel}{48}{section*.65}%
-\contentsline {paragraph}{Max Step}{48}{section*.66}%
-\contentsline {paragraph}{Polarity}{48}{section*.67}%
-\contentsline {subsection}{\numberline {3.4.6}Measured pulse shape}{48}{subsection.3.4.6}%
-\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{50}{subsection.3.4.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{51}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{51}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{51}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}Adding components}{51}{subsection.4.2.1}%
-\contentsline {subsection}{\numberline {4.2.2}Soldering}{52}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering anchors}{52}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo re-gluing}{55}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 motor}{57}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{58}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{61}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{62}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final test}{63}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{65}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{65}{section.5.1}%
-\contentsline {section}{\numberline {5.2}Contamination}{67}{section.5.2}%
-\contentsline {section}{\numberline {5.3}Penumbra}{68}{section.5.3}%
-\contentsline {section}{\numberline {5.4}Tilt}{74}{section.5.4}%
-\contentsline {section}{\numberline {5.5}Simulation}{76}{section.5.5}%
-\contentsline {paragraph}{Software improvements}{81}{section*.102}%
-\contentsline {chapter}{Conclusions and Outlook}{83}{chapter*.103}%
-\contentsline {chapter}{Bibliography}{84}{chapter*.104}%
-\contentsline {chapter}{List of Abbreviations}{86}{chapter*.105}%
-\contentsline {chapter}{\numberline {6}Appendix}{i}{chapter.6}%
-\contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.6.1}%
-\contentsline {section}{\numberline {B}Walker circuit diagrams}{i}{section.6.2}%
-\contentsline {section}{\numberline {C}New driver electronics}{v}{section.6.3}%
-\contentsline {paragraph}{pulse?}{v}{section*.106}%
-\contentsline {paragraph}{pol x}{v}{section*.107}%
-\contentsline {paragraph}{amp x}{v}{section*.108}%
-\contentsline {paragraph}{volt x}{v}{section*.109}%
-\contentsline {paragraph}{channel x}{v}{section*.110}%
-\contentsline {paragraph}{maxmstep x}{v}{section*.111}%
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-\contentsline {paragraph}{mstep x}{v}{section*.113}%
-\contentsline {paragraph}{cancel}{vi}{section*.114}%
-\contentsline {paragraph}{help}{vi}{section*.115}%
-\contentsline {section}{\numberline {D}Raycast Simulation}{vi}{section.6.4}%
-\contentsline {paragraph}{radius\_1}{vi}{section*.116}%
-\contentsline {paragraph}{angle}{vi}{section*.117}%
-\contentsline {paragraph}{radius\_mask}{vi}{section*.118}%
-\contentsline {paragraph}{distance\_circle\_mask}{vi}{section*.119}%
-\contentsline {paragraph}{distance\_sample}{vi}{section*.120}%
-\contentsline {paragraph}{rays\_per\_frame}{vi}{section*.121}%
-\contentsline {paragraph}{running\_time}{vi}{section*.122}%
-\contentsline {paragraph}{deposition\_gain}{vi}{section*.123}%
-\contentsline {paragraph}{penalize\_deposition}{vi}{section*.124}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vi}{section*.125}%
-\contentsline {paragraph}{oscillation\_period}{vi}{section*.126}%
-\contentsline {paragraph}{delay\_oscill\_time}{vii}{section*.127}%
-\contentsline {paragraph}{save\_in\_progress\_images}{vii}{section*.128}%
-\contentsline {paragraph}{save\_intervall}{vii}{section*.129}%
-\contentsline {paragraph}{oscillation\_dir}{vii}{section*.130}%
-\contentsline {paragraph}{oscillation\_rot\_s}{vii}{section*.131}%
-\contentsline {paragraph}{oscillation\_rot\_e}{vii}{section*.132}%
-\contentsline {paragraph}{random\_seed}{vii}{section*.133}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{vii}{section*.134}%
-\contentsline {paragraph}{resolution}{vii}{section*.135}%
-\contentsline {paragraph}{path}{vii}{section*.136}%
-\contentsline {chapter}{Acknowledgments}{viii}{chapter*.137}%
+\contentsline {chapter}{\numberline {1}Mask Aligner background}{5}{chapter.1}%
+\contentsline {section}{\numberline {1.1}Electron beam evaporation}{5}{section.1.1}%
+\contentsline {subsection}{\numberline {1.1.1}Mask Aligner lead evaporator}{7}{subsection.1.1.1}%
+\contentsline {section}{\numberline {1.2}Stencil lithography}{8}{section.1.2}%
+\contentsline {subsubsection}{Penumbra}{9}{section*.5}%
+\contentsline {subsubsection}{Tilt induced penumbra}{11}{section*.7}%
+\contentsline {section}{\numberline {1.3}Measurement techniques}{12}{section.1.3}%
+\contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{12}{subsection.1.3.1}%
+\contentsline {subsubsection}{Modes}{13}{section*.10}%
+\contentsline {paragraph}{Contact}{13}{section*.11}%
+\contentsline {paragraph}{Non-Contact}{13}{section*.12}%
+\contentsline {paragraph}{Tapping}{14}{section*.13}%
+\contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{15}{subsection.1.3.2}%
+\contentsline {chapter}{\numberline {2}Mask Aligner}{17}{chapter.2}%
+\contentsline {section}{\numberline {2.1}Molecular beam evaporation chamber}{19}{section.2.1}%
+\contentsline {section}{\numberline {2.2}Shadow mask alignment}{20}{section.2.2}%
+\contentsline {subsection}{\numberline {2.2.1}Motor calibration}{20}{subsection.2.2.1}%
+\contentsline {subsection}{\numberline {2.2.2}Optical alignment}{26}{subsection.2.2.2}%
+\contentsline {subsection}{\numberline {2.2.3}Approach curves}{28}{subsection.2.2.3}%
+\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{32}{subsection.2.2.4}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{32}{section*.30}%
+\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{34}{subsection.2.2.5}%
+\contentsline {paragraph}{Leakage current}{39}{section*.38}%
+\contentsline {paragraph}{Improved gold pin fitting}{39}{section*.39}%
+\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{39}{subsection.2.2.6}%
+\contentsline {paragraph}{High correlation between capacitance curves}{40}{section*.40}%
+\contentsline {paragraph}{Low correlation between capacitance curves}{40}{section*.41}%
+\contentsline {section}{\numberline {2.3}Mask Aligner operation}{40}{section.2.3}%
+\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{40}{subsection.2.3.1}%
+\contentsline {chapter}{\numberline {3}Electronics}{42}{chapter.3}%
+\contentsline {section}{\numberline {3.1}Slip stick principle}{42}{section.3.1}%
+\contentsline {section}{\numberline {3.2}RHK}{43}{section.3.2}%
+\contentsline {subsection}{\numberline {3.2.1}Overview}{43}{subsection.3.2.1}%
+\contentsline {paragraph}{amplitude}{43}{section*.43}%
+\contentsline {paragraph}{sweep period}{43}{section*.44}%
+\contentsline {paragraph}{time between sweeps}{43}{section*.45}%
+\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{43}{subsection.3.2.2}%
+\contentsline {section}{\numberline {3.3}KIM001}{44}{section.3.3}%
+\contentsline {subsection}{\numberline {3.3.1}Overview}{44}{subsection.3.3.1}%
+\contentsline {subsection}{\numberline {3.3.2}Pulse shape}{44}{subsection.3.3.2}%
+\contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{45}{subsection.3.3.3}%
+\contentsline {section}{\numberline {3.4}Mask Aligner controller "Walker"}{46}{section.3.4}%
+\contentsline {subsection}{\numberline {3.4.1}Overview}{46}{subsection.3.4.1}%
+\contentsline {subsection}{\numberline {3.4.2}Signal generation}{47}{subsection.3.4.2}%
+\contentsline {subsection}{\numberline {3.4.3}Fast flank}{48}{subsection.3.4.3}%
+\contentsline {subsection}{\numberline {3.4.4}Amplification}{49}{subsection.3.4.4}%
+\contentsline {subsection}{\numberline {3.4.5}Parameters}{49}{subsection.3.4.5}%
+\contentsline {paragraph}{Amplitude (amp)}{49}{section*.52}%
+\contentsline {paragraph}{Voltage (volt)}{50}{section*.53}%
+\contentsline {paragraph}{Channel}{50}{section*.54}%
+\contentsline {paragraph}{Max Step}{50}{section*.55}%
+\contentsline {paragraph}{Polarity}{50}{section*.56}%
+\contentsline {subsection}{\numberline {3.4.6}Measured pulse shape}{50}{subsection.3.4.6}%
+\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{52}{subsection.3.4.7}%
+\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{54}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Overview}{54}{section.4.1}%
+\contentsline {section}{\numberline {4.2}General UHV device preparation}{54}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}Adding components}{54}{subsection.4.2.1}%
+\contentsline {subsection}{\numberline {4.2.2}Soldering}{55}{subsection.4.2.2}%
+\contentsline {section}{\numberline {4.3}Soldering anchors}{55}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo re-gluing}{58}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 motor}{60}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{61}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{64}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{65}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final test}{66}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{68}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{68}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Contamination}{70}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Penumbra}{71}{section.5.3}%
+\contentsline {section}{\numberline {5.4}Tilt}{77}{section.5.4}%
+\contentsline {section}{\numberline {5.5}Simulation}{79}{section.5.5}%
+\contentsline {paragraph}{Software improvements}{84}{section*.90}%
+\contentsline {chapter}{Conclusions and Outlook}{86}{chapter*.91}%
+\contentsline {chapter}{Bibliography}{88}{chapter*.92}%
+\contentsline {chapter}{List of Abbreviations}{91}{chapter*.93}%
+\contentsline {chapter}{Appendix}{i}{chapter*.94}%
+\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*.97}%
+\contentsline {paragraph}{pol x}{vi}{section*.98}%
+\contentsline {paragraph}{amp x}{vi}{section*.99}%
+\contentsline {paragraph}{volt x}{vi}{section*.100}%
+\contentsline {paragraph}{channel x}{vi}{section*.101}%
+\contentsline {paragraph}{maxmstep x}{vi}{section*.102}%
+\contentsline {paragraph}{step x}{vi}{section*.103}%
+\contentsline {paragraph}{mstep x}{vi}{section*.104}%
+\contentsline {paragraph}{cancel}{vii}{section*.105}%
+\contentsline {paragraph}{help}{vii}{section*.106}%
+\contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
+\contentsline {paragraph}{radius\_1}{vii}{section*.107}%
+\contentsline {paragraph}{angle}{vii}{section*.108}%
+\contentsline {paragraph}{radius\_mask}{vii}{section*.109}%
+\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.110}%
+\contentsline {paragraph}{distance\_sample}{vii}{section*.111}%
+\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.112}%
+\contentsline {paragraph}{running\_time}{vii}{section*.113}%
+\contentsline {paragraph}{deposition\_gain}{vii}{section*.114}%
+\contentsline {paragraph}{penalize\_deposition}{vii}{section*.115}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.116}%
+\contentsline {paragraph}{oscillation\_period}{vii}{section*.117}%
+\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.118}%
+\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.119}%
+\contentsline {paragraph}{save\_intervall}{viii}{section*.120}%
+\contentsline {paragraph}{oscillation\_dir}{viii}{section*.121}%
+\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.122}%
+\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.123}%
+\contentsline {paragraph}{random\_seed}{viii}{section*.124}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.125}%
+\contentsline {paragraph}{resolution}{viii}{section*.126}%
+\contentsline {paragraph}{path}{viii}{section*.127}%
+\contentsline {chapter}{Acknowledgments}{ix}{chapter*.128}%