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diff --git a/appendix.tex b/appendix.tex
index 5aca1408481118c52e8835467cbbc0366429dfb9..5e385897c24b077b91cceea187bcefe043970d11 100644
--- a/appendix.tex
+++ b/appendix.tex
@@ -1,7 +1,13 @@
-\section{LockIn Amplifier Settings}
+\chapter*{Appendix}
+\pagenumbering{roman}
+%\sectionnumbering{roman} 
+\setcounter{section}{0}
+\renewcommand{\thesection}{\Alph{section}}
 
+\section{LockIn Amplifier Settings}\label{sec:appendix_lockIn}
 
-\section{New Driver Electronics}
+\section{New Driver Electronics}\label{sec:appendix_walker}
+The commands need to be sent to the new driver electronics using a serial interface with a baudrate of $115200$ and either new line or carriage return as line end characters. The easiest way to do this is via the Serial Monitor of the Arduino IDE.
 The new driver electronics have the following commands (as of 13.08.24) that can set the driving parameters:
 
 \paragraph{pulse?}
@@ -27,7 +33,7 @@ Displays a list of all commands along with short explanations on how to use them
 
 Any of the parameters that can set one of the values can be queried for their current value by using command? (for example pol?). 
 
-\section{Raycast Simulation}
+\section{Raycast Simulation}\label{sec:appendix_raycast}
 The raycasting simulation takes the following parameters:
 
 \paragraph{radius\_1}
diff --git a/bibliography.aux b/bibliography.aux
index 27e5aa109478ed228f394725a3cc05a8cd387ce1..71c33e1cfdc63ec672964537046b9cc8ae45cb83 100644
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-\bibcite{SEM_image_02}{{7}{}{{}}{{}}}
-\bibcite{SEM_book}{{8}{}{{}}{{}}}
-\bibcite{Mask_Aligner}{{9}{}{{}}{{}}}
-\bibcite{SiN_dielectric}{{10}{}{{}}{{}}}
-\bibcite{Beeker}{{11}{}{{}}{{}}}
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+\bibcite{Vapor_depo_princ}{{5}{}{{}}{{}}}
+\bibcite{florian_forster}{{6}{}{{}}{{}}}
+\bibcite{SEM_image_01}{{7}{}{{}}{{}}}
+\bibcite{SEM_image_02}{{8}{}{{}}{{}}}
+\bibcite{SEM_book}{{9}{}{{}}{{}}}
+\bibcite{Mask_Aligner}{{10}{}{{}}{{}}}
+\bibcite{SiN_dielectric}{{11}{}{{}}{{}}}
+\bibcite{Beeker}{{12}{}{{}}{{}}}
+\bibcite{switch_datasheet}{{13}{}{{}}{{}}}
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diff --git a/bibliography.bib b/bibliography.bib
index 8f295d18863c2cc109899ff7a3f4042e4a0fdbb4..c9f7c4ccfaba1f8acddba5a84f6075217b17cda2 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -39,7 +39,7 @@ doi = {10.1007/978-0-387-39620-0}
 }
 
 @book{AFM_book,
-  title={Atomic Force Microscopy},
+  title={{A}tomic {F}orce {M}icroscopy},
   author={Eaton, P. and West, P.},
   isbn={9780199570454},
   lccn={2010280406},
@@ -84,7 +84,7 @@ author       = {Bhaskar, Priyamvada},
 
 @thesis{Olschewski,
 	author = {Olschewski, Tim},
-	title = {Konstruktion und Aufbau eines Mask Aligners für Ultrahochvakuum},
+	title = {{K}onstruktion und {A}ufbau eines {M}ask {A}ligners für {U}ltrahochvakuum},
 	school       = {RWTH Aachen University},
 	type         = {Masters},
     address      = {Aachen},
@@ -129,7 +129,7 @@ doi = {10.1007/978-1-84628-669-8}
 }
 
 @book{Tungsten_evap,
-title = {Handbook of Chemical Compound Data for Process Safety},
+title = {{H}andbook of {C}hemical {C}ompound {D}ata for {P}rocess {S}afety},
 editor = {Carl L. Yaws},
 publisher = {Gulf Professional Publishing},
 address = {Houston},
@@ -142,7 +142,7 @@ url = {https://www.sciencedirect.com/science/article/pii/B9780884153818500152}
 
 @online{SEM_image_01,
   author = {Nicole Gleichmann},
-  title = {SEM vs TEM},
+  title = {{SEM} vs {TEM}},
   year = 2024,
   url = {https://www.technologynetworks.com/analysis/articles/sem-vs-tem-331262},
   urldate = {2024-01-24}
@@ -154,4 +154,42 @@ url = {https://www.sciencedirect.com/science/article/pii/B9780884153818500152}
   year = 2020,
   url = {https://commons.wikimedia.org/wiki/File:Electron-matter_interaction_volume_and_various_types_of_signal_generated_-_v2.svg},
   urldate = {2020-08-28}
-}
\ No newline at end of file
+}
+
+@article{tungsten_evaporation,
+  title={{T}he {E}lectron {B}eam {M}elting of {T}ungsten (The Electron Beam Melting of Refractory Metals (VIII))},
+  author={Tetsuya Takaai},
+  journal={Journal of the Japan Institute of Metals},
+  volume={30},
+  number={11},
+  pages={1027-1031},
+  year={1966},
+  doi={10.2320/jinstmet1952.30.11_1027}
+}
+
+@article{sputter_samage,
+title = {Sputtered transparent electrodes for optoelectronic devices: Induced damage and mitigation strategies},
+journal = {Matter},
+volume = {4},
+number = {11},
+pages = {3549-3584},
+year = {2021},
+issn = {2590-2385},
+doi = {https://doi.org/10.1016/j.matt.2021.09.021},
+url = {https://www.sciencedirect.com/science/article/pii/S2590238521004665},
+author = {Erkan Aydin and Cesur Altinkaya and Yury Smirnov and Muhammad A. Yaqin and Kassio P.S. Zanoni and Abhyuday Paliwal and Yuliar Firdaus and Thomas G. Allen and Thomas D. Anthopoulos and Henk J. Bolink and Monica Morales-Masis and Stefaan {De Wolf}},
+keywords = {sputtering, buffer layers, optoelectronic devices, perovskite/organic/silicon/chalcopyrite/chalcogenide/tandem solar cells, light-emitting diodes}
+}
+
+@article{CASINO,
+   title={Continuum variational and diffusion quantum Monte Carlo calculations},
+   volume={22},
+   ISSN={1361-648X},
+   url={http://dx.doi.org/10.1088/0953-8984/22/2/023201},
+   DOI={10.1088/0953-8984/22/2/023201},
+   number={2},
+   journal={Journal of Physics: Condensed Matter},
+   publisher={IOP Publishing},
+   author={Needs, R J and Towler, M D and Drummond, N D and López Ríos, P},
+   year={2009},
+   month=dec, pages={023201} }
diff --git a/bibliography.log b/bibliography.log
index f6f0babb8e686dc2d3bce2d74b4a04436aa2c800..edf21c73c5abf5c6c52b9f0354884eb9511c1289 100644
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-This is pdfTeX, Version 3.141592653-2.6-1.40.24 (MiKTeX 22.7) (preloaded format=pdflatex 2024.7.28)  13 AUG 2024 17:19
+This is pdfTeX, Version 3.141592653-2.6-1.40.24 (MiKTeX 22.7) (preloaded format=pdflatex 2024.7.28)  20 AUG 2024 14:30
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 \@setckpt{chap01}{
 \setcounter{page}{17}
@@ -100,7 +101,7 @@
 \setcounter{subfigure}{2}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{13}
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diff --git a/chap01.tex b/chap01.tex
index 027792429418158b2a7274ee7adf9ac183288e7d..ef03eef1bb654d985973c67870b49fe14bf64878 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -1,7 +1,7 @@
 % !TeX spellcheck = <en-US>
 Page left unintentionally blank
 \todo{This section needs citations}
-\chapter{Mask Aligner Background}
+\chapter{Mask Aligner background} \label{ch:}
 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}
@@ -30,18 +30,18 @@ The deposition rate of the evaporator can be measured using a molecular flux mon
 
 where $N$ is the number of gas molecules deposited, $A$ is the surface area, $t$ is time, $\alpha$ is the sticking parameter, $p$ is the gas pressure, $m$ is the mass of a single particle, $k_B$ is the Boltzmann constant and $T$ is the temperature. When the sticking coefficient of the material substrate is known the vapor pressure can be obtained from the particle flux measured per area. With this the total deposition rate can then be estimated. This parameter can be obtained via calibration measurement, where the particle flux is kept constant and the film thickness is measured after a certain time.
 
-Some of the advantages that e-beam evaporation has over other techniques such as thermal evaporation or sputtering \cite{} are that due to the high energy localized heating, materials, which require high temperature to reach their boiling point, like tungsten ($5828$ K)\cite{Tungsten_evap} or niobium ($5017$ K)\cite{Tungsten_evap} can be evaporated using e-beam evaporation. The deposition rate can also be controlled with high precision using the current applied to create the electron beam. \cite{Vapor_depo_princ} \\
-The high energy electron beam is directed directly at the source material and is unlikely to interact with the samples surface, unlike for example sputtering, where the high energy particles depositing the material can interact and either implant unwanted material or dislodge substrate material damaging the substrate surface. \cite{todo}\todo{citation}
+Some of the advantages that e-beam evaporation has over other techniques such as thermal evaporation or sputtering \cite{} are that due to the high energy localized heating, materials, which require high temperature to reach their boiling point, like tungsten ($5828$ K)\cite{Tungsten_evap} or niobium ($5017$ K)\cite{Tungsten_evap} can be evaporated using e-beam evaporation.\cite{tungsten_evaporation} The deposition rate can also be controlled with high precision using the current applied to create the electron beam. \cite{Vapor_depo_princ} \\
+The high energy electron beam is directed directly at the source material and is unlikely to interact with the samples surface, unlike for example sputtering, where the high energy particles depositing the material can interact and either implant unwanted material or dislodge substrate material damaging the substrate surface. \cite{sputter_damage}
 
-E-beam evaporation offers more control over deposition rate than thermal evaporation, and it is easier to evaporate material which require high evaporation temperatures with e-beam evaporation. \todo{citation}
+E-beam evaporation offers more control over deposition rate than thermal evaporation, and it is easier to evaporate material which require high evaporation temperatures with e-beam evaporation. \cite{Vapor_depo_princ}
 
 In order to control the length 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}
+\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, as is usual, is made from tungsten and 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. Additionally the system can be heated with radiative heat from the filament. This is also used to degas the system, when no evaporation is taking place. Surrounding the heating elements is a cooper cylinder, that functions as a heat sink for the system. The heatsink needs to be water cooled to prevent damage to the evaporator. In order to see if the cooling failed or too much current/voltage is applied to the controls, 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 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. \\
 
-\section{Stencil Lithography}
+\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, expect 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. \\
 Stencil Lithography can also be used for etching where patterns are cut into the substrates surface, using reactive ion etching, in the places where the mask has been patterned, while the rest of the sample remains protected. \\
 Stencil lithography requires no resist, heat or other chemical treatment and thus protects the substrate from possible contamination or damage that chemicals or heat can cause. Masks can also be reused many times and the process is relatively simple to use and fast in execution. In stencil lithography the fabrication speed is only limited by the possible deposition rate of the depositon material and the complexity of applying the mask to the sample and can be on the order of minutes.
@@ -71,7 +71,7 @@ The width of the penumbra $p$ is determined by the distance of the beam source t
 
 Usually when using stencil lithography it is desirable for the penumbra to be as small as possible. For the use case proposed for the Mask Aligner, a penumbra of $< 100$ nm is required.\cite{bhaskar} For this reason one tries to minimize the distance between mask and sample, as a certain size is required for the crucible to be able to evaporate lead efficiently and the distance to the beam source cannot be increased indefinitely since the amount of material that gets deposited on the sample falls off with the square of the distance to the sample. For our setup this quantities are approximately as follows: $b=6$ mm, $l=25$ cm. For a desired penumbra of $< 100$ nm a distance between mask and sample of at most $d=4$ $\mu$m is needed.\\
 
-\subsubsection{Tilt induced Penumbra}
+\subsubsection{Tilt induced penumbra}
 Previously the model for the penumbra assumed perfect alignment between mask and sample, but potentially large distance, but what can additionally happen is that the distance on one side of the mask is larger than that on the other side of the mask. 
 
 The mask and the sample also have to be kept parallel as a tilt would result in a large distance on one side $d_2$ even when the other is much a much closer $d_1$, which results in $2$ different penumbral lengths $p_1$ and $p_2$ along the major axis of the tilt an illustration of this can be seen in \ref{fig:penumbra_explanation_tilt_2d}. Along any other axis of the tilt other than the one where the tilt angle is largest however this will result in two new distances $d_1 '> d_1$ and $d_2 '< d_2$. This can be continued along a half circle until $d_1 ' = d_2 '$ where we have the situation similar to the aligned case again. Overall this results in a penumbra, which follows a "half-moon" shape. An illustration of this can be seen in \ref{fig:penumbra_explanation_tilt_3d}.\\
@@ -104,7 +104,7 @@ To analyse the penumbra, for a circular in this case since there are many differ
 
 However since the samples used for lithography are often very fragile and prone to contamination, hence directly contacting the sample with the mask should be avoided at all cost, while keeping the distance and tilt between the sample and the mask minimal.
 
-\section{Measurement Techniques}
+\section{Measurement techniques}
 For analyzing samples, various techniques can be used. In the following, the techniques used in this thesis and their working principles will be explained.
 \subsection{Atomic Force Microscopy}
 Atomic Force Microscopy (AFM) is a microscopy technique that uses the forces on a cantilever that appear near a sample's surface to measure a sample's height characteristics.
@@ -137,7 +137,7 @@ Tapping mode is a hybrid of both contact and non-contact modes. It is also somet
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.7\linewidth]{img/Plots/AFMPotential.pdf}
-    \caption{Schematic diagram of the Lennart Jones potential governing the interaction between tip and sample in an AFM. The 3 AFM Modes are marked \textcolor{tab_green}{contact}, \textcolor{tab_blue}{tapping} and \textcolor{tab_red}{non-contact} these regions are approximate. Units on both axis are arbitrary.}
+    \caption{Schematic diagram of the Lennart Jones potential governing the interaction between tip and sample in an AFM. The 3 AFM Modes are marked \textcolor{tab_green}{contact}, \textcolor{tab_blue}{tapping} and \textcolor{tab_red}{non-contact} these regions are approximate. Units on both axes are arbitrary.}
     \label{fig:afm_potential}
 \end{figure}
 
@@ -148,7 +148,7 @@ AFMs provide high resolution topographical images at the nanometer scale and all
 
 \subsection{Scanning Electron Microscopy} 
 \todo{Image of SEM Setup}
-A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope 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 with 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.
+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 with 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.
 
 \begin{figure}[H]
     \centering
@@ -162,17 +162,17 @@ A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope is a microscope in whi
 	\caption{}
 	\label{fig:sem_setup_interaction}
 	\end{subfigure}
-    \caption{The beam path for an SEM (\subref{fig:sem_setup_beam}). Multiple sets of magnetic lenses are used to focus the electron beam accurately. Accurate focussing of the electron beam is one of the major difficulties of SEM design and measurement uncertainty is usually dominated by optical artifacting from beam focus. The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the backscattering and X-ray detector. A diagram showing electron matter interactions (\subref{fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from \cite{SEM_image_01} and \cite{SEM_image_02}.}
+    \caption{The beam path for an SEM (\subref{fig:sem_setup_beam}). Multiple sets of magnetic lenses are used to focus the electron beam accurately. Accurate focusing of the electron beam is one of the major difficulties of SEM design and measurement uncertainty is usually dominated by optical artifacting from beam focus. The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the backscattering and X-ray detector. A diagram showing electron matter interactions (\subref{fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from \cite{SEM_image_01} and \cite{SEM_image_02}.}
     \label{fig:sem_setup}
 \end{figure}
 \todo{Placeholder}
 
-The electron beam of an SEM are created using an electron gun. The electron guns used are usually tungsten electrons for comparatively low cost and good reliability. Anoother possibility is using \textbf{f}ield \textbf{e}mission \textbf{e}lectron \textbf{g}uns.\cite{SEM_book} The beam emitted from the electron gun still has to large spread to be used for SEM imaging for this reason the beam must be focused using electron lenses. In principle electron lenses can use either electrostatic or magnetic fields, but in practice only magnetic lenses are used since they provide smaller lensing abberations. Multiple sets of lenses are used to magnetically focus the beam onto the sample.\cite{SEM_book} Due to the use of electromagnets for lensing the parameters can be controlled relatively easily. The different lenses are used to focus the image partially manually by the user to create a sharp and stable image.
+The electron beam of an SEM are created using an electron gun. The electron guns used are usually tungsten electrons for comparatively low cost and good reliability. Another possibility is using \textbf{f}ield \textbf{e}mission \textbf{e}lectron \textbf{g}uns.\cite{SEM_book} The beam emitted from the electron gun still has to large spread to be used for SEM imaging for this reason the beam must be focused using electron lenses. In principle electron lenses can use either electrostatic or magnetic fields, but in practice only magnetic lenses are used since they provide smaller lensing abberations. Multiple sets of lenses are used to magnetically focus the beam onto the sample.\cite{SEM_book} Due to the use of electromagnets for lensing the parameters can be controlled relatively easily. The different lenses are used to focus the image partially manually by the user to create a sharp and stable image.
 
 The main matter interaction that is measured in an SEM is the is inelastic scattering of the beam electron with a sample electron. The sample electron is ejected at a different angle from the incoming beam electron. This ejected electron is called secondary electron.\cite{SEM_book} The secondary electron are ejected from the sample at relatively low energy of $<50$ eV and can thus be attracted with a positive bias voltage ($>10$ kV) applied to a scintillator, which then converts the attracted electrons into light photons, which are then detected via \textbf{P}hoto \textbf{M}ultiplier \textbf{T}ube (PMT). Such a detector is called \textbf{E}verhart–\textbf{T}hornley detector (ET) detector.\cite{SEM_book} Using these detectors it is now possible to detect the amount of secondary electrons emitted at the current beam location. This amount is based on the surfaces topography and thus by measuring the voltage given at the PMT a topographical image of the sample can be obtained. Other types of electron are also emitted in beam sample interaction and can be detected in an SEM setup, but for this thesis only the secondary electrons are relevant.\\
 
 SEMs give high contrast large area images with good spatial resolution and were thus used in this thesis to initially locate evaporated fields on silicon samples, but SEM imaging comes with some downsides which is why they are not sufficient to fully characterize the samples in this thesis.
-On insulating or semi conducting 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 focussing 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.\todo{Maybe write cool things SEMs have accomplished}
+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.\todo{Maybe write cool things SEMs have accomplished}
 
 \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
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--- a/chap02.aux
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+\newlabel{eq:plate_capacitor}{{2.1}{28}{Approach curves}{equation.2.2.1}{}}
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 \citation{Beeker}
-\newlabel{eq:cap_slope_change}{{2.3}{30}{Approach Curves}{equation.2.2.3}{}}
+\newlabel{eq:cap_slope_change}{{2.3}{30}{Approach curves}{equation.2.2.3}{}}
 \citation{Beeker}
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 \@setckpt{chap02}{
 \setcounter{page}{41}
 \setcounter{equation}{4}
@@ -147,7 +147,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{35}
+\setcounter{@todonotes@numberoftodonotes}{33}
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diff --git a/chap02.tex b/chap02.tex
index e1ac8478178802a7d0219f69850f592205b1e0b1..cdda3f63218a7b1f6f4b7f0f2845aa009e68d584 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -39,7 +39,7 @@ The motor module of the Mask Aligner consists of $3$ motors of similar build. Th
 underside of the mask frame. The pivot points created by the $3$ motors neodym magnet connections to the mask frame approximately build an equilateral triangle with the mask position in the middle. When a motors sapphire prism now moves up the mask frame is tilted on the axis defined by the other two motor pivot points and the side of the mask moves closer to the sample. With this the tilt of the mask frame and thus the tilt of the mask can be controlled with precision in the order of $\approx 50$ nm steps. \\
 When moving the sapphire prism up the mask "approaches" the sample, due to this the movement direction is labeled approach, while the opposite is called retract. Often the direction is also specified by mathematical sign, where $-$ specifies the approach direction, while $+$ specifies retract.\\
 
-\section{Molecular Beam Evaporation Chamber}
+\section{Molecular beam evaporation chamber}
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.9\linewidth]{img/MaskAlignerChamber.pdf}
@@ -61,13 +61,12 @@ Another device, a gold evaporator, is connected to the vacuum system of the Mask
 \ref{fig:mask_aligner_chamber}. 
 \cite{Mask_Aligner}
 
-\section{Shadow Mask Alignment}
+\section{Shadow mask alignment}
 \subsection{Calibration}
 In order to use the Mask Aligner the different step sizes, i.e. the amount each
-motor moves when one pulse is applied, has to be measured. This should be done
-when performing repairs outside UHV, before putting the Mask Aligner into UHV in
+motor moves when one pulse is applied, has to be measured. This should be done in
 order to make sure all motors run with similar step sizes and inside UHV to
-determine the final step size for approach curves, which is used to determine a value for the distance of mask and sample, when the distance is small enough that it can no longer be optically determined.\\
+determine the final step size for approach curves, since in UHV the contribution to the step sizer from friction is increased. The calibration is used to determine a value for the distance of mask and sample, when the distance is small enough that it can no longer be optically determined.\\
 In order to make sure the motors can all give similar step sizes, there are 3
 screws, one on each motor's front plate, that can control the amount of force
 the front plate applies to the prism and thus the amount of friction the piezo
@@ -218,7 +217,7 @@ simultaneously. This should allow for corrections should the driving behavior
 of any of the motors change or if compensation for potential deviations in
 step size is needed.\\
 
-\subsection{Optical Alignment}
+\subsection{Optical alignment}
 To align mask and sample it is first necessary to get the sample aligned and
 within a distance of at least $50$ $\mu$m optically. A good optical alignment is
 necessary since at large distances $> 50$ $\mu$m the capacitance sensors give
@@ -292,7 +291,7 @@ possible optical accuracy.
 \end{figure}\todo{Placeholder}
 
 
-\subsection{Approach Curves}
+\subsection{Approach curves}
 
 \begin{figure}[H]
     \centering
@@ -699,9 +698,9 @@ curve and can use this to determine how close the mask to sample distance is.
 This is the easier and safer of the two scenarios, but it requires a good mask
 holder, which we currently do not have.\todo{Check}
 
-\section{Mask Aligner Operation}
+\section{Mask Aligner operation}
 
-\subsection{Sample Preparation}
+\subsection{Sample preparation}
 In order to get a clean interface, when evaporating a superconductor on any
 material a clean and contamination free sample surface is required. In this thesis only \ce{Si} samples were used. To clean a \ce{Si} sample the following steps have to be taken:
 
diff --git a/chap03.aux b/chap03.aux
index 62601d2e2348e1c6f47476d067a8bdc5db70f757..5ee28c4d1da57cc1dc3613feffc64d57973108ba 100644
--- a/chap03.aux
+++ b/chap03.aux
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+\newlabel{fig:kim0001_voltage_behaviour}{{3.6}{45}{4 Plots showing the Voltage of the retract steps of the KIM0001 after setting the Voltage to 125 on the device, after 1 step (a), ~50 steps (b), ~120 steps (c) and ~200 steps (d). The voltage spikes beyond the desired voltage at the start and after 200 steps settles on a voltage of ~118 V. Also noticeable is an inconsistency in peak shape in (c) as compared to the others. No settings were changed during the recording of this data}{figure.caption.85}{}}
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+\newlabel{fig:bessel_filter}{{3.8}{47}{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 our electronics and is simply for illustration purposes. After filtering, the signal appears very smooth and without sharp steps}{figure.caption.93}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {3.11}{\ignorespaces 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). The fast flank of the walker is more stable showing no signs of peaking, and it saturates at the desired voltage of 80 V, while the RHK signal over/undershoots the desired voltage, by about 20 V, before going back down/up.}}{51}{figure.caption.106}\protected@file@percent }
+\newlabel{fig:walker_pulse_shape_fast}{{3.11}{51}{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). The fast flank of the walker is more stable showing no signs of peaking, and it saturates at the desired voltage of 80 V, while the RHK signal over/undershoots the desired voltage, by about 20 V, before going back down/up}{figure.caption.106}{}}
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 \@writefile{toc}{\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{51}{subsection.3.4.7}\protected@file@percent }
 \@setckpt{chap03}{
 \setcounter{page}{52}
@@ -92,7 +92,7 @@
 \setcounter{subfigure}{2}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{48}
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diff --git a/chap03.tex b/chap03.tex
index 4e33e746372dcdd9956419107827fa3b21e6d841..dc05768b80b958410a6758642ceb503d1f364a00 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -1,6 +1,6 @@
 % !TeX spellcheck = <en-US>
 \chapter{Electronics}
-\section{Slip Stick Principle}
+\section{Slip stick principle}
 In order to control the movement of the mask stage using the mask aligner, 3 motors of 6 piezo stack made of 4 piezo crystals each are used. Piezo crystals expand/contract upon being supplied with a voltage. In order for the piezo crystals to now move the stage, a sapphire prism is set up in between the 6 piezo stacks. When one now applies a voltage to the piezo stacks, the prism is moved by the stacks when the piezo crystals  expand/contract. For this to result in a net movement of the prism, the slip stick principle is applied. The principle works as follows. First a slowly rising pulse is applied to the piezo moving the prism along with the piezo. This pulse is referred to as the "slow flank". Now a very fast pulse is applied, contracting the piezo back into its original position. The prism however due to its inertia cannot follow the piezo crystal's motion, and it remains in the position previously given by the piezo crystal's expansion. This pulse is referred to as the "fast flank". When done many times over, these results in the prism being moved upwards, or downward depending on signal polarity, by the piezo crystals. The principle is shown in Figure \ref{fig:slip_stick_diagram}. The simplest pulse shape allowing for this is the saw tooth wave.
 
 \begin{figure}[H]
@@ -84,7 +84,7 @@ The KIM001 device has a controllable parameter called voltage, which should in p
 \end{figure}
 
 
-\section{Mask Aligner Controller "Walker"}
+\section{Mask Aligner controller "Walker"}
 \subsection{Overview}
 In order to find a suitable replacement for the RHK Piezo Motor controller, we built a new device to drive control pulses to the piezo stacks in the mask aligner. The PCB is heavily based around the piezo Walker electronics designed to control the piezo walker for the\todo{find device}. 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 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. The frequency is fixed at 1 kHz. \todo{You say that later, me!}
 \begin{figure}[H]
@@ -152,7 +152,7 @@ The polarity of the generated signal. Negative polarity is chosen as an approach
 
 The frequency is not adjustable as of the writing of this thesis, though in principle multiples changable frequencies are possible to be implemented through code. Since all previous approach curves and alignment operations were always performed at $1$ kHz it was deemed not necessary to implement. Frequencies higher than $1$ kHz are also difficult, as the timing accuracy of the Arduino is already close to its limits and the signal would also lose sampling rate since the output rate of the DAC is fixed. 
 
-\subsection{Measured Pulse shape}
+\subsection{Measured pulse shape}
 In order to verify the ability to drive the Mask Aligner with the new electronics, test measurements of both the new Walker and the RHK were performed to see if the new Walker can support both the slip-stick behavior and give consistent pulse shape. For the Mask Aligner a voltage of 80 V was determined to be the default voltage to run experiments (see \ref{fig:calibration_voltage}) in, for this reason the comparisons will be made at 80 V, unless otherwise specified. \\
 A measurement of the slow flank, without any attached load, is shown in Figure (\ref{fig:walker_pulse_shape_slow}). The Walker compares favorably to the RHK. It has a more consistent peak shape and its peak voltage corresponds to the one given as a parameter more closely than the RHK, which both under- and overshoots the specified 80 V, by up to $\approx$20 V. The walker pulses are also more symmetric around the fast flank than the one from the RHK. Both the Walker and the RHK show no aliasing artifacts, that are not explainable with the limited time resolution of the oscilloscope. Given this data the Walker seems to outperform the RHK at least in the unloaded state and should give the same, or a better driving behavior as the RHK.\todo{This sentence}
 
diff --git a/chap04.aux b/chap04.aux
index 4ed92bd8c5e68400016c9d5cd7f5d6a8b83ac122..f489119d642e32ae6ba3f7aa4c509bdea22631ac 100644
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+\@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.}}{64}{figure.caption.135}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{64}{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.135}{}}
+\@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 measureable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{65}{table.caption.136}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{65}{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 measureable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.136}{}}
 \@setckpt{chap04}{
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@@ -102,7 +102,7 @@
 \setcounter{subfigure}{0}
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diff --git a/chap04.tex b/chap04.tex
index 48937ef5b7bd287d24ce369a703a4ec7f2c12685..db84a883da04c2644f7a09253212b98ff8c48dc1 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -1,5 +1,5 @@
 % !TeX spellcheck = <en-US>
-\chapter{Mask Aligner Repairs and Optimizations}
+\chapter{Mask Aligner repairs and optimizations}
 \section{Overview}
 
 \begin{figure}[H]
@@ -34,7 +34,7 @@ When using flux the flux has to be cleaned of thoroughly to avoid outgassing as
 	\item Remove the IPA residue with a heat gun. The heat gun should be set no higher than $80^\circ$ C and held about $10$ cm away from any components to avoid overheating. 
 \end{enumerate}
 
-\section{Soldering Anchors}
+\section{Soldering anchors}
 The soldering anchor points that were previously used on the Mask Aligner are small \todo{Measurements}(0.2 mm x mm x mm) ceramic pieces onto which a small piece of copper, pre-coated with solder, was glued using non-conductive EPO-TEK H70E.\todo{Check} Then all cables coming from the piezo motors can be soldered to this soldering anchor, allowing for shorter cables to be used and for the cables to be more cleanly routed around the Mask Aligners surface. The Ceramic piece was glued to the surface of the Mask Aligner using the same glue.\\ 
 However, over time and usage the glue on some of the soldering anchors had loosened to the point that the solder dots connecting the cables and the anchor where now sticking out from the surface of the Mask Aligner more, to the point of sometimes interfering with the Sapphire Prism that is used to drive the motion of the mask stage. This caused the mask stage to frequently get stuck, when driving the piezo motors. The Problem situation is depicted in Figure (\ref{fig:solder_anchors_diagram}\subref{fig:solder_anchors_diagram_base}).\\
 This behavior was worsening over time to the point of not allowing the motor Z1 to return the stage into the Mask extraction height. \\
@@ -99,7 +99,7 @@ Thorseal was instead used for all gluing purposes. Torr Seal is a two component
 All motors were checked for soldering anchor points that could potentially interfere with the prism, and one of these actions was taken for all ceramics where problems could be found.\todo{show examples} \\
 After this step, the prism would no longer get stuck when driving and could cleanly drive the whole range of possible motion. \\
 
-\section{Piezo Reglueing}
+\section{Piezo reglueing}
 The piezo motors of the 3 motor stacks in the Mask Aligner were glued in 2015\todo{check}\cite{olschewski} with the non-conductive EPO-TEK H70E glue. This glue has over time lost some of its sticking ability, even though the Mask Aligner is usually in UHV. For this reason, 2 of the piezo stacks, one on motor Z1 and one on Motor Z3, had by the time the previous repairs were performed completely detached. These stacks needed to be re-glued to the surface of the Mask Aligner Body, in order to provide proper support for the driving of the prisms. \\
 
 The EPO-TEK H70E glue would have been difficult to use for this, for the same reasons stated above, so again Torr Seal was used instead. Torr Seal was tested to have comparable elastic properties to the previously used glue and experiments to determine the right size of a glue dot in the middle of the piezo stack were performed to ensure a strong, but thin enough layer of Torr Seal. \\
@@ -136,7 +136,7 @@ The repair of the piezo on motor Z1 happened without problems, but on motor Z3 t
     \label{fig:Z3_after reglue}
 \end{figure}\todo{Draw in Angle}
 
-\section{Z3 Motor}
+\section{Z3 motor}
 After all repairs were performed, the motors Z1 and Z2 were performing as expected without any problems, but the motor Z3 would occasionally drive with massively reduced power.\todo{Find Plot of this} The speed of the prism driven by the Z3 motor would sometimes, without any noticeable change, drop to about half the expected value. Additionally, the difference in approach and retract speed between the motors Z2/Z1 was about a factor of 1.25, while the difference for Z3 was off by a factor of 2, regardless of screw configuration. This behaviour can be seen in Figure \ref{fig:Z3_screw_rot} This led to the conclusion, that Z3 had some sort of alignment issue, where sometimes randomly all the motors were in line with the prism and could drive at the appropriate power, while sometimes one of the motors would lose contact with the prism and now the prism would be driven by the other motors and the Z3 driving would no longer be symmetric. This conclusion was further corroborated, by the fact that the Z3 motor would at arbitrary times decrease its stepsize by about a factor of 2.
 The cause of this was determined to be the front plate of the Z3 motor, as switching the front plate of the Z1 and Z3 motors caused the problem to disappear on the Z3 motor. For this reason, the front plate had to be repaired.
 
@@ -147,7 +147,7 @@ The cause of this was determined to be the front plate of the Z3 motor, as switc
     \label{fig:Z3_screw_rot}
 \end{figure}\todo{Make those nicer}
 
-\subsection{Front Plate repair}
+\subsection{Front plate repair}
 In order to test the hypothesis, that the front plate of motor Z3 was causing the issues with said motor, the front plate of Z3 was exchanged for the front plate of motor Z1. Resoldering all the cables of the front plate to the solder anchors, in order to swap plates, would put the glue of the solder anchors at risk of failing and this would be required to be performed multiple times in order to do the full check. In order to prevent this new longer copper cables were created and the front plate of Z3 was directly connected to the vacuum feedthrough pins. After the plates were swapped the issues with motor Z3 were no longer observed and as seen in Figure \ref{} the performance of Z3 became more in line with the other 2 motors. The performance was in the firmer screw regime lower than that of Z2, but in the regime of normal operation (about 2-3 screw rotation in Figure \ref{}) the performance became very similar. The difference in this regime was determined to be not significant enough to require any more intervention. \\
 The problem on the Z3 front plate was likely a misalignment on one of the piezo stacks on the plate, leading to a slight shift of it on one of the sides. In order to check for the unevenness of the surface color, tests were performed, where the top of the piezo stacks was coated with color and then the plate was placed on a \ce{Al3O2} plate and moved in motor movement direction. This test was performed for both motor movement directions and repeated several times. For all cases the plate preferred to leave a mark where the lower of the piezo stacks was. \\
 The piezo stacks were taken off the front plate, and it was decided, that 2 of the 10 replacement piezos would be glued to the surface of the plate in order to function as the new plate. In order for the gluing to give good alignment, an alignment tool was produced by the workshop. \\
@@ -204,7 +204,7 @@ Afterward, changes in stray capacitance were measured and it compared to measure
 
 
 
-\section{Final Test}
+\section{Final test}
 In order to determine the proper screw setup and to test the function of the changes made to the Mask Aligner, a calibration was performed. This calibration shows similarity of performance between the 3 motors in the approach regime as seen in Figure \ref{fig:calibration_after_repair}. In approach direction the 3 motors deviate by about $3$ nm/step, which is at least within $2$ $\sigma$ of each other, when comparing Z1 to Z2 and Z2 to Z3. Z3 and Z1 however can deviate by up to $6$ nm/step, which is within $6$ $\sigma$ of each other. As a difference of $6 nm$, which is the worst case assumption given the data would give an angular tilt per step of $\approx (5.73 \! 10^{-6})^\circ$ or a difference in height on the sample of $\approx 0.5$ nm/step. This in turn would give a difference in penumbra of $1.2$ nm for every $100$ steps.\\
 In the retract regime the difference between motors is within margin of error for Z2 and Z1, but Z3 deviates by about $4 \sigma$ from the others. Since alignment happens with approach mostly and retract is only used to move the mask back from the sample after an evaporation this is of lesser importance than a deviation in approach behavior. After each evaporation the mask is retracted to about $50$ $\mu$m to ensure movement of the x piezo does not damage the sample. Within these a difference of $1.2$ $\mu$m would appear from side to side of the evaporation field, which corresponds to an angle of $\approx 0.004^\circ$. This difference should result in a difference of $\approx 38$ nm in penumbra for the evaporation, however by driving the Z1 and Z2 motors 100 steps up after the retraction this can be compensated almost fully and should result in an error of at most $\approx 6$ nm of additional penumbra induced by tilt. \\
 
diff --git a/chap05.aux b/chap05.aux
index adc66c3b4903aabbd3ea40a675d04218d1f999ed..ce6003d52f220203dcbd59697ec6b3764f66dbd1 100644
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+\newlabel{fig:evaporation_analysis}{{5.5}{72}{Example of the analysis performed on each of the recorded dots for a single line cut. (a) shows the raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) shows the cleaned image, as well as the line cut \textcolor {tab_green}{(green)} from which the line cut data (c) was obtained. The black lines show how multiple line cuts were obtained on a single image to obtain values for $\sigma _s$ and $\sigma _l$. The fit shows the two different penumbra widths induced by the tilt $\sigma _s$ and $\sigma _l$ for a single line cut}{figure.caption.145}{}}
+\newlabel{fig:evaporation_measured_penumbra_sigs}{{5.6a}{73}{\relax }{figure.caption.146}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_sigs}{{a}{73}{\relax }{figure.caption.146}{}}
+\newlabel{fig:evaporation_measured_penumbra_sigl}{{5.6b}{73}{\relax }{figure.caption.146}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_sigl}{{b}{73}{\relax }{figure.caption.146}{}}
+\newlabel{fig:evaporation_measured_penumbra_height}{{5.6c}{73}{\relax }{figure.caption.146}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_height}{{c}{73}{\relax }{figure.caption.146}{}}
+\newlabel{fig:evaporation_measured_penumbra_circle_r}{{5.6d}{73}{\relax }{figure.caption.146}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_circle_r}{{d}{73}{\relax }{figure.caption.146}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.6}{\ignorespaces 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}).}}{73}{figure.caption.146}\protected@file@percent }
+\newlabel{fig:evaporation_measured_penumbra}{{5.6}{73}{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})}{figure.caption.146}{}}
+\@writefile{tdo}{\contentsline {todo}{Check if script can fit negative penumbra}{73}{section*.147}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {5.4}Tilt}{75}{section.5.4}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {5.7}{\ignorespaces Image of the reconstruction of the tilt angle for Field 3 as an example (a) and the data given by all fields (b). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}}{75}{figure.caption.148}\protected@file@percent }
+\newlabel{fig:evaporation_tilts}{{5.7}{75}{Image of the reconstruction of the tilt angle for Field 3 as an example (a) and the data given by all fields (b). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case}{figure.caption.148}{}}
+\newlabel{fig:evaporation_SEM_sample}{{5.8a}{76}{\relax }{figure.caption.149}{}}
+\newlabel{sub@fig:evaporation_SEM_sample}{{a}{76}{\relax }{figure.caption.149}{}}
+\newlabel{fig:evaporation_SEM_mask}{{5.8b}{76}{\relax }{figure.caption.149}{}}
+\newlabel{sub@fig:evaporation_SEM_mask}{{b}{76}{\relax }{figure.caption.149}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces SEM images of field 2 on the sample (\subref  {fig:evaporation_SEM_sample}) and the mask (\subref  {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. 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.}}{76}{figure.caption.149}\protected@file@percent }
+\newlabel{fig:evaporation_SEM}{{5.8}{76}{SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. 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}{figure.caption.149}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog}{{5.9a}{77}{\relax }{figure.caption.150}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{77}{\relax }{figure.caption.150}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog_overlay}{{5.9b}{77}{\relax }{figure.caption.150}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog_overlay}{{b}{77}{\relax }{figure.caption.150}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces An example of the clogging noticed on $4$ of the mask holes (\subref  {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{77}{figure.caption.150}\protected@file@percent }
+\newlabel{fig:evaporation_SEM_analysis}{{5.9}{77}{An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields}{figure.caption.150}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {5.5}Simulation}{77}{section.5.5}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{place image of godot transform thing here}{78}{section*.151}\protected@file@percent }
+\citation{Bhaskar}
+\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.10a}{79}{\relax }{figure.caption.152}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{79}{\relax }{figure.caption.152}{}}
+\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.10b}{79}{\relax }{figure.caption.152}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{79}{\relax }{figure.caption.152}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces Comparison of an recorded AFM image (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 $.}}{79}{figure.caption.152}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare}{{5.10}{79}{Comparison of an recorded AFM image (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.152}{}}
+\@writefile{tdo}{\contentsline {todo}{Comparison of AFM Image and Simulation naive}{79}{section*.153}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Point at the images with arrows here}{79}{section*.154}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.11a}{80}{\relax }{figure.caption.155}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{80}{\relax }{figure.caption.155}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_inital}{{5.11b}{80}{\relax }{figure.caption.155}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_inital}{{b}{80}{\relax }{figure.caption.155}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.11c}{80}{\relax }{figure.caption.155}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{80}{\relax }{figure.caption.155}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\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 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}.}}{80}{figure.caption.155}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness}{{5.11}{80}{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 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.155}{}}
+\@writefile{tdo}{\contentsline {todo}{Comparison of AFM Image and Simulation implementing different sticking and irregular period}{80}{section*.156}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection_prev}{{5.12a}{81}{\relax }{figure.caption.157}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{81}{\relax }{figure.caption.157}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{5.12b}{81}{\relax }{figure.caption.157}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{81}{\relax }{figure.caption.157}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.12c}{81}{\relax }{figure.caption.157}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{81}{\relax }{figure.caption.157}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\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}.}}{81}{figure.caption.157}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{5.12}{81}{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.157}{}}
+\@writefile{tdo}{\contentsline {todo}{Not sure this is actually not nonsense}{81}{section*.158}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Image of final simulation with parameters given in }}{82}{figure.caption.159}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_progression}{{5.13}{82}{Image of final simulation with parameters given in}{figure.caption.159}{}}
+\@writefile{toc}{\contentsline {paragraph}{Software improvements}{82}{section*.160}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Link}{82}{section*.161}\protected@file@percent }
 \@setckpt{chap05}{
-\setcounter{page}{78}
+\setcounter{page}{83}
 \setcounter{equation}{1}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -72,17 +95,17 @@
 \setcounter{mpfootnote}{0}
 \setcounter{part}{0}
 \setcounter{chapter}{5}
-\setcounter{section}{1}
-\setcounter{subsection}{5}
+\setcounter{section}{5}
+\setcounter{subsection}{0}
 \setcounter{subsubsection}{0}
 \setcounter{paragraph}{0}
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-\setcounter{figure}{10}
+\setcounter{figure}{13}
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-\setcounter{bookmark@seq@number}{56}
+\setcounter{bookmark@seq@number}{55}
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@@ -91,7 +114,7 @@
 \setcounter{subfigure}{0}
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-\setcounter{@todonotes@numberoftodonotes}{76}
+\setcounter{@todonotes@numberoftodonotes}{73}
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diff --git a/chap05.tex b/chap05.tex
index 716599136d478fc3dd961221da31298bc10e2fcb..67f939650eee3ae36d620677879692d952518e6e 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -1,8 +1,6 @@
 % !TeX spellcheck = <en-US>
-\chapter{Evaporations and Measurement}
-
-\section{Silicon}
-\subsection{Evaporation Configuration}
+\chapter{Evaporations and measurement}
+\section{Evaporation configuration}
 
 As a test for positioning and as a test for the Mask Aligners capabilities after optimization evaporations were performed on a \ce{Si} sample. The sample was prepared and cleaned using the process described in \todo{Link Sample prep}. The 5 evaporations were performed across different points in the approach curve of this particular mask to see the difference in evaporation quality for the different criteria established for stopping the approach curve. The approach curve of this particular sample is shown in Figure \ref{fig:evaporation_approach}\\  
 
@@ -64,11 +62,11 @@ Figure \ref{fig:Evaporation_diagramm_sample_img} shows the positions of the evap
 \begin{figure}[H]
     \centering
     \includegraphics[width=\linewidth]{img/Evaporation/Approach_Curve_Field01.pdf}
-    \caption{The approach curve measured for Field 1 until full contact. }
+    \caption{The approach curve measured for Field 1 until full contact. Since the correlation between the 3 capacities is very high and the uncertainty on C2 and C3 is very large C1 was used for alignment primarily.}
     \label{fig:evaporation_approach_curve}
 \end{figure}
 
-\subsection{Contamination}
+\section{Contamination}
 The entire samples surface is contaminated with small particles, which are about $\approx 50$ nm in height and of a size on the order of $ 10$ nm. The contaminants are not visible in an optical microscope. After cleaning the sample was only checked optically, which is why it is unknown if they were present after cleaning or were deposited after. \todo{More}
 
 \begin{figure}[H]
@@ -81,7 +79,7 @@ The entire samples surface is contaminated with small particles, which are about
 Additionally the sample was contaminated with larger particles from long exposure at atmospheric conditions as well as being inside the Mask Aligner Chamber during bakeout on $2$ separate occasions. The size of these larger particles was approximately determined to be in the order of $\mathcal{O}(100 \text{ nm})$ using SEM. \todo{check}
 
 
-\subsection{Penumbra}
+\section{Penumbra}
 In order to obtain the width of the penumbra, as well as other characteristics of the performed evaporation AFM measurements were taken. For all fields at least one measurement was taken of the $4$ cardinal direction by first measuring a low resolution image of both the top right and the bottom left of the field and selecting a dot from left, right, top bottom, as well as one in the center. These do not necessarily are the ones in the middle of the $4$ cardinal directions. Dots were picked, which looked to have lower amount of contamination on them, as higher amount of particles make the analysis more difficult. \\
 First the data is cleaned by masking the contamination of the \ce{Si} sample. This works very well since the evaporated dots are of a height of $\approx 3$ nm, while the contamination particles are of the much greater height $\approx 50$ nm. The area under the mask is now interpolated in order to erase most of the particles. \\
 The width of the penumbra was then obtained by getting line cuts close to the line along which the tilt of the dots points and by fitting a gaussian fall of to the slopes of the resulting line cut. The fit function is
@@ -141,14 +139,18 @@ This process was performed for every recorded dot and with multiple line cuts ne
 	\end{subfigure}
 	\caption{Data obtained from the previously described method for each of the 5 evaporations, from evaporated dot each from the center of the field, the left, the right, the bottom and the top. The dot chosen depended on measurement condition such as contamination and phase characteristics of the dot. The data shows the smaller penumbra $\sigma_s$ (\subref{fig:evaporation_measured_penumbra_sigs}) the larger penumbra $\sigma_l$ (\subref{fig:evaporation_measured_penumbra_sigl}), the height of the dot (\subref{fig:evaporation_measured_penumbra_height}) and the diameter of the circle (\subref{fig:evaporation_measured_penumbra_circle_r}).}
     \label{fig:evaporation_measured_penumbra}
-\end{figure}\todo{Diameter currently wrong}
+\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 analyse. 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 $20$ 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.\\
 
-Figure \ref{fig:evaporation_measured_penumbra} shows the values obtained 
+The height of the dots (Figure \ref{fig:evaporation_measured_penumbra_height}) is spread around a mean value of $2.6 \pm 0.3$ nm and shows strong deviation from the expected $5$ nm, obtained from calibration measurements for the particle flux that was used in the evaporation. This seems to suggest a large amount of \ce{Pb} particles never reaches the mask even though they are expected to by the setup conditions. \\
 
-\subsection{Tilt}
-All evaporated dots, even when the capacitance signal was within the full contact regime showed signs of a tilt between mask hole and sample in the form of a half moon shaped second penumbra. If this was due to a misalignement between the entire mask and the sample one would expect the direction of the tilt to be the same for the entire evaporated field and the size of the second penumbra to diminish along the direction of the tilt. But as seen in Figure \ref{fig:evaporation_tilts} the direction of the tilt is not uniform and instead seems to point outwards for the dots on the edge. This suggests the mask itself is slightly bent towards the edges resulting in an alignment error. \\
+The diameter of the \ce{Pb} dots would by expectation decrease with subsequent evaporations due to clogging of the mask. This trend is mirrored in the data as the average diameter of evaporation decreases from $3.02 \pm 0.04$ for field $1$ to $2.947 \pm 0.008$ for field $4$ with a linear fit to the average values giving a decrease in diameter of $0.017 \pm 0.004$ $\mu$m per evaporation. \\
+
+The larger penumbra data (Figure \ref{fig:evaporation_measured_penumbra_sigl}) indicates no pattern for each field and only possibly a reduction in penumbra for the bottom and center dots. This might be due to different dots being chosen for each analysis, some of which are not completely at the top or bottom (or left and right), but one row below or above. In the following the penumbra and direction of tilt will be treated in a more thorough manner. \\
 
-The smallest minor that was found in the AFM data was $2.15 \pm 0.08$ $\mu$m against the $3.01\pm 0.05$ $\mu$m of the evaporated circle. This would imply a tilt from one side of the dot on the mask to the other of $44 \pm 9 ^\circ$, which implies a difference in mask sample distance from one side of the hole in the mask to the other side of it of $1.96 \pm 0.31$ $\mu$m. Even with a mask sample distance on average of $1$ $\mu$m this is still possible since one side can be retraced from the mask by $1.96 \pm 0.31$ $\mu$m rather than the other being closer, but this still implies a massive deformation of the mask membrane.
+\section{Tilt}
 
 \begin{figure}[H]
     \centering
@@ -164,32 +166,86 @@ The smallest minor that was found in the AFM data was $2.15 \pm 0.08$ $\mu$m aga
     \label{fig:evaporation_tilts}
 \end{figure}
 
-\subsection{Simulation}
+All evaporated dots, even when the capacitance signal was within the full contact regime showed signs of a tilt between mask hole and sample in the form of a half moon shaped second penumbra. If this was due to a misalignement between the entire mask and the sample one would expect the direction of the tilt to be the same for the entire evaporated field and the size of the second penumbra to diminish along the direction of the tilt. But as seen in Figure \ref{fig:evaporation_tilts} the direction of the tilt is not uniform and instead seems to point outwards for the dots on the edge. This suggests the mask itself is slightly bent towards the edges resulting in an alignment error. \\
+
+The smallest minor that was found in the AFM data was $2.15 \pm 0.08$ $\mu$m against the $3.01\pm 0.05$ $\mu$m of the evaporated circle. This would imply a tilt from one side of the dot on the mask to the other of $44 \pm 9 ^\circ$, which implies a difference in mask sample distance from one side of the hole in the mask to the other side of it of $2.08 \pm 0.31$ $\mu$m. Even with a mask sample distance on average of $1$ $\mu$m this is still possible since one side can be retracted from the mask by $2.08 \pm 0.31$ $\mu$m rather than the other being closer, but this still implies a massive deformation of the mask membrane.
+
+The different angles the tilt takes can be seen in Figure \ref{fig:evaporation_tilts}. All of the lead dots show a tilt and displacement as defined in Figure \ref{fig:penumbra_tilt_sigmas}, but noticeably the inner dots show lower tilt and displacement, than the ones on the outside of the field. The lead dots on the outer edge of the field point outwards from the field center, which could suggest an upwards bending of the mask towards the center of the field. \\
+
+\begin{figure}[H]
+    \centering
+	\begin{subfigure}{0.49\linewidth}
+		\centering
+    	\includegraphics[width=0.9\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}
+    	\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.}
+    \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. This could indicate different material being placed on the dot, but it can also be explained by a difference in growth direction, since for very thin films ($\mathit{O}(3 \text{ nm})$) a difference in growth direction would result in a difference in conductivity in the direction of the incoming electron beam. \\
+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}.
+
+\begin{figure}[H]
+    \centering
+	\begin{subfigure}{0.49\linewidth}
+		\centering
+    	\includegraphics[width=0.9\linewidth]{img/Evaporation/SEM/ShowingClog.pdf}
+    	\caption{}
+		\label{fig:evaporation_SEM_analysis_clog}
+	\end{subfigure}
+	\begin{subfigure}{0.49\linewidth}
+		\centering
+    	\includegraphics[width=0.9\linewidth]{img/Evaporation/SEM/SEM_CloggingOverlay.png}
+    	\caption{}
+		\label{fig:evaporation_SEM_analysis_clog_overlay}
+	\end{subfigure}
+	\caption{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.}
+    \label{fig:evaporation_SEM_analysis}
+\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 noticed bending 
+
+\section{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 generate, and from it a ray is cast to a point behind the sample choosing a random ray inside a possible cone with angle $\phi$, representing the different directions a molecule can take when being emitted from the sample. The ray is then checked against collision with a mask hole, which is represented by a cyclinder collider with very small height. When collision with the mask "hole" is determined the ray is cast again and the position at which the sample would be hit is determined. This position is then recorded as a hit in an array, that is structured like an image, spanning a user defined area around the middle of the sample and with user specified resolution. For each element in the array the amount of hits the "pixel" has received is stored. This step is repeated many times in a single time step.\\
+At a time $0$ at a distance $L$ from the sample a random point inside the circle is generate, and from it a ray is cast to a point behind the sample choosing a random ray inside a possible cone with angle $\phi$, representing the different directions a molecule can take when being emitted from the sample. 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}
 
-In order to simulate vibration effects the cyclinder collider for the mask can be moved and rotated in a periodic manner. The rotation, position and oscillation period are user parameters. And after each time step the collider is moved and in the next iteration the new collider position and rotation is checked against. This allows the simulation of $3$D vibrations in the resulting image. \\
+Objects in the Godot game engine are moved, rotated and scaled with a $3x4$ 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 components 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.
 
-After a user specified time has passed the amount of hits on each pixel is saved into a file and the image can then be displayed using a python script. For a more detailed look at the different parameters the script provides see the Appendix \todo{Appendix ref}\\
+In order to simulate vibration effects the cyclinder collider for the mask can be moved and rotated in a periodic manner. The rotation, position and oscillation period are user parameters. And after each time step the collider is moved and in the next iteration the new collider position and rotation is checked against. The position on the current time step is obtained by linear interpolation between the start position and tilt and the end position and tilt. The interpolation parameter is determined with the function $|\sin(\frac{t}{T})|$, where $T$ is the period of the oscillation in time steps and $t$ is the current time step. This allows the simulation of $3$D vibrations in the resulting image. \\
+
+After a user specified time has passed the amount of hits on each pixel is saved into a file and the image can then be displayed using a python script. For a more detailed look at the different parameters the script provides see the Appendix \ref{sec:appendix_raycast}.\\
 
 \begin{figure}[H]
     \centering
 	\begin{subfigure}{0.45\linewidth}
     	\includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right.png}
     	\caption{}
+		\label{fig:evaporation_simulation_first_compare_AFM}
 	\end{subfigure}
 	\begin{subfigure}{0.53\linewidth}
     	\includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple.pdf}
     	\caption{}
+		\label{fig:evaporation_simulation_first_compare_SIM}
 	\end{subfigure}
-	\caption{Comparison of an recorded AFM image (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 constant during the deposition and different sticking factors of \ce{Pb}-\ce{Si} and \ce{Pb}-\ce{Pb} were not considered.}
+	\caption{Comparison of an recorded AFM image (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 $\gamma$.}
     \label{fig:evaporation_simulation_first_compare}
 \end{figure}\todo{Comparison of AFM Image and Simulation naive}
 
-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}. 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 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. \todo{Point at the images with arrows here} The lower edge of the elliptical shape visible in the AFM dot below the circle is so faint as to be invisible in the AFM image, while it is very pronouced 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 $3.5 \pm 0.2$ \todo{check numbers}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.
+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 amplitude obtained in the PhD thesis of Priyamvada Bhaskar\cite{Bhaskar} for an active turbomolecular pump of $1$ $\mu$m. 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 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. \todo{Point at the images with arrows here} The lower edge of the elliptical shape visible in the AFM dot below the circle 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.
 
 \begin{figure}[H]
     \centering
@@ -208,22 +264,49 @@ The greater circle in the AFM has an average height for all dots of about $3.5 \
     	\caption{}
 		\label{fig:evaporation_simulation_sharpness_stick_power}
 	\end{subfigure}
-	\caption{}
+	\caption{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 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}.}
     \label{fig:evaporation_simulation_sharpness}
 \end{figure}\todo{Comparison of AFM Image and Simulation implementing different sticking and irregular period}
 
-The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_inital} 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 $\cos(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\cos(\frac{t}{T} + \phi)^p$ 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 the initial circular shape. 
+The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_inital} 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 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. \\
 
-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. 
+Lead or in general any deposited material deposits more easily, when there is already some of the same material deposited. This nucleation effect can be relatively simply be modeled in the simulation by penalizing deposition for pixels, where no material has been deposited previously. The probability to deposit on an empty surface is a user controlled parameter called "first\_layer\_depo\_prob". It controls the probability with which a particle hitting the sample is deposited, when no material has previously been deposited on the relevant pixel. \\
+
+\begin{figure}[H]
+    \centering
+	\begin{subfigure}{0.32\linewidth}
+    	\includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple_power.pdf}
+    	\caption{}
+		\label{fig:evaporation_simulation_rejection_prev}
+	\end{subfigure}
+	\begin{subfigure}{0.32\linewidth}
+    	\includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple_rejection.pdf}
+    	\caption{}
+		\label{fig:evaporation_simulation_rejection_after}
+	\end{subfigure}
+	\begin{subfigure}{0.32\linewidth}
+    	\includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right.png}
+    	\caption{}
+		\label{fig:evaporation_simulation_rejection_comparison}
+	\end{subfigure}
+	\caption{Simulated evaporation dots without (\subref{fig:evaporation_simulation_rejection_prev}) and with (\subref{fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref{fig:evaporation_simulation_rejection_comparison}) shows the AFM image 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}.}
+    \label{fig:evaporation_simulation_rejection}
+\end{figure}
+
+The results of adding this penalty for initial deposition are shown in Figure \ref{fig:evaporation_simulation_rejection_after}. As compared to the previous simulation step in Figure \ref{fig:evaporation_simulation_rejection_before} the dot appears more rough and the height has decreases. The outer tail of the ellipse dissapears nearly completely, these parameters match the deposition in the actual AFM image more closely, but crucially the decreased roughness of the elliptical part on the dot is not mirrored in the simulation, where the dot also appears rough. This however might come from the fact that upon deposition \ce{Pb} atoms might move and deposit on local minima of the height landscape since the potential effectively traps the atom there. \todo{Not sure this is actually not nonsense} The simulation does not take this effect into account at all.
 
 \begin{figure}[H]
     \centering
 	\includegraphics[width=0.9\linewidth]{img/Evaporation/Sim/Field3_right_sim_progression.pdf}
-	\caption{}
+	\caption{Image of final simulation with parameters given in }
     \label{fig:evaporation_simulation_progression}
-\end{figure}\todo{Showing simulation progression of evaporation}
+\end{figure}
+
+
 
-\paragraph{Improvements}
+\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 from the \todo{Link} Knudsen equation, but it does not currently take into account grain size and diffusion of particles, which makes the graininess of the image resolution dependent.\\
 The current way of implementing the simulation using Godot allowed for very quick implementation and bug fixing, but lacks in performance. Each ray is cast sequentially on the CPU and significant overhead is caused by the game engine computing things necessary for games, but unnecessary for the purposes of this simple simulation. This causes the render time of each image to be in the minute to hour range for images of higher resolutions. \\
 In order to improve performance a dedicated ray tracing engine with support for threading and maybe even parallel deployment on the GPU using for example CUDA or OpenCL could give massive performance improvements since rays many thousands of rays could be cast in parallel this way. This would most likely boost generation times by several orders of magnitude. \\
diff --git a/conclusion.aux b/conclusion.aux
index 7e1a988b76f34b7d7115bd8c5bc89e8e172c9d46..1301c19bab6c05f44405ad840eb5869389300a0d 100644
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+++ b/conclusion.aux
@@ -1,8 +1,8 @@
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diff --git a/img/Evaporation/Field3Angle.pdf b/img/Evaporation/Field3Angle.pdf
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diff --git a/thesis.bbl b/thesis.bbl
index 9fed95de4d1c53abe8955d0a8cf2a068e4c228d3..92cc906c6c16e660733bad13d35f7bed300cc5da 100644
--- a/thesis.bbl
+++ b/thesis.bbl
@@ -1,5 +1,12 @@
 \begin{thebibliography}{10}
 
+\bibitem{bhaskar}
+Priyamvada Bhaskar.
+\newblock {F}abrication and investigation of ultrahigh vacuum compatible
+  interfaces of topological insulators and superconductors, 2023.
+\newblock Published on the publication server of RWTH Aachen University;
+  Dissertation, RWTH Aachen University, 2023.
+
 \bibitem{Tungsten_melt}
 François Cardarelli.
 \newblock {\em Materials Handbook: A Concise Desktop Reference. Third Edition}.
@@ -7,9 +14,17 @@ François Cardarelli.
 
 \bibitem{Tungsten_evap}
 Carl~L. Yaws, editor.
-\newblock {\em Handbook of Chemical Compound Data for Process Safety}.
+\newblock {\em {H}andbook of {C}hemical {C}ompound {D}ata for {P}rocess
+  {S}afety}.
 \newblock Gulf Professional Publishing, Houston, 1997.
 
+\bibitem{tungsten_evaporation}
+Tetsuya Takaai.
+\newblock {T}he {E}lectron {B}eam {M}elting of {T}ungsten (the electron beam
+  melting of refractory metals (viii)).
+\newblock {\em Journal of the Japan Institute of Metals}, 30(11):1027--1031,
+  1966.
+
 \bibitem{Vapor_depo_princ}
 P.K.S.K.S.S. Harsha.
 \newblock {\em Principles of Vapor Deposition of Thin Films}.
@@ -21,16 +36,9 @@ Florian Forster.
 \newblock unpublished, but viewable on the Server of the 2nd institute of
   physics B.
 
-\bibitem{bhaskar}
-Priyamvada Bhaskar.
-\newblock {F}abrication and investigation of ultrahigh vacuum compatible
-  interfaces of topological insulators and superconductors, 2023.
-\newblock Published on the publication server of RWTH Aachen University;
-  Dissertation, RWTH Aachen University, 2023.
-
 \bibitem{SEM_image_01}
 Nicole Gleichmann.
-\newblock Sem vs tem, 2024.
+\newblock {SEM} vs {TEM}, 2024.
 
 \bibitem{SEM_image_02}
 Ponor.
@@ -69,8 +77,8 @@ Analog Devices Inc.
 
 \bibitem{olschewski}
 Tim Olschewski.
-\newblock Konstruktion und aufbau eines mask aligners für ultrahochvakuum,
-  2015.
+\newblock {K}onstruktion und {A}ufbau eines {M}ask {A}ligners für
+  {U}ltrahochvakuum, 2015.
 \newblock unpublished, but viewable on the Server of the 2nd institute of
   physics B.
 
diff --git a/thesis.blg b/thesis.blg
index 7e3859727351dcda0dc09d5f42a229ede734b98e..62362ff239418beb659125c9a7bd41d179019c47 100644
--- a/thesis.blg
+++ b/thesis.blg
@@ -15,6 +15,11 @@ Reallocating 'name_of_file' (item size: 1) to 11 items.
 A level-1 auxiliary file: chap04.aux
 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 56 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.
@@ -39,50 +44,50 @@ Warning--entry type for "SEM_image_01" isn't style-file defined
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 Warning--entry type for "SEM_image_02" isn't style-file defined
 --line 151 of file bibliography.bib
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-Warning--I didn't find a database entry for "todo"
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+Warning--I didn't find a database entry for "sputter_damage"
 Warning--empty publisher in Tungsten_melt
 Warning--empty publisher in SEM_book
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+You've used 14 entries,
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diff --git a/thesis.log b/thesis.log
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diff --git a/thesis.pdf b/thesis.pdf
index 3fb3739161a02c9c384b54582d55a0d74a631091..06c6e8548e823806e033108c0d516a6c4b96b669 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index cb84caaf74ff6d791b396a0bc4fa8fa3893fbd66..8c405a6186047b931e88a7dcc4248e24c0548822 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.tex b/thesis.tex
index 4e47e2cb908d1feb17074717b41b99a22fa09b70..20d9df561f995b49ec3a65dba616f71a7c723670 100644
--- a/thesis.tex
+++ b/thesis.tex
@@ -155,8 +155,6 @@ EDX = \textbf{E}nergy-\textbf{d}ispersive \textbf{X}-ray spectroscopy \\
 MC = \textbf{M}ain \textbf{C}hamber \\
 LL = \textbf{L}oad \textbf{L}ock
 
-
-
 \include{appendix}
 \include{acknowledgments}
 
diff --git a/thesis.toc b/thesis.toc
index c7a0ed1e166f9711b33010986340d516af3b280b..28aae5e11fbdaf9d423b455e716bd37ce9c12ada 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -1,116 +1,115 @@
 \contentsline {chapter}{Introduction}{3}{chapter*.2}%
-\contentsline {chapter}{\numberline {1}Mask Aligner Background}{5}{chapter.1}%
+\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}{7}{section.1.2}%
-\contentsline {subsubsection}{Penumbra}{8}{section*.9}%
-\contentsline {subsubsection}{Tilt induced Penumbra}{9}{section*.13}%
-\contentsline {section}{\numberline {1.3}Measurement Techniques}{11}{section.1.3}%
+\contentsline {subsection}{\numberline {1.1.1}Mask Aligner lead evaporator}{7}{subsection.1.1.1}%
+\contentsline {section}{\numberline {1.2}Stencil lithography}{7}{section.1.2}%
+\contentsline {subsubsection}{Penumbra}{8}{section*.7}%
+\contentsline {subsubsection}{Tilt induced penumbra}{9}{section*.11}%
+\contentsline {section}{\numberline {1.3}Measurement techniques}{11}{section.1.3}%
 \contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{11}{subsection.1.3.1}%
-\contentsline {subsubsection}{}{11}{section*.18}%
-\contentsline {subsubsection}{Modes}{12}{section*.20}%
-\contentsline {paragraph}{Contact}{12}{section*.21}%
-\contentsline {paragraph}{Non-Contact}{13}{section*.22}%
-\contentsline {paragraph}{Tapping}{13}{section*.23}%
+\contentsline {subsubsection}{}{11}{section*.16}%
+\contentsline {subsubsection}{Modes}{12}{section*.18}%
+\contentsline {paragraph}{Contact}{12}{section*.19}%
+\contentsline {paragraph}{Non-Contact}{13}{section*.20}%
+\contentsline {paragraph}{Tapping}{13}{section*.21}%
 \contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{14}{subsection.1.3.2}%
 \contentsline {subsection}{\numberline {1.3.3}Energy-dispersive X-ray spectroscopy}{16}{subsection.1.3.3}%
 \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 {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}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 {2.2.2}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}{31}{subsection.2.2.4}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{31}{section*.54}%
-\contentsline {subsubsection}{Reproducibility for different sample, but same mask}{33}{section*.59}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{31}{section*.52}%
+\contentsline {subsubsection}{Reproducibility for different sample, but same mask}{33}{section*.57}%
 \contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{33}{subsection.2.2.5}%
-\contentsline {paragraph}{Leakage current}{38}{section*.72}%
-\contentsline {paragraph}{Improved gold pin fitting}{38}{section*.73}%
+\contentsline {paragraph}{Leakage current}{38}{section*.70}%
+\contentsline {paragraph}{Improved gold pin fitting}{38}{section*.71}%
 \contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{39}{subsection.2.2.6}%
-\contentsline {paragraph}{High correlation between capacitance curves}{39}{section*.74}%
-\contentsline {paragraph}{Low correlation between capacitance curves}{39}{section*.77}%
-\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{39}{section.2.3}%
-\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{39}{subsection.2.3.1}%
+\contentsline {paragraph}{High correlation between capacitance curves}{39}{section*.72}%
+\contentsline {paragraph}{Low correlation between capacitance curves}{39}{section*.75}%
+\contentsline {section}{\numberline {2.3}Mask Aligner operation}{39}{section.2.3}%
+\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{39}{subsection.2.3.1}%
 \contentsline {chapter}{\numberline {3}Electronics}{41}{chapter.3}%
-\contentsline {section}{\numberline {3.1}Slip Stick Principle}{41}{section.3.1}%
+\contentsline {section}{\numberline {3.1}Slip stick principle}{41}{section.3.1}%
 \contentsline {section}{\numberline {3.2}RHK}{42}{section.3.2}%
 \contentsline {subsection}{\numberline {3.2.1}Overview}{42}{subsection.3.2.1}%
-\contentsline {paragraph}{amplitude}{42}{section*.80}%
-\contentsline {paragraph}{sweep period}{42}{section*.81}%
-\contentsline {paragraph}{time between sweeps}{42}{section*.82}%
+\contentsline {paragraph}{amplitude}{42}{section*.78}%
+\contentsline {paragraph}{sweep period}{42}{section*.79}%
+\contentsline {paragraph}{time between sweeps}{42}{section*.80}%
 \contentsline {subsection}{\numberline {3.2.2}Pulse shape}{42}{subsection.3.2.2}%
 \contentsline {section}{\numberline {3.3}KIM001}{43}{section.3.3}%
 \contentsline {subsection}{\numberline {3.3.1}Overview}{43}{subsection.3.3.1}%
 \contentsline {subsection}{\numberline {3.3.2}Pulse shape}{43}{subsection.3.3.2}%
 \contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{44}{subsection.3.3.3}%
-\contentsline {section}{\numberline {3.4}Mask Aligner Controller "Walker"}{45}{section.3.4}%
+\contentsline {section}{\numberline {3.4}Mask Aligner controller "Walker"}{45}{section.3.4}%
 \contentsline {subsection}{\numberline {3.4.1}Overview}{45}{subsection.3.4.1}%
 \contentsline {subsection}{\numberline {3.4.2}Signal generation}{46}{subsection.3.4.2}%
 \contentsline {subsection}{\numberline {3.4.3}Fast flank}{47}{subsection.3.4.3}%
 \contentsline {subsection}{\numberline {3.4.4}Amplification}{48}{subsection.3.4.4}%
 \contentsline {subsection}{\numberline {3.4.5}Parameters}{48}{subsection.3.4.5}%
-\contentsline {paragraph}{Amplitude (amp)}{48}{section*.100}%
-\contentsline {paragraph}{Voltage (volt)}{49}{section*.101}%
-\contentsline {paragraph}{Channel}{49}{section*.102}%
-\contentsline {paragraph}{Max Step}{49}{section*.103}%
-\contentsline {paragraph}{Polarity}{49}{section*.104}%
-\contentsline {subsection}{\numberline {3.4.6}Measured Pulse shape}{49}{subsection.3.4.6}%
+\contentsline {paragraph}{Amplitude (amp)}{48}{section*.98}%
+\contentsline {paragraph}{Voltage (volt)}{49}{section*.99}%
+\contentsline {paragraph}{Channel}{49}{section*.100}%
+\contentsline {paragraph}{Max Step}{49}{section*.101}%
+\contentsline {paragraph}{Polarity}{49}{section*.102}%
+\contentsline {subsection}{\numberline {3.4.6}Measured pulse shape}{49}{subsection.3.4.6}%
 \contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{51}{subsection.3.4.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner Repairs and Optimizations}{52}{chapter.4}%
+\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{52}{chapter.4}%
 \contentsline {section}{\numberline {4.1}Overview}{52}{section.4.1}%
 \contentsline {section}{\numberline {4.2}General UHV device preparation}{52}{section.4.2}%
 \contentsline {subsection}{\numberline {4.2.1}Adding components}{52}{subsection.4.2.1}%
 \contentsline {subsection}{\numberline {4.2.2}Soldering}{53}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering Anchors}{53}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo Reglueing}{57}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 Motor}{58}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front Plate repair}{59}{subsection.4.5.1}%
+\contentsline {section}{\numberline {4.3}Soldering anchors}{53}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo reglueing}{57}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 motor}{58}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{59}{subsection.4.5.1}%
 \contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{62}{subsection.4.5.2}%
 \contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{63}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final Test}{63}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and Measurement}{66}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Silicon}{66}{section.5.1}%
-\contentsline {subsection}{\numberline {5.1.1}Evaporation Configuration}{66}{subsection.5.1.1}%
-\contentsline {subsection}{\numberline {5.1.2}Contamination}{69}{subsection.5.1.2}%
-\contentsline {subsection}{\numberline {5.1.3}Penumbra}{70}{subsection.5.1.3}%
-\contentsline {subsection}{\numberline {5.1.4}Tilt}{73}{subsection.5.1.4}%
-\contentsline {subsection}{\numberline {5.1.5}Simulation}{74}{subsection.5.1.5}%
-\contentsline {paragraph}{Improvements}{77}{section*.160}%
-\contentsline {chapter}{Conclusions and Outlook}{78}{chapter*.162}%
-\contentsline {chapter}{Bibliography}{79}{chapter*.163}%
-\contentsline {chapter}{List of Abbreviations}{80}{chapter*.164}%
-\contentsline {section}{\numberline {5.2}LockIn Amplifier Settings}{81}{section.5.2}%
-\contentsline {section}{\numberline {5.3}New Driver Electronics}{81}{section.5.3}%
-\contentsline {paragraph}{pulse?}{81}{section*.165}%
-\contentsline {paragraph}{pol x}{81}{section*.166}%
-\contentsline {paragraph}{amp x}{81}{section*.167}%
-\contentsline {paragraph}{volt x}{81}{section*.168}%
-\contentsline {paragraph}{channel x}{81}{section*.169}%
-\contentsline {paragraph}{maxmstep x}{81}{section*.170}%
-\contentsline {paragraph}{step x}{81}{section*.171}%
-\contentsline {paragraph}{mstep x}{81}{section*.172}%
-\contentsline {paragraph}{cancel}{82}{section*.173}%
-\contentsline {paragraph}{help}{82}{section*.174}%
-\contentsline {section}{\numberline {5.4}Raycast Simulation}{82}{section.5.4}%
-\contentsline {paragraph}{radius\_1}{82}{section*.175}%
-\contentsline {paragraph}{angle}{82}{section*.176}%
-\contentsline {paragraph}{radius\_mask}{82}{section*.177}%
-\contentsline {paragraph}{distance\_circle\_mask}{82}{section*.178}%
-\contentsline {paragraph}{distance\_sample}{82}{section*.179}%
-\contentsline {paragraph}{rays\_per\_frame}{82}{section*.180}%
-\contentsline {paragraph}{running\_time}{82}{section*.181}%
-\contentsline {paragraph}{deposition\_gain}{82}{section*.182}%
-\contentsline {paragraph}{penalize\_deposition}{82}{section*.183}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{82}{section*.184}%
-\contentsline {paragraph}{oscillation\_period}{82}{section*.185}%
-\contentsline {paragraph}{delay\_oscill\_time}{83}{section*.186}%
-\contentsline {paragraph}{save\_in\_progress\_images}{83}{section*.187}%
-\contentsline {paragraph}{save\_intervall}{83}{section*.188}%
-\contentsline {paragraph}{oscillation\_dir}{83}{section*.189}%
-\contentsline {paragraph}{oscillation\_rot\_s}{83}{section*.190}%
-\contentsline {paragraph}{oscillation\_rot\_e}{83}{section*.191}%
-\contentsline {paragraph}{random\_seed}{83}{section*.192}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{83}{section*.193}%
-\contentsline {paragraph}{resolution}{83}{section*.194}%
-\contentsline {paragraph}{path}{83}{section*.195}%
-\contentsline {chapter}{Acknowledgments}{84}{chapter*.196}%
+\contentsline {section}{\numberline {4.7}Final test}{63}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{66}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{66}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Contamination}{69}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Penumbra}{70}{section.5.3}%
+\contentsline {section}{\numberline {5.4}Tilt}{75}{section.5.4}%
+\contentsline {section}{\numberline {5.5}Simulation}{77}{section.5.5}%
+\contentsline {paragraph}{Software improvements}{82}{section*.160}%
+\contentsline {chapter}{Conclusions and Outlook}{83}{chapter*.162}%
+\contentsline {chapter}{Bibliography}{84}{chapter*.163}%
+\contentsline {chapter}{List of Abbreviations}{85}{chapter*.164}%
+\contentsline {section}{\numberline {A}LockIn Amplifier Settings}{i}{section.5.1}%
+\contentsline {section}{\numberline {B}New Driver Electronics}{i}{section.5.2}%
+\contentsline {paragraph}{pulse?}{i}{section*.166}%
+\contentsline {paragraph}{pol x}{i}{section*.167}%
+\contentsline {paragraph}{amp x}{i}{section*.168}%
+\contentsline {paragraph}{volt x}{i}{section*.169}%
+\contentsline {paragraph}{channel x}{i}{section*.170}%
+\contentsline {paragraph}{maxmstep x}{i}{section*.171}%
+\contentsline {paragraph}{step x}{i}{section*.172}%
+\contentsline {paragraph}{mstep x}{ii}{section*.173}%
+\contentsline {paragraph}{cancel}{ii}{section*.174}%
+\contentsline {paragraph}{help}{ii}{section*.175}%
+\contentsline {section}{\numberline {C}Raycast Simulation}{ii}{section.5.3}%
+\contentsline {paragraph}{radius\_1}{ii}{section*.176}%
+\contentsline {paragraph}{angle}{ii}{section*.177}%
+\contentsline {paragraph}{radius\_mask}{ii}{section*.178}%
+\contentsline {paragraph}{distance\_circle\_mask}{ii}{section*.179}%
+\contentsline {paragraph}{distance\_sample}{ii}{section*.180}%
+\contentsline {paragraph}{rays\_per\_frame}{ii}{section*.181}%
+\contentsline {paragraph}{running\_time}{ii}{section*.182}%
+\contentsline {paragraph}{deposition\_gain}{ii}{section*.183}%
+\contentsline {paragraph}{penalize\_deposition}{ii}{section*.184}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{iii}{section*.185}%
+\contentsline {paragraph}{oscillation\_period}{iii}{section*.186}%
+\contentsline {paragraph}{delay\_oscill\_time}{iii}{section*.187}%
+\contentsline {paragraph}{save\_in\_progress\_images}{iii}{section*.188}%
+\contentsline {paragraph}{save\_intervall}{iii}{section*.189}%
+\contentsline {paragraph}{oscillation\_dir}{iii}{section*.190}%
+\contentsline {paragraph}{oscillation\_rot\_s}{iii}{section*.191}%
+\contentsline {paragraph}{oscillation\_rot\_e}{iii}{section*.192}%
+\contentsline {paragraph}{random\_seed}{iii}{section*.193}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{iii}{section*.194}%
+\contentsline {paragraph}{resolution}{iii}{section*.195}%
+\contentsline {paragraph}{path}{iii}{section*.196}%
+\contentsline {chapter}{Acknowledgments}{iv}{chapter*.197}%