diff --git a/acknowledgments.aux b/acknowledgments.aux
index 7a71cf8308dc6483afef7d0a72ebd9356b72d0c5..a530a4a2636f054af7e5bd220aed1073c438fde4 100644
--- a/acknowledgments.aux
+++ b/acknowledgments.aux
@@ -1,9 +1,6 @@
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 \providecommand\hyper@newdestlabel[2]{}
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-\@writefile{tdo}{\contentsline {todo}{Thank Jonas Duffhaus and Paul Dinslage}{ix}{section*.132}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Acknowledgments}{ix}{chapter*.127}\protected@file@percent }
 \@setckpt{acknowledgments}{
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 \setcounter{subfigure}{0}
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diff --git a/acknowledgments.tex b/acknowledgments.tex
index 0e6fc47e148dea87c9016a796bba5564f4acf398..6cac8a37d8f55ca635e32073deced201df0ae770 100644
--- a/acknowledgments.tex
+++ b/acknowledgments.tex
@@ -1,13 +1,26 @@
 \chapter*{Acknowledgments}
 \addcontentsline{toc}{chapter}{Acknowledgments}
 
-I want to thank Florian Muckel for teaching me all the techniques I needed for the repairs on the mask aligner, as well as general aid in the first half of my thesis.
+First and foremost, I want to thank Prof. Dr. Markus Morgenstern for giving me the opportunity to write this thesis and for the constant advice that he gave during the work on this thesis.
 
-For help with writing the software for the Walker and explanations of the existing Walker code, I want to thank Jonas Duffhaus. 
-For the building of the mask aligner controller and patience with debugging of the Walker software, I want to thank both Paul Dinslage and Uwe Wichmann.
+I want to thank Dr. Florian Muckel for teaching me all the techniques I needed for the repairs on the mask aligner, as well as general aid in the first half of my thesis. His expertise in the workings of the group and the repair and optimization of instruments have provided me with the resources needed to be able to work on the Mask Aligner and understand its mechanical workings.
+
+For help with writing the software for the Walker and explanations of the existing Walker code, I want to thank Jonas Duffhaus. Without the existing codebase and explanations of how some particular parts work, the programming would have taken much longer and been more difficult.
+For the building of the mask aligner controller and patience with debugging of the Walker software, I want to thank both Paul Dinslage and Uwe Wichmann. Without them the new Walker would not exist, and the hardware problems are not within my capability to solve.
+
+I would also like to express my gratitude to my supervisors, Jonas Beeker and Dr. Priyamvada Bhaskar, for their guidance and support throughout my master’s thesis. Their feedback and expertise have, I am particularly thankful for the time they dedicated to reviewing my work and providing feedback on the outline and writing of this thesis. As well as understanding the results better and coming to a conclusion about the measurements.
+
+For frequent discussion and general help, as well as the increase in pressure of my system, I want to thank Michiel Reul. Without his Gold evaporations the Mask Aligner lab would have been a lot more boring.
+
+For help regarding AFM results and Chamber operation (Leak-testing) I would also like to thank Dr. Marcus Liebmann and Dr. Marco Pratzer.
+
+For help with SEM measurement and other support, I want to thank Kanji Furuta and Thorben Frahm for the additional EDX measurement and clarifications regarding SEM measurements. 
+
+For the nice group atmosphere and interesting discussions I would like to thank the whole work group Jeff Strasdas, Benjamin Pestka, Michiel Reul, Tim Jacobs, Dishi Gingwar, Niklas Leuth, Marcus Eßer, Reza Habibipour.
+
+For the quick work and pleasant atmosphere during the creation and repair of parts, I want to thank the entire crew of the workshop 
+
+Lastly, I want to thank my family for proofreading this thesis and providing feedback, and emotional support during the creation of this thesis. In particular, I would like to thank my father for reading the thesis in full and pointing out errors and hard to understand sections.
 
 
-\todo{Thank Florian Muckel}
-\todo{Thank Jonas Beeker and Priya}
-\todo{Thank Jonas Duffhaus and Paul Dinslage}
 
diff --git a/appendix.aux b/appendix.aux
index 4a5718d30b3eaeae651a6648c7473be9ce2ffa7f..ab303364878758f27efaed0218ebda35bd2c852e 100644
--- a/appendix.aux
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diff --git a/appendix.tex b/appendix.tex
index 6cb16dddf3234ebf6dd063ab53a840056db8471f..e122f7a3b1394ac9a2eaf402fb15a70e1d7684f9 100644
--- a/appendix.tex
+++ b/appendix.tex
@@ -49,11 +49,11 @@ Changes the polarization direction. Default state is $1$, but can be set to $-1$
 \paragraph{amp x}
 Changes the amplitude of the internally generated pulse. This affects the output peak voltage. The maximum value is $100$, which corresponds to $120$ V peak to peak. The default value is $67$, which corresponds to $80.4$ V.
 \paragraph{volt x}
-Sets the output voltage of the signal generated. Internally this sets the amp parameter, which has limited precision. Due to this the voltage value input will only be output approximately. The possible range is $0$-$120$ V peak. The script will give back the actual voltage that will be output. Default is $80$ V.
+Sets the output voltage of the signal generated. Internally, this sets the amp parameter, which has limited precision. Due to this, the voltage value input will only be output approximately. The possible range is $0$-$120$ V peak. The script will give back the actual voltage that will be output. Default is $80$ V.
 \paragraph{channel x}
-Sets which channels should be output. X is of the form $z_1z_2z_3x$ where each value can be either $0$ to not pass any signal through or $1$ to pass signal through. For example activating only channels Z1 and X would be accomplished by "channel 1001". The command has an alias as "ch x", which can be used in exactly the same way.
+Sets which channels should be output. X is of the form $z_1z_2z_3x$ where each value can be either $0$ to not pass any signal through or $1$ to pass signal through. For example, activating only channels Z1 and X would be accomplished by "channel 1001". The command has an alias as "ch x", which can be used in exactly the same way.
 \paragraph{maxmstep x}
-Sets the maximum amount of steps that can be run at once. This is a safety measure to ensure no one accidentally types a value to large and crashes the mask into the sample. If the value of steps is exceeded the command will be ignored. This command has an alias as "maxsteps x", which can be used in exactly the same way. Allowed values are any positive integers.
+Sets the maximum amount of steps that can be run at once. This is a safety measure to ensure no one accidentally types a value too large and crashes the mask into the sample. If the value of steps is exceeded, the command will be ignored. This command has an alias as "maxsteps x", which can be used in exactly the same way. Allowed values are any positive integers.
 \paragraph{step x}
 Drives a single step in the specified direction. Allowed values are $1$ or $-1$. Direction of movement is determined by the "pol" parameter, by default $-1$ approaches and $1$ retracts.
 \paragraph{mstep x}
@@ -66,20 +66,20 @@ 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}\label{sec:appendix_raycast}
-The raycasting simulation takes the following parameters:
+The ray casting simulation takes the following parameters:
 
 \paragraph{radius\_1}
 The radius of the circle representing the crucible in Godot spacial units.
 \paragraph{angle}
 The angle of the cone in which rays are emitted from the crucible.
 \paragraph{radius\_mask}
-The radius of the cylinder collider representing the hole in the mask.
+The radius of the cylinder collider, representing the hole in the mask.
 \paragraph{distance\_circle\_mask}
 The distance between crucible and mask in Godot spacial units.
 \paragraph{distance\_sample}
 The distance between the sample and the mask in Godot spacial units.
 \paragraph{rays\_per\_frame}
-The amount of rays cast per time step of computation. Higher values means more "material" gets deposited.
+The amount of rays cast per time step of computation. Higher values mean more "material" gets deposited.
 \paragraph{running\_time}
 The amount of time steps the simulation is run for.
 \paragraph{deposition\_gain}
@@ -93,20 +93,21 @@ The period in time steps for the noise oscillation.
 \paragraph{delay\_oscill\_time}
 The time delay in time steps before the noise oscillation starts.
 \paragraph{save\_in\_progress\_images}
-Bollean value determining if images are stored before the full simulation time has elapsed. If false only one image is saved at the end.
+Boolean value, determining if images are stored before the full simulation time has elapsed. If false, only one image is saved at the end.
 \paragraph{save\_intervall}
-The intervall at which images are stored in time steps. Does nothing if save\_in\_progress\_images is false.
+The interval at which images are stored in time steps. Does nothing if save\_in\_progress\_images is false.
 \paragraph{oscillation\_dir}
-The direction of translational displacement enacted by the oscillation. After half a period the hole collider will be displaced by this amount. Oscillation always starts at the origin in x and z.
+The direction of translational displacement enacted by the oscillation. After half a period, the hole collider will be displaced by this amount. Oscillation always starts at the origin in x and z.
 \paragraph{oscillation\_rot\_s}
-The starting rotation of the hole in degrees. The hole collider oscillates between oscillation\_rot\_s and oscillation\_rot\_e. For constant tilt set them both the same.
+The starting rotation of the hole in degrees. The hole collider oscillates between oscillation\_rot\_s and oscillation\_rot\_e. For constant tilt, set them both the same.
 \paragraph{oscillation\_rot\_e}
-The ending rotation of the hole in degrees. The hole collider oscillates between oscillation\_rot\_s and oscillation\_rot\_e. For constant tilt set them both the same.
+The ending rotation of the hole in degrees. The hole collider oscillates between oscillation\_rot\_s and oscillation\_rot\_e. For constant tilt, set them both the same.
 \paragraph{random\_seed}
 The random seed for the pseudo random number generator used to generate rays. Can be set to get consistent results.
 \paragraph{x\_min, x\_max, y\_min, y\_max}
-The outer edges of the 2D image on the sample collider in godot spacial coordinates.
+The outer edges of the 2D image of the sample collider in Godot spacial coordinates.
 \paragraph{resolution}
 The resolution of the image in pixels.
 \paragraph{path}
-The path the images are saved to. In progress images are saved with an additional step number appended to the string before the file format. File format must be .csv otherwise script will fail.
\ No newline at end of file
+The path the images are saved to. In progress, images are saved with an additional step number appended to the string before the file format. File format must be .csv otherwise script will fail.
+
diff --git a/bibliography.aux b/bibliography.aux
index 5ad31777601bcf1a818d633a2a91412824b7fae3..f7d9f4bbdfb49526d837930a66aadb7103b6f7b3 100644
--- a/bibliography.aux
+++ b/bibliography.aux
@@ -14,7 +14,7 @@
 \bibcite{Tungsten_evap}{{10}{}{{}}{{}}}
 \bibcite{tungsten_evaporation}{{11}{}{{}}{{}}}
 \bibcite{Vapor_depo_princ}{{12}{}{{}}{{}}}
-\@writefile{toc}{\contentsline {chapter}{Bibliography}{88}{chapter*.93}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Bibliography}{90}{chapter*.91}\protected@file@percent }
 \bibcite{sputter_damage}{{13}{}{{}}{{}}}
 \bibcite{florian_forster}{{14}{}{{}}{{}}}
 \bibcite{afm_physics}{{15}{}{{}}{{}}}
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 \bibcite{arduino_cpu_datasheet}{{25}{}{{}}{{}}}
 \bibcite{switch_datasheet}{{26}{}{{}}{{}}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces Schematic diagram of a general E-beam evaporation chamber. The B-field is used to focus the beam onto the source. Alternatively, one can use a filament nearby and put the crucible under positive potential, which will attract the emitted electrons from the filament. The shutter is used to control when the beam can interact with the sample. The funnel is used to focus the vapor beam. }}{5}{figure.caption.3}\protected@file@percent }
 \providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
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+\newlabel{fig:e-beam_evap}{{1.1}{5}{Schematic diagram of a general E-beam evaporation chamber. The B-field is used to focus the beam onto the source. Alternatively, one can use a filament nearby and put the crucible under positive potential, which will attract the emitted electrons from the filament. The shutter is used to control when the beam can interact with the sample. The funnel is used to focus the vapor beam}{figure.caption.3}{}}
 \citation{CASINO}
 \citation{knudsen}
 \newlabel{eq:hertz_knudsen}{{1.1}{6}{Electron beam evaporation}{equation.1.1.1}{}}
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+\newlabel{fig:penumbra_explanation}{{1.3}{10}{Diagram showing the geometrical reason for the creation of a penumbra in the evaporation from a non point source. The crucible is placed at distance $l$ from the mask, and beams emit from either side of the crucible to each side of the hole in the mask. The area where only beams from one side of the crucible hit the sample receives fewer particles, and thus the deposition rate in the area decreases}{figure.caption.6}{}}
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diff --git a/chap01.tex b/chap01.tex
index b4004251114fb419fd620b6b130515e7c1495683..d7b9399b65483f7456df5c7a48cbfd93aab69d39 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -1,27 +1,27 @@
 % !TeX spellcheck = <en-US>
 \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.
+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 a sample surface, as well as explain the basic evaporation and alignment setup the Mask Aligner uses.
 
 \section{Electron beam evaporation}
 Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique used in vacuum and \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) conditions, to deposit material onto a substrates surface. 
 
 \begin{figure}[H]
     \centering
-y    \includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
-    \caption{Schematic diagram of a general E-beam evaporation chamber. The B-field is used to focus the beam onto the source. Alternatively one can use a filament nearby and put the crucible under positive potential, which will attract the emitted electrons from the filament. The shutter is used to control when the beam can interact with the sample. The funnel is used to focus the vapor beam. }
+    \includegraphics[width=0.5\linewidth]{img/EBeamDep.pdf}
+    \caption{Schematic diagram of a general E-beam evaporation chamber. The B-field is used to focus the beam onto the source. Alternatively, one can use a filament nearby and put the crucible under positive potential, which will attract the emitted electrons from the filament. The shutter is used to control when the beam can interact with the sample. The funnel is used to focus the vapor beam. }
     \label{fig:e-beam_evap}
 \end{figure}
  
-The general setup of an electron beam evaporator is seen in Figure \ref{fig:e-beam_evap}. The source material is placed inside a crucible as pellets of ultra pure ($>99$ \%) material.
+The general setup of an electron beam evaporator is seen in Figure \ref{fig:e-beam_evap}. The source material is placed inside a crucible as pellets of ultrapure ($>99$ \%) material.
 The crucible is also heated during the evaporation process, in order to prevent the crucible itself from being damaged a material with high melting point has to be chosen. Tungsten with a melting point of 3695 K \cite{Tungsten_melt} is usually chosen. Additionally, the crucible usually has to be water cooled to prevent damaging the system.
 
 In order to heat the source material locally beyond its boiling point it is hit with a high current electron beam ($\mathcal{O}$($1$ kV)), emitted by either an electron gun or a filament, this beam usually has to be focused using magnetic fields to hit the source material. The highly energetic electrons interact with the atomic nuclei and the atomic electrons of the source material and transfer energy. This energy transfer heats the hit atoms locally and eventually causes the system to reach its melting and then its boiling point, if enough current is applied to give the required heating power. \\
 
-The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)\cite{CASINO} so the heating occurs only very near to the source materials surface. This allows for less energy loss and more controlled evaporation as the crucible and the rest of the system is not heated by the electron beam directly, but only by the radiant heat emitted by the source material.\\
+The penetration depth of electron with ($<5$ kV) is less than 0.4 $\mu$m (estimated using CASINO Monte Carlo software)\cite{CASINO} so the heating occurs only very near to the source material's surface. This allows for less energy loss and more controlled evaporation as the crucible and the rest of the system is not heated by the electron beam directly, but only by the radiant heat emitted by the source material.\\
 
-When the material reaches its boiling point it forms a vapor, which is directed through a funnel to the samples surface. The sample is kept at a temperature much colder than the source materials boiling temperature, due to this the material beam will deposit and condense on the substrates surface forming a thin film. \\
+When the material reaches its boiling point, it forms a vapor, which is directed through a funnel to the sample's surface. The sample is kept at a temperature much colder than the source material's boiling temperature, due to this the material beam will deposit and condense on the substrate's surface forming a thin film. \\
 
-In order to ensure the material beam reaches the sample unperturbed the mean free path (MFP) of a traveling particle in the environment has to be larger than the distance to the samples surface. For this reason high vacuum (HV) (MFP of $10$ cm to $1$ km) or ultra high vacuum conditions (UHV) (MFP of $1$ km to $10^5$ km) are required for electron beam evaporation.
+In order to ensure the material beam reaches the sample unperturbed, the mean free path (MFP) of a traveling particle in the environment has to be larger than the distance to the sample's surface. For this reason, high vacuum (HV) (MFP of $10$ cm to $1$ km) or ultra-high vacuum conditions (UHV) (MFP of $1$ km to $10^5$ km) are required for electron beam evaporation.
 
 The deposition rate of the evaporator can be measured using a molecular flux monitor or a quartz balance. The deposition of a material follows the Hertz-Knudsen equation around the equilibrium gas pressure ($p_e$):
 \begin{equation}
@@ -29,17 +29,18 @@ The deposition rate of the evaporator can be measured using a molecular flux mon
 	\label{eq:hertz_knudsen}
 \end{equation}
 
-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 of the impinging gas, $m$ is the mass of a single particle, $k_B$ is the Boltzmann constant and $T$ is the temperature.\cite{knudsen} When the sticking parameter 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. In practice this is however difficult to estimate, since the pressure of the evaporant gas is difficult to determine. Instead, usually a calibration evaporations are performed for different particle fluxes and different times to determine the deposition rate for a given setup. Since the Hertz-Knudsen equation is linear in gas pressure this should give a linear dependence.
+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 of the impinging gas, $m$ is the mass of a single particle, $k_B$ is the Boltzmann constant and $T$ is the temperature.\cite{knudsen} When the sticking parameter 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. In practice, this is however difficult to estimate, since the pressure of the evaporant gas is difficult to determine. Instead, usually a calibration evaporations are performed for different particle fluxes and different times to determine the deposition rate for a given setup. Since the Hertz-Knudsen equation is linear in gas pressure, this should give a linear dependence.
 
 Some of the advantages that e-beam evaporation has over other techniques such as thermal evaporation or sputtering 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, in contrast to 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. \cite{Vapor_depo_princ}
 
-In order to control the duration of the evaporation precisely a shutter is usually included in the evaporation chamber which can be closed or opened to control when the sample is exposed to the vapor beam. This is also needed for improved deposition rate accuracy since the source material needs to initially heat up when the electron beam is started, which leads to unstable flux at the start of the evaporation. By closing the shutter this can be avoided.
+In order to control the duration of the evaporation precisely, a shutter is usually included in the evaporation chamber which can be closed or opened to control when the sample is exposed to the vapor beam. This is also needed for improved deposition rate accuracy, since the source material needs to initially heat up when the electron beam is started, which leads to unstable flux at the start of the evaporation. By closing the shutter, this can be avoided.
 
 \subsection{Mask Aligner lead evaporator}
-The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in $2009$.\cite{florian_forster} The crucible of this evaporator is made from tungsten. The evaporator uses a filament placed near the crucible to bombard the material placed inside the crucible with highly energetic electrons. To accomplish this a high current (up to $1$ kV) is applied between filament and crucible to emit electrons from the filament to the crucible. In addition, the system can be heated with radiative heat from the filament. This is also used to degas the evaporator and to prevent contaminants from settling on the filament, when no evaporation is taking place. The heating element and crucible are surrounded by a copper cylinder, that functions as a heat sink for the system. The heat sink needs to be water cooled to prevent damage to the evaporator. In order to prevent cooling failure, a thermal sensor measures the temperature of the copper cylinder. \\
+The electron beam evaporator used for the lead evaporation in the mask aligner chamber was built by Florian Forster in $2009$.\cite{florian_forster} The crucible of this evaporator is made from tungsten. The evaporator uses a filament placed near the crucible to bombard the material placed inside the crucible with highly energetic electrons. To accomplish this, a high current (up to $1$ kV) is applied between filament and crucible to emit electrons from the filament to the crucible. In addition, the system can be heated with radiative heat from the filament. This is also used to degas the evaporator and to prevent contaminants from settling on the filament, when no evaporation is taking place. The heating element and crucible are surrounded by a copper cylinder, that functions as a heat sink for the system. The heat sink needs to be water cooled to prevent damage to the evaporator. In order to prevent cooling failure, a thermal sensor measures the temperature of the copper cylinder. \\
+
 
 \begin{figure}[H]
     \centering
@@ -48,12 +49,12 @@ The electron beam evaporator used for the lead evaporation in the mask aligner c
     \label{fig:ma_evap}
 \end{figure}
 
-In order to control the molecular flow, one can change the current applied to the filament or the voltage accelerating the electron beam towards the source. Additionally, the crucible can be shifted on the z-axis closer to or further away from the filament, controlling the amount of heating that is received by the source material. This method of temperature control was unused in this thesis, as the distance was previously optimized already. In order to determine if the applied controls have the desired effect, the current of $\text{Pb}^+$ ions leaving the crucible is measured by a flux monitor positioned at the top of the evaporator, below the shutter, which can be used to open the molecular flow to the mask aligner chamber. An schematic of the evaporator can be seen in Figure \ref{fig:ma_evap}\\
+In order to control the molecular flow, one can change the current applied to the filament or the voltage accelerating the electron beam towards the source. Additionally, the crucible can be shifted on the z-axis closer to or further away from the filament, controlling the amount of heating that is received by the source material. This method of temperature control was unused in this thesis, as the distance was previously optimized already. In order to determine if the applied controls have the desired effect, the current of $\text{Pb}^+$ ions leaving the crucible is measured by a flux monitor positioned at the top of the evaporator, below the shutter, which can be used to open the molecular flow to the mask aligner chamber. A schematic of the evaporator can be seen in Figure \ref{fig:ma_evap}\\
 
 \section{Stencil lithography}
-Stencil lithography is a method of depositing patterned structures on a nanometer scale on substrates (sample) using a stencil. The stencil is made of a membrane of \ce{SiN} that is patterned with a lithography process such as electron beam lithography. Using e-beam lithography masks can be produced at sub micrometer scales \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) processes are used to deposit material on the substrates surface, while the mask is placed on top of the sample. The mask protects the substrate from the molecular beam, except in the places where the pattern has been cut into the mask. In this way the pattern is transferred from the mask to the sample. \\
-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. \\
+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 substrate's surface, while the mask is placed on top of the sample. The mask protects the substrate from the molecular beam, except in the places where the pattern has been cut into the mask. In this way, the pattern is transferred from the mask to the sample. \\
+Stencil Lithography can also be used for etching where patterns are cut into the substrate's 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. \\
 While versatile since any pattern can be deposited or etched using stencil lithography, stencil lithography comes with challenges. 
 Material is also deposited on the masks including in the aperture of the pattern, which reduces the effective aperture over time. This means that while masks can be reused, they cannot be reused indefinitely.
 One of the biggest challenges is that in order to get sharp patterns on the substrates surface the mask has ideally to be placed directly on the surface of the sample as otherwise effects resulting from the limited coherence length of the molecular beam used in physical vapor deposition result in a "blurring" of the structures. However, direct placement of the mask on the substrates surface has the potential to contaminate or damage both mask and sample and should be avoided for materials very sensitive to mechanical damage or when measurement of the sample in highly sensitive devices such as \textbf{S}canning \textbf{T}unneling \textbf{M}icroscopes (STMs) is intended.  \\
@@ -61,9 +62,9 @@ One of the biggest challenges is that in order to get sharp patterns on the subs
 The Mask Aligner is a tool designed to overcome the challenge of sample mask alignment, allowing precise control of mask sample distance. 
 
 \subsubsection{Penumbra}
-The molecular beam, the evaporator generates, is not a set of perfectly parallel beams rather it will be a spread of beams at slightly different angles. Its beam spread is determined by the size of the crucible in which the material evaporation takes place and is $a=5$ mm for the setup found on the Mask Aligner. For the purposes of this explanation the spread of different molecular beams will be modeled by its two extremal cones of parallel beams, created by the size of the crucible.\\
+The molecular beam, the evaporator generates, is not a set of perfectly parallel beams, rather it will be a spread of beams at slightly different angles. Its beam spread is determined by the size of the crucible in which the material evaporation takes place, and is $a=5$ mm for the setup found on the Mask Aligner. For the purposes of this explanation, the spread of different molecular beams will be modeled by its two extreme cones of parallel beams, created by the size of the crucible.\\
 
-The area where the cones of both beams overlap is called the "umbra" in analogy to the exact same phenomenon in optics. This can be seen in Figure \ref{fig:penumbra_explanation} as the red area. The region where only one of the cones hits the sample, but the other is blocked by the mask is called the "penumbra". This can be seen as the orange surface in Figure \ref{fig:penumbra_explanation}. Here the evaporated structure is smeared out similar to the edge of a soft shadow. \\
+The area where the cones of both beams overlap is called the "umbra" in analogy to the exact same phenomenon in optics. This can be seen in Figure \ref{fig:penumbra_explanation} as the red area. The region where only one of the cones hits the sample, but the other is blocked by the mask, is called the "penumbra". This can be seen as the orange surface in Figure \ref{fig:penumbra_explanation}. Here the evaporated structure is smeared out similar to the edge of a soft shadow. \\
 
 The width of the penumbra $p$ is determined by the distance of the beam source to the sample $l$, as with longer length the beams will be less coherent, the size of the crucible $b$ and the distance between mask and sample $d$. Given these parameters the size of the penumbra can be estimated using Figure \ref{fig:penumbra_explanation}, since $l >> a$ the rays coming from the crucible can be assumed to be approximately parallel:\\
 
@@ -74,16 +75,16 @@ The width of the penumbra $p$ is determined by the distance of the beam source t
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.5\linewidth]{img/Plots/Background/Penumbra_diagramm.pdf}
-    \caption{Diagram showing the geometrical reason for the creation of a penumbra in the evaporation from a non point source. The crucible is placed at distance $l$ from the mask and beams emit from either side of the crucible to each side of the hole in the mask. The area where only beams from one side of the crucible hit the sample receives fewer particles and thus the deposition rate in the area decreases.}
+    \caption{Diagram showing the geometrical reason for the creation of a penumbra in the evaporation from a non point source. The crucible is placed at distance $l$ from the mask, and beams emit from either side of the crucible to each side of the hole in the mask. The area where only beams from one side of the crucible hit the sample receives fewer particles, and thus the deposition rate in the area decreases.}
     \label{fig:penumbra_explanation}
 \end{figure}
 
-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.\\
+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, these 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}
 Formerly, the model for the penumbra assumed perfect alignment between mask and sample, but potentially large distance $d$, 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 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 Figure \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 Figure \ref{fig:penumbra_explanation_tilt_sim}.\\
+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 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 Figure \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 Figure \ref{fig:penumbra_explanation_tilt_sim}.\\
 
 \begin{figure}[H]
     \centering
@@ -97,22 +98,22 @@ The mask and the sample also have to be kept parallel as a tilt would result in
     \caption{}
 	\label{fig:penumbra_explanation_tilt_sim}
 	\end{subfigure}
-	\caption{A diagram of the evaporation happening with a tilted mask for only one hole (\subref{fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral radii that appear in a cross-section of the evaporation at the tilt angle. (\subref{fig:penumbra_explanation_tilt_sim}) shows a simulated evaporation with large penumbra for a tilt angle of $45^\circ$ the "half-moon" shaped penumbra, that is wider on one side than on the other, can be seen easily. The penumbra in the simulation is exaggerated for demonstrational purposes. Program used for simulation is described in Section \ref{sec:simulation}}
+	\caption{A diagram of the evaporation happening with a tilted mask for only one hole (\subref{fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral radii that appear in a cross-section of the evaporation at the tilt angle. (\subref{fig:penumbra_explanation_tilt_sim}) shows a simulated evaporation with large penumbra for a tilt angle of $45^\circ$ the "half-moon" shaped penumbra, that is wider on one side than on the other, can be seen easily. The penumbra in the simulation is exaggerated for demonstration purposes. Program used for simulation is described in Section \ref{sec:simulation}}
     \label{fig:penumbra_explanation_tilt}
 \end{figure}
 
 Since the evaporation effectively gives a projection of a circle through an aperture, the resulting image is a conical section. If the alignment between mask and sample is perfect the projection will thus give a circle, but if alignment is off the projection will instead be an ellipse.
 
-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.
+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}
 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}
 
-In order to measure a sample's topography \textbf{A}tomic \textbf{F}orce \textbf{M}icroscopy uses the \textbf{V}an \textbf{d}er \textbf{W}aals (VdW) forces the atoms of a sample enact upon a small scanning probe tip. 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.\\
-A cantilever, which has a small scanning probe tip at its top is suspended above the sample, when the cantilever now comes closer to the sample the tip is either attracted or repulsed by the sample, depending on distance, this causes the cantilever to bend slightly. This setup can be seen in Figure \ref{fig:afm_principle} The cantilever follows Hookes law $F = kx$ so if $k$ is known in principle the force can be determined from the displacement. The VdW force follows a Lennart Jones potential as seen in Figure \ref{fig:afm_potential}.\\
+In order to measure a sample's topography, \textbf{A}tomic \textbf{F}orce \textbf{M}icroscopy uses the \textbf{V}an \textbf{d}er \textbf{W}aals (VdW) forces the atoms of a sample enact upon a small scanning probe tip. 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.\\
+A cantilever, which has a small scanning probe tip at its top is suspended above the sample, when the cantilever now comes closer to the sample the tip is either attracted or repulsed by the sample, depending on distance, this causes the cantilever to bend slightly. This setup can be seen in Figure \ref{fig:afm_principle} The cantilever follows Hooke's law $F = kx$ so if $k$ is known in principle the force can be determined from the displacement. The VdW force follows a Lennart Jones potential as seen in Figure \ref{fig:afm_potential}.\\
 
-In order to detect this bending a laser is directed at the top of the cantilever and reflected to a mirror and then to a four quadrant photodiode, which then sees the bending as a deflection of the laser signal from the middle of the four quadrant sensor. In order to now determine the topography of a sample from the given diode signal there are various methods that can be used. These methods in this work called modes will be given a short explanation here.
+In order to detect this bending, a laser is directed at the top of the cantilever and reflected to a mirror and then to a four quadrant photodiode, which then sees the bending as a deflection of the laser signal from the middle of the four quadrant sensor. In order to now determine the topography of a sample from the given diode signal, there are various methods that can be used. These methods in this work called modes will be given a short explanation here.
 
 \begin{figure}[H]
     \centering
@@ -129,8 +130,8 @@ In contact mode the sample is directly contacted by the cantilever, this is achi
 The main disadvantage of contact mode is that since the cantilever contacts the sample constantly with a constant force both the sample and the cantilever will damage relatively quickly in the process, which is why this technique is only used when this damage to cantilever and sample is non-problematic or even desired. One can for example use contact mode to scratch the sample's surface in specific locations to etch patterns into the surface. \\
 In this thesis, however, both damage to cantilever and sample should be minimized, which is why contact mode is not used.
 \paragraph{Non-Contact}
-Another possible mode for AFM usage is non-contact mode. In this mode the cantilever does not touch the sample at all and instead the attractive potential of the surface to the cantilever is used to map the topography of the sample. In order to accomplish this the cantilever is oscillated near the samples surface close to its natural resonance frequency, like in tapping mode, when the cantilever now approaches the samples surface its resonance frequency is shifted towards a lower value, which then causes the oscillation amplitude to lower with distance to the samples surface, when the tip sample distance is increased the opposite happens. Now two approaches can be taken, either one can use phase or amplitude to determine deviations from the resonance frequency of the cantilever. By either keeping the phase between driving and response at 90° or the amplitude at a set value, both are accomplished by moving the z piezo as the cantilever is moved across the sample allowing the changes in z to give a topographical image of the samples surface. This is called the feedback loop as the feedback from the laser diode measurement drives the signal given to the z piezo to constantly keep the same tip sample distance.\\
-While non-contact mode does keep the tip and the sample undamaged in most cases it comes with the cost of added difficulty since the potential in the non-contact regime is relatively flat, which causes the signal given to the feedback loop to be small in scale and thus prone alterations from other sources, requiring high resolution frequency measurement from the 3d laser sensor or resulting in a low resolution image. Additionally this technique is very sensitive to humidity as in atmospheric conditions a thin water film is on the surface of the sample and the thickness of this film can vary with conditions in the room, for this reason non-contact mode is usually reserved for UHV environments. Instead a different, but similar technique is used for atmospheric conditions.
+Another possible mode for AFM usage is non-contact mode. In this mode the cantilever does not touch the sample at all and instead the attractive potential of the surface to the cantilever is used to map the topography of the sample. In order to accomplish this the cantilever is oscillated near the samples surface close to its natural resonance frequency, like in tapping mode, when the cantilever now approaches the samples surface its resonance frequency is shifted towards a lower value, which then causes the oscillation amplitude to lower with distance to the samples surface, when the tip sample distance is increased the opposite happens. Now two approaches can be taken, either one can use phase or amplitude to determine deviations from the resonance frequency of the cantilever. By either keeping the phase between driving and response at 90° or the amplitude at a set value, both are accomplished by moving the z piezo as the cantilever is moved across the sample, allowing the changes in z to give a topographical image of the sample's surface. This is called the feedback loop, as the feedback from the laser diode measurement drives the signal given to the z piezo to constantly keep the same tip sample distance.\\
+While non-contact mode does keep the tip and the sample undamaged in most cases it comes with the cost of added difficulty since the potential in the non-contact regime is relatively flat, which causes the signal given to the feedback loop to be small in scale and thus prone alterations from other sources, requiring high resolution frequency measurement from the 3d laser sensor or resulting in a low resolution image. Additionally, this technique is very sensitive to humidity as in atmospheric conditions a thin water film is on the surface of the sample and the thickness of this film can vary with conditions in the room, for this reason non-contact mode is usually reserved for UHV environments. Instead, a different, but similar technique is used for atmospheric conditions.
 \paragraph{Tapping}
 Tapping mode is a hybrid of both contact and non-contact modes. It is also sometimes called semi contact mode. Here the tip is oscillated near the resonance frequency again, but closer to the sample's surface, than in non-contact mode. This makes the oscillation see both the attractive and the repulsive part of the tip-surface potential. At the lower part of this oscillation, the tip contacts the surface, thus "tapping" it. The general idea behind the feedback loop from the non-contact mode is the same and a set point is constantly maintained, thus allowing the mapping of the surface. Due to the closer distance to the sample's surface however, both the resolution can be potentially higher and a transparency with regard to thin films on the samples surface can be achieved, at the cost of reducing the tip's lifespan, due to the tapping contacting the surface. The lifetime of the tip is however much longer, than that of contact mode and damage to the sample is, given correct operation, minimal. In this thesis, only the tapping mode of the AFM is used, as the sample was analyzed in atmospheric conditions.
 
@@ -143,11 +144,10 @@ Tapping mode is a hybrid of both contact and non-contact modes. It is also somet
 
 There are more ways to get useful sample information from an AFM, the tip can for example be coated in a magnetic coating in order to perform Magnetic Force Microscopy, but for the purposes of this thesis other uses will be neglected.
 
-AFMs provide high resolution topographical images at the nanometer scale and allow for accurate estimation of surface properties of a samples surface. Atomic force microscopy is a commonly used tool to characterize nano-lithography samples and has been extensively used in physics, material science and biology among others.\cite{afm_physics, afm_bio}
-
+AFMs provide high resolution topographical images at the nanometer scale and allow for accurate estimation of surface properties of a sample's surface. Atomic force microscopy is a commonly used tool to characterize nano-lithography samples and has been extensively used in physics, material science and biology among others.\cite{afm_physics, afm_bio}
 
 \subsection{Scanning Electron Microscopy} 
-A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope (SEM) is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this a sample is hit by a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample the electron can undergo various interactions with the sample.
+A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope (SEM) is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this, a sample is hit by a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample, the electron can undergo various interactions with the sample.
 
 \begin{figure}[H]
     \centering
@@ -161,15 +161,15 @@ A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope (SEM) is a microscope
 	\caption{}
 	\label{fig:sem_setup_interaction}
 	\end{subfigure}
-    \caption{The beam path for an SEM (\subref{fig:sem_setup_beam}). 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}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering 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}
 
-The electron beam of an SEM is 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 (FEEG).\cite{SEM_book} The beam emitted from the electron gun still has too large spread to be used for SEM imaging for this reason the beam must be focused using electron lenses. 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. 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} The different sets of lenses used to direct the beam to the sample can be seen in Figure \ref{fig:sem_setup_beam}. 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 is 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 (FEEG).\cite{SEM_book} The beam emitted from the electron gun still has too large spread to be used for SEM imaging for this reason the beam must be focused using electron lenses. Accurate focusing of the electron beam is one of the major difficulties of SEM design, and measurement uncertainty is usually dominated by optical artifacts from beam focus. 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} The different sets of lenses used to direct the beam to the sample can be seen in Figure \ref{fig:sem_setup_beam}. 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 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} This as well as the other processes that can be measured in an SEM can be seen in Figure \ref{fig:sem_setup_interaction} The secondary electrons 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. The detection of secondary electrons, back-scattered electrons and X-rays can be seen in Figure \ref{fig:sem_setup_beam}. 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.\\
+The main matter interaction that is measured in an SEM is the 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} This as well as the other processes that can be measured in an SEM can be seen in Figure \ref{fig:sem_setup_interaction} The secondary electrons 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 surface's topography, and thus by measuring the voltage given at the PMT a topographical image of the sample can be obtained. The detection of secondary electrons, back-scattered electrons and X-rays can be seen in Figure \ref{fig:sem_setup_beam}. 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 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. \\
+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 semiconducting samples, the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason, the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focusing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference, and thus they are not sufficient for sample characterization. \\
 
 SEM images and in particular the related technologies of \textbf{T}ransmission \textbf{E}lectron \\ \textbf{M}icroscopy and \textbf{S}canning \textbf{Tunneling} \textbf{E}lectron \textbf{M}icroscopy have been used to characterize properties of thin films and characterize interfaces down to the single atomic scale.\cite{self_epitaxy}\\
diff --git a/chap02.aux b/chap02.aux
index 4cd01de9bb2f098fa463cc0f98abe80e21229664..c615cebee3ac7f0afdd8a862c5a7873a00c79be7 100644
--- a/chap02.aux
+++ b/chap02.aux
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 \citation{Beeker}
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-\newlabel{fig:leakage_current}{{2.17}{35}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.33}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{36}{table.caption.34}\protected@file@percent }
-\newlabel{tab:cross_cap}{{2.1}{36}{Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII}{table.caption.34}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty.}}{37}{figure.caption.35}\protected@file@percent }
-\newlabel{fig:mask_old_caps}{{2.18}{37}{The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty}{figure.caption.35}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{38}{figure.caption.36}\protected@file@percent }
-\newlabel{fig:mask_old_correl}{{2.19}{38}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.36}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger.}}{39}{figure.caption.37}\protected@file@percent }
-\newlabel{fig:cross_cap_diagramm}{{2.20}{39}{Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger}{figure.caption.37}{}}
-\@writefile{toc}{\contentsline {paragraph}{Leakage current}{39}{section*.38}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{39}{section*.39}\protected@file@percent }
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-\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{40}{subsection.2.3.1}\protected@file@percent }
-\newlabel{sec:sample_prep}{{2.3.1}{40}{Sample preparation}{subsection.2.3.1}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless.}}{33}{figure.caption.29}\protected@file@percent }
+\newlabel{fig:approach_subsequent}{{2.14}{33}{Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless}{figure.caption.29}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{33}{subsection.2.2.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{33}{section*.30}\protected@file@percent }
+\newlabel{fig:approach_replicability_cap}{{2.15a}{34}{\relax }{figure.caption.31}{}}
+\newlabel{sub@fig:approach_replicability_cap}{{a}{34}{\relax }{figure.caption.31}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.15b}{34}{\relax }{figure.caption.31}{}}
+\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{34}{\relax }{figure.caption.31}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces 3 subsequent approach curves \subref  {fig:approach_replicability_cap} and differences in capacitance for each step \subref  {fig:approach_replicability_cap_diff} recorded. \textcolor {tab_green}{Green} is initial curve. \textcolor {tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier.}}{34}{figure.caption.31}\protected@file@percent }
+\newlabel{fig:approach_replicability}{{2.15}{34}{3 subsequent approach curves \subref {fig:approach_replicability_cap} and differences in capacitance for each step \subref {fig:approach_replicability_cap_diff} recorded. \textcolor {tab_green}{Green} is initial curve. \textcolor {tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.31}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{35}{subsection.2.2.5}\protected@file@percent }
+\newlabel{subsec:cross_cap}{{2.2.5}{35}{Cross capacitances}{subsection.2.2.5}{}}
+\newlabel{fig:cross_cap_approach_difference}{{2.16a}{35}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:cross_cap_approach_difference}{{a}{35}{\relax }{figure.caption.32}{}}
+\newlabel{fig:cross_cap_approach_difference_2}{{2.16b}{35}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:cross_cap_approach_difference_2}{{b}{35}{\relax }{figure.caption.32}{}}
+\newlabel{fig:cross_cap_approach_sim}{{2.16c}{35}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:cross_cap_approach_sim}{{c}{35}{\relax }{figure.caption.32}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref  {fig:cross_cap_approach_difference}, \subref  {fig:cross_cap_approach_difference_2}). (\subref  {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case.}}{35}{figure.caption.32}\protected@file@percent }
+\newlabel{fig:cross_cap_approach}{{2.16}{35}{The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref {fig:cross_cap_approach_difference}, \subref {fig:cross_cap_approach_difference_2}). (\subref {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case}{figure.caption.32}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask, allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample.}}{36}{figure.caption.33}\protected@file@percent }
+\newlabel{fig:leakage_current}{{2.17}{36}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask, allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.33}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{37}{table.caption.34}\protected@file@percent }
+\newlabel{tab:cross_cap}{{2.1}{37}{Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII}{table.caption.34}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same, sharing all features and general shape. The main difference is the scale of the y-axis, and due to this the scale of the uncertainty.}}{38}{figure.caption.35}\protected@file@percent }
+\newlabel{fig:mask_old_caps}{{2.18}{38}{The 3 capacitance curves of the Mask labeled "old", the plots look the same, sharing all features and general shape. The main difference is the scale of the y-axis, and due to this the scale of the uncertainty}{figure.caption.35}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less than $1$ \%.}}{39}{figure.caption.36}\protected@file@percent }
+\newlabel{fig:mask_old_correl}{{2.19}{39}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less than $1$ \%}{figure.caption.36}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger.}}{40}{figure.caption.37}\protected@file@percent }
+\newlabel{fig:cross_cap_diagramm}{{2.20}{40}{Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger}{figure.caption.37}{}}
+\@writefile{toc}{\contentsline {paragraph}{Leakage current}{40}{section*.38}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{40}{section*.39}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{40}{subsection.2.2.6}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{High correlation between capacitance curves}{41}{section*.40}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Low correlation between capacitance curves}{41}{section*.41}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}Mask Aligner operation}{41}{section.2.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{41}{subsection.2.3.1}\protected@file@percent }
+\newlabel{sec:sample_prep}{{2.3.1}{41}{Sample preparation}{subsection.2.3.1}{}}
 \@setckpt{chap02}{
-\setcounter{page}{42}
+\setcounter{page}{43}
 \setcounter{equation}{4}
 \setcounter{enumi}{10}
 \setcounter{enumii}{0}
diff --git a/chap02.tex b/chap02.tex
index 52c8ecff2f5836ba97784090c2ec0f836d2b1c04..f8becf7ca4e5be4182a50e4bdce7a1b2f14e264d 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -1,7 +1,6 @@
 % !TeX spellcheck = <en-US>
 \chapter{Mask Aligner}
 
-
 \begin{figure}[H]
     \centering
 	\begin{subfigure}{0.42\textwidth}
@@ -35,30 +34,30 @@ The sample module is used for the stable fitting of the sample and the movement
 
 The mask module consists of the mask frame (Fig. \ref{fig:mask_aligner_nomenclature_components} H), which holds the mask shuttle (Fig. \ref{fig:mask_aligner_nomenclature_components} J) in place using spring tension and provides \ce{CuBe} contacts for the $3$ capacitance detectors on the mask used for capacitive distance measurement. The contacts are connected to shielded coaxial cables that take the capacitance signal from the mask to the vacuum feedthroughs. The coaxial cables are grounded to the Mask Aligner body (Fig. \ref{fig:mask_aligner_nomenclature_components} P). \\
 
-The motor module of the Mask Aligner consists of $3$ motors of similar build. The motors move the mask on the z axis $3$ different pivot points, due to this the $3$ motors are labeled Z1, Z2 and Z3. The order of the $3$ motors is pictured in Figure \ref{fig:mask_aligner_nomenclature_motors}. Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components} O) that is held in place by $6$ piezostack (made up of $4$ $\approx 0.4$ nF piezo plates each). $4$ of these are attached directly to the Mask Aligner body. While the last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components} N), which is pressed against the sapphire prism using a \ce{CuBe} spring (Fig. \ref{fig:mask_aligner_nomenclature_components} M). The tension of the spring keeps the saphhire prism in its place while still allowing movement of the sapphire prism using the piezostacks. To control the amount of tension the \ce{CuBe} spring provides, it is affixed using a screw, which can be made more firm or loose to provide more or less tension on the sapphire prism. On top of the sapphire prism a \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components} L) is attached, which has a small groove in the middle. A neodym magnet (Fig. \ref{fig:mask_aligner_nomenclature_components} K) is located in the groove of the plate and connects the motor to the mask frame, where a similar \ce{Al2O3} plate setup is placed on the 
-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. \\
+The motor module of the Mask Aligner consists of $3$ motors of similar build. The motors move the mask on the z axis $3$ different pivot points, due to this the $3$ motors are labeled Z1, Z2 and Z3. The order of the $3$ motors is pictured in Figure \ref{fig:mask_aligner_nomenclature_motors}. Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components} O) that is held in place by $6$ piezo stack (made up of $4$ $\approx 0.4$ nF piezo plates each). $4$ of these are attached directly to the Mask Aligner body. While the last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components} N), which is pressed against the sapphire prism using a \ce{CuBe} spring (Fig. \ref{fig:mask_aligner_nomenclature_components} M). The tension of the spring keeps the sapphire prism in its place while still allowing movement of the sapphire prism using the piezo stacks. To control the amount of tension the \ce{CuBe} spring provides, it is affixed using a screw, which can be made more firm or loose to provide more or less tension on the sapphire prism. On top of the sapphire prism, a \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components} L) is attached, which has a small groove in the middle. A neodym magnet (Fig. \ref{fig:mask_aligner_nomenclature_components} K) is located in the groove of the plate and connects the motor to the mask frame, where a similar \ce{Al2O3} plate setup is placed on the 
+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 motor's 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}
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.9\linewidth]{img/MaskAlignerChamber.pdf}
     \caption{Circuit diagram of the mask aligner and its associated vacuum
 system. The system consists of the mask aligner chamber, the main chamber, the
-Pb evaporator and the AU evaporator. The AU evporator is attached to the same vacuum system, but is unrelated to the Mask Aligner. The configuration depicted is used for
+Pb evaporator and the AU evaporator. The AU evaporator is attached to the same vacuum system, but is unrelated to the Mask Aligner. The configuration depicted is used for
 evaporation. The section labeled load lock is a vacuum suitcase and can be
 detached. The \textcolor{tab_green}{green} path shows the sample/mask extraction
-and insertion path with the wobblestick. The black arrow shows the molecular beam
+and insertion path with the wobble stick. The black arrow shows the molecular beam
 path from the \ce{Pb} evaporator.}
     \label{fig:mask_aligner_chamber}
 \end{figure}
 
-The Mask Aligner vacuum system consists of three distinct vacuum chambers that can be separated with vacuum gate valves.\cite{Mask_Aligner} The first part is the \textbf{M}ain \textbf{C}hamber (MC), in which the Mask Aligner is located and the evaporator chamber used to create a molecular beam into the main chamber, secondly the \textbf{L}oad \textbf{L}ock (LL), which is a vacuum suitcase that is used to insert new samples and masks into the system and thirdly a Turbomolecular pump loop used to pump the system down to UHV vacuum pressures. The main chamber is equipped with an Ion Getter Pump, due to this the system can be separated from the main pumping loop of the Turbo molecular pump, without loss of vacuum pressure. The system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV), one located directly on the main chamber and one separating the evaporator from the Turbomolecular pump loop. Additionally, the Load Lock and the main chamber are separated using a Gate Valve. In order to detect leaks in the vacuum system a mass spectrometer is also attached to the main chamber. \\
-The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV pressures for extended periods of time, even while separated from the main pump loop. A garage with spaces for up to $10$ samples and $4$ additional spaces for Omicron samples is part of the Load Lock. This allows insertion of multiple samples and masks, that can then be later inserted into the main chamber. For insertion and removal of masks and sample a wobble stick is attached to the Load Lock chamber. The sample/mask insertion path of the wobblestick can be seen in \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. The Load Lock is designed to be a detachable vacuum suitcase, allowing samples to be stored in the garage and then transported with the suitcase to another vacuum system without intermediate exposure to ambient conditions.\\
+The Mask Aligner vacuum system consists of three distinct vacuum chambers that can be separated with vacuum gate valves.\cite{Mask_Aligner} The first part is the \textbf{M}ain \textbf{C}hamber (MC), in which the Mask Aligner is located, and the evaporator chamber used to create a molecular beam into the main chamber, secondly the \textbf{L}oad \textbf{L}ock (LL), which is a vacuum suitcase that is used to insert new samples and masks into the system and thirdly a Turbomolecular pump loop used to pump the system down to UHV vacuum pressures. The main chamber is equipped with an Ion Getter Pump, due to this the system can be separated from the main pumping loop of the Turbo molecular pump, without loss of vacuum pressure. The system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV), one located directly on the main chamber and one separating the evaporator from the Turbomolecular pump loop. Additionally, the Load Lock and the main chamber are separated using a Gate Valve. In order to detect leaks in the vacuum system, a mass spectrometer is also attached to the main chamber. \\
+The Load Lock is equipped with a small ion getter pump, that runs on its own, allowing it to keep UHV pressures for extended periods of time, even while separated from the main pump loop. A garage with spaces for up to $10$ samples and $4$ additional spaces for Omicron samples is part of the Load Lock. This allows insertion of multiple samples and masks, that can then be later inserted into the main chamber. For insertion and removal of masks and sample, a wobble stick is attached to the Load Lock chamber. The sample/mask insertion path of the wobble stick can be seen in \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. The Load Lock is designed to be a detachable vacuum suitcase, allowing samples to be stored in the garage and then transported with the suitcase to another vacuum system without intermediate exposure to ambient conditions.\\
 The main pump loop consists of a rotary vane prepump and a turbomolecular pump. Between prepump and turbo molecular pump is a pressure sensor to determine if the prepump is providing suitable backing pressure and a valve, which can be opened to a Nitrogen bottle to allow the system to be vented to atmospheric pressure with an inert gas. \\
 The 3 parts are seen as distinct, as the 3 components can be decoupled safely once the entire system is pumped to UHV without risk of losing vacuum pressure since no part of the system is not pumped. \\ 
-Another device, unrelated to this thesis, a gold evaporator, is connected to the vacuum system of the Mask Aligner, but it can be currently run fully separately, as it has its own Turbomolecular pump with attached prepump. As such the system is completely independent and only needs to be opened to the Mask Aligner system to check its pressure, since it currently is not equipped with any pressure sensor of its own. The pressure sensor is however not needed, since in testing the turbomolecular pump can pump the system down to the necessary pressures in very short time. Opening to the Mask Aligner system would only be needed in case there is a suspected leak. \\
-
+Another device, unrelated to this thesis, a gold evaporator, is connected to the vacuum system of the Mask Aligner, but it can be currently run fully separately, as it has its own Turbomolecular pump with attached prepump. As such, the system is completely independent and only needs to be opened to the Mask Aligner system to check its pressure, since it currently is not equipped with any pressure sensor of its own. The pressure sensor is however not needed, since in testing the turbomolecular pump can pump the system down to the necessary pressures in very short time. Opening to the Mask Aligner system would only be needed in case there is a suspected leak. \\
 
 \section{Shadow mask alignment}
 \subsection{Motor calibration}
@@ -92,8 +91,8 @@ amount of time and allowing for quick iteration. \\
 
 In order to do a final calibration to obtain the step sizes, one has to measure
 the distance driven for specific given amount of steps driven. This is done
-optically with the camera. To do so the camera first has to be calibrated with
-an object of known size. For this a good choice are the \ce{Nd} magnets on top
+optically with the camera. To do so, the camera first has to be calibrated with
+an object of known size. For this, a good choice are the \ce{Nd} magnets on top
 of the prisms as their diameter is known to be $5$ mm and they are always in
 view when looking at the motors separately. \\
  In order to do measure the distance each motor travels in a given amount of
@@ -101,12 +100,12 @@ steps, a specific remarkable point has to be found, that does not change upon
 motor movement and that can be observed after and before a given amount of steps
 were driven. Outside UHV the best points are small scratches on the prisms
 \ce{Al2O3} plate, since these are already in a focal plane with the motors,
-and it is easy to determine their center since their are usually only a few
+and it is easy to determine their center since they are usually only a few
 pixels in diameter, while remaining stable after driving. However, when scratches
-in the metal are chosen as a point of reference the lighting conditions must not
-be changed during the calibration as this can hinder their visibility.\\
+in the metal are chosen as a point of reference, the lighting conditions must not
+be changed during the calibration, as this can hinder their visibility.\\
 Inside UHV it is a little more complicated since only one angle is available for
-the camera. For Z1 the previously mentioned notches on the Z1 Motor itself can
+the camera. For Z1, the previously mentioned notches on the Z1 Motor itself can
 be chosen, since it is directly in view, but for the motors Z2 and Z3 this
 procedure is not possible since they cannot be directly seen. Instead, the 2
 screws very close to the motors are chosen (seen in Figure
@@ -123,7 +122,7 @@ little closer to the camera than the motors themselves, if one neglects the smal
     \label{fig:calibration_screw_diff_explain}
 \end{figure}
 
-With this one gets that for each unit of distance the motor moves the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. With this the actual movement on the motor can be obtained. \\
+With this one gets that for each unit of distance the motor moves, the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. With this, the actual movement on the motor can be obtained. \\
 
 \begin{figure}[H]
     \centering
@@ -137,14 +136,13 @@ With this one gets that for each unit of distance the motor moves the screws mov
     \caption{}
 	\label{fig:calibration_uhv_points_of_interest_z2z3}
 	\end{subfigure}
-	\caption{Points of interest for the the calibration of the 3 piezo motors ion
+	\caption{Points of interest for the calibration of the 3 piezo motors ion
 UHV. (a) shows measurement point \textcolor{tab_green}{green} and object that is
 chosen for measurement \textcolor{tab_green}{red} for calibration of Z1. (b)
 shows the same for Z2 and Z3.}
     \label{fig:calibration_uhv_points_of_interest}
 \end{figure}
 
-
 When good measurement points are found the procedure is very simple: $2000$, $4000$,
 $6000$, $8000$ and $10000$ steps are driven and after each set of steps the distance
 the chosen point has traveled in camera view is measured. An example for motor Z1 and Z2 can be seen in Figure \ref{fig:calibration_uhv_example_driving} for a $1000$ step measurement. \\
@@ -180,7 +178,7 @@ is on the order of $10$ nm/step.
     \centering
     \includegraphics[width=0.8\linewidth]{img/Plots/Calibrations/80V.pdf}
     \caption{Example of a linear fit for the measured calibration data. From the
-slope of the fit, the step size of a single step can be obtained. This
+slope of the fit, the step size of a single step, can be obtained. This
 calibration was performed during a time in which repairs at the Z3 motor were
 performed. The Z3 motor has a stronger difference in step size between
 approach/retract than the other motors here.}
@@ -200,9 +198,9 @@ seen in Figure \ref{fig:calibration_voltage}
 \end{figure}
 
 The behavior is linear in the voltage, but the slope is slightly different for
-each motor causing an optimum voltage for driving all 3 motors with the same
+each motor, causing an optimum voltage for driving all 3 motors with the same
 voltage to be around $80$ V. Also noticeable is a strong difference in slope for
-Z3. Z3 is much more influenced by voltage than the other motors where the
+Z3. Z3 is much more influenced by voltage than the other motors, where the
 step size/V is larger by $\approx 0.3$. From this plot the
 slope for each motor can be obtained and with this possible variations in motor
 behavior can be compensated by adjusting the voltage to each channel. This has
@@ -213,21 +211,21 @@ of the motors change or if compensation for potential deviations in
 step size is needed.\\
 
 \subsection{Optical alignment}
-To align mask and sample it is first necessary to get the sample aligned and
+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
 small signal, which will then be noise dominated and thus unusable for
 alignment. \\
-To do this a Bresser MicroCam II camera with a resolution of $20$ megapixel is
+To do this, a Bresser MicroCam II camera with a resolution of $20$ megapixel is
 mounted on a stand in front of the window of the mask aligner chamber. The
 mounting of it can be controlled via 3 micrometer screws in x, y and z
 direction. Additionally, the camera can be rotated on $2$ axes allowing full
 control of the camera angle. No optical adjustment can be done
 in the axis, in which the camera is pointed as depth information is difficult to
-obtain. For this reason the sample has to be aligned so that its surface normal
-is perpendicular to the cameras view direction i.e. no sample surface can be
+obtain. For this reason, the sample has to be aligned so that its surface normal
+is perpendicular to the camera's view direction, i.e. no sample surface can be
 seen in camera view and no upwards tilt can be observed when viewing the side
-edge of the sample, and the upper side of the sample holder cannot be observed.
+edge of the sample, and the upper side of the sample holder, cannot be observed.
 \\
 
 \begin{figure}[H]
@@ -249,21 +247,20 @@ placed or angled too low (a), too high (b) and placed in good alignment (c). In
 (a) the surface of the sample can be seen, which means the camera is not in line
 with the sample, but rather tilted too far up or too low. In (b) one
 can see the surface of the sample holder on the upper side as well as an upwards
-shift on the side of the sample indicating that the sample is tilted with
+shift on the side of the sample, indicating that the sample is tilted with
 respect to the camera, this is caused by a camera too high up or tilted too far
 down.}
     
     \label{fig:camera_alignment_example}
 \end{figure}
 
-
 When the camera is aligned with the sample, the mask can now be moved close to
 the sample leaving a decently sized gap between mask and sample still. Now the
 mask is aligned until only a very small gap can be seen. The size of the gap can
 be optically estimated using the Bresser software. A known length can be used to
-calibrate lengths within the software. As an object of known length the sample
+calibrate lengths within the software. As an object of known length, the sample
 can be for example chosen since its edge is known to be $5940 \pm 20 $ $\mu$m.
-In camera view direction the mask and sample should now be aligned within
+In camera view direction, the mask and sample should now be aligned within
 achievable optical accuracy. The progression of this can be seen in Figure \ref{fig:optical_approach}
  
 \begin{figure}[H]
@@ -280,7 +277,7 @@ achievable optical accuracy. The progression of this can be seen in Figure \ref{
     \includegraphics[width=\linewidth]{img/OpticalAlign03.png}
     \caption{}
 	\end{subfigure}
-	\caption{The progression of optical alignment up from $65 \pm 5$ $\mu$m (a) to $25 \pm 5$ $\mu$m (c) mask sample distance. Measurement was obtained optically using measurement software and the samples edge as a reference length.}
+	\caption{The progression of optical alignment up from $65 \pm 5$ $\mu$m (a) to $25 \pm 5$ $\mu$m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length.}
     \label{fig:optical_approach}
 \end{figure}
 
@@ -288,7 +285,7 @@ achievable optical accuracy. The progression of this can be seen in Figure \ref{
 
 \subsection{Approach curves}
 
-After optical alignment the final step towards an aligned sample comes via
+After optical alignment, the final step towards an aligned sample comes via
 capacitive measurement to obtain the distance to the sample surface. The 3
 capacitive sensors on the mask are aligned with the 3 motors of the Mask Aligner
 and are labeled as seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_motors}. The masks consist of a $200$ $\mu$m thick \ce{Si} body. A small $100\times100$ $\mu$m \ce{SiN} membrane, with $3$ $\mu$m holes each $10$ $\mu$m apart, is situated in the middle of the body. The \ce{SiN} actually covers the whole mask and is $1$ $\mu$m thick, but only the center part has holes and a trench below it. Around the hole membrane are $3$ gold pads, that function as the aforementioned capacitive sensors. The \ce{Au} of the gold pads is placed below an insulating $\approx 100$ nm layer of \ce{SiO2} at the bottom of a trench in the \ce{Si} body. They are at a distance of $0.7$ mm from the hole membrane and are located in an equilateral triangle around it. The dimensions of the mask and the capacitive sensors on the mask can be seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}.
@@ -306,10 +303,10 @@ and are labeled as seen in Figure \ref{fig:mask_aligner_nomenclature_capacitance
 		\label{fig:mask_aligner_nomenclature_capacitances_mask}
 	\end{subfigure}
 	\label{fig:mask_aligner_nomenclature_capacitances}
-	\caption{(\subref{fig:mask_aligner_nomenclature_capacitances_motors}) shows a cross section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor{tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref{fig:mask_aligner_nomenclature_capacitances_mask}) shows an diagram of the masks dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is actually used to create patterns.}
+	\caption{(\subref{fig:mask_aligner_nomenclature_capacitances_motors}) shows a cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor{tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref{fig:mask_aligner_nomenclature_capacitances_mask}) shows a diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is actually used to create patterns.}
 \end{figure}
 
-The readout of the capacitance sensors is performed with a Lock-in amplifier and the movement of the piezo motor stacks is done with the RHK piezo motor controller. Communication with both the RHK and the Lock-in amplifier is done with a Matlab script. The communication with the RHK is done via a network interface while the Lock-in uses a serial interface. Figure \ref{fig:diagram_MA_circ} shows a diagram of the communication circuit. Settings of the Lock-in amplifier are available in Appendix \ref{app:lock_in}.
+The readout of the capacitance sensors is performed with a Lock-in amplifier, and the movement of the piezo motor stacks is done with the RHK piezo motor controller. Communication with both the RHK and the Lock-in amplifier is done with a Matlab script. The communication with the RHK is done via a network interface, while the Lock-in uses a serial interface. Figure \ref{fig:diagram_MA_circ} shows a diagram of the communication circuit. Settings of the Lock-in amplifier are available in Appendix \ref{app:lock_in}.
 
 \begin{figure}[H]
     \centering
@@ -338,10 +335,10 @@ capacitance readout should increase by
 	C' = \epsilon_0 \epsilon_r \frac{A}{r + r'} \Rightarrow \frac{1}{C'} =
 \frac{1}{C} + \epsilon_0 \epsilon_r \frac{A}{r'}
 \end{equation}
-$r$ here has to be split into the distance of $1$ $\mu$m of \ce{SiN} on the masks surface and the rest of the mask sample distance in vacuum. The $\epsilon_r$ value for \ce{SiN} is $6.06$ (for a thin film of $437$ nm)\cite{SiN_dielectric} and the value for UHV can be approximated to very good accuracy as $1$, since the system is at a pressure of at least $10^{-8}$ mbar and even for atmospheric conditions $\epsilon_r \approx 1$.
+$r$ here has to be split into the distance of $1$ $\mu$m of \ce{SiN} on the mask's surface and the rest of the mask sample distance in vacuum. The $\epsilon_r$ value for \ce{SiN} is $6.06$ (for a thin film of $437$ nm)\cite{SiN_dielectric} and the value for UHV can be approximated to very good accuracy as $1$, since the system is at a pressure of at least $10^{-8}$ mbar and even for atmospheric conditions $\epsilon_r \approx 1$.
 The capacitance increases with a $\frac{1}{r}$ dependence. This holds true until
-the masks surface makes contact with the sample or any contamination particles
-on the samples or the masks surface. 
+the mask's surface makes contact with the sample or any contamination particles
+on the samples or the mask's surface. 
 
 \begin{figure}[H]
     \centering
@@ -378,7 +375,7 @@ an example (a) and the difference of each capacitance value to the last (b).
 Only one sensor is pictured. Marked are the important point where the slope of
 the $\frac{1}{r}$ curve changes. These points, where the geometry of the
 alignment process changes are marked labeled First, Second and Full contact.
-Before each of these points the difference goes to a local maximum. These are
+Before each of these points, the difference goes to a local maximum. These are
 marked with blue dashed lines. Below are images of the geometry between mask and
 sample at First (c), Second (d) and Full contact (e). Red lines or points mark
 where the mask is touching the sample.}
@@ -393,7 +390,7 @@ this is seen in Figure \ref{fig:approach_curve_example_first} This will inhibit
 the movement of the mask on the side associated, which results in a changed
 step size. Since all motors move the mask frame and the mask is in the middle of
 it this will affect all motors step sizes, albeit in differing amounts. Due to
-this step size change the slope of the approach curve changes (shown in Eq.
+this step size change, the slope of the approach curve changes (shown in Eq.
 \ref{eq:cap_slope_change}), as seen in Figure
 \ref{fig:approach_curve_example_cap} with the label "First contact".
 
@@ -405,14 +402,14 @@ this step size change the slope of the approach curve changes (shown in Eq.
 \end{equation}
 
 Where $C''$ is the final capacitance, $r$ is the distance to first contact, $r'$ is the distance since first contact and $d$ is the parameter by which the step size changes.
-When now approaching the surface further the mask will then contact the surface
+When now approaching the surface further, the mask will then contact the surface
 with another point, which now puts and edge in contact with the sample (see
 Figure \ref{fig:approach_curve_example_second}). This will have the same effect
 of changing the slope of the curve again, labeled in Figure
 \ref{fig:approach_curve_example_cap} as "Second contact". If the sample is now
-approached further the only axis of movement left for the mask is the one
+approached further, the only axis of movement left for the mask is the one
 aligning the mask to the sample perfectly, illustrated in Figure
-\ref{fig:approach_curve_example_full}. At this point the capacitance value no
+\ref{fig:approach_curve_example_full}. At this point, the capacitance value no
 longer changes since the distance between mask and sample can no longer be
 decreased. This point is labeled "Full contact" in Figure
 \ref{fig:approach_curve_example_cap}. \\
@@ -436,20 +433,20 @@ the sample is contacted. This peak value of capacitance difference is called a
 In an ideal scenario where the mask is perfect and the only capacitance values
 to consider are the ones from the gold pads to the sample, the distance to the
 sample could be read off from the capacitance value via Eq.
-\ref{eq:plate_capacitor}. However with real masks the capacitance values can
-deviate drastically from the ideally expected ones so without any point of
-reference no statement about the absolute distance can be made.
-For this reason the approach curve of any mask sample combination has to be
+\ref{eq:plate_capacitor}. However, with real masks the capacitance values can
+deviate drastically from the ideally expected ones, so without any point of
+reference, no statement about the absolute distance can be made.
+For this reason, the approach curve of any mask sample combination has to be
 recorded first as a calibration curve. This requires contacting the sample at
-least once. However this calibration can still not be used to obtain absolute
+least once. However, this calibration can still not be used to obtain absolute
 distance values for the given capacitance since upon retraction and subsequent
-approach the capacitance values drop as seen in Figure
+approach, the capacitance values drop as seen in Figure
 \ref{fig:approach_subsequent}. This is either due to accumulation of
-misalignement due to small errors in the different Z motor stepsizes and/or
+misalignement due to small errors in the different Z motor step sizes and/or
 accumulation of particles on the sample/mask surface due to contacting the
 sample. \\
-In order to still get a good replicable alignement instead the difference in
-capacitance is used and the stop condition is used to determine good alignement
+In order to still get a good replicable alignment instead, the difference in
+capacitance is used, and the stop condition is used to determine good alignment
 \cite{Beeker}. 
 
 \begin{figure}[H]
@@ -467,13 +464,13 @@ measurement to the other regardless.}
 \subsection{Reproducibility}
 One of the questions about the efficacy of Mask Aligner as an alignment tool is
 the reproducibility of approach curves with regard to different samples and
-other differences in conditions. In the masters thesis of Jonas Beeker the
+other differences in conditions. In the master’s thesis of Jonas Beeker the
 reproducibility of different masks, different locations, different approaches
 and a comparison before and after evaporation was discussed.\cite{Beeker}
 
 \subsubsection{Reproducibility when removing sample/mask}
 
-One question concerning reproducibility is whether the approach curve is strongly affected by the exchange of mask or sample or even just the reinsertion of mask or sample. This is important since an exchange of sample to perform a new evaporation is a common operation in the creation of patterned samples. 
+One question concerning reproducibility is whether the approach curve is strongly affected by the exchange of mask or sample, or even just the reinsertion of mask or sample. This is important since an exchange of sample to perform a new evaporation is a common operation in the creation of patterned samples. 
 
 \begin{figure}[H]
     \centering
@@ -491,24 +488,25 @@ One question concerning reproducibility is whether the approach curve is strongl
     \label{fig:approach_replicability}
 \end{figure} 
 
-The reproducibility when exchanging just the mask and sample and reinserting it is looked at. When reinserting the mask the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}. This might be feature of the particular batch of masks this thesis worked with as the gold pins connecting the mask holder and mask stage do not have fully stable contact between the male and female side and allow for a certain level of movement. The process of moving the mask out and back in to the mask frame might induce enough perturbation to the mask holder to move it slightly in the mask. This fault could potentially be fixed with better gold pin design, when designing newer mask mentioned further in \ref{subsec:cross_cap}\\
+The reproducibility when exchanging just the mask and sample and reinserting it is looked at. When reinserting the mask, the approach curve changed drastically, which can likely be attributed to newly induced tilt on the mask. This can be seen in the shift between the \textcolor{tab_green}{green} and \textcolor{tab_red}{red} curves in Figure \ref{fig:approach_replicability}. This might be a feature of the particular batch of masks this thesis worked with, as the gold pins connecting the mask holder and mask stage do not have fully stable contact between the male and female side and allow for a certain level of movement. The process of moving the mask out and back in to the mask frame might induce enough perturbation to the mask holder to move it slightly in the mask. This fault could potentially be fixed with better gold pin design, when designing newer mask mentioned further in \ref{subsec:cross_cap}\\
+
 
 Another reason might be small movement of the mask frame on the \ce{Nd} magnets tilting the mask, when reinserting the mask. This problem cannot be fixed without a complete redesign of the Mask Aligner. \\
 
-Reinserting the sample also induced a difference in approach curves, but the difference is much smaller as can be seen in \textcolor{tab_blue}{blue} and \textcolor{tab_green}{green}, but the same curve is followed and the point of first contact has only shifted upwards slightly. In the difference curve it is clear that the stop condition however changed by some amount. A stop condition developed on the peak of the \textcolor{tab_green}{green} curve (for example $0.04$ pF) would overshoot the point of first contact on the \textcolor{tab_blue}{blue} curve and the stop condition would never trigger. If left unsupervised the mask would in this instance eventually crash into the sample, unless a point near the point of second or full contact satisfies the stop condition as well. This should be taken into account when deciding on a stop condition. \\
+Reinserting the sample also induced a difference in approach curves, but the difference is much smaller as can be seen in \textcolor{tab_blue}{blue} and \textcolor{tab_green}{green}, but the same curve is followed and the point of first contact has only shifted upwards slightly. In the difference curve, it is clear that the stop condition however changed by some amount. A stop condition developed on the peak of the \textcolor{tab_green}{green} curve (for example $0.04$ pF) would overshoot the point of first contact on the \textcolor{tab_blue}{blue} curve and the stop condition would never trigger. If left unsupervised, the mask would in this instance eventually crash into the sample, unless a point near the point of second or full contact satisfies the stop condition as well. This should be taken into account when deciding on a stop condition. \\
 
 
 \subsection{Cross capacitances} \label{subsec:cross_cap}
 The biggest problem with the for alignment with current set of masks is that the
 approach curves obtained for aligning masks with them, show heavy correlation
 between the sensors, $C_i$ see Figure \ref{fig:cross_cap_approach}~\subref{fig:cross_cap_approach_difference}-\subref{fig:cross_cap_approach_difference_2}. If
-alignment were perfect these curves should indeed appear to be very similar
+alignment were perfect, these curves should indeed appear to be very similar
 since moving any of the motors affects all capacitance sensors due to the
 geometry of the mask stage, but each of the capacitance sensors should
 independently give a curve, which follows a $\frac{1}{r}$ behavior. From this
 follows, that if alignment is not perfect and the distances from the \ce{Si} are
 indeed different for each of the sensors the behavior of the 3 different curves
-should be much more different. A simulated approach curve for a difference of $440$ nm between $C_1$ and $C_2$ and $560$ nm between $C_1$ and $C_3$ can be seen in Figure \ref{fig:cross_cap_approach_sim}. The model assumes no capacitance between the 3 capacitance sensors and no capacitance to the environment. Additionally, the model assumes all motors drive exactly the same. This assumes the mask first makes contact with the sample at the corner that is aligned with $C_1$ such that the motor aligned with $C_1$ stops moving the stage up. After that the same happens for $C_2$.
+should be much more different. A simulated approach curve for a difference of $440$ nm between $C_1$ and $C_2$ and $560$ nm between $C_1$ and $C_3$ can be seen in Figure \ref{fig:cross_cap_approach_sim}. The model assumes no capacitance between the 3 capacitance sensors and no capacitance to the environment. Additionally, the model assumes all motors drive exactly the same. This assumes the mask first makes contact with the sample at the corner that is aligned with $C_1$ such that the motor aligned with $C_1$ stops moving the stage up. After that, the same happens for $C_2$.
 
 \begin{figure}[H]
     \centering
@@ -531,21 +529,21 @@ should be much more different. A simulated approach curve for a difference of $4
 	\label{fig:cross_cap_approach}
 \end{figure}
 
-The model assumes the gold plates behave as plate capacitors with the and the
-difference in distance for the capacitors is assumed to be $440$ nm each, so
+The model assumes the gold plates behave as plate capacitors, with the
+difference in distance for the capacitors assumed to be $440$ nm each, so
 that the distance between C1 and C3 is $560$ nm. A distance that is well within the maximal optical accuracy of $\approx 5$ $\mu$m for maximal zoom and resolution. Even for such a small
-difference the measured deviance between the curves should be very visible. The
+difference, the measured deviance between the curves, should be very visible. The
 values for the capacitances obtained should approximately follow the formula for
 a plate capacitor \ref{eq:plate_capacitor}. \\
-However, the curves measured for capacitance show a deviation in behavior from the model. Figure \ref{fig:cross_cap_approach_difference} shows this. The curves of the 3 capacitances were normalized to bring them into the same range. The different capacitances vary by $1$-$2$ order of magnitude. The largest capacitance was measured to $19.12$ pF. It starts with the capacitances with large difference and merges together for small distance. This is the opposite to the expected behavior. The general shape of the curve also is identical between all $3$, while it is expected that first contact affects the $3$ capacitances differently. Another mask (Figure \ref{fig:cross_cap_approach_difference_2}) shows behavior more close to the expected with a difference for the $3$ capacitances at first contact. However, $C_2$ and $C_3$ behave identically again. Here again the largest capacitance was measured to be $19.78$ pF and $C_2$ and $C_3$ varied by $2$ orders of magnitude from $C_1$.
-For the gold pads this would give a capacitance value of $\approx 0.40$ fF at a
+However, the curves measured for capacitance show a deviation in behavior from the model. Figure \ref{fig:cross_cap_approach_difference} shows this. The curves of the 3 capacitances were normalized to bring them into the same range. The different capacitances vary by $1$-$2$ order of magnitude. The largest capacitance was measured to $19.12$ pF. It starts with the capacitances with large difference and merges together for small distance. This is the opposite to the expected behavior. The general shape of the curve also is identical between all $3$, while it is expected that first contact affects the $3$ capacitances differently. Another mask (Figure \ref{fig:cross_cap_approach_difference_2}) shows behavior more close to the expected, with a difference for the $3$ capacitances at first contact. However, $C_2$ and $C_3$ behave identically again. Here again the largest capacitance was measured to be $19.78$ pF and $C_2$ and $C_3$ varied by $2$ orders of magnitude from $C_1$.
+For the gold pads, this would give a capacitance value of $\approx 0.40$ fF at a
 distance of $50$ micron, but at a distance of $\approx 50$ micron, as measured
 optically, the capacitance values of the curve $C_1$ measured was $\approx 2.4$
 pF, which deviates by 4 order of magnitude. This corresponds more closely to the
 value expected for capacitance from the \ce{Si} of the mask to the \ce{Si} of
 the sample, where the expected value for a plate capacitor would be $\approx
 1.44$ pF. The deviation in this case can be explained by the oversimplification
-of the model, which does not take into account any stray capacitances the system
+of the model, which does not take into account any stray capacitances of the system
 might have, as well as assume perfectly aligned plate capacitors. 
 
 %\begin{figure}[H]
@@ -570,7 +568,7 @@ more closely, suggesting this is the cause.
     \includegraphics[width=0.65\linewidth]{img/LeakageCurrent.pdf}
     \caption{Diagram showing one possible explanation for the large correlation
 in Capacitance readings. A small Tear in the \ce{SiNi} layer removes insulation
-between the gold wire and the Si of the Mask allowing current to travel through.
+between the gold wire and the Si of the Mask, allowing current to travel through.
 This causes the capacitance to reflect the much larger capacitance between the
 Si of the Mask and that of the sample, instead of the desired Capacitance
 between the gold pad and the Si of the sample.}
@@ -618,15 +616,15 @@ capacitances were obtained for $3$ masks holders inside mask shuttles, as well a
     \centering
     \includegraphics[width=0.9\linewidth]{img/Plots/Mask_Old_Caps.pdf}
     \caption{The 3 capacitance curves of the Mask labeled "old", the plots look
-the same sharing all features and general shape. The main difference is the
-scale of the y-axis and due to this the scale of the uncertainty.}
+the same, sharing all features and general shape. The main difference is the
+scale of the y-axis, and due to this the scale of the uncertainty.}
     \label{fig:mask_old_caps}
 \end{figure}
 
 The shuttles on their own have a cross capacitance values that is of the order
 of the expected capacitance from the measurement itself. When adding the mask
 the cross capacitances increase often dramatically, but when compared with the
-approach curve the mask labeled old had the highest correlation between
+approach curve, the mask labeled old had the highest correlation between
 capacitances, see Figure \ref{fig:mask_old_caps}, of any measured in this thesis,
 whilst the cross capacitance values seem much lower the for example mask $3$. This
 seems to suggest, that while the cross capacitances have a strong influence on
@@ -640,11 +638,11 @@ mask often determine the shape.
     \caption{The 3 capacitance curves of the Mask labeled "old" scaled to be
 within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit
 to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars
-and overall within less then $1$ \%.}
+and overall within less than $1$ \%.}
     \label{fig:mask_old_correl}
 \end{figure}
 
-To further corroborate the similarity between the different capacitance sensors signals the data of each was overlaid over one another. Since the capacitance ranges vary between sensors the signals have to first be normalized to fall in the same range. Then additionally an offset has to be fitted, since they are also offset by each other. The result of this can be seen in Figure \ref{fig:mask_old_correl}. This shows even more clearly that the $3$ different capacitances give the same signal within error. Systematic deviations in the residuals are only visible near the jump in capacitance signal, which is of unknown cause. The deviations are within $0.1$ \%, which is on the same order as the expected measurement error for the given LockIn parameters. 
+To further corroborate the similarity between the different capacitance sensors signals, the data of each was overlaid over one another. Since the capacitance ranges vary between sensors, the signals have to first be normalized to fall in the same range. Then additionally an offset has to be fitted, since they are also offset by each other. The result of this can be seen in Figure \ref{fig:mask_old_correl}. This shows even more clearly that the $3$ different capacitances give the same signal within error. Systematic deviations in the residuals are only visible near the jump in capacitance signal, which is of unknown cause. The deviations are within $0.1$ \%, which is on the same order as the expected measurement error for the given LockIn parameters. 
 
 The data seems to suggest multiple sources for the strong correlation between the 3 capacitance curves. Figure \ref{fig:cross_cap_diagramm} shows a circuit diagram for the known sources of capacitance correlation. In order to improve these capacitance values, a couple of this have to be done.
 
@@ -683,7 +681,7 @@ wiggling the mask sometimes.
 
 \subsection{Stop Conditions}
 When doing an approach for evaporation, first an approach on a mask has to be
-performed as a calibration. Here two different scenarios can arise:
+performed as a calibration. Here, two different scenarios can arise:
 
 \paragraph{High correlation between capacitance curves}
 When all 3 capacitance curves are heavily correlated, no alignment information
@@ -716,7 +714,7 @@ petri dish should be cleaned using acetone and then IPA in an ultrasonic bath.
 	\item Carefully grab the silicon chip with a soft tip tweezer and while
 ensuring stable grip, carefully blow any coarse particles from the surface of the
 chip using pressurized nitrogen. Do not blow the nitrogen at the surface, but
-across it as otherwise the chip will just fall from the tweezer.
+across it, as otherwise the chip will just fall from the tweezer.
 	\item Place the chip in a beaker filled with pure acetone and put it in an
 ultrasonic bath. Heat the acetone using the heating function of the ultrasonic
 bath, ensuring however that $55^\circ$ C are never exceeded, for 10 minutes.
@@ -728,7 +726,4 @@ bath, ensuring however that $55^\circ$ C are never exceeded, for 10 minutes.
 	\item Document the sample's surface cleanliness using an optical microscope image and an AFM image
 	\item Place the sample as quickly as possible in the Mask Aligner Load Lock and pump the system down to avoid further contamination.
 \end{enumerate}
-If the sample is intended to be analyzed in an STM, the sample preparation should happen in a UHV environment to ensure further cleanliness and the sample should be transported directly via the Load Lock UHV suitcase attached to the Mask Aligner Chamber. 
-
-
-
+If the sample is intended to be analyzed in an STM, the sample preparation should happen in a UHV environment to ensure further cleanliness and the sample should be transported directly via the Load Lock UHV suitcase attached to the Mask Aligner Chamber. 
\ No newline at end of file
diff --git a/chap03.aux b/chap03.aux
index eb6e158f7602ff4dbd142b8d0bb900dda15d446c..6fec2f63601147104101f4024763052ef1269bfd 100644
--- a/chap03.aux
+++ b/chap03.aux
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+\newlabel{fig:walker_pulse_shape_fast}{{3.9}{53}{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both approach (a) and retract (b), for a nominal voltage of 80 V (without load)}{figure.caption.58}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {3.10}{\ignorespaces Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order. }}{54}{figure.caption.59}\protected@file@percent }
+\newlabel{fig:diagram_MA_circ_walker}{{3.10}{54}{Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order}{figure.caption.59}{}}
 \@setckpt{chap03}{
-\setcounter{page}{54}
+\setcounter{page}{55}
 \setcounter{equation}{1}
 \setcounter{enumi}{10}
 \setcounter{enumii}{0}
diff --git a/chap03.tex b/chap03.tex
index f46e33825a949b6e17dc1a516336ba4ebfab4af4..5065e300dad016640fc7874544f5c37ddce6c64b 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -12,9 +12,9 @@ In order to control the movement of the mask stage using the mask aligner, 3 mot
 
 \section{RHK}
 \subsection{Overview}
-The PMC100 Piezo motor controller by RHK technologies is a piezo motor controller designed for operating nanoscale motion in Scanning Probe systems. The piezo motor controller is capable of sending signals to $9$ separate motors at the same time. For each of these nine channels and for both direction there are $3$ parameters that can be changed:
+The PMC100 Piezo motor controller by RHK technologies is a piezo motor controller designed for operating nanoscale motion in Scanning Probe systems. The piezo motor controller is capable of sending signals to $9$ separate motors at the same time. For each of these nine channels and for both direction, there are $3$ parameters that can be changed:
 \paragraph{amplitude}
-The amplitude is the peak voltage of the pulse given in V. The default voltage for the mask aligner setup is $80$ V.
+The amplitude is the peak voltage of the pulse, given in V. The default voltage for the mask aligner setup is $80$ V.
 \paragraph{sweep period}
 The sweep period is the time a single pulse lasts, given in ms, with a minimum of 1 ms. The mask aligner setup uses a frequency of 1 kHz by default, which results in a sweep time period of 1 ms.
 \paragraph{time between sweeps}
@@ -61,7 +61,7 @@ It is noticeable that the pulse shapes for approach and retract are similar, but
 The KIM001 Kinesis® K-Cube™ Piezo Inertia Actuator Controller by Thorlabs was a piezo motor controller that was initially considered as a replacement driver motor to the RHK.\\
 
 \subsection{Pulse shape}
-The KIM001 Kinesis® K-Cube™ Piezo Inertia Actuator Controller provides a monomodal piezo driver signal in a sawtooth-like shape that can be used to drive piezo motors in a slip stick fashion. A measurement of the pulse shape for both retraction and approach of the mask aligner is seen in Figure (\ref{fig:kim0001_pulse_shape}). The pulse shapes for both approach and retract are very different, with the approach step having a large plateau at the top while the retract step is lacking such a feature. The slow flank also has different slope for approach and retract. \\
+The KIM001 Kinesis® K-Cube™ Piezo Inertia Actuator Controller provides a monomodal piezo driver signal in a sawtooth-like shape that can be used to drive piezo motors in a slip stick fashion. A measurement of the pulse shape for both retraction and approach of the mask aligner is seen in Figure (\ref{fig:kim0001_pulse_shape}). The pulse shapes for both approach and retract are very different, with the approach step having a large plateau at the top, while the retract step is lacking such a feature. The slow flank also has different slope for approach and retract. \\
 Both approach and retract show heavy aliasing artifacts, which could, due to the sharp slope at that specific point, lead to the piezo behaving unpredictable, since it might be in the slip regime. 
 
 \begin{figure}[H]
@@ -82,7 +82,7 @@ Both approach and retract show heavy aliasing artifacts, which could, due to the
 
 
 \subsection{Voltage behavior}
-The KIM001 device has a controllable parameter called voltage, which should in principle control the output signal voltage between $85$ V and $125$ V, but in testing it was found to not in fact control the output voltage at all. When changing the voltage parameter the KIM001 device will give a pulse with a peak voltage very high ( $>150$ V) if the voltage parameter specified is $125$ V and very low (approx. $85$ V) when the specified voltage is $85$ V, but when driving pulses in retract direction the signal peak will (within a few $100$ steps) drift back to a voltage of approx. $118$ V. This behavior is shown in Figure (\ref{fig:kim0001_voltage_behaviour}). This led to the conclusion that the KIM001 device is unusable for our purposes, since a variable voltage is in some situations necessary for driving the Mask Aligner appropriately. Also noticeable is an inconsistency in peak shape in the signal after 100 steps (\textcolor{tab_green}{green}) as compared to the others. No settings were changed during the recording of this data.
+The KIM001 device has a controllable parameter called voltage, which should in principle control the output signal voltage between $85$ V and $125$ V, but in testing it was found to not in fact control the output voltage at all. When changing the voltage parameter the KIM001 device will give a pulse with a peak voltage very high ( $>150$ V) if the voltage parameter specified is $125$ V and very low (approx. $85$ V) when the specified voltage is $85$ V, but when driving pulses in retract direction the signal peak will (within a few $100$ steps) drift back to a voltage of approx. $118$ V. This behavior is shown in Figure (\ref{fig:kim0001_voltage_behaviour}). This led to the conclusion that the KIM001 device is unusable for our purposes, since a variable voltage is in some situations necessary for driving the Mask Aligner appropriately. Also, noticeable is an inconsistency in peak shape in the signal after 100 steps (\textcolor{tab_green}{green}) as compared to the others. No settings were changed during the recording of this data.
 
 \begin{figure}[H]
     \centering
@@ -95,7 +95,7 @@ Due to the aforementioned behaviors of the KIM001 device, the device was found t
 
 \section{Mask Aligner controller "Walker"}
 \subsection{Overview}
-In order to find a suitable replacement for the RHK Piezo Motor controller, a new device to drive control pulses to the piezo stacks in the mask aligner was built. The PCB is heavily based around the piezo Walker electronics designed to control the piezo Walker used for SEM control. Due to this the device is often referred to as the "Mask Aligner Walker", even though it is not a walker or stepper motor controller. Adaptations were made to adjust it to the desired slip-stick behavior needed for application in the mask aligner. The Controller takes a serial input command and then drives sinusoidal steps with a sharp fast flank in the middle of them. Controllable are the amplitude of the signal and the number of steps. A simplified overview of the entire signal generation process is shown in Appendix \ref{app:walker_diagram}. The following section will look at each part of the process depicted in detail.
+In order to find a suitable replacement for the RHK Piezo Motor controller, a new device to drive control pulses to the piezo stacks in the mask aligner was built. The PCB is heavily based around the piezo Walker electronics designed to control the piezo Walker used for SEM control. Due to this, the device is often referred to as the "Mask Aligner Walker", even though it is not a walker or stepper motor controller. Adaptations were made to adjust it to the desired slip-stick behavior needed for application in the mask aligner. The Controller takes a serial input command and then drives sinusoidal steps with a sharp fast flank in the middle of them. Controllable are the amplitude of the signal and the number of steps. A simplified overview of the entire signal generation process is shown in Appendix \ref{app:walker_diagram}. The following section will look at each part of the process depicted in detail.
 
 \subsection{Signal generation}
 The core of the Mask aligner controller is an Arduino DUE.~\cite{arduino_datasheet} The  \textbf{C}entral to \textbf{P}rocessing \textbf{U}nit CPU of the Arduino DUE the "Atmel SAM3X8E ARM Cortex-M3 CPU" is a $32$-Bit ARM-Core microcontroller. Intgrated into the CPU is a $12$-Bit \textbf{D}igital to \textbf{A}nalog \textbf{C}onverter (DAC).~\cite{arduino_cpu_datasheet} The DAC comes with two output channels that can be controlled to output a signal simultaneously. The Arduino CPU is responsible for the generation of the original signal shape in software. The Arduino generates a signal internally with a sampling rate of $404$ kHz with the shape given by:
@@ -103,7 +103,7 @@ The core of the Mask aligner controller is an Arduino DUE.~\cite{arduino_datashe
      S = 4095 * \frac{A}{2 \pi} * \sin(2 \pi * t/P) + t/P
 \end{equation}
 
-Where $A$ is an amplitude parameter given by the user, that controls the voltage given at the output. $t$ is the time elapsed since the start of the current step, and $P$ is the period of a single step. The value $4095$ is chosen to use the full range of the $12$-Bit accuracy the Arduino DUE DAC provides. This gives a sinus-like shape of the pulse depicted in Figure \ref{fig:bessel_filter_unfiltered}, that closely matches the pulse shape given by the RHK. Due to this similar behavior is expected. This signal is then output on the DAC 0 pin of the Arduino. Since the Arduino can only output one polarity of voltage, but our final signal is intended to be bipolar, another signal is generated on DAC 1 with $1 - S$ as the given function. If one now subtracts the signals as depicted in Figure \ref{fig:bessel_filter_unfiltered} gets a bipolar signal following the desired sinusoidal shape. This is done via a hardware subtractor. \\
+Where $A$ is an amplitude parameter given by the user, that controls the voltage given at the output. $t$ is the time elapsed since the start of the current step, and $P$ is the period of a single step. The value $4095$ is chosen to use the full range of the $12$-Bit accuracy the Arduino DUE DAC provides. This gives a sinus-like shape of the pulse depicted in Figure \ref{fig:bessel_filter_unfiltered}, that closely matches the pulse shape given by the RHK. Due to this, similar behavior is expected. This signal is then output on the DAC 0 pin of the Arduino. Since the Arduino can only output one polarity of voltage, but our final signal is intended to be bipolar, another signal is generated on DAC 1 with $1 - S$ as the given function. If one now subtracts the signals as depicted in Figure \ref{fig:bessel_filter_unfiltered} gets a bipolar signal following the desired sinusoidal shape. This is done via a hardware subtractor. \\
 The Signal given by the Arduino contains aliasing artifacts from the digital to analog conversion. Aliasing leads to sharp very short steps in the signal, this could potentially put the piezo movement into the slip rather than the stick regime. In order to prevent that, the aliasing steps in the signal have to be smoothed out. This is done by applying an 8th order Bessel filter to the signal. The effect of this can be seen in Figure \ref{fig:bessel_filter_filter}.
 
 \begin{figure}[H]
@@ -124,7 +124,7 @@ The Signal given by the Arduino contains aliasing artifacts from the digital to
 
 \subsection{Fast flank}
 
-After this step the signal is bimodal and of the correct shape, but for the desired slip-stick behavior this only gives the slow flank. The fast flank is achieved by taking the signal given here and feeding it into a hardware inverter, whilst retaining both the original (normal) and the inverted signal. The retained signals can be seen in Figure \ref{fig:signal_switch_entry} When the signal is at its plateau, a hardware switch is used to change from the normal to the inverted signal. Examples of the signal are shown in Figure \ref{fig:signal_switch_switched}. The switching is achieved via a ADG1436 switch that has a transition time of $<200$ ns \cite{switch_datasheet}, this puts it well within the $<1$ $\mu$s time span required for the slip behavior of the signals fast flank. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
+After this step the signal is bimodal and of the correct shape, but for the desired slip-stick behavior this only gives the slow flank. The fast flank is achieved by taking the signal given here and feeding it into a hardware inverter, whilst retaining both the original (normal) and the inverted signal. The retained signals can be seen in Figure \ref{fig:signal_switch_entry} When the signal is at its plateau, a hardware switch is used to change from the normal to the inverted signal. Examples of the signal are shown in Figure \ref{fig:signal_switch_switched}. The switching is achieved via a ADG1436 switch that has a transition time of $<200$ ns \cite{switch_datasheet}, this puts it well within the $<1$ $\mu$s time span required for the slip behavior of the signal's fast flank. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
 
 \begin{figure}[H]
     \centering
@@ -145,7 +145,7 @@ After this step the signal is bimodal and of the correct shape, but for the desi
 The signal is then controlled by $2$ switches that are controlled by the Arduino digital output pins $22$, $24$, $26$ and $28$ and that lead the signal to $4$ different channels that go to the $4$ different output channels of the controller. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.
 
 \subsection{Amplification}
-The final step needed to get the desired signal for driving the piezo motors, is amplification. Currently, the signal is still in the -$3.3$ to $3.3$ V range supplied by the Arduino DUE, but for this application a driving signal between $-120$ to $120$ V ($240$ V peak to peak) is needed. In order to do that, the signal for each channel is separately amplified. This is done on a separate PCB that is exclusively for amplifying the signal and outputting it to the 4 outputs. It uses several high voltage Opamps and a high voltage transformer to boost the signal into the desired range. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.\\
+The final step, needed to get the desired signal for driving the piezo motors, is amplification. Currently, the signal is still in the -$3.3$ to $3.3$ V range supplied by the Arduino DUE, but for this application a driving signal between $-120$ to $120$ V ($240$ V peak to peak) is needed. In order to do that, the signal for each channel is separately amplified. This is done on a separate PCB that is exclusively for amplifying the signal and outputting it to the 4 outputs. It uses several high voltage opamps and a high voltage transformer to boost the signal into the desired range. Circuits diagrams for this can be found in Appendix \ref{app:circuit_electronics}.\\
 Afterward there are 4 relays, one for each channel that can be shut to prevent any current from being on the output leads, this is mainly a safety measure. The 4 relays are also controlled by the Arduino from the digital outputs 53, 51, 49 and 47 for the channels Z1, Z2, Z3 and X respectively.
 
 \subsection{Parameters}
@@ -153,19 +153,19 @@ The following parameters can be controlled with the new electronics:
 \paragraph{Amplitude (amp)}
 The amplitude of the generated signal within the Arduino given as $4095 * \text{amp} / 100$. An amplitude of $100$ results in a signal of $240$ V peak to peak at the output and as such can be treated as an output voltage as long as the internal potentiometers are not changed to a different voltage. 
 \paragraph{Voltage (volt)}
-Instead of setting the amp parameter to a given values, which corresponds to a output voltage. The voltage can be set directly. Internally this sets the amp parameter. Due to limited integer precision in the amp parameter not all voltages can be accurately chosen. The script will chose the closest voltage to the input one. The range is $0$ - $120$ V. The default value is $80$ V. 
+Instead of setting the amp parameter to a given value, which corresponds to an output voltage. The voltage can be set directly. Internally, this sets the amp parameter. Due to limited integer precision in the amp parameter, not all voltages can be accurately chosen. The script will choose the closest voltage to the input one. The range is $0$ - $120$ V. The default value is $80$ V. 
 \paragraph{Channel}
-The channels the generated signal is output to. The system can output 4 channels of signal, where each can be turned of separately. 
+The channels the generated signal is output to. The system can output 4 channels of signal, where each can be turned off separately. 
 \paragraph{Max Step}
-The maximum number of pulses the controller is allowed to run in succession. By default this value is set to 10000. This is a safety to ensure no accidental inputs crash the mask into the sample.
+The maximum number of pulses the controller is allowed to run in succession. By default, this value is set to 10000. This is a safety to ensure no accidental inputs crash the mask into the sample.
 \paragraph{Polarity}
-The polarity of the generated signal. Negative polarity is chosen as an approach signal while positive polarity represents the retract signal. The polarity can also be changed by specifying "step -1" for example, but this parameter is a global toggle, that changes the behavior for the entire program.
+The polarity of the generated signal. Negative polarity is chosen as an approach signal, while positive polarity represents the retract signal. The polarity can also be changed by specifying "step -1" for example, but this parameter is a global toggle, that changes the behavior for the entire program.
 
-The frequency is not adjustable as of the writing of this thesis, though in principle multiples changeable 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. 
+The frequency is not adjustable as of the writing of this thesis, though in principle changeable 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}
 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 optimum voltage to run experiments (see point of intercept in Figure \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 keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walkers pulse. 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 by 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 than the RHK.
+A measurement of the slow flank, without any attached load, is shown in Figure (\ref{fig:walker_pulse_shape_slow}).  The Walker keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walker's pulse. 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 by 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 than the RHK.
 
 \begin{figure}[H]
     \centering
@@ -181,7 +181,7 @@ A measurement of the slow flank, without any attached load, is shown in Figure (
     \label{fig:walker_pulse_shape_slow}
 \end{figure}
 
-The slow flank was also measured for both the RHK and the Walker, again in an unloaded state. The results can be seen in Figure (\ref{fig:walker_pulse_shape_fast}). 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. The Walkers fast flank drops from $80$ to $-80$ within $\approx 0.5 \mu$s while the RHK needs nearly $\approx 2 \mu$s on the falling flank and the Walker takes $\approx 1.7 \mu$s to reach $80$ V for the rising slope, while the RHK takes $\approx 2.2 \mu$s. Until the Walker signal fully stabilizes at the desired voltage another $\approx 1 \mu$s passes for the falling/rising flank, where the falling flank has the stronger undershoot/ringing. The RHK signal does not stabilize for another $\approx 2 \mu$s at least. As before the Walker either meets or outperforms the RHK in its pulse shape behavior and should thus drive the piezo motor appropriately.
+The slow flank was also measured for both the RHK and the Walker, again in an unloaded state. The results can be seen in Figure (\ref{fig:walker_pulse_shape_fast}). 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. The Walker's fast flank drops from $80$ to $-80$ within $\approx 0.5 \mu$s while the RHK needs nearly $\approx 2 \mu$s on the falling flank and the Walker takes $\approx 1.7 \mu$s to reach $80$ V for the rising slope, while the RHK takes $\approx 2.2 \mu$s. Until the Walker signal fully stabilizes at the desired voltage, another $\approx 1 \mu$s passes for the falling/rising flank, where the falling flank has the stronger undershoot/ringing. The RHK signal does not stabilize for another $\approx 2 \mu$s at least. As before, the Walker either meets or outperforms the RHK in its pulse shape behavior and should thus drive the piezo motor appropriately.
 
 \begin{figure}[H]
     \centering
@@ -197,7 +197,6 @@ The slow flank was also measured for both the RHK and the Walker, again in an un
     \label{fig:walker_pulse_shape_fast}
 \end{figure}
 
-
 \subsection{Driving the Mask Aligner}
 The communication diagram with the Walker looks slightly different from the one in Figure \ref{fig:diagram_MA_circ}, since the RHK relay is no longer needed since the Walker can take over its function. The new diagram can be seen in Figure \ref{fig:diagram_MA_circ_walker}
 
@@ -208,5 +207,4 @@ The communication diagram with the Walker looks slightly different from the one
     \label{fig:diagram_MA_circ_walker}
 \end{figure}
 
-Due to hardware issues with the Walker, no final test with the Mask Aligner attached as a load could not be performed and the driving performance could not be tested. Some hardware failure caused the positive polarity to no longer reach full $120$ V peak and with a load attached it could no longer reach beyond $0$ V giving a unipolar piezo driving signal in approach direction and no slip stick driving signal in retract.
-
+Due to hardware issues with the Walker, no final test with the Mask Aligner attached as a load could not be performed, and the driving performance could not be tested. Some hardware failure caused the positive polarity to no longer reach full $120$ V peak and with a load attached it could no longer reach beyond $0$ V giving a unipolar piezo driving signal in approach direction and no slip stick driving signal in retract.
diff --git a/chap04.aux b/chap04.aux
index 0b17fb588b79126c1e7245c31ac1f60a2c89e92d..d4b68f34858c5d8bfa97ccae638090e464dc8ddb 100644
--- a/chap04.aux
+++ b/chap04.aux
@@ -1,81 +1,79 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{54}{chapter.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{55}{chapter.4}\protected@file@percent }
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
-\@writefile{toc}{\contentsline {section}{\numberline {4.1}Overview}{54}{section.4.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.1}{\ignorespaces \relax }}{54}{figure.caption.60}\protected@file@percent }
-\newlabel{fig:Repair_Diagram}{{4.1}{54}{\relax }{figure.caption.60}{}}
-\@writefile{tdo}{\contentsline {todo}{Add image of Solidworks or sth. next to it.}{54}{section*.61}\protected@file@percent }
-\@writefile{toc}{\contentsline {section}{\numberline {4.2}General UHV device preparation}{54}{section.4.2}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.2.1}Adding components}{54}{subsection.4.2.1}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.2.2}Soldering}{55}{subsection.4.2.2}\protected@file@percent }
-\@writefile{tdo}{\contentsline {todo}{Check UHV solder}{55}{section*.62}\protected@file@percent }
-\@writefile{toc}{\contentsline {section}{\numberline {4.3}Soldering anchors}{55}{section.4.3}\protected@file@percent }
-\newlabel{fig:solder_anchors_diagram_base}{{4.2a}{56}{\relax }{figure.caption.63}{}}
-\newlabel{sub@fig:solder_anchors_diagram_base}{{a}{56}{\relax }{figure.caption.63}{}}
-\newlabel{fig:solder_anchors_diagram_SmallerDot}{{4.2b}{56}{\relax }{figure.caption.63}{}}
-\newlabel{sub@fig:solder_anchors_diagram_SmallerDot}{{b}{56}{\relax }{figure.caption.63}{}}
-\newlabel{fig:solder_anchors_diagram_AlO}{{4.2c}{56}{\relax }{figure.caption.63}{}}
-\newlabel{sub@fig:solder_anchors_diagram_AlO}{{c}{56}{\relax }{figure.caption.63}{}}
-\newlabel{fig:solder_anchors_diagram_GlueTop}{{4.2d}{56}{\relax }{figure.caption.63}{}}
-\newlabel{sub@fig:solder_anchors_diagram_GlueTop}{{d}{56}{\relax }{figure.caption.63}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref  {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref  {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref  {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref  {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref  {fig:solder_anchors_diagram_SmallerDot}-\subref  {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref  {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably. }}{56}{figure.caption.63}\protected@file@percent }
-\newlabel{fig:solder_anchors_diagram}{{4.2}{56}{Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref {fig:solder_anchors_diagram_SmallerDot}-\subref {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably}{figure.caption.63}{}}
-\newlabel{fig:solder_anchors_examples_glue_bottom}{{4.3a}{57}{\relax }{figure.caption.64}{}}
-\newlabel{sub@fig:solder_anchors_examples_glue_bottom}{{a}{57}{\relax }{figure.caption.64}{}}
-\newlabel{fig:solder_anchors_examples_AlO}{{4.3b}{57}{\relax }{figure.caption.64}{}}
-\newlabel{sub@fig:solder_anchors_examples_AlO}{{b}{57}{\relax }{figure.caption.64}{}}
-\newlabel{fig:solder_anchors_examples_shear_01}{{4.3c}{57}{\relax }{figure.caption.64}{}}
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-\newlabel{fig:solder_anchors_examples}{{4.3}{57}{Examples for the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely}{figure.caption.64}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {4.1}{\ignorespaces \relax }}{55}{figure.caption.60}\protected@file@percent }
+\newlabel{fig:Repair_Diagram}{{4.1}{55}{\relax }{figure.caption.60}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.2}General UHV device preparation}{55}{section.4.2}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2.1}Adding components}{55}{subsection.4.2.1}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.2.2}Soldering}{56}{subsection.4.2.2}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {4.3}Soldering anchors}{56}{section.4.3}\protected@file@percent }
+\newlabel{fig:solder_anchors_diagram_base}{{4.2a}{57}{\relax }{figure.caption.61}{}}
+\newlabel{sub@fig:solder_anchors_diagram_base}{{a}{57}{\relax }{figure.caption.61}{}}
+\newlabel{fig:solder_anchors_diagram_SmallerDot}{{4.2b}{57}{\relax }{figure.caption.61}{}}
+\newlabel{sub@fig:solder_anchors_diagram_SmallerDot}{{b}{57}{\relax }{figure.caption.61}{}}
+\newlabel{fig:solder_anchors_diagram_AlO}{{4.2c}{57}{\relax }{figure.caption.61}{}}
+\newlabel{sub@fig:solder_anchors_diagram_AlO}{{c}{57}{\relax }{figure.caption.61}{}}
+\newlabel{fig:solder_anchors_diagram_GlueTop}{{4.2d}{57}{\relax }{figure.caption.61}{}}
+\newlabel{sub@fig:solder_anchors_diagram_GlueTop}{{d}{57}{\relax }{figure.caption.61}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref  {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref  {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref  {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref  {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref  {fig:solder_anchors_diagram_SmallerDot}-\subref  {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref  {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably. }}{57}{figure.caption.61}\protected@file@percent }
+\newlabel{fig:solder_anchors_diagram}{{4.2}{57}{Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref {fig:solder_anchors_diagram_SmallerDot}-\subref {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably}{figure.caption.61}{}}
+\newlabel{fig:solder_anchors_examples_glue_bottom}{{4.3a}{58}{\relax }{figure.caption.62}{}}
+\newlabel{sub@fig:solder_anchors_examples_glue_bottom}{{a}{58}{\relax }{figure.caption.62}{}}
+\newlabel{fig:solder_anchors_examples_AlO}{{4.3b}{58}{\relax }{figure.caption.62}{}}
+\newlabel{sub@fig:solder_anchors_examples_AlO}{{b}{58}{\relax }{figure.caption.62}{}}
+\newlabel{fig:solder_anchors_examples_shear_01}{{4.3c}{58}{\relax }{figure.caption.62}{}}
+\newlabel{sub@fig:solder_anchors_examples_shear_01}{{c}{58}{\relax }{figure.caption.62}{}}
+\newlabel{fig:solder_anchors_examples_shear_02}{{4.3d}{58}{\relax }{figure.caption.62}{}}
+\newlabel{sub@fig:solder_anchors_examples_shear_02}{{d}{58}{\relax }{figure.caption.62}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.3}{\ignorespaces Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref  {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref  {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref  {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref  {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely.}}{58}{figure.caption.62}\protected@file@percent }
+\newlabel{fig:solder_anchors_examples}{{4.3}{58}{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely}{figure.caption.62}{}}
 \citation{olschewski}
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-\newlabel{sub@fig:Z3_reglue_process_off}{{a}{59}{\relax }{figure.caption.65}{}}
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-\newlabel{sub@fig:Z3_reglue_process_dot}{{c}{59}{\relax }{figure.caption.65}{}}
-\newlabel{fig:Z3_reglue_process_down}{{4.4d}{59}{\relax }{figure.caption.65}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move.}}{59}{figure.caption.65}\protected@file@percent }
-\newlabel{fig:Z3_reglue_process}{{4.4}{59}{The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move}{figure.caption.65}{}}
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-\newlabel{fig:Z3_after reglue}{{4.5}{60}{The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $}{figure.caption.66}{}}
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-\newlabel{fig:Z3_screw_rot}{{4.6}{61}{Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after}{figure.caption.67}{}}
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-\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{62}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.68}{}}
-\newlabel{fig:Front_plate_repair_tool}{{4.8a}{63}{\relax }{figure.caption.69}{}}
-\newlabel{sub@fig:Front_plate_repair_tool}{{a}{63}{\relax }{figure.caption.69}{}}
-\newlabel{fig:Front_plate_repair_plate}{{4.8b}{63}{\relax }{figure.caption.69}{}}
-\newlabel{sub@fig:Front_plate_repair_plate}{{b}{63}{\relax }{figure.caption.69}{}}
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-\newlabel{fig:Front_plate_repair}{{4.8}{63}{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled}{figure.caption.69}{}}
-\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{64}{subsection.4.5.2}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezos stacks of the motor Z3. }}{64}{figure.caption.70}\protected@file@percent }
-\newlabel{fig:Z3_weaker_stack}{{4.9}{64}{The measured capacitance values for the piezos stacks of the motor Z3}{figure.caption.70}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{65}{section.4.6}\protected@file@percent }
-\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{65}{\relax }{figure.caption.71}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{65}{\relax }{figure.caption.71}{}}
-\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{65}{\relax }{figure.caption.71}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{65}{\relax }{figure.caption.71}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces Left (\subref  {fig:Feedthrough_Repairs_left}) and right (\subref  {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding.}}{65}{figure.caption.71}\protected@file@percent }
-\newlabel{fig:Feedthrough_Repairs}{{4.10}{65}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.71}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{66}{table.caption.72}\protected@file@percent }
-\newlabel{tab:cross_cap_after_repair}{{4.1}{66}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.72}{}}
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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.}}{66}{figure.caption.73}\protected@file@percent }
-\newlabel{fig:calibration_after_repair}{{4.11}{66}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.73}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.4}Piezo re-gluing}{59}{section.4.4}\protected@file@percent }
+\newlabel{sec:piezo_reglue}{{4.4}{59}{Piezo re-gluing}{section.4.4}{}}
+\newlabel{fig:Z3_reglue_process_off}{{4.4a}{60}{\relax }{figure.caption.63}{}}
+\newlabel{sub@fig:Z3_reglue_process_off}{{a}{60}{\relax }{figure.caption.63}{}}
+\newlabel{fig:Z3_reglue_process_scratched}{{4.4b}{60}{\relax }{figure.caption.63}{}}
+\newlabel{sub@fig:Z3_reglue_process_scratched}{{b}{60}{\relax }{figure.caption.63}{}}
+\newlabel{fig:Z3_reglue_process_dot}{{4.4c}{60}{\relax }{figure.caption.63}{}}
+\newlabel{sub@fig:Z3_reglue_process_dot}{{c}{60}{\relax }{figure.caption.63}{}}
+\newlabel{fig:Z3_reglue_process_down}{{4.4d}{60}{\relax }{figure.caption.63}{}}
+\newlabel{sub@fig:Z3_reglue_process_down}{{d}{60}{\relax }{figure.caption.63}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of Torr Seal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move.}}{60}{figure.caption.63}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{4.4}{60}{The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of Torr Seal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move}{figure.caption.63}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.5}{\ignorespaces The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $.}}{61}{figure.caption.64}\protected@file@percent }
+\newlabel{fig:Z3_after reglue}{{4.5}{61}{The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $}{figure.caption.64}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{61}{section.4.5}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after.}}{62}{figure.caption.65}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot}{{4.6}{62}{Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after}{figure.caption.65}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{62}{subsection.4.5.1}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces Screw rotation calibration data for Z2 and Z3 after front plate repairs.}}{63}{figure.caption.66}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{63}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.66}{}}
+\newlabel{fig:Front_plate_repair_tool}{{4.8a}{64}{\relax }{figure.caption.67}{}}
+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{64}{\relax }{figure.caption.67}{}}
+\newlabel{fig:Front_plate_repair_plate}{{4.8b}{64}{\relax }{figure.caption.67}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{64}{\relax }{figure.caption.67}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref  {fig:Front_plate_repair_tool}). (\subref  {fig:Front_plate_repair_plate}) shows final front plate assembled.}}{64}{figure.caption.67}\protected@file@percent }
+\newlabel{fig:Front_plate_repair}{{4.8}{64}{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled}{figure.caption.67}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{65}{subsection.4.5.2}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezo stacks of the motor Z3. }}{65}{figure.caption.68}\protected@file@percent }
+\newlabel{fig:Z3_weaker_stack}{{4.9}{65}{The measured capacitance values for the piezo stacks of the motor Z3}{figure.caption.68}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{66}{section.4.6}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{66}{\relax }{figure.caption.69}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{66}{\relax }{figure.caption.69}{}}
+\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{66}{\relax }{figure.caption.69}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{66}{\relax }{figure.caption.69}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces Left (\subref  {fig:Feedthrough_Repairs_left}) and right (\subref  {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding.}}{66}{figure.caption.69}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs}{{4.10}{66}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.69}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{67}{table.caption.70}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{67}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.70}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{67}{section.4.7}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.11}{\ignorespaces The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions.}}{67}{figure.caption.71}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{67}{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.71}{}}
 \@setckpt{chap04}{
-\setcounter{page}{68}
+\setcounter{page}{69}
 \setcounter{equation}{0}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -104,7 +102,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
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diff --git a/chap04.tex b/chap04.tex
index 90a29417fc189aa7ce3fdd38a738b05a6175ee36..0d93ca5676e3add09d8629c0c0fd7b01f61ec3ba 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -8,26 +8,25 @@
     \caption{}
     \label{fig:Repair_Diagram}
 \end{figure}
-\todo{Add image of Solidworks or sth. next to it.}
 
 \section{General UHV device preparation}
 \subsection{Adding components}
-When adding components to a UHV device especially machined parts, a cleaning procedure has to be followed to ensure the part does not strongly outgass in the UHV environment. When working on steel and other materials workshops use oils that heavily outgass in UHV environments. Before using any components that were treated beforehand, like store bought screws or nuts, and any components for which the cleanliness is unknown the following cleaning procedure should be followed:
+When adding components to a UHV device, especially machined parts, a cleaning procedure has to be followed to ensure the part does not strongly outgass in the UHV environment. When working on steel and other materials, workshops use oils that heavily outgass in UHV environments. Before using any components that were treated beforehand, like store bought screws or nuts, and any components for which the cleanliness is unknown, the following cleaning procedure should be followed:
 \begin{enumerate}
-	\item Submerge the component in demineralized water mixed with laboratory grade cleaning detergent and put it in the ultrasonic bath for 10 minutes. This step is to wash of any oils and greases on the components surface.
-	\item Remove the component from the beaker and taking a clean beaker repeat the same step with demineralized water without any detergent.
+	\item Submerge the component in demineralized water mixed with laboratory grade cleaning detergent and put it in the ultrasonic bath for 10 minutes. This step is to wash off any oils and greases on the component's surface.
+	\item Remove the component from the beaker and taking a clean beaker, repeat the same step with demineralized water without any detergent.
 	\item Repeat the previous step with pure acetone
 	\item Repeat the previous step with IPA
 \end{enumerate} 
 The properly cleaned component can now be used in parts that are permanently exposed to vacuum.
 
-Only materials that have been cleared for use in UHV environments should be used. Especially materials that leave residues, like adhesive tapes should be chosen with this in mind. 
+Only materials that have been cleared for use in UHV environments should be used. Especially materials that leave residues, like adhesive tapes, should be chosen with this in mind. 
 
 \subsection{Soldering}
-When soldering any part that is exposed to UHV only solder tins, which are cleared for use in UHV environments should be used. The soldering irons for UHV use should never be used with non-UHV solder in order to ensure no non-UHV solder may be deposited on UHV components. This means that no solder containing lead can be used. \todo{Check UHV solder}.\\
-When using flux the flux has to be cleaned of thoroughly to avoid outgassing as well as short circuiting from stray flux. To do this the following steps have to be followed:
+When soldering any part that is exposed to UHV only solder tins, which are cleared for use in UHV environments, should be used. The soldering irons for UHV use should never be used with non-UHV solder, in order to ensure no non-UHV solder may be deposited on UHV components. This means that no solder containing lead can be used. \\
+When using flux, the flux has to be cleaned off thoroughly to avoid outgassing as well as short-circuiting from stray flux. To do this, the following steps have to be followed:
 \begin{enumerate}
-	\item Using laboratory cleaning swabs and demineralized water mixed with laboratory detergent the surface that was solder on should be cleaned thoroughly, but carefully. After cleaning with the laboratory swab rinse the surface.
+	\item Using laboratory cleaning swabs and demineralized water mixed with laboratory detergent the surface that was solder on should be cleaned thoroughly, but carefully. After cleaning with the laboratory swab, rinse the surface.
 	\item The previous step should be repeated with demineralized water without any detergent
 	\item Rinse the surface with IPA to wash off water residue 
 	\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. 
@@ -66,7 +65,7 @@ However, over time and usage the glue on some of the soldering anchors had loose
 This behavior was worsening over time to the point of not allowing the motor Z1 to return the stage into the Mask extraction height. \\
 In order to optimize this behavior, 3 possible courses of action can be taken.
 First, the size of the solder dots on the anchor could be decreased until it no longer interfered with the prism. This process often involved re-soldering the respective cable, since carving away material often proved impossible. This action was taken when the ceramic still seemed stable and soldering on it did not cause the glue to detach the anchor. This course of action is pictured in Figure (\ref{fig:solder_anchors_diagram_SmallerDot}).\\
-Another course of action that could be taken is to completely replace the soldering anchor with a much thinner \ce{Al2O3} plate, where the size of the solder dot no longer mattered, as long as it is within reasonable measures. This action was taken, when the solder ceramic was no longer stably attached to the Mask Aligner body. This can be seen in Figure (\ref{fig:solder_anchors_diagram_AlO}).\\ 
+Another course of action that could be taken is to completely replace the soldering anchor with a much thinner \ce{Al2O3} plate, where the size of the solder dot no longer mattered, as long as it is within reasonable measures. This action was taken, when the solder ceramic was no longer stably attached to the Mask Aligner body. In Figure (\ref{fig:solder_anchors_diagram_AlO}) this is shown.\\ 
 The last course of action that could be taken was to glue the soldering anchor on the top/bottom side of the ceramic, here care has to be taken that the layer of glue between the walls of the Mask Aligner and the anchor is thick enough to provide proper insulation. This last solution is somewhat inelegant, but was used as a quick optimization, since the functional solder anchor could often be reused without having to detach all cables. This can be seen in Figure (\ref{fig:solder_anchors_diagram_GlueTop}). \\
 
 \begin{figure}[H]
@@ -95,15 +94,15 @@ The last course of action that could be taken was to glue the soldering anchor o
         \caption{}
         \label{fig:solder_anchors_examples_shear_02}
     \end{subfigure}
-    \caption{Examples for the different approaches taken to solve the issues with the solder anchor points. (\subref{fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref{fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce{Al2O3} plate.  (\subref{fig:solder_anchors_examples_shear_01}) and  shows the initial state of a solder ceramic interfering with the prism and then (\subref{fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely.}
+    \caption{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref{fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref{fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce{Al2O3} plate.  (\subref{fig:solder_anchors_examples_shear_01}) and  shows the initial state of a solder ceramic interfering with the prism and then (\subref{fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely.}
     \label{fig:solder_anchors_examples}
 \end{figure}
 
 Examples for all the different approaches taken on the Mask Aligner can be seen in Figure \ref{fig:solder_anchors_examples}
-Figure \ref{fig:solder_anchors_examples_AlO} is a somewhat inelegant example, since the TorrSeal use is a bit excessive since it was very difficult to apply constant pressure at this angle. This is also the reason why the new anchor is placed differently. Here the problem was actually not that the solder anchor interfered with the prism, but that the glue on the old ceramic no longer held the solder anchor in place. Due to remaining glue on the solder ceramic gluing a new solder anchor proved difficult, since the glue sticks poorly to glue residue.
+Figure \ref{fig:solder_anchors_examples_AlO} is a somewhat inelegant example, since the Torr Seal use is a bit excessive since it was very difficult to apply constant pressure at this angle. This is also the reason why the new anchor is placed differently. Here the problem was actually not that the solder anchor interfered with the prism, but that the glue on the old ceramic no longer held the solder anchor in place. Due to remaining glue on the solder ceramic, gluing a new solder anchor proved difficult, since the glue sticks poorly to glue residue.
 
 EPO-TEK H70E is recommended to cure at $150$°C for at least 1 hour, since it would be difficult and dangerous to heat the entire Mask Aligner to $150$°C, since the piezo stacks depolarize at temperatures near $150$°C, and it would be also difficult to heat the glue locally to $150$°C, it was determined that a different glue should be used. \\
-Torr Seal was instead used for all gluing purposes. Torr Seal is a two component epoxy, that can cure at room temperature and follows the requirements, with regard to out gassing, that allows usage in UHV conditions. It however has the disadvantage of reaching its flash point at $175$°C, for this reason soldering on anything affixed with Torr Seal should be done with care as prolonged exposure to the heat of a soldering iron will lead the glue to deteriorate quickly. Also of note is that Torr Seal cannot operate at temperatures below $-45$°C, so usage in a cryonically cooled environment is no longer possible. Since the Mask Aligner is however not intended for usage in a cooled environment anyway this was determined not to be an issue.
+Torr Seal was instead used for all gluing purposes. Torr Seal is a two component epoxy, that can cure at room temperature and follows the requirements, with regard to out gassing, that allows usage in UHV conditions. It however has the disadvantage of reaching its flash point at $175$°C, for this reason soldering on anything affixed with Torr Seal should be done with care as prolonged exposure to the heat of a soldering iron will lead the glue to deteriorate quickly. Also of note is that Torr Seal cannot operate at temperatures below $-45$°C, so usage in a cryonically cooled environment is no longer possible. Since the Mask Aligner is however not intended for usage in a cooled environment anyway, this was determined not to be an issue.
 
 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. An example for a problematic anchor is shown in Figure \ref{fig:solder_anchors_examples_shear_01}. The state after taking of some of the solder is shown in Figure \ref{fig:solder_anchors_examples_shear_02}\\\
 After this step, the prism would no longer get stuck when driving and could cleanly drive the whole range of possible motion. \\
@@ -137,13 +136,13 @@ The piezo motors of the 3 motor stacks in the Mask Aligner were glued in 2015 wi
     	\caption{}
 		\label{fig:Z3_reglue_process_down}
     \end{subfigure}
-    \caption{The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move.}
+    \caption{The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of Torr Seal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move.}
     \label{fig:Z3_reglue_process}
 \end{figure}
 
 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. \\
 
-To perform the actual gluing of the piezo stack, first all traces of remaining glue were scratched of the surface of the affected piezo stack. Afterward a small dot of Torr Seal was put on the underside of the piezo stack, and it was carefully put in place, the Mask Aligner was rotated via a clamp so that gravity kept the piezo stack in the place it is intended to stay. In order to provide pressure on the piezo stack, so that the glue can evenly spread and properly stick to the surface of the Mask Aligner, the prism was reinserted into the motor and was weighed down with nuts. The entire process can be seen in Figure \ref{fig:Z3_reglue_process}.\\ 
+To perform the actual gluing of the piezo stack, first all traces of remaining glue were scratched off the surface of the affected piezo stack. Afterward a small dot of Torr Seal was put on the underside of the piezo stack, and it was carefully put in place, the Mask Aligner was rotated via a clamp so that gravity kept the piezo stack in the place it is intended to stay. In order to provide pressure on the piezo stack, so that the glue can evenly spread and properly stick to the surface of the Mask Aligner, the prism was reinserted into the motor and was weighed down with nuts. The entire process can be seen in Figure \ref{fig:Z3_reglue_process}.\\ 
 The repair of the piezo on motor Z1 happened without problems, but on motor Z3 the piezo turned by about $\approx 4.5^\circ \pm 0.5^\circ$ during the curing process. Since $\cos(5^\circ) \approx 0.996$ this should not majorly affect the performance of the Z3 motor.
 
 \begin{figure}[H]
@@ -167,8 +166,8 @@ This behavior can be seen in Figure \ref{fig:Z3_screw_rot} (compare \textcolor{t
 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.
 
 \subsection{Front plate repair}
-In order to test the hypothesis, that the front plate of motor Z3 was causing the issues, the front plate of Z3 was exchanged for the front plate of motor Z1. Re-soldering 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{fig:Z3_screw_rot_after_rep} (\textcolor{tab_green}{green} and \textcolor{tab_red}{red}) 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{fig:Z3_screw_rot_after_rep}) 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. \\
+In order to test the hypothesis, that the front plate of motor Z3 was causing the issues, the front plate of Z3 was exchanged for the front plate of motor Z1. Re-soldering 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{fig:Z3_screw_rot_after_rep} (\textcolor{tab_green}{green} and \textcolor{tab_red}{red}) 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{fig:Z3_screw_rot_after_rep}) 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. \\
 
 \begin{figure}[H]
     \centering
@@ -177,12 +176,12 @@ The problem on the Z3 front plate was likely a misalignment on one of the piezo
     \label{fig:Z3_screw_rot_after_rep}
 \end{figure}
 
-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. An Solidworks image of the alignment tool can be seen in Figure \ref{fig:Front_plate_repair_tool} \\
+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. A Solidworks image of the alignment tool can be seen in Figure \ref{fig:Front_plate_repair_tool} \\
 Since the plate is separate from the rest of the Mask Aligner, the plate could be cured inside an oven at $150$°C easily. For this reason it was decided, that EPO-TEK H70E would be used, since this was used previously and would result in a quicker curing time as well as more similarity to the other $2$ front plates. \\
 
 During the gluing process, a mistake was made, that was only noticed after curing. During the setup of the new front plate it was assumed, that the replacement piezos and the original piezos of the Mask Aligner were identical, where both sides were polished, so that they can be used as sliding surfaces, but the replacement piezos have one sliding surface, which is polished and one gluing surface, which is not polished and as such is more rough. This can be seen in the different texture the top and bottom piezo stacks have in Figure \ref{fig:Front_plate_repair_plate}. This could potentially negatively affect the performance of the new front plate. \\
 The solder ceramics on the front plate had to be detached for the creation of the new front plate, as the alignment tool was designed without them in mind. This was not an issue however as they had similar problems to the other solder ceramics in previous chapters and replacement was deemed to be an improvement. The ceramics were replaced with a long \ce{Al2O3} plate, which was attached using Torr Seal. The results of the full assembly of the front plate can be seen in Figure \ref{fig:Front_plate_repair_plate}.\\
-In testing with the newly made front plate the performance of Z3 was comparable with Z2, although it had a slightly larger deviance between approach and retract movement and a slightly decreased performance for very firm screw. Regardless the difference in performance was deemed to be immaterial as a point of common step size could be found in the step size tests as seen in Figure \ref{fig:Z3_screw_rot_after_rep}. In the range of 2.5 screw rotations the performance matched between Z2 and Z3 and thus this screw setting was chosen for optimization of these 2 motors. Z1 was then compared to both motors and a fitting screw setting was chosen for it as well. 
+In testing with the newly made front plate, the performance of Z3 was comparable with Z2, although it had a slightly larger deviance between approach and retract movement and a slightly decreased performance for very firm screw. Regardless, the difference in performance was deemed to be immaterial as a point of common step size could be found in the step size tests as seen in Figure \ref{fig:Z3_screw_rot_after_rep}. In the range of 2.5 screw rotations the performance matched between Z2 and Z3 and thus this screw setting was chosen for optimization of these 2 motors. Z1 was then compared to both motors and a fitting screw setting was chosen for it as well. 
 
 
 \begin{figure}[H]
@@ -203,22 +202,22 @@ In testing with the newly made front plate the performance of Z3 was comparable
     \label{fig:Front_plate_repair}
 \end{figure}
 
-In order to prevent the now longer cables of the front plates of Z1 and Z3 to interfere with Mask Aligner operation the cables were guided around the Mask Aligner body in ways such that they would not interfere with normal operation. This includes in particular not being within field of vision of the camera pointed at the sample (see \ref{camera_dings}) as well as not interfering with the wobblestick path when removing or adding samples/masks from the mask aligner. For this reason the cables of Z1 were moved towards the left side, when viewing Z1 from the front, and then guided to the top of the Mask Aligner body, close to the X piezo and from there to the vacuum feed through pins. Z3 was guided to the upper side of the stoppers and then directly to the vacuum feed through pins. In order to ensure the cables would not move from these positions, they were glued in place using TorrSeal.
+In order to prevent the now longer cables of the front plates of Z1 and Z3 to interfere with Mask Aligner operation, the cables were guided around the Mask Aligner body in ways such that they would not interfere with normal operation. This includes in particular not being within the field of vision of the camera pointed at the sample (see \ref{camera_dings}) as well as not interfering with the wobble stick path when removing or adding samples/masks from the mask aligner. For this reason the cables of Z1 were moved towards the left side, when viewing Z1 from the front, and then guided to the top of the Mask Aligner body, close to the X piezo and from there to the vacuum feed through pins. Z3 was guided to the upper side of the stoppers and then directly to the vacuum feed through pins. In order to ensure the cables would not move from these positions, they were glued in place using Torr Seal.
 
 \subsection{Small capacitance stack}
-During the investigation into the problems with the driving of the Z3 motor the capacitance values for the piezo stacks of the Z3 motors were determined. Since the cables had to be re-soldered they could be measured separately. The motor that was re-glued in Section \ref{sec:piezo_reglue} has a lower capacitance value than the surrounding piezo stacks. The value of $1.05$ nF is lower by approximately the amount a single piezo has of $0.4$ nF from the expected $1.6 \pm 0.4$ nF (the range is not an measurement uncertainty, but due to variance in temperature). The different capacitances measured for all the piezo stacks can be seen in Figure \ref{fig:Z3_weaker_stack}. The piezo stacks both showing $1.62$ nF were only measured together since they were always wired in parallel, when measurements were taken. The plate stacks were also only measured together. Measurements were taken by measuring capacitance of the entire motor Z3 with the piezos detached from the circuit. \\
+During the investigation into the problems with the driving of the Z3 motor, the capacitance values for the piezo stacks of the Z3 motors were determined. Since the cables had to be re-soldered, they could be measured separately. The motor that was re-glued in Section \ref{sec:piezo_reglue} has a lower capacitance value than the surrounding piezo stacks. The value of $1.05$ nF is lower by approximately the amount a single piezo has of $0.4$ nF from the expected $1.6 \pm 0.4$ nF (the range is not a measurement uncertainty, but due to variance in temperature). The different capacitances measured for all the piezo stacks can be seen in Figure \ref{fig:Z3_weaker_stack}. The piezo stacks both showing $1.62$ nF were only measured together since they were always wired in parallel, when measurements were taken. The plate stacks were also only measured together. Measurements were taken by measuring capacitance of the entire motor Z3 with the piezos detached from the circuit. \\
 
-The deviation of the upper left piezo stack would imply that one of the piezo layers has depolarized and is no longer functioning, this could lead to slight deviances in the driving behavior of Z3 at low screw firmness, but was determined to not be an issue. It should however be mentioned in case of future problems with the Z3 motor, so it can be determined if it can be a source of the issue.
+The deviation of the upper left piezo stack would imply that one of the piezo layers has depolarized and is no longer functioning, this could lead to a slight deviance in the driving behavior of Z3 at low screw firmness, but was determined to not be an issue. It should however be mentioned in case of future problems with the Z3 motor, so it can be determined if it can be a source of the issue.
 
 \begin{figure}[H]
     \centering
     \includegraphics[width=0.45\linewidth]{img/Repairs/WeakerCapacitor.pdf}
-    \caption{The measured capacitance values for the piezos stacks of the motor Z3. }
+    \caption{The measured capacitance values for the piezo stacks of the motor Z3. }
     \label{fig:Z3_weaker_stack}
 \end{figure}
 
 \section{Feed through cabling optimizations}
-A last step of optimization that was performed was on the feedthroughts that lead the signal coming from the capacitance sensors on the mask to the outside of the Mask Aligner flange, so the signal can be finally read out with the LockIn Amplifier. The cables for the capacitance signals are coaxial cables with a shielding to prevent stray influences from the system affecting the readout. These cables were noticed to be overly long and only one of the cables shielding was grounded on the feedthrough side, instead the shielding of the other cables was grounded on the Mask Stage side, to the Mask Aligner Body. The shielding was also stripped from a large part of the cable near the feedthrough exposing the cable near the metal body of the feedthrough flange.
+A last step of optimization that was performed was on the feedthroughts that lead the signal coming from the capacitance sensors on the mask to the outside of the Mask Aligner flange, so the signal can be finally read out with the Lock-in Amplifier. The cables for the capacitance signals are coaxial cables with a shielding to prevent stray influences from the system affecting the readout. These cables were noticed to be overly long and only one of the cables shielding was grounded on the feedthrough side, instead the shielding of the other cables was grounded on the Mask Stage side, to the Mask Aligner Body. The shielding was also stripped from a large part of the cable near the feedthrough exposing the cable near the metal body of the feedthrough flange.
 
 
 \begin{figure}[H]
@@ -237,7 +236,7 @@ A last step of optimization that was performed was on the feedthroughts that lea
     \label{fig:Feedthrough_Repairs}
 \end{figure}
 
-In order to reduce possible interference on the signal, the cables were shortened and were properly grounded on the feedthroughs. In order to connect the feedthroughs to the body of the feedthroughs, a gold pin was soldered to the inside of the feedthrough and the male end was soldered to the coaxial cable shielding with a short copper cable. This is easier than soldering the shielding to the body directly since a large solder amount of solder is required to properly stick to the smooth steel surface. Only the small part near the gold pins, that connect the coaxial cable to the feedthrough is now without shielding.\\
+In order to reduce possible interference to the signal, the cables were shortened and were properly grounded on the feedthroughs. In order to connect the feedthroughs to the body of the feedthroughs, a gold pin was soldered to the inside of the feedthrough and the male end was soldered to the coaxial cable shielding with a short copper cable. This is easier than soldering the shielding to the body directly, since a large solder amount of solder is required to properly stick to the smooth steel surface. Only the small part near the gold pins, that connect the coaxial cable to the feedthrough is now without shielding.\\
 
 \begin{table}[H]
 \centering
@@ -265,7 +264,5 @@ In order to determine the proper screw setup and to test the function of the cha
     \label{fig:calibration_after_repair}
 \end{figure}
 
-This calibration shows similarity of performance between the 3 motors in the approach regime as seen in Figure \ref{fig:calibration_after_repair}. In approach direction the 3 motors deviate by about $3$ nm/step, which is at least within $2$ $\sigma$ of each other, when comparing Z1 to Z2 and Z2 to Z3. Z3 and Z1 however can deviate by up to $6$ nm/step, which is within $6$$\sigma$ of each other. Assuming a difference of $6 nm$, as the worst case, the data would give an angular tilt per step of $\approx (5.73 \times 10^{-6})^\circ$ or a difference in height on the sample of $\approx 0.5$ nm/step. This in turn would give a difference in penumbra of $1.2$ nm for every $100$ steps.\\
-In the retract regime the difference between motors is within margin of error for Z2 and Z1, but Z3 deviates by about $4 \sigma$ from the others. Since alignment happens with approach mostly and retract is only used to move the mask back from the sample after an evaporation this is of lesser importance than a deviation in approach behavior. After each evaporation the mask is retracted to about $50$ $\mu$m to ensure movement of the x piezo does not damage the sample. Within these a difference of $1.2$ $\mu$m would appear from side to side of the evaporation field, which corresponds to an angle of $\approx 0.004^\circ$. This difference should result in a deviation of $\approx 38$ nm in penumbra for the evaporation, however by driving the Z1 and Z2 motors $100$ steps up after the retraction this can be compensated almost fully and should result in an error of at most $\approx 6$ nm of additional penumbra induced by tilt. \\
-
-
+This calibration shows similarity of performance between the 3 motors in the approach regime, as seen in Figure \ref{fig:calibration_after_repair}. In approach direction the 3 motors deviate by about $3$ nm/step, which is at least within $2$ $\sigma$ of each other, when comparing Z1 to Z2 and Z2 to Z3. Z3 and Z1 however can deviate by up to $6$ nm/step, which is within $6$$\sigma$ of each other. Assuming a difference of $6 nm$, as the worst case, the data would give an angular tilt per step of $\approx (5.73 \times 10^{-6})^\circ$ or a difference in height on the sample of $\approx 0.5$ nm/step. This in turn would give a difference in penumbra of $1.2$ nm for every $100$ steps.\\
+In the retract regime, the difference between motors is within the margin of error for Z2 and Z1, but Z3 deviates by about $4 \sigma$ from the others. Since alignment happens with approach mostly and retract is only used to move the mask back from the sample after an evaporation, this is of lesser importance than a deviation in approach behavior. After each evaporation, the mask is retracted to about $50$ $\mu$m to ensure movement of the x piezo does not damage the sample. Within these, a difference of $1.2$ $\mu$m would appear from side to side of the evaporation field, which corresponds to an angle of $\approx 0.004^\circ$. This difference should result in a deviation of $\approx 38$ nm in penumbra for the evaporation, however by driving the Z1 and Z2 motors $100$ steps up after the retraction this can be compensated almost fully and should result in an error of at most $\approx 6$ nm of additional penumbra induced by tilt. \\
diff --git a/chap05.aux b/chap05.aux
index b0f0aa485ca702ccde7678f7124edf34cd5d1636..9b657b2f5935fb10539ca9d63b100c162c5cb0ec 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -1,99 +1,99 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{\numberline {5}Evaporations and measurement}{68}{chapter.5}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{\numberline {5}Evaporations and measurement}{69}{chapter.5}\protected@file@percent }
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+\newlabel{fig:evaporation_tilts_all}{{5.8b}{78}{\relax }{figure.caption.80}{}}
+\newlabel{sub@fig:evaporation_tilts_all}{{b}{78}{\relax }{figure.caption.80}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces Image of the reconstruction of the tilt angle for Field 3 as an example (\subref  {fig:evaporation_tilts_example}) and the data given by all fields (\subref  {fig:evaporation_tilts_all}). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}}{78}{figure.caption.80}\protected@file@percent }
+\newlabel{fig:evaporation_tilts}{{5.8}{78}{Image of the reconstruction of the tilt angle for Field 3 as an example (\subref {fig:evaporation_tilts_example}) and the data given by all fields (\subref {fig:evaporation_tilts_all}). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case}{figure.caption.80}{}}
+\newlabel{fig:evaporation_SEM_sample}{{5.9a}{79}{\relax }{figure.caption.81}{}}
+\newlabel{sub@fig:evaporation_SEM_sample}{{a}{79}{\relax }{figure.caption.81}{}}
+\newlabel{fig:evaporation_SEM_mask}{{5.9b}{79}{\relax }{figure.caption.81}{}}
+\newlabel{sub@fig:evaporation_SEM_mask}{{b}{79}{\relax }{figure.caption.81}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces SEM images of field 2 on the sample (\subref  {fig:evaporation_SEM_sample}) and the mask (\subref  {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects.}}{79}{figure.caption.81}\protected@file@percent }
+\newlabel{fig:evaporation_SEM}{{5.9}{79}{SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects}{figure.caption.81}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog}{{5.10a}{80}{\relax }{figure.caption.82}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{80}{\relax }{figure.caption.82}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog_overlay}{{5.10b}{80}{\relax }{figure.caption.82}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog_overlay}{{b}{80}{\relax }{figure.caption.82}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces An example of the clogging noticed on $4$ of the mask holes (\subref  {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{80}{figure.caption.82}\protected@file@percent }
+\newlabel{fig:evaporation_SEM_analysis}{{5.10}{80}{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.82}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {5.5}Simulation}{80}{section.5.5}\protected@file@percent }
+\newlabel{sec:simulation}{{5.5}{80}{Simulation}{section.5.5}{}}
+\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.11a}{82}{\relax }{figure.caption.83}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{82}{\relax }{figure.caption.83}{}}
+\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.11b}{82}{\relax }{figure.caption.83}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{82}{\relax }{figure.caption.83}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $.}}{82}{figure.caption.83}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare}{{5.11}{82}{Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $}{figure.caption.83}{}}
 \citation{Bhaskar}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask. }}{82}{figure.caption.86}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_overlap}{{5.12}{82}{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask}{figure.caption.86}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.13a}{82}{\relax }{figure.caption.87}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{82}{\relax }{figure.caption.87}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.13b}{82}{\relax }{figure.caption.87}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{82}{\relax }{figure.caption.87}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.13c}{82}{\relax }{figure.caption.87}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{82}{\relax }{figure.caption.87}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref  {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ (\subref  {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{82}{figure.caption.87}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness}{{5.13}{82}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.87}{}}
-\newlabel{fig:evaporation_simulation_rejection_prev}{{5.14a}{83}{\relax }{figure.caption.88}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{83}{\relax }{figure.caption.88}{}}
-\newlabel{fig:evaporation_simulation_rejection_after}{{5.14b}{83}{\relax }{figure.caption.88}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{83}{\relax }{figure.caption.88}{}}
-\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.14c}{83}{\relax }{figure.caption.88}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{83}{\relax }{figure.caption.88}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Simulated evaporation dots without (\subref  {fig:evaporation_simulation_rejection_prev}) and with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{83}{figure.caption.88}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_rejection}{{5.14}{83}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.88}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.15}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$.}}{84}{figure.caption.89}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_progression}{{5.15}{84}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$}{figure.caption.89}{}}
-\@writefile{toc}{\contentsline {paragraph}{Software improvements}{84}{section*.90}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Conclusion}{85}{section*.91}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask. }}{83}{figure.caption.84}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_overlap}{{5.12}{83}{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask}{figure.caption.84}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.13a}{84}{\relax }{figure.caption.85}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{84}{\relax }{figure.caption.85}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.13b}{84}{\relax }{figure.caption.85}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{84}{\relax }{figure.caption.85}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.13c}{84}{\relax }{figure.caption.85}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{84}{\relax }{figure.caption.85}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref  {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ (\subref  {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{84}{figure.caption.85}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness}{{5.13}{84}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.85}{}}
+\newlabel{fig:evaporation_simulation_rejection_prev}{{5.14a}{85}{\relax }{figure.caption.86}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{85}{\relax }{figure.caption.86}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{5.14b}{85}{\relax }{figure.caption.86}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{85}{\relax }{figure.caption.86}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.14c}{85}{\relax }{figure.caption.86}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{85}{\relax }{figure.caption.86}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Simulated evaporation dots without (\subref  {fig:evaporation_simulation_rejection_prev}) and with (\subref  {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref  {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{85}{figure.caption.86}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{5.14}{85}{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.86}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.15}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$.}}{86}{figure.caption.87}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_progression}{{5.15}{86}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$}{figure.caption.87}{}}
+\@writefile{toc}{\contentsline {paragraph}{Software improvements}{86}{section*.88}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Conclusion}{87}{section*.89}\protected@file@percent }
 \@setckpt{chap05}{
-\setcounter{page}{86}
+\setcounter{page}{88}
 \setcounter{equation}{1}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -122,7 +122,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{0}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap05.tex b/chap05.tex
index d1d6c448b708b335d68bf5227f22fb6d6624cf6b..58e50da93070eee8139629cdea0da2e72e59d6d9 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -11,7 +11,7 @@ As a test for positioning and as a test for the Mask Aligners capabilities after
     \label{fig:evaporation_approach_curve}
 \end{figure}
 
-Five subsequent evaporations were performed at different lateral positions on the sample. Each field was evaporated at different mask sample distances as described by the approach curve. The approach curve to full contact of this particular sample is shown in Figure \ref{fig:evaporation_approach_curve} \\  
+Five subsequent evaporations were performed at different lateral positions on the sample. Each field was evaporated at different mask sample distances, as described by the approach curve. The approach curve to full contact of this particular sample is shown in Figure \ref{fig:evaporation_approach_curve} \\  
 
 \begin{itemize}
 	\item Field 1: Full contact
@@ -33,7 +33,7 @@ The evaporation parameters are shown in Table \ref{tab:evaporation_settings}.
 		Evap. 4 & $40$             & $1.75$        & $10.0-4.9$      & $460-510$       &$2.99 \times 10^{-9}$& $24$                   \\ \hline
 		Evap. 5 & $40$             & $1.75$        & $6.8-4.7$       & $450-500$       &$2.86 \times 10^{-9}$& $24$                   \\ \hline
 	\end{tabular}
-	\caption{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}
+	\caption{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}
 	\label{tab:evaporation_settings}
 \end{table}
 
@@ -46,7 +46,7 @@ The evaporation parameters are shown in Table \ref{tab:evaporation_settings}.
 
 Figure \ref{fig:evaporation_chamber_status} shows the vacuum chamber status when the evaporation was performed. The turbomolecular pump was not turned off. The gold evaporator attached to the system was in use during the evaporations, requiring the system to be vented and pumped multiple times in the $2$ days, during which the 5 fields were evaporated. These two factors could have affected the evaporation performance.
 
-The pressure of the main chamber before each of the evaporations was $4.5 \times 10^{-10}$ mbar. The pressure during each evaporation was recorded, with the exception of evaporation 4, where the software crashed during saving, corrupting the file. In this case only the highest pressure value was recorded.
+The pressure of the main chamber before each of the evaporations was $4.5 \times 10^{-10}$ mbar. The pressure during each evaporation was recorded, except for evaporation 4, where the software crashed during saving, corrupting the file. In this case, only the highest pressure value was recorded.
 
 \begin{figure}[H]
     \centering
@@ -63,11 +63,11 @@ The pressure of the main chamber before each of the evaporations was $4.5 \times
 		\label{fig:Evaporation_diagramm_mask_img}
 	\end{subfigure}
     
-    \caption{Diagram showing the Evaporation performed on the sample (\subref{fig:Evaporation_diagramm_sample_img}). Red squares represent the evaporation fields. The number shows the order of evaporations. Distances are measured using optical microscope. Fields are at a $10^\circ$ angle with respect to the sample holder. (\subref{fig:Evaporation_diagramm_mask_img}) shows a microscope image of the mask taken before evaporation. The mask holder is placed straight in the microscope. The mask itself is angled on the mask holder.}
+    \caption{Diagram showing the Evaporation performed on the sample (\subref{fig:Evaporation_diagramm_sample_img}). Red squares represent the evaporation fields. The number shows the order of evaporations. Distances are measured using an optical microscope. Fields are at a $10^\circ$ angle with respect to the sample holder. (\subref{fig:Evaporation_diagramm_mask_img}) shows a microscope image of the mask taken before evaporation. The mask holder is placed straight in the microscope. The mask itself is angled on the mask holder.}
     \label{fig:Evaporation_diagramm}
 \end{figure}
 
-Figure \ref{fig:Evaporation_diagramm_sample_img} shows the positions of the evaporated fields with regards to the sample edges and each other. 
+Figure \ref{fig:Evaporation_diagramm_sample_img} shows the positions of the evaporated fields in regard to the sample edges and each other. 
 
 \section{Contamination}
 The entire sample's 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. 
@@ -112,7 +112,7 @@ To analyze the penumbra, for a circular in this case since there are many differ
 	\label{fig:Evaporation_diagramm_field}
 	\end{subfigure}
     
-    \caption{AFM image of evaporated \ce{Pb} dot (\subref{fig:penumbra_tilt_sigmas}) illustrating the penumbral widths used for evaporation analysis $\sigma_s$ and $\sigma_l$, depicted in \textcolor{tab_red}{red}, and the major axis of the tilt \textcolor{tab_green}{(green)}.  $\sigma_s$ is drawn larger than actually measured, since the measured value would be hardly visible. The \textcolor{tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data stems from Evaporation 5 In Chapter 5. (\subref{fig:Evaporation_diagramm_field}) shows an AFM image of the top right part of the evaporated field labeled $3$. Grains were reduced using post processing. Black circles show the dots chosen for further examination on this particular field.}
+    \caption{AFM image of evaporated \ce{Pb} dot (\subref{fig:penumbra_tilt_sigmas}) illustrating the penumbral widths used for evaporation analysis $\sigma_s$ and $\sigma_l$, depicted in \textcolor{tab_red}{red}, and the major axis of the tilt \textcolor{tab_green}{(green)}.  $\sigma_s$ is drawn larger than actually measured, since the measured value would be hardly visible. The \textcolor{tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data stems from Evaporation 5 In Chapter 5. (\subref{fig:Evaporation_diagramm_field}) shows an AFM image of the top right part of the evaporated field labeled $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field.}
     \label{fig:penumbra_tilt_sigmas_and_field_show}
 \end{figure}
 
@@ -130,7 +130,7 @@ The width of the penumbra was then obtained by getting line cuts close to the li
 
 where $r$ is the radius of the dot, $b$ is an offset from $0$, $\mu$ is the midpoint of the dot, $h$ is the height of the dot and $\sigma_s$ and $\sigma_l$ are the two different penumbras. This fit function allows the determination of the height, radius and penumbra of each dot 
 
-An example is shown in Figure \ref{fig:evaporation_analysis}. In the example, the "Half Moon" shape of the dot, induced by a tilt, can be easily seen in both image and line cut. This results in $2$ extremal penumbra widths that were separately fitted.
+An example is shown in Figure \ref{fig:evaporation_analysis}. In the example, the "Half Moon" shape of the dot, induced by a tilt, can be easily seen in both image and line cut. This results in $2$ extreme penumbra widths that were separately fitted.
 Also obtained by this method are the height and the diameter of each dot.
  
 \begin{figure}[H]
@@ -184,9 +184,10 @@ This process was performed for every recorded dot and with multiple line cuts ne
 Figure \ref{fig:evaporation_measured_penumbra} shows the values obtained from analysis of exemplary \ce{Pb} dots of each field. For each field a dot on the top of the field, one on the bottom, one near the center and on each on the left and the right were chosen to analyze. The dots were chosen based on how contaminated the data looked in an AFM image of the top right and bottom left of the field, and if the phase showed line artifacts. \\
 The data in Figure \ref{fig:evaporation_measured_penumbra_sigs} shows that for the smaller penumbra values of well below the threshold of $100$ nm can be found, with most of the fields lying near $50$ nm. Showing that the evaporation gave very sharp interfaces. From the evaporation conditions it would be expected, that field $1$ and field $5$ should be very similar and both should show smaller penumbra than the other fields, but this does not appear to be the case. While field $5$ shows some of the smallest penumbras, its behavior seems to be more akin to field $3$ than $1$. Field $4$ also has the largest penumbras, which is unexpected since it was evaporated at the point of second contact and should thus perform better than both field $3$ and field $2$. Both field $2$ and $4$ have the largest uncertainties, due to more noisy data, which could explain this discrepancy. The difference between top, bottom, right, left and center seems to be within measurement uncertainty and thus no conclusive statements can be made about it.\\
 
+
 The height of the dots (Figure \ref{fig:evaporation_measured_penumbra_height}) is spread around a mean value of $2.6 \pm 0.3$ nm and shows strong deviation from the expected $5$ nm, obtained from calibration measurements for the particle flux that was used in the evaporation. This seems to suggest a large amount of \ce{Pb} particles never reaches the mask, even though they are expected to by the setup conditions. \\
 
-The diameter of the \ce{Pb} dots would be expected to decrease with subsequent evaporation due to clogging of the mask. This trend is mirrored in the data as the average diameter of evaporation decreases from $3.02 \pm 0.04$ 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 eccentricity of the dots outer shape was determined by measuring the diameter for multiple line cuts on the circle via fit and comparing measurements of perpendicular line cuts. The resulting eccentricity was as in the weighted mean $0.2 \pm 0.1$, which suggest that the dots are circular within measurement accuracy. This means the outer dot shape does not seem to be affected by the tilting effects.\\
+The diameter of the \ce{Pb} dots would be expected to decrease with subsequent evaporation due to clogging of the mask. This trend is mirrored in the data as the average diameter of evaporation decreases from $3.02 \pm 0.04$ 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 eccentricity of the dot's outer shape was determined by measuring the diameter of multiple line cuts on the circle via fit and comparing measurements of perpendicular line cuts. The resulting eccentricity was as in the weighted mean $0.2 \pm 0.1$, which suggest that the dots are circular within measurement accuracy. This means the outer dot shape does not seem to be affected by the tilting effects.\\
 
 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. \\
 
@@ -254,7 +255,7 @@ The image of the mask (Figure \ref{fig:evaporation_SEM_mask}) shows no damage to
 \end{figure}
 
 An example of this clogging in the SEM image is shown in Figure \ref{fig:evaporation_SEM_analysis_clog}
-To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. It also mostly points outwards. For a lot of points the clogging is not clearly visible in the image however so no strong conclusion can be made from the SEM image alone.
+To further check if the clogging artifacts correspond to the directions of tilt shown in Figure \ref{fig:evaporation_tilts} the directions are overlayed in Figure \ref{fig:evaporation_SEM_analysis_clog_overlay}. The directions correspond to the direction shown in the SEM image, except for some outliers. It also mostly points outwards. For a lot of points the clogging is not clearly visible in the image however, so no strong conclusion can be made from the SEM image alone.
 
 \section{Simulation} \label{sec:simulation}
 In order to gain more information about the different hypothesis for the tilted evaporation dots, a simple evaporation simulation was written. The simulation is based on ray tracing and is written in the open source Godot game engine, since game engines support checking of rays against collision natively and thus a ray tracing simulation could be implemented quickly. \\
@@ -275,7 +276,6 @@ In order to simulate vibration effects, the cylinder collider for the mask can b
 
 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}
@@ -294,7 +294,7 @@ After a user specified time has passed, the amount of hits on each pixel is save
 
 An image of a simple simulation for an oscillating mask dot with parameters obtained from the AFM measurement can be seen in Figure \ref{fig:evaporation_simulation_first_compare_SIM}. The parameters for the amplitude of the oscillation were extracted from the AFM image shown in Figure \ref{fig:evaporation_simulation_first_compare_AFM}. The values were $0.143$ $\mu$m in x and $-0.358$ $\mu$m in z direction and a tilt of $-41.12^\circ$ in $\alpha$ and $31^\circ$ in $\gamma$. \\
 
-The mask being deformed by nearly $45^\circ$ at a single hole site locally would induce large strain upon the mask. The visible tilt is most likely an outcome of both an x-y displacement and a bending of the mask. If there was just a displacement due to the vibration the mask would shift between 2 lateral positions with a certain frequency. If there is strong overlap the $2$ extreme positions would have a certain overlap, which is elliptical. If there is now an additional displacement component in the z direction this causes a smaller circle on top of the flat mask position. It is likely that the effect on the edge is an overlap of both a bending of the mask giving the mask some angle and an additional contribution from the displacement in both x-y and z direction. A simulated of this is shown in Figure \ref{fig:evaporation_simulation_overlap}
+The mask being deformed by nearly $45^\circ$ at a single hole site locally would induce large strain upon the mask. The visible tilt is most likely an outcome of both an x-y displacement and a bending of the mask. If there was just a displacement due to the vibration, the mask would shift between 2 lateral positions with a certain frequency. If there is strong overlap, the $2$ extreme positions would have a certain overlap, which is elliptical. If there is now an additional displacement component in the z direction, this causes a smaller circle on top of the flat mask position. It is likely that the effect on the edge is an overlap of both a bending of the mask giving the mask some angle and an additional contribution from the displacement in both x-y and z direction. A simulation of this is shown in Figure \ref{fig:evaporation_simulation_overlap}
 
 \begin{figure}[H]
     \centering
@@ -305,7 +305,7 @@ The mask being deformed by nearly $45^\circ$ at a single hole site locally would
 
 The amplitude of displacement in the case in Figure \ref{fig:evaporation_simulation_first_compare_SIM} is $\approx 0.4$ $\mu$m, this is in line with the peak to peak amplitude of an active turbomolecular pump given by $1$ $\mu$m, obtained in the PhD thesis of Priyamvada Bhaskar.~\cite{Bhaskar} Some features of the AFM measurement are mirrored in the simulation, however it does not match the simulated image in a decent number of characteristics. The "half moon" shaped penumbra (\textcolor{tab_red}{red} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) in the AFM image is very rough, but on average of equal height, while in the simulation the penumbra gradually lowers from the highest part. The lower edge of the elliptical shape visible in the AFM dot below the circle (\textcolor{tab_cyan}{cyan} in Figure \ref{fig:evaporation_simulation_first_compare_AFM}) is so faint as to be invisible in the AFM image, while it is very pronounced in the simulated image and the lower edge is sharp in the AFM image $61 \pm 9$ nm while it is smeared out in the simulated image. \\
 
-The different roughness from circle and ellipse might suggest different possible reasons. First it could be a chronological effect where the circle is deposited first and the ellipse is deposited second. Another possiblity is that the vibration cause the displacement and bending of the mask in an pattern that is anharmonic, which causes the extreme points of the oscillation to be preferred. In order to investigate possible sources of this effect the simulation was amended. \\
+The different roughness from circle and ellipse might suggest different possible reasons. First it could be a chronological effect where the circle is deposited first, and the ellipse is deposited second. Another possibility is that the vibration cause the displacement and bending of the mask in a pattern that is anharmonic, which causes the extreme points of the oscillation to be preferred. In order to investigate possible sources of this effect, the simulation was amended. \\
 
 \begin{figure}[H]
     \centering
@@ -328,7 +328,7 @@ The different roughness from circle and ellipse might suggest different possible
     \label{fig:evaporation_simulation_sharpness}
 \end{figure}
 
-The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_initial} compared with the simpler model Figure \ref{fig:evaporation_simulation_sharpness_stick_simple}) this gives an image more simple to the AFM measurement. Another possibility is an oscillation, which is not harmonic. For this instead of choosing the oscillation as $\sin(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\sin(\frac{t}{T} + \phi)^p$ with $p$ being the oscillation power. The resulting image can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_power}. The effect of this is very similar to the initial circular shape. The vibrations causing the deformation and tilt are unlikely to be very anharmonic, but due to growth of thin films happening near grains the actual growth of \ce{Pb} on the \ce{Si} is concentrated near the extreme positions of the oscillation.
+The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_initial} compared with the simpler model Figure \ref{fig:evaporation_simulation_sharpness_stick_simple}) this gives an image more simple to the AFM measurement. Another possibility is an oscillation, which is not harmonic. For this instead of choosing the oscillation as $\sin(\frac{t}{T} + \phi)$ with $t$ being current time, $T$ the oscillation period and $\phi$ being a phase shift, the oscillation is instead parametrized as $\sin(\frac{t}{T} + \phi)^p$ with $p$ being the oscillation power. The resulting image can be seen in Figure \ref{fig:evaporation_simulation_sharpness_stick_power}. The effect of this is very similar to the initial circular shape. The vibrations causing the deformation and tilt are unlikely to be very anharmonic, but due to growth of thin films happening near grains, the actual growth of \ce{Pb} on the \ce{Si} is concentrated at the extreme positions of the oscillation.
 
 When looking at the measured AFM image, it is very noticeable, that the surface of the "half moon" is rougher than the surface of the inner circle. On average, the roughness is $1.7 \pm 0.4$ times higher. This could be due to the \ce{Pb} preferring already established particle sites to diffuse and grow near another possible reason is a chronology of events where the growth happens first on the outer circle and then on the elliptical shape, as previously looked at.\\
 
@@ -355,7 +355,7 @@ Lead or in general any deposited material deposits more easily, when there is al
     \label{fig:evaporation_simulation_rejection}
 \end{figure}
 
-The results of adding this penalty for initial deposition are shown in Figure \ref{fig:evaporation_simulation_rejection_after}. As compared to the previous simulation step in Figure \ref{fig:evaporation_simulation_rejection_prev} the dot appears more rough and the height has decreases. The outer tail of the ellipse 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. Typically, growth prefers to occur at grains, since these function as nucleation sites. Particles impinging on the surface will diffuse to a nearby large nucleation site. The simulation does not take this effect into account at all. Though it could be implemented, by having each pixel interact with neighboring pixels. \\
+The results of adding this penalty for initial deposition are shown in Figure \ref{fig:evaporation_simulation_rejection_after}. As compared to the previous simulation step in Figure \ref{fig:evaporation_simulation_rejection_prev} the dot appears more rough and the height has decreases. The outer tail of the ellipse disappears nearly completely, these parameters match the deposition in the actual AFM image more closely, but crucially the decreased roughness of the elliptical part of the dot is not mirrored in the simulation, where the dot also appears rough. Typically, growth prefers to occur at grains, since these function as nucleation sites. Particles impinging on the surface will diffuse to a nearby large nucleation site. The simulation does not take this effect into account at all. Though it could be implemented, by having each pixel interact with neighboring pixels. \\
 
 The simulation image matches the one given by the AFM measurement pretty well, which shows that vibrations bending the holey part of the mask induced by the vibrations of the turbomolecular pump are a plausible explanation for the abberant penumbra of the measured dots. 
 
@@ -366,7 +366,7 @@ The simulation image matches the one given by the AFM measurement pretty well, w
     \label{fig:evaporation_simulation_progression}
 \end{figure}
 
-The simulation allows for taking in progress images at specified time intervals, with this a progression of the evaporation can be created. An example for the previously discussed example can be seen in Figure \ref{fig:evaporation_simulation_progression}. With this the chronology of events can be made visible more easily and visualizations could easily be created. \\
+The simulation allows for taking in progress images at specified time intervals, with this a progression of the evaporation can be created. An example for the previously discussed example can be seen in Figure \ref{fig:evaporation_simulation_progression}. With this, the chronology of events can be made visible more easily and visualizations could easily be created. \\
 
 \paragraph{Software improvements}
 The simulation is accurate in geometrical configuration of the Mask Aligner setup, but it assumes each particle hitting the surface either sticks to it or is rejected with a certain probability, which is a reasonable approximation as it follows the linear behavior from the Knudsen equation (Eq. \ref{eq:hertz_knudsen}), but it does not currently take into account grain size and diffusion of particles, which makes the graininess of the image resolution dependent.\\
@@ -376,4 +376,4 @@ Since Godot uses its own units for length measurement, which are stored as $32$-
 
 \paragraph{Conclusion}
 
-The results of the simulation show that a x-y-z vibration with a component of "bending" simulated as a strong tilt can explain the shape of the penumbra obtained in the AFM and that its peak to peak amplitude is within the expected for this system. This also shows that the sharper penumbra edge, which for this evaporation was measured to be $\approx 60$ nm is penumbras that would likely be obtained had there been no vibrational influence on the experiment. This shows that the Mask Aligner is capable of creating sharp interfaces, that fall within the superconductors coherence length. \\
\ No newline at end of file
+The results of the simulation show that a x-y-z vibration with a component of "bending" simulated as a strong tilt can explain the shape of the penumbra obtained in the AFM, and that its peak to peak amplitude is within the expected for this system. This also shows that the sharper penumbra edge, which for this evaporation was measured to be $\approx 60$ nm is penumbras that would likely be obtained had there been no vibrational influence on the experiment. This shows that the Mask Aligner is capable of creating sharp interfaces, that fall within the superconductors coherence length. \\
\ No newline at end of file
diff --git a/conclusion.aux b/conclusion.aux
index ba78265c013598470022511908a00e8c44f5cc1a..a7c35315edd9c009d1871639804cc5ff40e5f400 100644
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+++ b/conclusion.aux
@@ -1,9 +1,9 @@
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 \citation{self_epitaxy}
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diff --git a/conclusion.tex b/conclusion.tex
index d1931a818a991cb65e2bb1c779d46551ab4a66b7..9b5855244693fcc69b0f0030f4e32210851f2b64 100644
--- a/conclusion.tex
+++ b/conclusion.tex
@@ -19,3 +19,4 @@ In future the Mask Aligner will be first used to test evaporation properties of
 Characterization of these new samples using a low temperature STM to record a superconducting gap is also a subject of future research. The determination of properties, such as appearance of a wetting layer is another important factor that will be done in STM analysis, as the appearance of a wetting layer across the sample's surface would make \ce{Pb} a bad candidate for Majorana Zero Mode research.\\
 
 Another possible candidate for evaporation on a topological insulator seems to be \ce{Pd}. As recent papers have shown it to have interesting self epitaxial growth properties when evaporated on the topological insulator \ce{(Bi_{1-x}Sb_{x})2Te3}.\cite{self_epitaxy} This could be a good candidate for further research. The current evaporator attached is unable to perform palladium evaporation. If \ce{Pd} were chosen over \ce{Pb} a new evaporator need to be connected to the Mask Aligner system.
+
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 \contentsline {paragraph}{Non-Contact}{13}{section*.12}%
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-\contentsline {paragraph}{Software improvements}{84}{section*.90}%
-\contentsline {paragraph}{Conclusion}{85}{section*.91}%
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-\contentsline {chapter}{Bibliography}{88}{chapter*.93}%
-\contentsline {chapter}{List of Abbreviations}{91}{chapter*.94}%
-\contentsline {chapter}{Appendix}{i}{chapter*.95}%
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+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{66}{section.4.6}%
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+\contentsline {chapter}{Conclusions and Outlook}{88}{chapter*.90}%
+\contentsline {chapter}{Bibliography}{90}{chapter*.91}%
+\contentsline {chapter}{List of Abbreviations}{93}{chapter*.92}%
+\contentsline {chapter}{Appendix}{i}{chapter*.93}%
 \contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
 \contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
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