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 \bibcite{Tungsten_evap}{{10}{}{{}}{{}}}
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diff --git a/chap02.tex b/chap02.tex
index 14758a1ea4cfaad202b2f482ef9ca573a6d8bdc8..67046964c521aef014e0c1f085a5eaf6491a60df 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -64,8 +64,8 @@ The motor module consists of $3$ piezo motors. They move the mask along the z ax
 Often the direction is specified by mathematical sign, where $-$ specifies the approach direction, while $+$ specifies retract (Fig. \ref{fig:mask_aligner_nomenclature_motors}).\\
 
 \section{Slip stick principle}
-In order to control the movement of the mask stage using the mask aligner, $3$ motors of $6$ piezo stack made of $4$ piezo crystals each are used. Piezo crystals expand/contract upon being supplied with a DC voltage. In order for the piezo crystals to move the stage, a sapphire prism is clamped between the $6$ piezo stacks. When one now applies a voltage amplitude to the piezo stacks, the prism is moved by the stacks. An illustration of the principle is shown in Figure \ref{fig:slip_stick_diagram}. \\
-First a slowly rising pulse is applied to the piezo moving the prism along with the piezo. This pulse is referred to as the "slow flank". Afterward, a very fast pulse ($<1$ $\mu$s) is applied, contracting the piezo back into its original position. The prism however due to inertia remains in position. This pulse is referred to as the "fast flank". When done many times over, the prism can be moved larger distances. The direction depends on the voltage amplitude signal polarity. The simplest pulse shape allowing for this is the saw tooth wave, but other signal shapes that follow the principle can be used.
+In order to control the movement of the mask stage using the mask aligner, $3$ motors of $6$ piezo stack made of $4$ piezo crystals each are used. Piezo crystals expand/contract upon being supplied with a DC voltage. To enable the piezo crystals to move the stage, a sapphire prism is clamped between the $6$ piezo stacks. When one now applies a voltage amplitude to the piezo stacks, the prism is moved by the stacks. An illustration of the principle is shown in Figure \ref{fig:slip_stick_diagram}. \\
+First a slowly rising pulse is applied to the piezo moving the prism along with the piezo. This pulse is referred to as the "slow flank". Afterward, a very fast pulse ($<1$ $\mu$s) is applied, contracting the piezo back into its original position. The prism however due to inertia remains in position. This pulse is referred to as the "fast flank". When repeated, the prism can be moved. The direction depends on the voltage amplitude signal polarity. The simplest pulse shape allowing for this is the saw tooth wave, but other signal shapes that follow the principle can be used.
 
 \begin{figure}[H]
     \centering
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+\newlabel{fig:walker_pulse_shape_slow}{{3.7}{49}{Plots showing both an approach step (a) and a retract step (b) for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly}{figure.caption.64}{}}
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+\newlabel{fig:walker_pulse_shape_fast}{{3.8}{50}{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.65}{}}
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+\newlabel{fig:diagram_MA_circ_walker}{{3.9}{51}{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.66}{}}
 \@setckpt{chap03}{
-\setcounter{page}{53}
+\setcounter{page}{52}
 \setcounter{equation}{1}
 \setcounter{enumi}{10}
 \setcounter{enumii}{0}
@@ -97,7 +99,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{5}
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diff --git a/chap03.tex b/chap03.tex
index 01e465991e8a1e64a5644859b2cdeb897dafdcd0..4f3659da41c758844def4b4cea2ab651e4210b8b 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -1,6 +1,6 @@
 % !TeX spellcheck = <en-US>
 \chapter{Electronics}
-\section{RHK}
+\section{RHK piezo motor controller}
 \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:
 \paragraph{amplitude}
@@ -8,7 +8,8 @@ The amplitude is the peak voltage of the pulse, given in V. The default voltage
 \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}
-The time between sweeps is a time in between each pulse where no voltage is given as the output signal. It is given in ms and in the mask aligner setup is kept at 0 ms.
+The "time between sweeps" is the time between each pulse where no voltage is applied. It is given in ms and in the mask aligner setup is kept at 0 ms.
+\todo{Maybe image explanation}
 
 \subsection{Pulse shape}
 \begin{figure}[H]
@@ -23,11 +24,11 @@ The time between sweeps is a time in between each pulse where no voltage is give
     \caption{}
 	\label{fig:RHK_pulse_shape_retract}
     \end{subfigure}
-    \caption{Oscilloscope data showing both an approach step (\subref{fig:RHK_pulse_shape_approach}) and a retract step (\subref{fig:RHK_pulse_shape_retract}) for the RHK Piezo motor controller given at a voltage of $80$ V, as specified per settings. }
+    \caption{Oscilloscope data showing both an approach step (\subref{fig:RHK_pulse_shape_approach}) and a retract step (\subref{fig:RHK_pulse_shape_retract}) for the RHK Piezo motor controller given at a voltage of $80$ V, as specified per setting. }
     \label{fig:RHK_pulse_shape}
 \end{figure}
 
-Figure \ref{fig:RHK_pulse_shape} shows the voltage against time signal of a single RHK driving pulse, for both an approach step and a retract step.
+Figure \ref{fig:RHK_pulse_shape} shows the voltage against time of a single RHK driving pulse, for both an approach step and a retract step.
 It is noticeable that the pulse shapes for approach and retract are similar, but swapped in polarity, as such only a small difference in behavior between approach and retract is expected. After the fast flank the voltage is also overshot by nearly $7.5$ V and on the other side of the fast flank undershot by the same $7.5$ V.
 
 \begin{figure}[H]
@@ -48,11 +49,11 @@ It is noticeable that the pulse shapes for approach and retract are similar, but
 
 \section{KIM001}
 \subsection{Overview}
-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.\\
+The KIM001 Kinesis® K-Cube™ Piezo Inertia Actuator Controller by Thorlabs is 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. \\
-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. 
+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 shown Figure (\ref{fig:kim0001_pulse_shape}). The pulse shapes for both approach and retract are very different. The approach step has 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 lead to the piezo behaving unpredictable, since it might be in the slip regime. 
 
 \begin{figure}[H]
     \centering
@@ -72,7 +73,9 @@ 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 is supposed to control the output signal voltage amplitude between $85$ V and $125$ V. In testing it was found to not in fact control the output voltage at all. When the voltage parameter is set to $125$ V the voltage amplitude will be a value $> 150$ V. This value is not consistent and varies by $\pm 25 V$.  When the voltage parameter is set to $80$ V the output voltage amplitude is $\approx 80$ V.\\
+
+In both cases if driving pulses in retract direction are driven. The signal 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 cannot be used for our purposes. 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, although no settings were changed during the recording of this data.
 
 \begin{figure}[H]
     \centering
@@ -81,20 +84,21 @@ The KIM001 device has a controllable parameter called voltage, which should in p
     \label{fig:kim0001_voltage_behaviour}
 \end{figure}
 
-Due to the aforementioned behaviors of the KIM001 device, the device was found to be unable to provide the capabilities a piezo motor controller for the Mask Aligner would need and was thus deprecated.
+Due to the aforementioned behaviors of the KIM001 device, the device was found to be incapable of providing driving pulses for the Mask Aligner and was thus deprecated.
 
 \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 \textbf{P}rinted \textbf{C}ircuit \textbf{B}oard (PCB) is based on the piezo Walker electronics designed to control the piezo Walker used for STM control.\todo{Check if erklärt} 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 at the center of the period. 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 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:
+The core of the Mask aligner controller is an Arduino DUE~\cite{arduino_datasheet}. The  \textbf{C}entral \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. Integrated 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 output simultaneously. The signal provided to the DAC is generated via software. The Arduino generates a signal internally with a sampling rate of $404$ kHz with the shape given by:
 \begin{equation}
      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. \\
-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}.
+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 (Fig. \ref{fig:RHK_pulse_shape}). Similar behavior is expected. \\
+This signal is then output on the DAC 0 pin of the Arduino. The Arduino can only output one polarity of voltage, but our final signal is intended to be bimodal. Therefore, another signal is generated on DAC 1 with $1 - S$ as the given function. The two signals are now subtracted from each other as depicted in Figure \ref{fig:bessel_filter_unfiltered}. This gives 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, which 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]
     \centering
@@ -108,13 +112,13 @@ The Signal given by the Arduino contains aliasing artifacts from the digital to
     \caption{}
 	\label{fig:bessel_filter_filter}
     \end{subfigure}
-    \caption{Plots showing both an aliased signal (a) and the same signal, but smoothed out with an 8th order Bessel filter (b). The amount of aliasing is not representative of the Walker electronics and is simply for illustration purposes. After filtering, the signal appears very smooth and without sharp steps.}
+    \caption{Plots showing both an aliased signal (a) and the same signal, but smoothed out with an 8th order Bessel filter (b). The amount of aliasing is exaggerated to be more easily visible. }
     \label{fig:bessel_filter}
 \end{figure}
 
 \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 signal's 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 provides only the slow flank. The fast flank is achieved by taking the signal given 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
@@ -132,11 +136,10 @@ After this step the signal is bimodal and of the correct shape, but for the desi
     \label{fig:signal_switch}
 \end{figure}
 
-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}.\\
-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.
+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. For this application a driving signal between of $240$ 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 Arduino digital output pins $22$, $24$, $26$ and $28$ control, which channels receive any output signal. 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. The relays are switched off after a waiting period of $2$ seconds after no signal is supplied to the given channel. 
 
 \subsection{Parameters}
 The following parameters can be controlled with the new electronics:
@@ -147,15 +150,15 @@ Instead of setting the amp parameter to a given value, which corresponds to an o
 \paragraph{Channel}
 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 measure 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 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. 
+The frequency is not adjustable as of the writing of this thesis, though in principle changeable frequencies could be implemented. Since all previous approach curves and alignment operations were always performed at $1$ kHz, it was deemed unnecessary. Frequencies higher than $1$ kHz are also difficult, as the timing accuracy of the Arduino is already close to its limits. 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 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.
+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. 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}), 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 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. It both under- and overshoots the specified $80$ V, by up to $\approx20$ 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. Steps visible in Figure \ref{fig:walker_pulse_shape_slow} are due to the limited resolution of the oscilloscope (see Fig. \ref{fig:walker_pulse_shape_fast}). Given this data the Walker seems to outperform the RHK in the unloaded state and should give the same, or a better driving behavior than the RHK.
 
 \begin{figure}[H]
     \centering
@@ -171,7 +174,7 @@ 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 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.
+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. 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 motors appropriately.
 
 \begin{figure}[H]
     \centering
@@ -188,7 +191,7 @@ The slow flank was also measured for both the RHK and the Walker, again in an un
 \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}
+The communication diagram with the Walker looks slightly different from the one in Figure \ref{fig:diagram_MA_circ}. The RHK relay is no longer needed since the Walker can take over its function. The new diagram can be seen in Figure \ref{fig:diagram_MA_circ_walker}
 
 \begin{figure}[H]
     \centering
@@ -197,4 +200,4 @@ 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. The actual driving performance could not be tested. Hardware failure caused the positive polarity to no longer reach full $120$ V peak and with a load attached. It stayed below $0$ V giving a single polarity of piezo driving signal in approach direction and no fast flank at all in retract.
diff --git a/chap04.aux b/chap04.aux
index 6c76f0c4b02d7aae9c3b3ed1302f536c3e45c0a3..913bbc54ad74695912c4b0b02c8c85b10adb3b58 100644
--- a/chap04.aux
+++ b/chap04.aux
@@ -1,85 +1,86 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
 \citation{Olschewski}
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-\newlabel{sub@fig:Front_plate_repair_tool}{{a}{63}{\relax }{figure.caption.72}{}}
-\newlabel{fig:Front_plate_repair_plate}{{4.8b}{63}{\relax }{figure.caption.72}{}}
-\newlabel{sub@fig:Front_plate_repair_plate}{{b}{63}{\relax }{figure.caption.72}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref  {fig:Front_plate_repair_tool}). (\subref  {fig:Front_plate_repair_plate}) shows final front plate assembled.}}{63}{figure.caption.72}\protected@file@percent }
-\newlabel{fig:Front_plate_repair}{{4.8}{63}{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled}{figure.caption.72}{}}
-\@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 piezo stacks of the motor Z3. }}{64}{figure.caption.73}\protected@file@percent }
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-\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{65}{\relax }{figure.caption.74}{}}
-\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{65}{\relax }{figure.caption.74}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{65}{\relax }{figure.caption.74}{}}
-\@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.74}\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.74}{}}
-\@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.75}\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.75}{}}
-\@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{66}{section.4.7}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.11}{\ignorespaces The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions.}}{66}{figure.caption.76}\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.76}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.4}Piezo re-gluing}{57}{section.4.4}\protected@file@percent }
+\newlabel{sec:piezo_reglue}{{4.4}{57}{Piezo re-gluing}{section.4.4}{}}
+\newlabel{fig:Z3_reglue_process_off}{{4.4a}{58}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:Z3_reglue_process_off}{{a}{58}{\relax }{figure.caption.71}{}}
+\newlabel{fig:Z3_reglue_process_scratched}{{4.4b}{58}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:Z3_reglue_process_scratched}{{b}{58}{\relax }{figure.caption.71}{}}
+\newlabel{fig:Z3_reglue_process_dot}{{4.4c}{58}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:Z3_reglue_process_dot}{{c}{58}{\relax }{figure.caption.71}{}}
+\newlabel{fig:Z3_reglue_process_down}{{4.4d}{58}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:Z3_reglue_process_down}{{d}{58}{\relax }{figure.caption.71}{}}
+\@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) shows detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. 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.}}{58}{figure.caption.71}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{4.4}{58}{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) shows detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. 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}{figure.caption.71}{}}
+\@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 $.}}{59}{figure.caption.72}\protected@file@percent }
+\newlabel{fig:Z3_after reglue}{{4.5}{59}{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.72}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{59}{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.}}{60}{figure.caption.73}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot}{{4.6}{60}{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.73}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{60}{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.}}{61}{figure.caption.74}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{61}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.74}{}}
+\newlabel{fig:Front_plate_repair_tool}{{4.8a}{62}{\relax }{figure.caption.75}{}}
+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{62}{\relax }{figure.caption.75}{}}
+\newlabel{fig:Front_plate_repair_plate}{{4.8b}{62}{\relax }{figure.caption.75}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{62}{\relax }{figure.caption.75}{}}
+\@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.}}{62}{figure.caption.75}\protected@file@percent }
+\newlabel{fig:Front_plate_repair}{{4.8}{62}{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.75}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{63}{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. }}{63}{figure.caption.76}\protected@file@percent }
+\newlabel{fig:Z3_weaker_stack}{{4.9}{63}{The measured capacitance values for the piezo stacks of the motor Z3}{figure.caption.76}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{63}{section.4.6}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{64}{\relax }{figure.caption.77}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{64}{\relax }{figure.caption.77}{}}
+\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{64}{\relax }{figure.caption.77}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{64}{\relax }{figure.caption.77}{}}
+\@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.}}{64}{figure.caption.77}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs}{{4.10}{64}{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.77}{}}
+\@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.}}{64}{table.caption.78}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{64}{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.78}{}}
+\@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{65}{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.}}{65}{figure.caption.79}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{65}{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.79}{}}
 \@setckpt{chap04}{
-\setcounter{page}{68}
+\setcounter{page}{67}
 \setcounter{equation}{0}
 \setcounter{enumi}{4}
 \setcounter{enumii}{0}
@@ -108,7 +109,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{5}
+\setcounter{@todonotes@numberoftodonotes}{8}
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diff --git a/chap04.tex b/chap04.tex
index fdf5967ddbaf87084601c076c3f998b02545fa81..a8f31d32d69f56af0215b2dfc343932bd81225dc 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -2,7 +2,7 @@
 \chapter{Mask Aligner repairs and optimizations}
 \section{Overview}
 
-The Mask Aligner was built in 2015~\cite{Olschewski}. Since then some problems had developed with the function of the Mask Aligner and its performance was limited. In order to alleviate and prevent further problems, repairs had to be performed on several of the piezo motor stacks. In order to possibly prevent further problems from occurring, various measures were taken as preemptive measures. The following chapter will detail the repairs and optimizations that were performed on the Mask Aligner. 
+The Mask Aligner was built in 2015~\cite{Olschewski}. Since then some problems had developed with the Mask Aligner and its performance was limited. In order to alleviate and prevent further problems, repairs had to be performed on several of the piezo motor stacks. The following chapter will detail the repairs and optimizations that were performed on the Mask Aligner. 
 
 \begin{figure}[H]
     \centering
@@ -16,11 +16,11 @@ The Mask Aligner was built in 2015~\cite{Olschewski}. Since then some problems h
 		\caption{}
 		\label{fig:Repair_Diagram_image}
 	\end{subfigure}
-    \caption{Diagram showing the names given to the different parts of a motor of the mask aligner (\subref{fig:Repair_Diagram_diagram}). (\subref{fig:Repair_Diagram_image}) shows a roughly corresponding image as a photo of the Mask Aligner. The lower right solder anchor is detached in the image and the lower left solder anchor is bridged with a technique discussed in Section \ref{ch:solder_anchors}}
+    \caption{(\subref{fig:Repair_Diagram_diagram}) diagram of front view of a single piezo motor with associated nomenclature. Front plate is turned around and moved to the side. (\subref{fig:Repair_Diagram_image}) shows a roughly corresponding image as a photo of the Mask Aligner. The lower right solder anchor is detached in the image and the lower left solder anchor is bridged with a technique discussed in Section \ref{ch:solder_anchors}}
     \label{fig:Repair_Diagram}
 \end{figure}
 
-The mask aligners optimization and repair often involves mentioning specific piezo stacks. To aid in understanding, which piezo stack or part of the motor is meant Figure \ref{fig:Repair_Diagram_diagram} shows the nomenclature used in this thesis for the different parts of a single motor. Figure \ref{fig:Repair_Diagram_image} shows a photo with a similar configuration as the diagram as its counterpart on the Mask Aligner to make clear what it looks like in the actual motor.
+The nomenclature for the piezo motors used in the following is described in Figure \ref{fig:Repair_Diagram_diagram}. It shows  for the different parts of a single motor. Figure \ref{fig:Repair_Diagram_image} shows a photo with a similar configuration as the diagram to make clear what it corresponds to.
 
 \section{General UHV device preparation}
 \subsection{Adding components}
@@ -37,7 +37,7 @@ Only materials that have been cleared for use in UHV environments should be used
 
 \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. \\
-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:
+When using flux, the flux has to be cleaned off thoroughly to avoid outgassing as well as short-circuiting from stray flux. 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 The previous step should be repeated with demineralized water without any detergent
@@ -46,7 +46,10 @@ When using flux, the flux has to be cleaned off thoroughly to avoid outgassing a
 \end{enumerate}
 
 \section{Soldering anchors} \label{ch:solder_anchors}
-The soldering anchor points that were previously used on the Mask Aligner are small ($2$ mm x $2$ mm x $6$ mm) ceramic pieces onto which a small piece of copper, pre-coated with solder, was glued using non-conductive EPO-TEK H70E. Then all cables coming from the piezo motors can be soldered to this soldering anchor, allowing for shorter cables to be used and for the cables to be more cleanly routed around the Mask Aligners surface. The Ceramic piece was glued to the surface of the Mask Aligner using the same glue.\\ 
+The soldering anchor points that were previously used on the Mask Aligner are small ($2$ mm x $2$ mm x $6$ mm) ceramic pieces onto which a small piece of copper, pre-coated with solder, was glued using non-conductive EPO-TEK H70E. All cables coming from the piezo motors can be soldered to this soldering anchor. This allows usage of shorter cables and for the cables to be more cleanly routed. The Ceramic piece was glued to the surface of the Mask Aligner using the same glue.\\
+
+EPO-TEK H70E is recommended to cure at $150$°C for at least 1 hour. For repairs would be difficult and dangerous to heat the entire Mask Aligner to $150$°C, since the piezo stacks depolarize at temperatures near $150$°C. It is also difficult to heat the glue locally to $150$°C. Due to this it was determined that a different glue should be used. \\
+Torr Seal was determined to have all the necessary qualities and was used as a replacement universally. Torr Seal is a two component epoxy, that can cure at room temperature. It fulfills UHV outgassing requirements\todo{Cite Torrseal data}. 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 to deterioration. Also of note is that Torr Seal cannot operate at temperatures below $-45$°C, so usage in a very low temperature environment is no longer possible. This is not an issue since the Mask Aligner is not intended for use in cooled environments.\\ 
 
 \begin{figure}[H]
     \centering
@@ -70,58 +73,58 @@ The soldering anchor points that were previously used on the Mask Aligner are sm
         \caption{}
         \label{fig:solder_anchors_diagram_GlueTop}
     \end{subfigure}
-    \caption{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. }
+    \caption{(\subref{fig:solder_anchors_diagram_base}) solder anchor interfering with the prism due to deterioration over time. (\subref{fig:solder_anchors_diagram_SmallerDot}) making the solder dot smaller. (\subref{fig:solder_anchors_diagram_AlO}) replacing the solder anchor ceramic with a much smaller \ce{Al2O3} plate. (\subref{fig:solder_anchors_diagram_GlueTop}) putting the anchor with glue on the top/bottom of the solder ceramic. 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. }
     \label{fig:solder_anchors_diagram}
 \end{figure}
 
-However, over time and usage the glue on some of the soldering anchors had loosened to the point that the solder dots connecting the cables and the anchor were now sticking out from the surface of the Mask Aligner more, to the point of sometimes interfering with the Sapphire Prism that is used to drive the motion of the mask stage. This caused the mask stage to frequently get stuck, when driving the piezo motors. The Problem situation is depicted in Figure (\ref{fig:solder_anchors_diagram_base}).\\
-This behavior was worsening over time to the point of not allowing the motor Z1 to return the stage into the Mask extraction height. \\
-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. 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}). \\
+However, over time and usage the glue on some of the soldering anchors had loosened to the point that the solder dots connecting the cables and the anchor were sticking out from the surface of the Mask Aligner. Sometimes to the point of interfering with the Sapphire Prism. This caused the mask stage to frequently get stuck, when driving the piezo motors. The Problem situation is depicted in Figure (\ref{fig:solder_anchors_diagram_base}).
+This problem would culminate in the motor Z1 getting completely stuck, when driven down to mask extraction height. \\
+
+In order to optimize this behavior, the following 3 actions can be taken.
+First, the size of solder on the anchor can be reduced until it no longer interferes. This process often involved re-soldering the respective cable, since carving away material without disconnecting the cable often proved impossible. This was done when the anchor has not lost adhesion to the MA body. This is pictured in Figure (\ref{fig:solder_anchors_diagram_SmallerDot}). \\
+
+Another procedure is to completely replace the soldering anchor with a much thinner \ce{Al2O3} plate. The size of the solder dot can in this case be quite large before interfering. When the solder ceramic was no longer stably attached to the Mask Aligner body this procedure is used (\ref{fig:solder_anchors_diagram_AlO}). \\ 
+
+The third procedure is to glue the soldering anchor on the top/bottom side of the ceramic. 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 inelegant, but was used as a quick optimization. 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]
     \centering
-    \begin{subfigure}{0.35\textwidth}
+	\begin{subfigure}{0.35\textwidth}
 		\centering
-        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/GlueBelow.png}
+        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/Solder_shear_big.png}
         \caption{}
-        \label{fig:solder_anchors_examples_glue_bottom}
+        \label{fig:solder_anchors_examples_shear_01}
     \end{subfigure}
     \begin{subfigure}{0.35\textwidth}
 		\centering
-        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/AlO.png}
+        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/Solder_shear_smaller.png}
         \caption{}
-        \label{fig:solder_anchors_examples_AlO}
+        \label{fig:solder_anchors_examples_shear_02}
     \end{subfigure}
     \begin{subfigure}{0.35\textwidth}
 		\centering
-        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/Solder_shear_big.png}
+        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/GlueBelow.png}
         \caption{}
-        \label{fig:solder_anchors_examples_shear_01}
+        \label{fig:solder_anchors_examples_glue_bottom}
     \end{subfigure}
     \begin{subfigure}{0.35\textwidth}
 		\centering
-        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/Solder_shear_smaller.png}
+        \includegraphics[width=0.9\linewidth]{img/Repairs/SolderAnchors/AlO.png}
         \caption{}
-        \label{fig:solder_anchors_examples_shear_02}
+        \label{fig:solder_anchors_examples_AlO}
     \end{subfigure}
-    \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.}
+    \caption{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref{fig:solder_anchors_examples_shear_01}) and  shows the initial state of a solder ceramic interfering with the prism. (\subref{fig:solder_anchors_examples_shear_02}) shows the solder ceramic from before after some of the solder was carefully taken off. (\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. }
     \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 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.
+Examples for all the different measures 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 Torr Seal use is a bit excessive. It was very difficult to apply constant pressure at the angle given. This is also the reason why the new anchor is placed differently. In this instance the problem was not that the solder anchor interference, but the glue on the old ceramic no longer holding. Due to remaining glue on the solder ceramic, gluing a new solder anchor proved difficult, since the glue sticks poorly to glue residue.
 
-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. \\
+All motors were checked for soldering anchor points that could potentially interfere with the prism. 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 prisms would no longer get stuck when driving and could cleanly drive the whole range of possible motion. A lot of the solder ceramics were no longer attached well, due to this in future others might fail. To ensure correct driving it is recommended that all solder ceramics, not just interfering ones, should be replaced. This however goes beyond the work in this thesis. \\
 
 \section{Piezo re-gluing} \label{sec:piezo_reglue}
-The piezo motors of the 3 motor stacks in the Mask Aligner were glued in 2015 with the non-conductive EPO-TEK H70E glue~\cite{Olschewski}. This glue has over time lost some of its sticking ability, even though the Mask Aligner is usually in UHV. For this reason, 2 of the piezo stacks, one on motor Z1 and one on Motor Z3, had by the time previous repairs were performed completely detached. These stacks needed to be re-glued to the surface of the Mask Aligner Body, in order to provide proper support for the driving of the prisms. \\
+The piezo stacks in the Mask Aligner were also glued in 2015 with the non-conductive EPO-TEK H70E glue~\cite{Olschewski}. For this reason, $2$ of the piezo stacks, one on motor Z1 and one on Motor Z3, had completely detached. These stacks needed to be re-glued to the surface of the Mask Aligner Body. \\
 
 \begin{figure}[H]
     \centering
@@ -149,14 +152,14 @@ 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 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.}
+    \caption{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) shows detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. 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.}
     \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. \\
+Torr Seal was used for this again. Tests and the datasheet showed that Torr Seal has similar elastic properties to H70E. The right size for a glue dot was determined via testing of spread and comparison with previous glue dot size. \\
 
-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.
+To perform the actual gluing of the piezo stack, all traces of remaining glue were scratched off the surface of the affected piezo stack (Fig. \ref{fig:Z3_reglue_process_scratched}). Afterward a small dot of Torr Seal was put on the underside of the piezo stack, and it was carefully put in place (Fig. \ref{fig:Z3_reglue_process_dot}). The Mask Aligner was rotated with a clamp so that gravity kept the piezo stack in the place. In order to provide pressure on the piezo stack, the prism was reinserted into the motor and was weighed down with comparatively large nuts (Fig. \ref{fig:Z3_reglue_process_down}). 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 significantly affect the performance of the Z3 motor.
 
 \begin{figure}[H]
     \centering
@@ -166,7 +169,7 @@ The repair of the piezo on motor Z1 happened without problems, but on motor Z3 t
 \end{figure}
 
 \section{Z3 motor}
-After all repairs were performed, the motors Z1 and Z2 were performing as expected without any problems, but the motor Z3 would occasionally drive with reduced step size. The speed of the prism driven by the Z3 motor would sometimes, without any noticeable change, drop to about half the expected value. Additionally, the difference in approach and retract speed between the motors Z2/Z1 was about a factor of $1.25$, while the difference for Z3 was off by a factor of $2$, regardless of screw configuration. 
+After repairs, the motors Z1 and Z2 were performing as expected, but the motor Z3 would occasionally drive with reduced step size. The step size of motor Z3 would occasionally drop by approximately one half. This happened randomly. Additionally, the ratio of approach/retract speed was much higher for Z3 than for Z1/Z2 ($2$ instead of $1.25$), regardless of screw configuration. This behavior can be seen in Figure \ref{fig:Z3_screw_rot} (compare \textcolor{tab_blue}{blue} and \textcolor{tab_orange}{orange} to \textcolor{tab_purple}{purple} and \textcolor{tab_brown}{brown}).
 
 \begin{figure}[H]
     \centering
@@ -175,12 +178,15 @@ After all repairs were performed, the motors Z1 and Z2 were performing as expect
     \label{fig:Z3_screw_rot}
 \end{figure}
 
-This behavior can be seen in Figure \ref{fig:Z3_screw_rot} (compare \textcolor{tab_blue}{blue} and \textcolor{tab_orange}{orange} to \textcolor{tab_purple}{purple} and \textcolor{tab_brown}{brown}) This led to the conclusion, that Z3 had some sort of alignment issue, where sometimes randomly all the motors were in line with the prism and could drive at the appropriate power, while sometimes one of the motors would lose contact with the prism and now the prism would be driven by the other motors and the Z3 driving would no longer be symmetric. This conclusion was further corroborated, by the fact that the Z3 motor would at arbitrary times decrease its step size by about a factor of $2$.
-The cause of this was determined to be the front plate of the Z3 motor, as switching the front plate of the Z1 and Z3 motors caused the problem to disappear on the Z3 motor. For this reason, the front plate had to be repaired.
+This led to the conclusion, that Z3 had some sort of alignment issue. Sometimes randomly all the motors were in line with the prism and could drive at the appropriate power, while sometimes one of the motors would lose contact with the prism. 
+The cause of this was hypothesized to be the front plate of 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. This detaching and reattaching needed to be done multiple times in order to do the full check. In order to prevent risks, 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 (Fig. \ref{fig:Z3_screw_rot} \textcolor{tab_green}{green} and \textcolor{tab_red}{red} against \textcolor{tab_blue}{blue} and \textcolor{tab_orange}{orange}). \\
+
+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. 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. To check for the unevenness of the surface, 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 color remained on the same piezo, suggesting improper alignment. \\
 
 \begin{figure}[H]
     \centering
@@ -189,13 +195,14 @@ 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. A 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. Two of the ten replacement piezos would be glued to the surface of the plate in order to function as the new plate. 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. 
+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. Both sides of the piezos used originally were polished, so that they can be used as sliding surfaces, but the replacement piezos have only one sliding surface. This can be seen in the different texture of the top and bottom piezo stacks 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 sections. 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 configuration. Regardless, the difference in performance was deemed to be insignificant as a point of common step size could be found (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 similar screw setting was chosen for it as well. 
 
 \begin{figure}[H]
     \centering
@@ -215,7 +222,9 @@ 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 the field of vision of the camera pointed at the sample 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.
+In order to prevent the longer cables of the front plates of Z1 and Z3 from interfering with Mask Aligner operation, the cables were guided around the Mask Aligner body. This includes in particular not being within the field of vision of the camera pointed at the sample as well as not interfering with the wobble stick path. 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.
+
+\todo{Maybe image}
 
 \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 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. \\
diff --git a/chap05.aux b/chap05.aux
index 44af917505f17b4e2d5a133594d9b3af65062d5f..0e980f1095347b0b95078fc392045943b709819b 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -1,101 +1,101 @@
 \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}{67}{chapter.5}\protected@file@percent }
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
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-\newlabel{fig:evaporation_approach_curve}{{5.1}{68}{The approach curve measured for Field 1 until full contact. Since the 3 capacitance sensors appear correlated and the uncertainty on C2 and C3 is an order of magnitude larger than the difference of the current to the last step, C1 was used for alignment primarily}{figure.caption.77}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}}{69}{table.caption.78}\protected@file@percent }
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-\@writefile{lof}{\contentsline {figure}{\numberline {5.3}{\ignorespaces Diagram showing the Evaporation performed on the sample (\subref  {fig:Evaporation_diagramm_sample_img}). Red squares represent the positions of the evaporated 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.}}{70}{figure.caption.80}\protected@file@percent }
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-\@writefile{lof}{\contentsline {figure}{\numberline {5.4}{\ignorespaces (\subref  {fig:evaporation_contamination_img}) shows an AFM image of field $3$ without any grain removal applied. Data was obtained on multiple different spots on the sample. (\subref  {fig:evaporation_contamination_anal}) shows line cuts obtained from contamination particles. \textcolor {tab_red}{Red} and \textcolor {tab_green}{green} lines show the average height and width of the contamination particles obtained from peak fits.}}{71}{figure.caption.81}\protected@file@percent }
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diff --git a/thesis.pdf b/thesis.pdf
index d82c96f737b3b2e936fbd21288f87ec357c9ee61..86d394b4151f1f24f39ddb653f87cf9ce0253fed 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index 62a08e2723e940c3288c4403101598463bd59398..68949005b95f75ef21ceec0fd9276a51752113ad 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.toc b/thesis.toc
index f372b1ec409dd9aa9843b9e737ee39387d24f032..461ea7e960bf7084558c1e44639e4a27c84e0962 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -31,7 +31,7 @@
 \contentsline {section}{\numberline {2.4}Mask Aligner operation}{40}{section.2.4}%
 \contentsline {subsection}{\numberline {2.4.1}Sample preparation}{40}{subsection.2.4.1}%
 \contentsline {chapter}{\numberline {3}Electronics}{42}{chapter.3}%
-\contentsline {section}{\numberline {3.1}RHK}{42}{section.3.1}%
+\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{42}{section.3.1}%
 \contentsline {subsection}{\numberline {3.1.1}Overview}{42}{subsection.3.1.1}%
 \contentsline {paragraph}{amplitude}{42}{section*.48}%
 \contentsline {paragraph}{sweep period}{42}{section*.49}%
@@ -43,77 +43,77 @@
 \contentsline {subsection}{\numberline {3.2.3}Voltage behavior}{44}{subsection.3.2.3}%
 \contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{45}{section.3.3}%
 \contentsline {subsection}{\numberline {3.3.1}Overview}{45}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Signal generation}{46}{subsection.3.3.2}%
+\contentsline {subsection}{\numberline {3.3.2}Signal generation}{45}{subsection.3.3.2}%
 \contentsline {subsection}{\numberline {3.3.3}Fast flank}{47}{subsection.3.3.3}%
-\contentsline {subsection}{\numberline {3.3.4}Amplification}{48}{subsection.3.3.4}%
+\contentsline {subsection}{\numberline {3.3.4}Amplification}{47}{subsection.3.3.4}%
 \contentsline {subsection}{\numberline {3.3.5}Parameters}{48}{subsection.3.3.5}%
-\contentsline {paragraph}{Amplitude (amp)}{48}{section*.57}%
-\contentsline {paragraph}{Voltage (volt)}{49}{section*.58}%
-\contentsline {paragraph}{Channel}{49}{section*.59}%
-\contentsline {paragraph}{Max Step}{49}{section*.60}%
-\contentsline {paragraph}{Polarity}{49}{section*.61}%
-\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{49}{subsection.3.3.6}%
-\contentsline {subsection}{\numberline {3.3.7}Driving the Mask Aligner}{51}{subsection.3.3.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{53}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{53}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{54}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}Adding components}{54}{subsection.4.2.1}%
-\contentsline {subsection}{\numberline {4.2.2}Soldering}{54}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering anchors}{55}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo re-gluing}{58}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 motor}{60}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{61}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{64}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{65}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final test}{66}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{68}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{68}{section.5.1}%
-\contentsline {section}{\numberline {5.2}Contamination}{71}{section.5.2}%
-\contentsline {section}{\numberline {5.3}Penumbra}{72}{section.5.3}%
-\contentsline {section}{\numberline {5.4}Tilt and deformation}{77}{section.5.4}%
-\contentsline {section}{\numberline {5.5}Simulation}{79}{section.5.5}%
-\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{79}{subsection.5.5.1}%
-\contentsline {subsection}{\numberline {5.5.2}Results}{81}{subsection.5.5.2}%
-\contentsline {subsection}{\numberline {5.5.3}Software improvements}{85}{subsection.5.5.3}%
-\contentsline {subsection}{\numberline {5.5.4}Final Remark}{86}{subsection.5.5.4}%
-\contentsline {chapter}{Conclusions and Outlook}{87}{chapter*.93}%
-\contentsline {chapter}{Bibliography}{89}{chapter*.94}%
-\contentsline {chapter}{List of Abbreviations}{92}{chapter*.95}%
-\contentsline {chapter}{Appendix}{i}{chapter*.96}%
+\contentsline {paragraph}{Amplitude (amp)}{48}{section*.59}%
+\contentsline {paragraph}{Voltage (volt)}{48}{section*.60}%
+\contentsline {paragraph}{Channel}{48}{section*.61}%
+\contentsline {paragraph}{Max Step}{48}{section*.62}%
+\contentsline {paragraph}{Polarity}{48}{section*.63}%
+\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{48}{subsection.3.3.6}%
+\contentsline {subsection}{\numberline {3.3.7}Driving the Mask Aligner}{50}{subsection.3.3.7}%
+\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{52}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Overview}{52}{section.4.1}%
+\contentsline {section}{\numberline {4.2}General UHV device preparation}{53}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}Adding components}{53}{subsection.4.2.1}%
+\contentsline {subsection}{\numberline {4.2.2}Soldering}{53}{subsection.4.2.2}%
+\contentsline {section}{\numberline {4.3}Soldering anchors}{54}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo re-gluing}{57}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 motor}{59}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{60}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{63}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{63}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final test}{65}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{67}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{67}{section.5.1}%
+\contentsline {section}{\numberline {5.2}Contamination}{70}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Penumbra}{71}{section.5.3}%
+\contentsline {section}{\numberline {5.4}Tilt and deformation}{76}{section.5.4}%
+\contentsline {section}{\numberline {5.5}Simulation}{78}{section.5.5}%
+\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{78}{subsection.5.5.1}%
+\contentsline {subsection}{\numberline {5.5.2}Results}{80}{subsection.5.5.2}%
+\contentsline {subsection}{\numberline {5.5.3}Software improvements}{84}{subsection.5.5.3}%
+\contentsline {subsection}{\numberline {5.5.4}Final Remark}{85}{subsection.5.5.4}%
+\contentsline {chapter}{Conclusions and Outlook}{86}{chapter*.96}%
+\contentsline {chapter}{Bibliography}{88}{chapter*.97}%
+\contentsline {chapter}{List of Abbreviations}{91}{chapter*.98}%
+\contentsline {chapter}{Appendix}{i}{chapter*.99}%
 \contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
 \contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
 \contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}%
 \contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}%
-\contentsline {paragraph}{pulse?}{vi}{section*.99}%
-\contentsline {paragraph}{pol x}{vi}{section*.100}%
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-\contentsline {paragraph}{volt x}{vi}{section*.102}%
-\contentsline {paragraph}{channel x}{vi}{section*.103}%
-\contentsline {paragraph}{maxmstep x}{vi}{section*.104}%
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-\contentsline {paragraph}{mstep x}{vi}{section*.106}%
-\contentsline {paragraph}{cancel}{vii}{section*.107}%
-\contentsline {paragraph}{help}{vii}{section*.108}%
+\contentsline {paragraph}{pulse?}{vi}{section*.102}%
+\contentsline {paragraph}{pol x}{vi}{section*.103}%
+\contentsline {paragraph}{amp x}{vi}{section*.104}%
+\contentsline {paragraph}{volt x}{vi}{section*.105}%
+\contentsline {paragraph}{channel x}{vi}{section*.106}%
+\contentsline {paragraph}{maxmstep x}{vi}{section*.107}%
+\contentsline {paragraph}{step x}{vi}{section*.108}%
+\contentsline {paragraph}{mstep x}{vi}{section*.109}%
+\contentsline {paragraph}{cancel}{vii}{section*.110}%
+\contentsline {paragraph}{help}{vii}{section*.111}%
 \contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
-\contentsline {paragraph}{radius\_1}{vii}{section*.109}%
-\contentsline {paragraph}{angle}{vii}{section*.110}%
-\contentsline {paragraph}{radius\_mask}{vii}{section*.111}%
-\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.112}%
-\contentsline {paragraph}{distance\_sample}{vii}{section*.113}%
-\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.114}%
-\contentsline {paragraph}{running\_time}{vii}{section*.115}%
-\contentsline {paragraph}{deposition\_gain}{vii}{section*.116}%
-\contentsline {paragraph}{penalize\_deposition}{vii}{section*.117}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.118}%
-\contentsline {paragraph}{oscillation\_period}{vii}{section*.119}%
-\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.120}%
-\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.121}%
-\contentsline {paragraph}{save\_intervall}{viii}{section*.122}%
-\contentsline {paragraph}{oscillation\_dir}{viii}{section*.123}%
-\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.124}%
-\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.125}%
-\contentsline {paragraph}{random\_seed}{viii}{section*.126}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.127}%
-\contentsline {paragraph}{resolution}{viii}{section*.128}%
-\contentsline {paragraph}{path}{viii}{section*.129}%
-\contentsline {chapter}{Acknowledgments}{ix}{chapter*.130}%
+\contentsline {paragraph}{radius\_1}{vii}{section*.112}%
+\contentsline {paragraph}{angle}{vii}{section*.113}%
+\contentsline {paragraph}{radius\_mask}{vii}{section*.114}%
+\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.115}%
+\contentsline {paragraph}{distance\_sample}{vii}{section*.116}%
+\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.117}%
+\contentsline {paragraph}{running\_time}{vii}{section*.118}%
+\contentsline {paragraph}{deposition\_gain}{vii}{section*.119}%
+\contentsline {paragraph}{penalize\_deposition}{vii}{section*.120}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.121}%
+\contentsline {paragraph}{oscillation\_period}{vii}{section*.122}%
+\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.123}%
+\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.124}%
+\contentsline {paragraph}{save\_intervall}{viii}{section*.125}%
+\contentsline {paragraph}{oscillation\_dir}{viii}{section*.126}%
+\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.127}%
+\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.128}%
+\contentsline {paragraph}{random\_seed}{viii}{section*.129}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.130}%
+\contentsline {paragraph}{resolution}{viii}{section*.131}%
+\contentsline {paragraph}{path}{viii}{section*.132}%
+\contentsline {chapter}{Acknowledgments}{ix}{chapter*.133}%