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diff --git a/appendix.tex b/appendix.tex
index 0560bd3400f95d38e065b120db4a1490436ccd27..5dccf76f834dfafadd55af2df14a8fbe2bafcf86 100644
--- a/appendix.tex
+++ b/appendix.tex
@@ -1 +1,46 @@
-\section{New Driver Electronics}
\ No newline at end of file
+\section{New Driver Electronics}
+\section{Raycast Simulation}
+The raycasting simulation takes the following parameters:
+
+\paragraph{radius\_1}
+The radius of the circle representing the crucible in Godot spacial units.
+\paragraph{angle}
+The angle of the cone in which rays are emitted from the crucible.
+\paragraph{radius\_mask}
+The radius of the cylinder collider representing the hole in the mask.
+\paragraph{distance\_circle\_mask}
+The distance between crucible and mask in Godot spacial units.
+\paragraph{distance\_sample}
+The distance between the sample and the mask in Godot spacial units.
+\paragraph{rays\_per\_frame}
+The amount of rays cast per time step of computation. Higher values means more "material" gets deposited.
+\paragraph{running\_time}
+The amount of time steps the simulation is run for.
+\paragraph{deposition\_gain}
+A multiplier to the amount of "material" that gets deposited for every ray that hits the sample. High values lead to grainier image, but allow for less computation time.
+\paragraph{penalize\_deposition}
+A boolean value that determines if a ray hitting a spot on the sample where previously nothing was deposited is less likely to deposit, than one that already has a deposit on the pixel for that spot.
+\paragraph{first\_layer\_deposition\_prob}
+The probability that material gets deposited on a pixel when previously no material had been deposited there. Does nothing if penalize\_deposition is false.
+\paragraph{oscillation\_period}
+The period in time steps for the noise oscillation.
+\paragraph{delay\_oscill\_time}
+The time delay in time steps before the noise oscillation starts.
+\paragraph{save\_in\_progress\_images}
+Bollean value determining if images are stored before the full simulation time has elapsed. If false only one image is saved at the end.
+\paragraph{save\_intervall}
+The intervall at which images are stored in time steps. Does nothing if save\_in\_progress\_images is false.
+\paragraph{oscillation\_dir}
+The direction of translational displacement enacted by the oscillation. After half a period the hole collider will be displaced by this amount. Oscillation always starts at the origin in x and z.
+\paragraph{oscillation\_rot\_s}
+The starting rotation of the hole in degrees. The hole collider oscillates between oscillation\_rot\_s and oscillation\_rot\_e. For constant tilt set them both the same.
+\paragraph{oscillation\_rot\_e}
+The ending rotation of the hole in degrees. The hole collider oscillates between oscillation\_rot\_s and oscillation\_rot\_e. For constant tilt set them both the same.
+\paragraph{random\_seed}
+The random seed for the pseudo random number generator used to generate rays. Can be set to get consistent results.
+\paragraph{x\_min, x\_max, y\_min, y\_max}
+The outer edges of the 2D image on the sample collider in godot spacial coordinates.
+\paragraph{resolution}
+The resolution of the image in pixels.
+\paragraph{path}
+The path the images are saved to. In progress images are saved with an additional step number appended to the string before the file format. File format must be .csv otherwise script will fail.
\ No newline at end of file
diff --git a/bibliography.aux b/bibliography.aux
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diff --git a/bibliography.bib b/bibliography.bib
index 2b272c0abe3ccd171392a1720eb57629f2a4bce5..51099e0bcb2de4fb7cc77a53b42d4561e1801865 100644
--- a/bibliography.bib
+++ b/bibliography.bib
@@ -139,3 +139,39 @@ isbn = {978-0-88415-381-8},
doi = {https://doi.org/10.1016/B978-088415381-8/50015-2},
url = {https://www.sciencedirect.com/science/article/pii/B9780884153818500152}
}
+
+@online{SEM_image_01,
+ALTauthor = {author},
+ALTeditor = {editor},
+title = {title},
+date = {date},
+url = {url},
+OPTsubtitle = {subtitle},
+OPTtitleaddon = {titleaddon},
+OPTlanguage = {language},
+OPTversion = {version},
+OPTnote = {note},
+OPTorganization = {organization},
+OPTdate = {date},
+OPTmonth = {month},
+OPTyear = {year},
+OPTaddendum = {addendum},
+OPTpubstate = {pubstate},
+OPTurldate = {urldate},
+}
+
+@online{SEM_image_01,
+ author = {Nicole Gleichmann},
+ title = {SEM vs TEM},
+ year = 2024,
+ url = {https://www.technologynetworks.com/analysis/articles/sem-vs-tem-331262},
+ urldate = {2024-01-24}
+}
+
+@online{SEM_image_02,
+ author = {Ponor},
+ title = {Electron-matter interaction volume and various types of signal generated - v2.svg},
+ year = 2020,
+ url = {https://commons.wikimedia.org/wiki/File:Electron-matter_interaction_volume_and_various_types_of_signal_generated_-_v2.svg},
+ urldate = {2020-08-28}
+}
\ No newline at end of file
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diff --git a/chap01.tex b/chap01.tex
index eea82506a292fdf1630806d3fd159be12a69abec..9c9c23ce58ee72ca7fc00d5b90244f66f03d8296 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -144,10 +144,36 @@ Tapping mode is a hybrid of both contact and non-contact modes. It is also somet
There are more ways to get useful sample information from an AFM, the tip can for example be coated in a magnetic coating in order to perform Magnetic Force Microscopy, but for the purposes of this thesis other uses will be neglected.
+AFMs provide high resolution topographical images at the nanometer scale and allow for accurate estimation of surface properties of a samples surface.
+\todo{Maybe write cool things AFMs have accomplished}
+
\subsection{Scanning Electron Microscopy}
\todo{Image of SEM Setup}
-A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this a sample is hit with a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample the electron can undergo various interactions with the sample. The main matter interaction that is measured in an SEM is the is inelastic scattering of the beam electron with a sample electron. The sample electron is ejected at a different angle from the incoming beam electron. This ejected electron is called secondary electron.\cite{SEM_book} The secondary electron are ejected from the sample at relatively low energy of $<50$ eV and can thus be attracted with a positive bias voltage ($>10$ kV) applied to a scintillator, which then converts the attracted electrons into light photons, which are then detected via photo multiplier tube (PMT). Such a detector is called Everhart–Thornley detector (ET) detector. Using these detectors it is now possible to detect the amount of secondary electrons emitted at the current beam location. This amount is based on the surfaces topography and thus by measuring the voltage given at the PMT a topographical image of the sample can be obtained. Other types of electron are also emitted in beam sample interaction and can be detected in an SEM setup, but for this thesis only the secondary electrons are relevant.\\
+A \textbf{S}canning \textbf{E}lectron \textbf{M}icroscope is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this a sample is hit with a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample the electron can undergo various interactions with the sample.
+
+\begin{figure}[H]
+ \centering
+ \begin{subfigure}{0.45\linewidth}
+ \includegraphics[width=0.9\linewidth]{img/Plots/Background/SEMSetup.png}
+ \caption{}
+ \label{fig:sem_setup_beam}
+ \end{subfigure}
+ \begin{subfigure}{0.45\linewidth}
+ \includegraphics[width=0.9\linewidth]{img/Plots/Background/Electron_Beam_Matter_Interaction.pdf}
+ \caption{}
+ \label{fig:sem_setup_interaction}
+ \end{subfigure}
+ \caption{The beam path for an SEM (\subref{fig:sem_setup_beam}). Multiple sets of magnetic lenses are used to focus the electron beam accurately. Accurate focussing of the electron beam is one of the major difficulties of SEM design and measurement uncertainty is usually dominated by optical artifacting from beam focus. The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the backscattering and X-ray detector. A diagram showing electron matter interactions (\subref{fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from \cite{SEM_image_01} and \cite{SEM_image_02}.}
+ \label{fig:sem_setup}
+\end{figure}
+\todo{Placeholder}
+
+The electron beam of an SEM are created using an electron gun. The electron guns used are usually tungsten electrons for comparatively low cost and good reliability. Anoother possibility is using \textbf{f}ield \textbf{e}mission \textbf{e}lectron \textbf{g}uns.\cite{SEM_book} The beam emitted from the electron gun still has to large spread to be used for SEM imaging for this reason the beam must be focused using electron lenses. In principle electron lenses can use either electrostatic or magnetic fields, but in practice only magnetic lenses are used since they provide smaller lensing abberations. Multiple sets of lenses are used to magnetically focus the beam onto the sample.\cite{SEM_book} Due to the use of electromagnets for lensing the parameters can be controlled relatively easily. The different lenses are used to focus the image partially manually by the user to create a sharp and stable image.
+
+The main matter interaction that is measured in an SEM is the is inelastic scattering of the beam electron with a sample electron. The sample electron is ejected at a different angle from the incoming beam electron. This ejected electron is called secondary electron.\cite{SEM_book} The secondary electron are ejected from the sample at relatively low energy of $<50$ eV and can thus be attracted with a positive bias voltage ($>10$ kV) applied to a scintillator, which then converts the attracted electrons into light photons, which are then detected via \textbf{P}hoto \textbf{M}ultiplier \textbf{T}ube (PMT). Such a detector is called \textbf{E}verhart–\textbf{T}hornley detector (ET) detector.\cite{SEM_book} Using these detectors it is now possible to detect the amount of secondary electrons emitted at the current beam location. This amount is based on the surfaces topography and thus by measuring the voltage given at the PMT a topographical image of the sample can be obtained. Other types of electron are also emitted in beam sample interaction and can be detected in an SEM setup, but for this thesis only the secondary electrons are relevant.\\
+
SEMs give high contrast large area images with good spatial resolution and were thus used in this thesis to initially locate evaporated fields on silicon samples, but SEM imaging comes with some downsides which is why they are not sufficient to fully characterize the samples in this thesis.
-On insulating or semi conducting samples the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focussing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference and thus they are not sufficient for sample characterization.
+On insulating or semi conducting samples the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focussing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference and thus they are not sufficient for sample characterization.\todo{Maybe write cool things SEMs have accomplished}
\subsection{Energy-dispersive X-ray spectroscopy}
+\textbf{E}nergy \textbf{d}ispersive \textbf{X}-ray spectroscopy (EDX)
\ No newline at end of file
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+\newlabel{fig:approach_curve_example}{{2.12}{29}{A capacitance (approach) curve, for one of the capacitive sensors, as an example (a) and the difference of each capacitance value to the last (b). Only one sensor is pictured. Marked are the important point where the slope of the $\frac {1}{r}$ curve changes. These points, where the geometry of the alignment process changes are marked labeled First, Second and Full contact. Before each of these points the difference goes to a local maximum. These are marked with blue dashed lines. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points mark where the mask is touching the sample}{figure.caption.51}{}}
\citation{Beeker}
-\newlabel{eq:cap_slope_change}{{2.3}{28}{Approach Curves}{equation.2.2.3}{}}
+\newlabel{eq:cap_slope_change}{{2.3}{30}{Approach Curves}{equation.2.2.3}{}}
\citation{Beeker}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless.}}{29}{figure.caption.47}\protected@file@percent }
-\newlabel{fig:approach_subsequent}{{2.13}{29}{Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless}{figure.caption.47}{}}
-\@writefile{tdo}{\contentsline {todo}{Plot too smol}{29}{section*.48}\protected@file@percent }
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-\@writefile{tdo}{\contentsline {todo}{If you do not have data for this maybe scratch line, me!}{29}{section*.50}\protected@file@percent }
-\newlabel{fig:approach_replicability_cap}{{2.14a}{30}{\relax }{figure.caption.51}{}}
-\newlabel{sub@fig:approach_replicability_cap}{{a}{30}{\relax }{figure.caption.51}{}}
-\newlabel{fig:approach_replicability_cap_diff}{{2.14b}{30}{\relax }{figure.caption.51}{}}
-\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{30}{\relax }{figure.caption.51}{}}
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-\newlabel{fig:approach_replicability}{{2.14}{30}{3 subsequent approach curves \subref {fig:approach_replicability_cap} and differences in capacitance for each step \subref {fig:approach_replicability_cap_diff} recorded. \textcolor {tab_green}{Green} is initial curve. \textcolor {tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.51}{}}
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-\newlabel{fig:cross_cap_approach_sim}{{2.16}{32}{The 3 capacitance curves of one example measurement multiplied with a factor, found by fitting, to ensure same scale (upper), the differences from $C_1$ to $C_2$ and $C_3$ (lower left) and the differences $C_2$ to $C_3$ (lower right). The plot shows heavy correlation between $C_1$, $C_2$ and $C_3$, since the shape of the graph is nearly identical. Most approach curves obtained with the newer mask holders are of similar shape}{figure.caption.58}{}}
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-\newlabel{fig:leakage_current}{{2.17}{33}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.60}{}}
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the error.}}{35}{figure.caption.62}\protected@file@percent }
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-\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via linear fit, first to C2 and C3 fit to C1 and then C3 fit to C2. If the function follows a $\frac {1}{r}$ shape, one should not be able to fit the plots to each other, via a linear function, unless they are heavily correlated. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{35}{figure.caption.63}\protected@file@percent }
-\newlabel{fig:mask_old_correl}{{2.19}{35}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via linear fit, first to C2 and C3 fit to C1 and then C3 fit to C2. If the function follows a $\frac {1}{r}$ shape, one should not be able to fit the plots to each other, via a linear function, unless they are heavily correlated. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.63}{}}
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-\@writefile{tdo}{\contentsline {todo}{Check}{37}{section*.73}\protected@file@percent }
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+\newlabel{fig:approach_subsequent}{{2.13}{31}{Plot of data of approach curves recorded on two different days. The second curve was recorded after retraction and subsequent approach. The 2 curves do not start at the same distance away from sample, which is why they are not aligned on the x-axis. A clear drop in capacitance can be observed from one measurement to the other regardless}{figure.caption.52}{}}
+\@writefile{tdo}{\contentsline {todo}{Plot too smol}{31}{section*.53}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{31}{subsection.2.2.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{31}{section*.54}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{If you do not have data for this maybe scratch line, me!}{31}{section*.55}\protected@file@percent }
+\newlabel{fig:approach_replicability_cap}{{2.14a}{32}{\relax }{figure.caption.56}{}}
+\newlabel{sub@fig:approach_replicability_cap}{{a}{32}{\relax }{figure.caption.56}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.14b}{32}{\relax }{figure.caption.56}{}}
+\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{32}{\relax }{figure.caption.56}{}}
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+\newlabel{fig:approach_replicability}{{2.14}{32}{3 subsequent approach curves \subref {fig:approach_replicability_cap} and differences in capacitance for each step \subref {fig:approach_replicability_cap_diff} recorded. \textcolor {tab_green}{Green} is initial curve. \textcolor {tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.56}{}}
+\@writefile{tdo}{\contentsline {todo}{Plot needs labels and bigger}{32}{section*.57}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Find chapter ref}{32}{section*.58}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility for different sample, but same mask}{33}{section*.59}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Plot too smol}{33}{section*.60}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{33}{subsection.2.2.5}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces \relax }}{33}{figure.caption.61}\protected@file@percent }
+\newlabel{fig:explanation_curve_difference}{{2.15}{33}{\relax }{figure.caption.61}{}}
+\@writefile{tdo}{\contentsline {todo}{Better plort}{33}{section*.62}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces The 3 capacitance curves of one example measurement multiplied with a factor, found by fitting, to ensure same scale (upper), the differences from $C_1$ to $C_2$ and $C_3$ (lower left) and the differences $C_2$ to $C_3$ (lower right). The plot shows heavy correlation between $C_1$, $C_2$ and $C_3$, since the shape of the graph is nearly identical. Most approach curves obtained with the newer mask holders are of similar shape.}}{34}{figure.caption.63}\protected@file@percent }
+\newlabel{fig:cross_cap_approach_sim}{{2.16}{34}{The 3 capacitance curves of one example measurement multiplied with a factor, found by fitting, to ensure same scale (upper), the differences from $C_1$ to $C_2$ and $C_3$ (lower left) and the differences $C_2$ to $C_3$ (lower right). The plot shows heavy correlation between $C_1$, $C_2$ and $C_3$, since the shape of the graph is nearly identical. Most approach curves obtained with the newer mask holders are of similar shape}{figure.caption.63}{}}
+\@writefile{tdo}{\contentsline {todo}{Plot of heavily correlated approach curves}{34}{section*.64}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample.}}{35}{figure.caption.65}\protected@file@percent }
+\newlabel{fig:leakage_current}{{2.17}{35}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the SiNi layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.65}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {2.1}{\ignorespaces Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII.}}{36}{table.caption.66}\protected@file@percent }
+\newlabel{tab:cross_cap}{{2.1}{36}{Table of cross capacitance measurement to determine possible causes for large values in approach curves. All measurements were done with Mask shuttle in Mask aligner and sample at $0.3$ mm distance. The distance was determined optically with Bresser MicroCam II and MikroCamLabII}{table.caption.66}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the error.}}{37}{figure.caption.67}\protected@file@percent }
+\newlabel{fig:mask_old_caps}{{2.18}{37}{The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the error}{figure.caption.67}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via linear fit, first to C2 and C3 fit to C1 and then C3 fit to C2. If the function follows a $\frac {1}{r}$ shape, one should not be able to fit the plots to each other, via a linear function, unless they are heavily correlated. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{37}{figure.caption.68}\protected@file@percent }
+\newlabel{fig:mask_old_correl}{{2.19}{37}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via linear fit, first to C2 and C3 fit to C1 and then C3 fit to C2. If the function follows a $\frac {1}{r}$ shape, one should not be able to fit the plots to each other, via a linear function, unless they are heavily correlated. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.68}{}}
+\@writefile{tdo}{\contentsline {todo}{Axis labels}{37}{section*.69}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.20}{\ignorespaces Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger.}}{38}{figure.caption.70}\protected@file@percent }
+\newlabel{fig:cross_cap_diagramm}{{2.20}{38}{Circuit diagram of the measurement setup with the cross capacitances and parasitic capacitances for the mask shuttle. The $C_i$ refer to the main capacitances that are used for mask alignment. $C_{ij}$ refers to a cross capacitance between capacitance sensor $i$ and sensor $j$. $C_{mask-sample}$ refers to the capacitance between the Si of the Mask and the Si of the Sample, usually this should not be measured since the Si of the Mask is separated from the gold pads with a SiN layer, but should that layer be pierced or otherwise allow a leakage current (if the resistances $R_{i, Leak}$ are small enough) this will be measured instead of $C_i$, since it is an order of magnitude larger}{figure.caption.70}{}}
+\@writefile{tdo}{\contentsline {todo}{Make into 1 curve}{38}{section*.71}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Leakage current}{38}{section*.72}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{38}{section*.73}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{39}{subsection.2.2.6}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{High correlation between capacitance curves}{39}{section*.74}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Write this but understandable}{39}{section*.75}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Plot stop condition}{39}{section*.76}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Low correlation between capacitance curves}{39}{section*.77}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Check}{39}{section*.78}\protected@file@percent }
+\@writefile{toc}{\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{39}{section.2.3}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{39}{subsection.2.3.1}\protected@file@percent }
\@setckpt{chap02}{
-\setcounter{page}{39}
+\setcounter{page}{41}
\setcounter{equation}{4}
\setcounter{enumi}{10}
\setcounter{enumii}{0}
@@ -146,7 +147,7 @@
\setcounter{subfigure}{0}
\setcounter{subtable}{0}
\setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{31}
+\setcounter{@todonotes@numberoftodonotes}{35}
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diff --git a/chap02.tex b/chap02.tex
index 62fcbe1c769047f40911a93aff7252adb37e193c..e1ac8478178802a7d0219f69850f592205b1e0b1 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -1,15 +1,15 @@
% !TeX spellcheck = <en-US>
-\chapter{Mask Aligner Setup}
+\chapter{Mask Aligner}
\begin{figure}[H]
\centering
- \begin{subfigure}{0.49\textwidth}
+ \begin{subfigure}{0.42\textwidth}
\includegraphics[width=\linewidth]{img/MA/NomenclatureMaskAlignerFront.pdf}
\caption{}
\label{fig:mask_aligner_nomenclature_motors}
\end{subfigure}
- \begin{subfigure}{0.49\textwidth}
+ \begin{subfigure}{0.42\textwidth}
\includegraphics[width=\linewidth]{img/MA/NomenclatureMaskAlignerCrossSec.pdf}
\caption{}
@@ -27,33 +27,17 @@ spring, \textbf{N} piezo motor front plate, \textbf{O} sapphire prism,
\textbf{P} Mask Aligner lower body. In \textcolor{tab_red}{red} the molecular
beam path to the mask is displayed.}
\label{fig:mask_aligner_nomenclature}
-\end{figure}\todo{Probably better as 2 Figures}
-
-The Mask Aligner is as the name implies a tool for aligning shadow masks in
-order to perform stencil lithography. 3 separate motors made up of 6 piezostacks
-each move a sapphire prism up or down. The is 3 prisms are each coupled to 3
-spots on the Mask frame of the Mask Aligner, via a neodym magnet. So that moving
-one of the motors tilts the frame (see
-Figure\ref{fig:mask_aligner_nomenclature_components} H). With the piezo motors
-the mask frame can be moved in steps of $\approx 50$ nm, which allows precise
-control of the distance between the mask and the sample, by tilting the frame on
-3 axis in z-axis direction. For this reason these motors are called Z1, Z2 and
-Z3 as seen in Figure \ref{fig:mask_aligner_nomenclature_motors}. The sample is
-attached with the sample stage and held in place with spring force. In addition
-the sample frame can be moved laterally in x direction with regard to the mask
-with a fourth piezo motor attached on the upper side of the mask aligner. This
-motor is referred to as the X motor also seen in Figure
-\ref{fig:mask_aligner_nomenclature_motors}. \\
-In order to measure the distance between mask an sample each mask is patterned
-with 3 gold pads, which serve as capacitive sensors, measuring the capacitance
-between the respective gold pad and the \ce{Si} of the sample. The labelling of
-the capacitance sensors can be seen The gold pads are electrically coupled to
-the Mask holder via gold cables that are glued to both the gold pads and to male
-gold pins, which are directly contacted to the female gold pins of the sample
-holder. Finally the signal is taken from the mask frame to the vacuum
-feedthroughs via shielded coaxial cables. The cable shielding is there in order
-to minimize noise and potentially prevent stray capacitances from influencing
-the measurement. \\
+\end{figure}
+
+The Mask Aligner is made up of components that can be separated into 3 sections:
+The sample module (Figure \ref{fig:mask_aligner_nomenclature_components} A-G), the central (mask) module (Figure \ref{fig:mask_aligner_nomenclature_components} I-J) and the lower (motor) module (Figure \ref{fig:mask_aligner_nomenclature_components} K-P). \\
+The sample module is concerned with the stable fitting of the sample and the movement of the sample in the x direction. For this reason the sample module is fitted with a sliding rail (Fig. \ref{fig:mask_aligner_nomenclature_components} D) along which the sample stage (Fig. \ref{fig:mask_aligner_nomenclature_components} E) can be moved, by applying voltage pulses. This setup is referred to as a motor and this motor is labeled X, since it moves the sample in x direction, the movement is pictured inf Figure \ref{fig:mask_aligner_nomenclature_motors}. The sample holder itself is held in place with spring tension inside the sample stage, allowing the sample to remain firm in its position, while it still remains easy to withdraw and insert the sample. \\
+
+The mask module consists of the mask frame (Fig. \ref{fig:mask_aligner_nomenclature_components} H), which holds the mask shuttle (Fig. \ref{fig:mask_aligner_nomenclature_components} J) in place using spring tension and provides \ce{CuBe} contacts for the $3$ capacitance detectors on the mask used for capacitive distance measurement. The contacts are connected to shielded coaxial cables that take the capacitance signal from the mask to the vacuum feedthroughs. The coaxial cables are grounded to the Mask Aligner body ((Fig. \ref{fig:mask_aligner_nomenclature_components} P)). \\
+
+The motor module of the Mask Aligner consists of $3$ motors of similar build. The motors move the mask on the z axis $3$ different pivot points, due to this the $3$ motors are labelled Z1, Z2 and Z3. The order of the $3$ motors is pictured in Figure \ref{fig:mask_aligner_nomenclature_motors}. Each motor consists of a sapphire prism (Fig. \ref{fig:mask_aligner_nomenclature_components} O) that is held in place by $6$ piezostack (made up of $4$ $\approx 0.4$ nF piezo plates each). $4$ of these are attached directly to the Mask Aligner body. While the last two are attached to a metal plate (Fig. \ref{fig:mask_aligner_nomenclature_components} N), which is pressed against the sapphire prism using a \ce{CuBe} spring (Fig. \ref{fig:mask_aligner_nomenclature_components} M). The tension of the spring keeps the saphhire prism in its place while still allowing movement of the sapphire prism using the piezostacks. To control the amount of tension the \ce{CuBe} spring provides, it is affixed using a screw, which can be made more firm or loose to provide more or less tension on the sapphire prism. On top of the sapphire prism a \ce{Al2O3} plate (Fig. \ref{fig:mask_aligner_nomenclature_components} L) is attached, which has a small groove in the middle. A neodym magnet (Fig. \ref{fig:mask_aligner_nomenclature_components} K) sits in the groove of the plate and connects the motor to the mask frame, where a similar \ce{Al2O3} plate setup is placed on the
+underside of the mask frame. The pivot points created by the $3$ motors neodym magnet connections to the mask frame approximately build an equilateral triangle with the mask position in the middle. When a motors sapphire prism now moves up the mask frame is tilted on the axis defined by the other two motor pivot points and the side of the mask moves closer to the sample. With this the tilt of the mask frame and thus the tilt of the mask can be controlled with precision in the order of $\approx 50$ nm steps. \\
+When moving the sapphire prism up the mask "approaches" the sample, due to this the movement direction is labeled approach, while the opposite is called retract. Often the direction is also specified by mathematical sign, where $-$ specifies the approach direction, while $+$ specifies retract.\\
\section{Molecular Beam Evaporation Chamber}
\begin{figure}[H]
@@ -62,30 +46,28 @@ the measurement. \\
\caption{Circuit diagram of the mask aligner and its associated vacuum
system. The system consists of the mask aligner chamber, the main chamber, the
Pb evaporator and the AU evaporator. The configuration depicted is used for
-evaporation. The section labelled load lock is a vacuum suitcase and can be
+evaporation. The section labeled load lock is a vacuum suitcase and can be
detached. The \textcolor{tab_green}{green} path shows the sample/mask extraction
and insertion path with the wobblestick. The gray arrow shows the molecular beam
path from the \ce{Pb} evaporator.}
\label{fig:mask_aligner_chamber}
\end{figure}
-The Mask Aligner is housed within a electron beam evaporation chamber so that
-once mask and sample have been aligned the evaporator attached to the Mask
-Aligner chamber can be used to evaporate material upon the sample. Currently the
-evaporator is used with \ce{Pb} as it was intended to evaporate superconducting
-islands onto a magnetic topological insulator. So far however only tests on
-\ce{Si} have been performed.\todo{bad} The chamber layout can be seen in Figure
+The Mask Aligner vacuum system consists of three distinct vacuum chambers that can be separated with vacuum gate valves. The first part is the \textbf{M}ain \textbf{C}hamber (MC), in which the Mask Aligner is located and the evaporator chamber used to create a molecular beam into the main chamber, secondly the \textbf{L}oad \textbf{L}ock (LL), which is a vacuum suitcase that is used to insert new samples and masks into the system and thirdly a Turbomolecular pump loop used to pump the system down to UHV vacuum pressures. The main chamber is equipped with an Ion Getter Pump, due to this the system can be seperated from the main pumping loop of the Turbo molecular pump, without loss of vacuum pressure. The system is separated via $2$ \textbf{A}ll \textbf{M}etal \textbf{C}orner \textbf{V}alves (AMCV), one located directly on the main chamber and one separating the evaporator from the Turbomolecular pump loop. Additionally the Load Lock and the main chamber are separated using a Gate Valve. In order to detect leaks in the vacuum system a mass spectrometer is also attached to the main chamber. \\
+The Load Lock is equipped with a small ion getter pump, that runs on of its own allowing it to keep UHV pressures for extended periods of time, even while separated from the main pump loop. A garage with spaces for up to \todo{check number} samples and 4 additional spaces for \todo{name} samples is part of the Load Lock. This allows insertion of multiple samples and masks, that can then be later inserted into the main chamber. For insertion and removal of masks and sample a wobble stick is attached to the Load Lock chamber. The sample/mask insertion path of the wobblestick can be seen in \textcolor{tab_green}{green} in Figure \ref{fig:mask_aligner_chamber}. The Load Lock is designed to be a detachable vacuum suitcase, allowing samples to be stored in the garage and then transported with the suitcase to another vacuum system without intermediate exposure to ambient conditions.\\
+The main pump loop consists of a rotary vane prepump and a turbomolecular pump \todo{Look up exact model}. Between prepump and turbo molecular pump is a pressure sensor to determine if the prepump is providing suitable backing pressure and a valve, which can be opened to a Nitrogen bottle to allow the system to be vented to atmospheric pressure with an inert gas. \\
+The 3 parts are seen as distinct, as the 3 components can be decoupled safely once the entire system is pumped to UHV without risk of losing vacuum pressure since no part of the system is not pumped. \\
+Another device, a gold evaporator, is connected to the vacuum system of the Mask Aligner, but it can be currently run fully separately, as it has its own Turbomolecular pump with attached prepump. As such the system is completely independent and only needs to be opened to the Mask Aligner system to check its pressure, since it currently is not equipped with any pressure sensor of its own. The pressure sensor is however not needed, since in testing the turbomolecular pump can pump the system down to the necessary pressures in very short time. Opening to the Mask Aligner system would only be needed in case there is a suspected leak. \\
\ref{fig:mask_aligner_chamber}.
\cite{Mask_Aligner}
\section{Shadow Mask Alignment}
\subsection{Calibration}
-In order to use the Mask Aligner the different step sizes, i.e. the amount the
+In order to use the Mask Aligner the different step sizes, i.e. the amount each
motor moves when one pulse is applied, has to be measured. This should be done
when performing repairs outside UHV, before putting the Mask Aligner into UHV in
order to make sure all motors run with similar step sizes and inside UHV to
-determine the final step size for approach curves, which gives information on
-how close the mask is to the sample at any given point. \\
+determine the final step size for approach curves, which is used to determine a value for the distance of mask and sample, when the distance is small enough that it can no longer be optically determined.\\
In order to make sure the motors can all give similar step sizes, there are 3
screws, one on each motor's front plate, that can control the amount of force
the front plate applies to the prism and thus the amount of friction the piezo
@@ -143,7 +125,7 @@ little closer to the camera than the motors themselves, if one neglects the smal
\includegraphics[width=0.6\linewidth]{img/Plots/Calibrations/screw_diff_explain.pdf}
\caption{Diagram explaining how to derive the deviation of measured step size on the screws near the Z2 and Z3 motors from the actual step size of the motors.}
\label{fig:calibration_screw_diff_explain}
-\end{figure} \todo{Maybe leave out}
+\end{figure} \todo{Maybe leave out or put tranparent image of motor below}
With this one gets that for each unit of distance the motor moves the screws move by $h' = \frac{17.8}{23.74} \approx 0.75$. With this the actual movement on the motor can be obtained. \\
diff --git a/chap03.aux b/chap03.aux
index 267a3335ecbf31fbe6a520454ab4f4c426933ed2..62601d2e2348e1c6f47476d067a8bdc5db70f757 100644
--- a/chap03.aux
+++ b/chap03.aux
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+\newlabel{fig:walker_pulse_shape_slow}{{3.10}{50}{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. The Walker keeps the Voltage of 80 V both in the maxima and minima, while the RHK undershoots in the maximum for approach and overshoots in the minimum and vice versa in the retract. Noticeable is a voltage peak in the RHK behavior after the fast flank, that is absent in the Walkers pulse}{figure.caption.106}{}}
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index 1fa7e663ea17da8fc5962909c4ef24a59978e9fb..6844bbe190513453a5f01a2ccf24f9b0fedb5b03 100644
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index 5a7060a4478e097389e8cb798edc7f42c8ef44cc..5988652c5c7340d2044cefcb333a892b6e6c7736 100644
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diff --git a/chap05.tex b/chap05.tex
index 1f4b5cf64dbb88ac37104baa5ddd9232df3f79c4..7e684c442f5d7c5af504536d87cff21f262ffa7e 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -2,7 +2,7 @@
\chapter{Evaporations and Measurement}
\section{Silicon}
-\subsection{Sample Preparation}
+\subsection{Evaporation Configuration}
As a test for positioning and as a test for the Mask Aligners capabilities after optimization evaporations were performed on a \ce{Si} sample. The sample was prepared and cleaned using the process described in \todo{Link Sample prep}. The 5 evaporations were performed across different points in the approach curve of this particular mask to see the difference in evaporation quality for the different criteria established for stopping the approach curve. The approach curve of this particular sample is shown in Figure \ref{fig:evaporation_approach}\\
@@ -33,8 +33,18 @@ The evaporation conditions were as follows:
\begin{figure}[H]
\centering
- \includegraphics[width=0.4\linewidth]{img/Plots/Evaporation/SampleImage.pdf}
- \caption{Diagram showing the Evaporation performed on the sample. Red squares represent the evaporation fields. The number shows the order of evaporations. Distances are measured using optical microscope. Fields are at a $10^\circ$ angle with respect to the sample holder.}
+ \begin{subfigure}{0.45\linewidth}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/SampleImage.pdf}
+ \caption{}
+ \label{fig:Evaporation_diagramm_sample_img}
+ \end{subfigure}
+ \begin{subfigure}{0.45\linewidth}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Mask02_Aspect.png}
+ \caption{}
+ \label{fig:Evaporation_diagramm_mask_img}
+ \end{subfigure}
+
+ \caption{Diagram showing the Evaporation performed on the sample (\subref{fig:Evaporation_diagramm_sample_img}). Red squares represent the evaporation fields. The number shows the order of evaporations. Distances are measured using optical microscope. Fields are at a $10^\circ$ angle with respect to the sample holder. An optical microscope image of the mask taken before evaporation (\subref{fig:Evaporation_diagramm_mask_img})}
\label{fig:Evaporation_diagramm}
\end{figure}
@@ -43,7 +53,7 @@ The entire samples surface is contaminated with small particles, which are about
\begin{figure}[H]
\centering
- \includegraphics[width=0.9\linewidth]{img/Plots/Evaporation/Contamination.pdf}
+ \includegraphics[width=0.9\linewidth]{img/Evaporation/Contamination.pdf}
\caption{Line cuts obtained from contamination particles. The data shows that the particles are up to $\approx 40$ nm in height and with an average height of $20 \pm 10$ nm. The particles are on average $40 \pm 10$ in width. height and width were obtained by fitting flattened gaussian functions to the particles line cuts and extracting $2\sigma$ as well as the height of the peak.}
\label{fig:evaporation_contamination}
\end{figure}
@@ -59,22 +69,22 @@ Also obtained by this method are the height and the umbral width of each dot.
\begin{figure}[H]
\centering
\begin{subfigure}{0.4\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Field5_top_demo01.png}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Field5_top_demo01.png}
\caption{}
\end{subfigure}
\begin{subfigure}{0.4\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Field5_top_demo02.png}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Field5_top_demo02.png}
\caption{}
\end{subfigure}
\begin{subfigure}{0.6\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/TopField5Fit.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/TopField5Fit.pdf}
\caption{}
\end{subfigure}
\caption{Example of the analysis performed on each of the recorded dots for a single line cut. (a) shows the raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) shows the cleaned image, as well as the line (red) from which the line cut data (c) was obtained. The fit shows the two different penumbra widths induced by the tilt $\sigma_l$ and $\sigma_r$.}
\label{fig:evaporation_analysis}
\end{figure}
-This process was performed for every recorded dot and with multiple line cuts near the line in which the tilt is pointing as well as for both trace and retrace images. This gives multiple datapoints for each image for both $\sigma_s$ and $\sigma_l$.
+This process was performed for every recorded dot and with multiple line cuts near the line in which the tilt is pointing as well as for both trace and retrace images. This gives multiple data points for each image for both $\sigma_s$ and $\sigma_l$.
\subsection{Tilt}
All evaporated dots, even when the capacitance signal was within the full contact regime showed signs of a tilt between mask hole and sample in the form of a half moon shaped second penumbra. If this was due to a misalignement between the entire mask and the sample one would expect the direction of the tilt to be the same for the entire evaporated field and the size of the second penumbra to diminish along the direction of the tilt. But as seen in Figure \ref{fig:evaporation_tilts} the direction of the tilt is not uniform and instead seems to point outwards for the dots on the edge. This suggests the mask itself is slightly bent towards the edges resulting in an alignment error. \\
@@ -85,11 +95,11 @@ The smallest minor that was found in the AFM data was $2.15 \pm 0.08$ $\mu$m aga
\begin{figure}[H]
\centering
\begin{subfigure}{0.495\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Field3Angle.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Field3Angle.pdf}
\caption{}
\end{subfigure}
\begin{subfigure}{0.495\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/FieldsAngle.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/FieldsAngle.pdf}
\caption{}
\end{subfigure}
\caption{Image of the reconstruction of the tilt angle for Field 3 as an example (a) and the data given by all fields (b). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}
@@ -109,11 +119,11 @@ After a user specified time has passed the amount of hits on each pixel is saved
\begin{figure}[H]
\centering
\begin{subfigure}{0.45\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Sim/Field3_right.png}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right.png}
\caption{}
\end{subfigure}
\begin{subfigure}{0.53\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Sim/Field3_right_sim_simple.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple.pdf}
\caption{}
\end{subfigure}
\caption{Comparison of an recorded AFM image (a) (grains were removed using interpolation during post processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be constant during the deposition and different sticking factors of \ce{Pb}-\ce{Si} and \ce{Pb}-\ce{Pb} were not considered.}
@@ -126,17 +136,17 @@ The greater circle in the AFM has an average height for all dots of about $3.5 \
\begin{figure}[H]
\centering
\begin{subfigure}{0.32\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Sim/Field3_right_sim_simple.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple.pdf}
\caption{}
\label{fig:evaporation_simulation_sharpness_stick_simple}
\end{subfigure}
\begin{subfigure}{0.32\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Sim/Field3_right_sim_simple_initial.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple_initial.pdf}
\caption{}
\label{fig:evaporation_simulation_sharpness_stick_inital}
\end{subfigure}
\begin{subfigure}{0.32\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Plots/Evaporation/Sim/Field3_right_sim_simple_power.pdf}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Sim/Field3_right_sim_simple_power.pdf}
\caption{}
\label{fig:evaporation_simulation_sharpness_stick_power}
\end{subfigure}
@@ -149,7 +159,7 @@ The effect of this can be seen in Figure \ref{fig:evaporation_simulation_sharpne
\begin{figure}[H]
\centering
- \includegraphics[width=0.9\linewidth]{img/Plots/Evaporation/Sim/Field3_right_sim_progression.pdf}
+ \includegraphics[width=0.9\linewidth]{img/Evaporation/Sim/Field3_right_sim_progression.pdf}
\caption{}
\label{fig:evaporation_simulation_progression}
\end{figure}\todo{Showing simulation progression of evaporation}
diff --git a/conclusion.aux b/conclusion.aux
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diff --git a/thesis.bbl b/thesis.bbl
index 48d941c4c7dc7e26f72ccbd0debab8c2c2dc9db8..fc1cca821bb0441849e11016372de9daa26e4b03 100644
--- a/thesis.bbl
+++ b/thesis.bbl
@@ -34,6 +34,14 @@ W.~Zhou and Z.L. Wang.
Applications}.
\newblock 01 2007.
+\bibitem{SEM_image_01}
+title.
+
+\bibitem{SEM_image_02}
+Ponor.
+\newblock Electron-matter interaction volume and various types of signal
+ generated - v2.svg, 2020.
+
\bibitem{Mask_Aligner}
Priyamvada Bhaskar, Simon Mathioudakis, Tim Olschewski, Florian Muckel,
Jan~Raphael Bindel, Marco Pratzer, Marcus Liebmann, and Markus Morgenstern.
diff --git a/thesis.blg b/thesis.blg
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Chapter 3.
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Chapter 4.
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diff --git a/thesis.pdf b/thesis.pdf
index 187d7fc9f52787124e65cce3559788f361858189..16cd766a1c7d9e03300bc93157d728e3d04cce3c 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index bd929c413ba6c172b18e5e057a03d3d5ad017fa0..f0dc6d5139c8e30ab45f8d582e87612046ef828b 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.tex b/thesis.tex
index 4c07ef58dae940e33e5da5341792ed40eb2d3f03..d366e676c3dc65aa96dd6142eeee6987709de7f0 100644
--- a/thesis.tex
+++ b/thesis.tex
@@ -150,11 +150,13 @@ PMT = \textbf{P}hoto\textbf{m}ultiplier \textbf{T}ube \\
ET detector = \textbf{E}verhart-\textbf{T}hornley detector \\
RIE = \textbf{R}eactive \textbf{I}on \textbf{E}tching \\
Opamp = \textbf{O}perational \textbf{A}mplifier \\
+EDX = \textbf{E}nergy-\textbf{d}ispersive \textbf{X}-ray spectroscopy \\
+MC = \textbf{M}ain \textbf{C}hamber
+LL = \textbf{L}oad \textbf{L}ock
+
\include{appendix}
-\todo{Circuit Diagramms Mask Aligner}
-\todo{Instructions new Driver electronics}
\include{acknowledgments}
%%% Attachments to the bachelor thesis, if any. Each attachment must be
diff --git a/thesis.toc b/thesis.toc
index 5a5ea4451993d43090d6aa2cef7b291e2ebc9158..4ba637d00e243c1ca0541c859f96a58e5d9eaf68 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -13,71 +13,93 @@
\contentsline {paragraph}{Non-Contact}{13}{section*.22}%
\contentsline {paragraph}{Tapping}{13}{section*.23}%
\contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{14}{subsection.1.3.2}%
-\contentsline {subsection}{\numberline {1.3.3}Energy-dispersive X-ray spectroscopy}{15}{subsection.1.3.3}%
-\contentsline {chapter}{\numberline {2}Mask Aligner Setup}{16}{chapter.2}%
-\contentsline {section}{\numberline {2.1}Molecular Beam Evaporation Chamber}{18}{section.2.1}%
-\contentsline {section}{\numberline {2.2}Shadow Mask Alignment}{19}{section.2.2}%
-\contentsline {subsection}{\numberline {2.2.1}Calibration}{19}{subsection.2.2.1}%
-\contentsline {subsection}{\numberline {2.2.2}Optical Alignment}{24}{subsection.2.2.2}%
-\contentsline {subsection}{\numberline {2.2.3}Approach Curves}{26}{subsection.2.2.3}%
-\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{29}{subsection.2.2.4}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{29}{section*.49}%
-\contentsline {subsubsection}{Reproducibility for different sample, but same mask}{31}{section*.54}%
-\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{31}{subsection.2.2.5}%
-\contentsline {paragraph}{Leakage current}{36}{section*.67}%
-\contentsline {paragraph}{Improved gold pin fitting}{36}{section*.68}%
-\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{37}{subsection.2.2.6}%
-\contentsline {paragraph}{High correlation between capacitance curves}{37}{section*.69}%
-\contentsline {paragraph}{Low correlation between capacitance curves}{37}{section*.72}%
-\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{37}{section.2.3}%
-\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{37}{subsection.2.3.1}%
-\contentsline {chapter}{\numberline {3}Electronics}{39}{chapter.3}%
-\contentsline {section}{\numberline {3.1}Slip Stick Principle}{39}{section.3.1}%
-\contentsline {section}{\numberline {3.2}RHK}{40}{section.3.2}%
-\contentsline {subsection}{\numberline {3.2.1}Overview}{40}{subsection.3.2.1}%
-\contentsline {paragraph}{amplitude}{40}{section*.75}%
-\contentsline {paragraph}{sweep period}{40}{section*.76}%
-\contentsline {paragraph}{time between sweeps}{40}{section*.77}%
-\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{40}{subsection.3.2.2}%
-\contentsline {section}{\numberline {3.3}KIM001}{41}{section.3.3}%
-\contentsline {subsection}{\numberline {3.3.1}Overview}{41}{subsection.3.3.1}%
-\contentsline {subsection}{\numberline {3.3.2}Pulse shape}{41}{subsection.3.3.2}%
-\contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{42}{subsection.3.3.3}%
-\contentsline {section}{\numberline {3.4}Mask Aligner Controller "Walker"}{43}{section.3.4}%
-\contentsline {subsection}{\numberline {3.4.1}Overview}{43}{subsection.3.4.1}%
-\contentsline {subsection}{\numberline {3.4.2}Signal generation}{44}{subsection.3.4.2}%
-\contentsline {subsection}{\numberline {3.4.3}Fast flank}{45}{subsection.3.4.3}%
-\contentsline {subsection}{\numberline {3.4.4}Amplification}{46}{subsection.3.4.4}%
-\contentsline {subsection}{\numberline {3.4.5}Parameters}{46}{subsection.3.4.5}%
-\contentsline {paragraph}{Amplitude (amp)}{46}{section*.95}%
-\contentsline {paragraph}{Voltage (volt)}{47}{section*.96}%
-\contentsline {paragraph}{Channel}{47}{section*.97}%
-\contentsline {paragraph}{Max Step}{47}{section*.98}%
-\contentsline {paragraph}{Polarity}{47}{section*.99}%
-\contentsline {subsection}{\numberline {3.4.6}Measured Pulse shape}{47}{subsection.3.4.6}%
-\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{49}{subsection.3.4.7}%
-\contentsline {chapter}{\numberline {4}Mask Aligner Repairs and Optimizations}{50}{chapter.4}%
-\contentsline {section}{\numberline {4.1}Overview}{50}{section.4.1}%
-\contentsline {section}{\numberline {4.2}General UHV device preparation}{50}{section.4.2}%
-\contentsline {subsection}{\numberline {4.2.1}Adding components}{50}{subsection.4.2.1}%
-\contentsline {subsection}{\numberline {4.2.2}Soldering}{51}{subsection.4.2.2}%
-\contentsline {section}{\numberline {4.3}Soldering Anchors}{51}{section.4.3}%
-\contentsline {section}{\numberline {4.4}Piezo Reglueing}{54}{section.4.4}%
-\contentsline {section}{\numberline {4.5}Z3 Motor}{56}{section.4.5}%
-\contentsline {subsection}{\numberline {4.5.1}Front Plate repair}{57}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{60}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{61}{section.4.6}%
-\contentsline {section}{\numberline {4.7}Final Test}{61}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and Measurement}{64}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Silicon}{64}{section.5.1}%
-\contentsline {subsection}{\numberline {5.1.1}Sample Preparation}{64}{subsection.5.1.1}%
-\contentsline {subsection}{\numberline {5.1.2}Contamination}{65}{subsection.5.1.2}%
-\contentsline {subsection}{\numberline {5.1.3}Penumbra}{66}{subsection.5.1.3}%
-\contentsline {subsection}{\numberline {5.1.4}Tilt}{68}{subsection.5.1.4}%
-\contentsline {subsection}{\numberline {5.1.5}Simulation}{69}{subsection.5.1.5}%
-\contentsline {paragraph}{Improvements}{72}{section*.152}%
-\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.153}%
-\contentsline {chapter}{Bibliography}{74}{chapter*.154}%
-\contentsline {chapter}{List of Abbreviations}{75}{chapter*.155}%
-\contentsline {section}{\numberline {5.2}New Driver Electronics}{76}{section.5.2}%
-\contentsline {chapter}{Acknowledgments}{78}{chapter*.158}%
+\contentsline {subsection}{\numberline {1.3.3}Energy-dispersive X-ray spectroscopy}{16}{subsection.1.3.3}%
+\contentsline {chapter}{\numberline {2}Mask Aligner}{17}{chapter.2}%
+\contentsline {section}{\numberline {2.1}Molecular Beam Evaporation Chamber}{19}{section.2.1}%
+\contentsline {section}{\numberline {2.2}Shadow Mask Alignment}{20}{section.2.2}%
+\contentsline {subsection}{\numberline {2.2.1}Calibration}{20}{subsection.2.2.1}%
+\contentsline {subsection}{\numberline {2.2.2}Optical Alignment}{26}{subsection.2.2.2}%
+\contentsline {subsection}{\numberline {2.2.3}Approach Curves}{28}{subsection.2.2.3}%
+\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{31}{subsection.2.2.4}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{31}{section*.54}%
+\contentsline {subsubsection}{Reproducibility for different sample, but same mask}{33}{section*.59}%
+\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{33}{subsection.2.2.5}%
+\contentsline {paragraph}{Leakage current}{38}{section*.72}%
+\contentsline {paragraph}{Improved gold pin fitting}{38}{section*.73}%
+\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{39}{subsection.2.2.6}%
+\contentsline {paragraph}{High correlation between capacitance curves}{39}{section*.74}%
+\contentsline {paragraph}{Low correlation between capacitance curves}{39}{section*.77}%
+\contentsline {section}{\numberline {2.3}Mask Aligner Operation}{39}{section.2.3}%
+\contentsline {subsection}{\numberline {2.3.1}Sample Preparation}{39}{subsection.2.3.1}%
+\contentsline {chapter}{\numberline {3}Electronics}{41}{chapter.3}%
+\contentsline {section}{\numberline {3.1}Slip Stick Principle}{41}{section.3.1}%
+\contentsline {section}{\numberline {3.2}RHK}{42}{section.3.2}%
+\contentsline {subsection}{\numberline {3.2.1}Overview}{42}{subsection.3.2.1}%
+\contentsline {paragraph}{amplitude}{42}{section*.80}%
+\contentsline {paragraph}{sweep period}{42}{section*.81}%
+\contentsline {paragraph}{time between sweeps}{42}{section*.82}%
+\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{42}{subsection.3.2.2}%
+\contentsline {section}{\numberline {3.3}KIM001}{43}{section.3.3}%
+\contentsline {subsection}{\numberline {3.3.1}Overview}{43}{subsection.3.3.1}%
+\contentsline {subsection}{\numberline {3.3.2}Pulse shape}{43}{subsection.3.3.2}%
+\contentsline {subsection}{\numberline {3.3.3}Voltage behavior}{44}{subsection.3.3.3}%
+\contentsline {section}{\numberline {3.4}Mask Aligner Controller "Walker"}{45}{section.3.4}%
+\contentsline {subsection}{\numberline {3.4.1}Overview}{45}{subsection.3.4.1}%
+\contentsline {subsection}{\numberline {3.4.2}Signal generation}{46}{subsection.3.4.2}%
+\contentsline {subsection}{\numberline {3.4.3}Fast flank}{47}{subsection.3.4.3}%
+\contentsline {subsection}{\numberline {3.4.4}Amplification}{48}{subsection.3.4.4}%
+\contentsline {subsection}{\numberline {3.4.5}Parameters}{48}{subsection.3.4.5}%
+\contentsline {paragraph}{Amplitude (amp)}{48}{section*.100}%
+\contentsline {paragraph}{Voltage (volt)}{49}{section*.101}%
+\contentsline {paragraph}{Channel}{49}{section*.102}%
+\contentsline {paragraph}{Max Step}{49}{section*.103}%
+\contentsline {paragraph}{Polarity}{49}{section*.104}%
+\contentsline {subsection}{\numberline {3.4.6}Measured Pulse shape}{49}{subsection.3.4.6}%
+\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{51}{subsection.3.4.7}%
+\contentsline {chapter}{\numberline {4}Mask Aligner Repairs and Optimizations}{52}{chapter.4}%
+\contentsline {section}{\numberline {4.1}Overview}{52}{section.4.1}%
+\contentsline {section}{\numberline {4.2}General UHV device preparation}{52}{section.4.2}%
+\contentsline {subsection}{\numberline {4.2.1}Adding components}{52}{subsection.4.2.1}%
+\contentsline {subsection}{\numberline {4.2.2}Soldering}{53}{subsection.4.2.2}%
+\contentsline {section}{\numberline {4.3}Soldering Anchors}{53}{section.4.3}%
+\contentsline {section}{\numberline {4.4}Piezo Reglueing}{56}{section.4.4}%
+\contentsline {section}{\numberline {4.5}Z3 Motor}{58}{section.4.5}%
+\contentsline {subsection}{\numberline {4.5.1}Front Plate repair}{59}{subsection.4.5.1}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{62}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{63}{section.4.6}%
+\contentsline {section}{\numberline {4.7}Final Test}{63}{section.4.7}%
+\contentsline {chapter}{\numberline {5}Evaporations and Measurement}{66}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Silicon}{66}{section.5.1}%
+\contentsline {subsection}{\numberline {5.1.1}Evaporation Configuration}{66}{subsection.5.1.1}%
+\contentsline {subsection}{\numberline {5.1.2}Contamination}{67}{subsection.5.1.2}%
+\contentsline {subsection}{\numberline {5.1.3}Penumbra}{68}{subsection.5.1.3}%
+\contentsline {subsection}{\numberline {5.1.4}Tilt}{70}{subsection.5.1.4}%
+\contentsline {subsection}{\numberline {5.1.5}Simulation}{71}{subsection.5.1.5}%
+\contentsline {paragraph}{Improvements}{74}{section*.157}%
+\contentsline {chapter}{Conclusions and Outlook}{75}{chapter*.158}%
+\contentsline {chapter}{Bibliography}{76}{chapter*.159}%
+\contentsline {chapter}{List of Abbreviations}{77}{chapter*.160}%
+\contentsline {section}{\numberline {5.2}New Driver Electronics}{78}{section.5.2}%
+\contentsline {section}{\numberline {5.3}Raycast Simulation}{78}{section.5.3}%
+\contentsline {paragraph}{radius\_1}{78}{section*.161}%
+\contentsline {paragraph}{angle}{78}{section*.162}%
+\contentsline {paragraph}{radius\_mask}{78}{section*.163}%
+\contentsline {paragraph}{distance\_circle\_mask}{78}{section*.164}%
+\contentsline {paragraph}{distance\_sample}{78}{section*.165}%
+\contentsline {paragraph}{rays\_per\_frame}{78}{section*.166}%
+\contentsline {paragraph}{running\_time}{78}{section*.167}%
+\contentsline {paragraph}{deposition\_gain}{78}{section*.168}%
+\contentsline {paragraph}{penalize\_deposition}{78}{section*.169}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{78}{section*.170}%
+\contentsline {paragraph}{oscillation\_period}{78}{section*.171}%
+\contentsline {paragraph}{delay\_oscill\_time}{78}{section*.172}%
+\contentsline {paragraph}{save\_in\_progress\_images}{78}{section*.173}%
+\contentsline {paragraph}{save\_intervall}{79}{section*.174}%
+\contentsline {paragraph}{oscillation\_dir}{79}{section*.175}%
+\contentsline {paragraph}{oscillation\_rot\_s}{79}{section*.176}%
+\contentsline {paragraph}{oscillation\_rot\_e}{79}{section*.177}%
+\contentsline {paragraph}{random\_seed}{79}{section*.178}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{79}{section*.179}%
+\contentsline {paragraph}{resolution}{79}{section*.180}%
+\contentsline {paragraph}{path}{79}{section*.181}%
+\contentsline {chapter}{Acknowledgments}{80}{chapter*.182}%