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diff --git a/chap01.tex b/chap01.tex
index 4870ec9b3b1d31f1b216377ffbb1b5796b4e3ca0..5362f90b0010b71c296247eed721fd2065208b27 100644
--- a/chap01.tex
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@@ -89,7 +89,7 @@ The mask and the sample also have to be kept parallel as a tilt would result in
\caption{}
\label{fig:penumbra_explanation_tilt_sim}
\end{subfigure}
- \caption{A diagram of the evaporation happening with a tilted mask for only one hole (\subref{fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral radii that appear in a cross-section of the evaporation at the tilt angle. (\subref{fig:penumbra_explanation_tilt_sim}) shows a simulated evaporation with large penumbra for a tilt angle of $45^\circ$ the "half-moon" shaped penumbra, that is wider on one side than on the other, can be seen easily. The penumbra in the simulation is exaggerated for demonstrational purposes.}
+ \caption{A diagram of the evaporation happening with a tilted mask for only one hole (\subref{fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral radii that appear in a cross-section of the evaporation at the tilt angle. (\subref{fig:penumbra_explanation_tilt_sim}) shows a simulated evaporation with large penumbra for a tilt angle of $45^\circ$ the "half-moon" shaped penumbra, that is wider on one side than on the other, can be seen easily. The penumbra in the simulation is exaggerated for demonstrational purposes. Program used for simulation is described in Section \ref{sec:simulation}}
\label{fig:penumbra_explanation_tilt}
\end{figure}
@@ -139,7 +139,6 @@ AFMs provide high resolution topographical images at the nanometer scale and all
\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 (SEM) is a microscope in which an image of the topography of a sample is created via a focused electron beam. In order to do this a sample is hit by a focused beam of electrons, while suspended in vacuum. When an electron hits the surface of the sample the electron can undergo various interactions with the sample.
\begin{figure}[H]
@@ -165,7 +164,7 @@ The main matter interaction that is measured in an SEM is the inelastic scatteri
SEMs give high contrast large area images with good spatial resolution and were thus used in this thesis to initially locate evaporated fields on silicon samples, but SEM imaging comes with some downsides which is why they are not sufficient to fully characterize the samples in this thesis.
On insulating or semiconducting samples the electron beam of the SEM causes areas of the sample to charge up, which changes the SEM image over time and can potentially cause damage to the sample. For this reason the electron beam has to be operated at the lower end of beam energy. In theory this limits the spatial resolution as higher energy electron have a better De-Broglie wavelength, but optical effects arising from focusing the electron beam bottleneck the resolution rather than wavelength. SEMs give good topographical images, but exact quantitative heights of features cannot be directly obtained from an SEM image without a known reference, and thus they are not sufficient for sample characterization. \\
-SEM images and in particular the related technologies of \textbf{T}ransmission \textbf{E}lectron \textbf{M}icroscopy and \textbf{S}canning \textbf{Tunneling} \textbf{E}lectron \textbf{M}icroscopy have been used to characterize properties of thin films and characterize interfaces down to the single atomic scale.\cite{self_epitaxy}\\
+SEM images and in particular the related technologies of \textbf{T}ransmission \textbf{E}lectron \\ \textbf{M}icroscopy and \textbf{S}canning \textbf{Tunneling} \textbf{E}lectron \textbf{M}icroscopy have been used to characterize properties of thin films and characterize interfaces down to the single atomic scale.\cite{self_epitaxy}\\
%\subsection{Energy-dispersive X-ray spectroscopy}
%\textbf{E}nergy \textbf{d}ispersive \textbf{X}-ray spectroscopy (EDX)
\ No newline at end of file
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.1}{\ignorespaces The nomenclature for the various parts of the Mask Aligner. The four movement axes and their names from the viewport perspective (\subref {fig:mask_aligner_nomenclature_motors}). The various components of the Mask Aligner (\subref {fig:mask_aligner_nomenclature_components}) \textbf {A} carrying frame \textbf {B} piezo stack, \textbf {C} stoppers, \textbf {D} Sliding Rail for x-movement, \textbf {E} sample stage, \textbf {F} sample \textbf {G} sample holder, \textbf {H} Mask Frame, \textbf {I} Mask, \textbf {J} Mask Shuttle, \textbf {K} neodym magnet, \textbf {L} \ce {Al2O3} plate, \textbf {M} \ce {CuBe} 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.}}{16}{figure.caption.17}\protected@file@percent }
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\citation{Mask_Aligner}
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+\newlabel{fig:calibration_uhv_example_driving_z1}{{2.6a}{23}{\relax }{figure.caption.24}{}}
+\newlabel{sub@fig:calibration_uhv_example_driving_z1}{{a}{23}{\relax }{figure.caption.24}{}}
+\newlabel{fig:calibration_uhv_example_driving_z2}{{2.6b}{23}{\relax }{figure.caption.24}{}}
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+\@writefile{lof}{\contentsline {figure}{\numberline {2.6}{\ignorespaces Examples showing the measurement of step sizes during driving at the previously specified points of interest. (\subref {fig:calibration_uhv_example_driving_z1}) shows the point of interest of Z1 and in the inset shows an example of how the driving looks after $1000$ approach steps, as well as the measurement. The image before and after are superimposed. (\subref {fig:calibration_uhv_example_driving_z2}) shows a measurement of the screw at Z2. The inset shows the measurements over an image of the final state after driving $1000$ steps in approach and then $1000$ steps in retract.}}{23}{figure.caption.24}\protected@file@percent }
+\newlabel{fig:calibration_uhv_example_driving}{{2.6}{23}{Examples showing the measurement of step sizes during driving at the previously specified points of interest. (\subref {fig:calibration_uhv_example_driving_z1}) shows the point of interest of Z1 and in the inset shows an example of how the driving looks after $1000$ approach steps, as well as the measurement. The image before and after are superimposed. (\subref {fig:calibration_uhv_example_driving_z2}) shows a measurement of the screw at Z2. The inset shows the measurements over an image of the final state after driving $1000$ steps in approach and then $1000$ steps in retract}{figure.caption.24}{}}
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+\newlabel{fig:camera_alignment_example}{{2.9}{25}{Examples of camera views for different alignment situations. Camera placed or angled too low (a), too high (b) and placed in good alignment (c). In (a) the surface of the sample can be seen, which means the camera is not in line with the sample, but rather tilted too far up or too low. In (b) one can see the surface of the sample holder on the upper side as well as an upwards shift on the side of the sample indicating that the sample is tilted with respect to the camera, this is caused by a camera too high up or tilted too far down}{figure.caption.28}{}}
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\citation{SiN_dielectric}
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-\newlabel{eq:cap_slope_change}{{2.3}{28}{Approach curves}{equation.2.2.3}{}}
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+\newlabel{sub@fig:approach_curve_example_full}{{e}{28}{\relax }{figure.caption.31}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\ignorespaces 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.}}{28}{figure.caption.31}\protected@file@percent }
+\newlabel{fig:approach_curve_example}{{2.12}{28}{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.31}{}}
\citation{Beeker}
+\newlabel{eq:cap_slope_change}{{2.3}{29}{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.}}{30}{figure.caption.33}\protected@file@percent }
-\newlabel{fig:approach_subsequent}{{2.13}{30}{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.33}{}}
-\@writefile{tdo}{\contentsline {todo}{Plot too smol}{30}{section*.34}\protected@file@percent }
+\@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.}}{30}{figure.caption.32}\protected@file@percent }
+\newlabel{fig:approach_subsequent}{{2.13}{30}{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.32}{}}
+\@writefile{tdo}{\contentsline {todo}{Plot too smol}{30}{section*.33}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{30}{subsection.2.2.4}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.35}\protected@file@percent }
-\@writefile{tdo}{\contentsline {todo}{If you do not have data for this maybe scratch line, me!}{30}{section*.36}\protected@file@percent }
-\newlabel{fig:approach_replicability_cap}{{2.14a}{31}{\relax }{figure.caption.37}{}}
-\newlabel{sub@fig:approach_replicability_cap}{{a}{31}{\relax }{figure.caption.37}{}}
-\newlabel{fig:approach_replicability_cap_diff}{{2.14b}{31}{\relax }{figure.caption.37}{}}
-\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{31}{\relax }{figure.caption.37}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces 3 subsequent approach curves \subref {fig:approach_replicability_cap} and differences in capacitance for each step \subref {fig:approach_replicability_cap_diff} recorded. \textcolor {tab_green}{Green} is initial curve. \textcolor {tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier.}}{31}{figure.caption.37}\protected@file@percent }
-\newlabel{fig:approach_replicability}{{2.14}{31}{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.37}{}}
-\@writefile{tdo}{\contentsline {todo}{Plot needs labels and bigger}{31}{section*.38}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.34}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{If you do not have data for this maybe scratch line, me!}{30}{section*.35}\protected@file@percent }
+\newlabel{fig:approach_replicability_cap}{{2.14a}{31}{\relax }{figure.caption.36}{}}
+\newlabel{sub@fig:approach_replicability_cap}{{a}{31}{\relax }{figure.caption.36}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.14b}{31}{\relax }{figure.caption.36}{}}
+\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{31}{\relax }{figure.caption.36}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces 3 subsequent approach curves \subref {fig:approach_replicability_cap} and differences in capacitance for each step \subref {fig:approach_replicability_cap_diff} recorded. \textcolor {tab_green}{Green} is initial curve. \textcolor {tab_blue}{Blue} curve is after sample has been carefully removed and reinserted. For \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier.}}{31}{figure.caption.36}\protected@file@percent }
+\newlabel{fig:approach_replicability}{{2.14}{31}{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.36}{}}
+\@writefile{tdo}{\contentsline {todo}{Plot needs labels and bigger}{31}{section*.37}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{32}{subsection.2.2.5}\protected@file@percent }
\newlabel{subsec:cross_cap}{{2.2.5}{32}{Cross capacitances}{subsection.2.2.5}{}}
-\newlabel{fig:cross_cap_approach_difference}{{2.15a}{32}{\relax }{figure.caption.39}{}}
-\newlabel{sub@fig:cross_cap_approach_difference}{{a}{32}{\relax }{figure.caption.39}{}}
-\newlabel{fig:cross_cap_approach_difference_2}{{2.15b}{32}{\relax }{figure.caption.39}{}}
-\newlabel{sub@fig:cross_cap_approach_difference_2}{{b}{32}{\relax }{figure.caption.39}{}}
-\newlabel{fig:cross_cap_approach_sim}{{2.15c}{32}{\relax }{figure.caption.39}{}}
-\newlabel{sub@fig:cross_cap_approach_sim}{{c}{32}{\relax }{figure.caption.39}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref {fig:cross_cap_approach_difference}, \subref {fig:cross_cap_approach_difference_2}). (\subref {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case.}}{32}{figure.caption.39}\protected@file@percent }
-\newlabel{fig:cross_cap_approach}{{2.15}{32}{The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref {fig:cross_cap_approach_difference}, \subref {fig:cross_cap_approach_difference_2}). (\subref {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case}{figure.caption.39}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample.}}{34}{figure.caption.40}\protected@file@percent }
-\newlabel{fig:leakage_current}{{2.16}{34}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.40}{}}
-\@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.}}{34}{table.caption.41}\protected@file@percent }
-\newlabel{tab:cross_cap}{{2.1}{34}{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.41}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty.}}{35}{figure.caption.42}\protected@file@percent }
-\newlabel{fig:mask_old_caps}{{2.17}{35}{The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty}{figure.caption.42}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{36}{figure.caption.43}\protected@file@percent }
-\newlabel{fig:mask_old_correl}{{2.18}{36}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.43}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\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.}}{37}{figure.caption.44}\protected@file@percent }
-\newlabel{fig:cross_cap_diagramm}{{2.19}{37}{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.44}{}}
-\@writefile{toc}{\contentsline {paragraph}{Leakage current}{37}{section*.45}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.46}\protected@file@percent }
+\newlabel{fig:cross_cap_approach_difference}{{2.15a}{32}{\relax }{figure.caption.38}{}}
+\newlabel{sub@fig:cross_cap_approach_difference}{{a}{32}{\relax }{figure.caption.38}{}}
+\newlabel{fig:cross_cap_approach_difference_2}{{2.15b}{32}{\relax }{figure.caption.38}{}}
+\newlabel{sub@fig:cross_cap_approach_difference_2}{{b}{32}{\relax }{figure.caption.38}{}}
+\newlabel{fig:cross_cap_approach_sim}{{2.15c}{32}{\relax }{figure.caption.38}{}}
+\newlabel{sub@fig:cross_cap_approach_sim}{{c}{32}{\relax }{figure.caption.38}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref {fig:cross_cap_approach_difference}, \subref {fig:cross_cap_approach_difference_2}). (\subref {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case.}}{32}{figure.caption.38}\protected@file@percent }
+\newlabel{fig:cross_cap_approach}{{2.15}{32}{The 3 capacitance curves of two example measurements of 2 different masks normalized to ensure same scale (\subref {fig:cross_cap_approach_difference}, \subref {fig:cross_cap_approach_difference_2}). (\subref {fig:cross_cap_approach_sim}) shows a simple simulation of how the approach with tilted sample would look in an ideal case}{figure.caption.38}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample.}}{34}{figure.caption.39}\protected@file@percent }
+\newlabel{fig:leakage_current}{{2.16}{34}{Diagram showing one possible explanation for the large correlation in Capacitance readings. A small Tear in the \ce {SiNi} layer removes insulation between the gold wire and the Si of the Mask allowing current to travel through. This causes the capacitance to reflect the much larger capacitance between the Si of the Mask and that of the sample, instead of the desired Capacitance between the gold pad and the Si of the sample}{figure.caption.39}{}}
+\@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.}}{34}{table.caption.40}\protected@file@percent }
+\newlabel{tab:cross_cap}{{2.1}{34}{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.40}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.17}{\ignorespaces The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty.}}{35}{figure.caption.41}\protected@file@percent }
+\newlabel{fig:mask_old_caps}{{2.17}{35}{The 3 capacitance curves of the Mask labeled "old", the plots look the same sharing all features and general shape. The main difference is the scale of the y-axis and due to this the scale of the uncertainty}{figure.caption.41}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.18}{\ignorespaces The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%.}}{36}{figure.caption.42}\protected@file@percent }
+\newlabel{fig:mask_old_correl}{{2.18}{36}{The 3 capacitance curves of the Mask labeled "old" scaled to be within same range, via normalization and subsequent fit of offset parameter, first to C2 and C3 fit to C1 and then C3 fit to C2. The lower plots show residuals. The residuals show the variation to be well within the error bars and overall within less then $1$ \%}{figure.caption.42}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.19}{\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.}}{37}{figure.caption.43}\protected@file@percent }
+\newlabel{fig:cross_cap_diagramm}{{2.19}{37}{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.43}{}}
+\@writefile{toc}{\contentsline {paragraph}{Leakage current}{37}{section*.44}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.45}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{37}{subsection.2.2.6}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{High correlation between capacitance curves}{38}{section*.47}\protected@file@percent }
-\@writefile{tdo}{\contentsline {todo}{Plot stop condition}{38}{section*.48}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Low correlation between capacitance curves}{38}{section*.49}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{High correlation between capacitance curves}{38}{section*.46}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Plot stop condition}{38}{section*.47}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Low correlation between capacitance curves}{38}{section*.48}\protected@file@percent }
\@writefile{toc}{\contentsline {section}{\numberline {2.3}Mask Aligner operation}{38}{section.2.3}\protected@file@percent }
\@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{38}{subsection.2.3.1}\protected@file@percent }
\newlabel{sec:sample_prep}{{2.3.1}{38}{Sample preparation}{subsection.2.3.1}{}}
@@ -137,7 +139,7 @@
\setcounter{subfigure}{0}
\setcounter{subtable}{0}
\setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{10}
+\setcounter{@todonotes@numberoftodonotes}{9}
\setcounter{float@type}{8}
\setcounter{AM@survey}{0}
\setcounter{thm}{0}
diff --git a/chap02.tex b/chap02.tex
index 4a4ab69239f2495bc717cbe1d04bab0bd4cb08d8..b17f2f14b1777ac129be18d0642140bd5cd975bd 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -61,7 +61,7 @@ Another device, unrelated to this thesis, a gold evaporator, is connected to the
\section{Shadow mask alignment}
-\subsection{Calibration}
+\subsection{Motor calibration}
In order to use the Mask Aligner the different step sizes, i.e. the amount each
motor moves when one pulse is applied, has to be measured. This should be done in
order to make sure all motors run with similar step sizes and inside UHV to
@@ -145,10 +145,29 @@ shows the same for Z2 and Z3.}
\end{figure}
-When good measurement points are found the procedure is very simple: 2000, 4000,
-6000, 8000 and 10000 steps are driven and after each set of steps the distance
-the chosen point has traveled in camera view is measured, afterward a linear
-fit is performed from the given data and from the slope of the fit the step size
+When good measurement points are found the procedure is very simple: $2000$, $4000$,
+$6000$, $8000$ and $10000$ steps are driven and after each set of steps the distance
+the chosen point has traveled in camera view is measured. An example for motor Z1 and Z2 can be seen in Figure \ref{fig:calibration_uhv_example_driving} for a $1000$ step measurement. \\
+
+\begin{figure}[H]
+ \centering
+ \begin{subfigure}{0.495\textwidth}
+ \centering
+ \includegraphics[width=\linewidth]{img/MA/CalibrationZ1.pdf}
+ \caption{}
+ \label{fig:calibration_uhv_example_driving_z1}
+ \end{subfigure}
+ \begin{subfigure}{0.495\textwidth}
+ \centering
+ \includegraphics[width=\linewidth]{img/MA/CalibrationZ2.pdf}
+ \caption{}
+ \label{fig:calibration_uhv_example_driving_z2}
+ \end{subfigure}
+ \caption{Examples showing the measurement of step sizes during driving at the previously specified points of interest. (\subref{fig:calibration_uhv_example_driving_z1}) shows the point of interest of Z1 and in the inset shows an example of how the driving looks after $1000$ approach steps, as well as the measurement. The image before and after are superimposed. (\subref{fig:calibration_uhv_example_driving_z2}) shows a measurement of the screw at Z2. The inset shows the measurements over an image of the final state after driving $1000$ steps in approach and then $1000$ steps in retract.}
+ \label{fig:calibration_uhv_example_driving}
+\end{figure}
+
+Afterward a linear fit is performed from the given data and from the slope of the fit the step size
for a single step can be determined. After each set of steps driven it has to be ensured, that the mask frame not tilted, as excessive tilt will affect the step size. It should also be taken care that the movement range of the piezos is not exceeded. This means that the piezos should not drive so far down, that the \ce{Nd} detaches from the stage or that the frame is driven so far up, that it interferes with the sample stage. Under no circumstance should the motors be driven so far down, that the sapphire prism might fall out of the motor. This has to be done for both driving
directions separately, since in one gravity affects the movement positively and
in one negatively, and thus the step sizes will be different for both approach
@@ -157,26 +176,7 @@ obtained is shown in Figure \ref{fig:calibration_example}. In this image it can
be seen, that the positive direction has larger step sizes and that steps size
is on the order of $10$ nm/step.
-\begin{figure}[H]
- \centering
- \begin{subfigure}{0.45\textwidth}
- \includegraphics[width=\linewidth]{img/CalibrationUHV_Z1.png}
- \caption{}
- \label{fig:calibration_uhv_example_driving_start}
- \end{subfigure}
- \begin{subfigure}{0.45\textwidth}
- \includegraphics[width=\linewidth]{img/CalibrationUHV_Z2_Z3.png}
- \caption{}
- \label{fig:calibration_uhv_example_driving_up}
- \end{subfigure}
- \begin{subfigure}{0.45\textwidth}
- \includegraphics[width=\linewidth]{img/CalibrationUHV_Z2_Z3.png}
- \caption{}
- \label{fig:calibration_uhv_example_driving_down}
- \end{subfigure}
- \caption{}
- \label{fig:calibration_uhv_example_driving}
-\end{figure}
+
\begin{figure}[H]
\centering
@@ -291,25 +291,30 @@ achievable optical accuracy. The progression of this can be seen in Figure \ref{
\subsection{Approach curves}
+
+After optical alignment the final step towards an aligned sample comes via
+capacitive measurement to obtain the distance to the sample surface. The 3
+capacitive sensors on the mask are aligned with the 3 motors of the Mask Aligner
+and are labeled as seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_motors}. The masks consist of a $200$ $\mu$m thick \ce{Si} body. A small $100\times100$ $\mu$m \ce{SiN} membrane, with $3$ $\mu$m holes each $10$ $\mu$m apart, is situated in the middle of the body. The \ce{SiN} actually covers the whole mask and is $1$ $\mu$m thick, but only the center part has holes and a trench below it. Around the hole membrane are $3$ gold pads, that function as the aforementioned capacitive sensors. The \ce{Au} of the gold pads is placed below an insulating $\approx 100$ nm layer of \ce{SiO2} at the bottom of a trench in the \ce{Si} body. They are at a distance of $0.7$ mm from the hole membrane and are located in an equilateral triangle around it. The dimensions of the mask and the capacitive sensors on the mask can be seen in Figure \ref{fig:mask_aligner_nomenclature_capacitances_mask}.
+
\begin{figure}[H]
\centering
-
-\includegraphics[width=0.5\linewidth]{img/MA/NomeclatureMotorsAndCapacitance.pdf}
- \caption{Cross section of the Mask Aligner showing the labeling and rough
-positioning of the capacitance sensors on the mask (inner
-\textcolor{tab_red}{red} triangle)} in relation to the $3$ piezo motor stacks.
+ \begin{subfigure}{0.495\textwidth}
+ \includegraphics[width=\linewidth]{img/MA/NomeclatureMotorsAndCapacitance.pdf}
+ \caption{}
+ \label{fig:mask_aligner_nomenclature_capacitances_motors}
+ \end{subfigure}
+ \begin{subfigure}{0.38\textwidth}
+ \includegraphics[width=0.9\linewidth]{img/MA/Mask.pdf}
+ \caption{}
+ \label{fig:mask_aligner_nomenclature_capacitances_mask}
+ \end{subfigure}
\label{fig:mask_aligner_nomenclature_capacitances}
+ \caption{(\subref{fig:mask_aligner_nomenclature_capacitances_motors}) shows a cross section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor{tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref{fig:mask_aligner_nomenclature_capacitances_mask}) shows an diagram of the masks dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is actually used to create patterns.}
\end{figure}
-After optical alignment the final step towards an aligned sample comes via
-capacitive measurement to obtain the distance to the sample surface. The 3
-capacitive sensors on the mask are aligned with the 3 motors of the Mask Aligner
-and are labeled as seen in Figure
-\ref{fig:mask_aligner_nomenclature_capacitances}.
Note that this diagram is not true for all masks, since some were assembled with
-the capacitance sensors pointed in the wrong direction. But for the masks used
-in this thesis it was accurate.
-
+the capacitance sensors pointed in the wrong direction.
The capacitance of each of the $3$ sensors can be approximated using a simple
plate capacitor model where the gold pad is one plate of the capacitor and the
overlap of its bounds with the \ce{Si} sample can be seen as the other plate of
@@ -445,7 +450,7 @@ capacitance is used and the stop condition is used to determine good alignement
\begin{figure}[H]
\centering
-\includegraphics[width=0.8\linewidth]{img/MA/SubsequentApproachDeviation.pdf}
+\includegraphics[width=0.9\linewidth]{img/MA/SubsequentApproachDeviation.pdf}
\caption{Plot of data of approach curves recorded on two different days. The
second curve was recorded after retraction and subsequent approach. The 2 curves
do not start at the same distance away from sample, which is why they are not
diff --git a/chap03.aux b/chap03.aux
index fe6574c1bad18d10edd6a4453bb9f02b11367fb4..f4ab96cd0bf60ec2107ac9205676233be08d07c0 100644
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\citation{arduino_cpu_datasheet}
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-\newlabel{fig:solder_anchors_diagram}{{4.2}{53}{Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref {fig:solder_anchors_diagram_SmallerDot}-\subref {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably}{figure.caption.74}{}}
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-\newlabel{fig:solder_anchors_examples}{{4.3}{54}{Examples for the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely}{figure.caption.75}{}}
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+\newlabel{fig:solder_anchors_diagram}{{4.2}{53}{Depiction of the problem with the solder anchors, that emerged with the Mask Aligner over time (\subref {fig:solder_anchors_diagram_base}) as well as the $3$ different measures that were taken to fix the problem. Making the solder point smaller (\subref {fig:solder_anchors_diagram_SmallerDot}), replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate (\subref {fig:solder_anchors_diagram_AlO}) or putting the anchor with glue on the top/bottom of the solder ceramic (\subref {fig:solder_anchors_diagram_GlueTop}). The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray. All 3 measures (\subref {fig:solder_anchors_diagram_SmallerDot}-\subref {fig:solder_anchors_diagram_GlueTop}) fix the same issue depicted in (\subref {fig:solder_anchors_diagram_base}) where the solder anchor used for cabling interferes with the prism causing the motor to drive unpredictably}{figure.caption.73}{}}
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+\newlabel{fig:solder_anchors_examples}{{4.3}{54}{Examples for the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_glue_bottom}) shows attaching a solder anchor to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) shows the replacement of a solder ceramic with a thinner \ce {Al2O3} plate. (\subref {fig:solder_anchors_examples_shear_01}) and shows the initial state of a solder ceramic interfering with the prism and then (\subref {fig:solder_anchors_examples_shear_02}) shows the solder ceramic after some of the solder was carefully taken off, allowing the prism to now move freely}{figure.caption.74}{}}
\citation{olschewski}
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+\@writefile{lof}{\contentsline {figure}{\numberline {4.4}{\ignorespaces The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move.}}{56}{figure.caption.75}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{4.4}{56}{The re gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body (a). Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. In (b) the remains were scratched off carefully to ensure no large height discrepancy is introduced. (c) shows the applied dot of TorrSeal epoxy glue applied to the piezo stack before being carefully put in place. In order for the glue to have a force applied to it during the curing process two nuts and the prism were used as weights, while the prism was put into the Aligner to ensure proper alignment with the prism the stacks are supposed to move}{figure.caption.75}{}}
+\@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 $.}}{57}{figure.caption.76}\protected@file@percent }
+\newlabel{fig:Z3_after reglue}{{4.5}{57}{The final glued position of the upper Z3 motor after re-gluing. Red line shows the deviation from the other piezo stack. The angle $\alpha $ is about $ \approx 4.5^\circ \pm 0.5^\circ $}{figure.caption.76}{}}
\@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{57}{section.4.5}\protected@file@percent }
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-\newlabel{fig:Z3_screw_rot}{{4.6}{58}{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.78}{}}
+\@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.}}{58}{figure.caption.77}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot}{{4.6}{58}{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.77}{}}
\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{58}{subsection.4.5.1}\protected@file@percent }
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-\@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.}}{62}{table.caption.83}\protected@file@percent }
-\newlabel{tab:cross_cap_after_repair}{{4.1}{62}{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.83}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces Screw rotation calibration data for Z2 and Z3 after front plate repairs.}}{59}{figure.caption.78}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{59}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.78}{}}
+\newlabel{fig:Front_plate_repair_tool}{{4.8a}{60}{\relax }{figure.caption.79}{}}
+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{60}{\relax }{figure.caption.79}{}}
+\newlabel{fig:Front_plate_repair_plate}{{4.8b}{60}{\relax }{figure.caption.79}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{60}{\relax }{figure.caption.79}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled.}}{60}{figure.caption.79}\protected@file@percent }
+\newlabel{fig:Front_plate_repair}{{4.8}{60}{Solidworks explosive diagram of the Z3 front plate with the alignment tool (\subref {fig:Front_plate_repair_tool}). (\subref {fig:Front_plate_repair_plate}) shows final front plate assembled}{figure.caption.79}{}}
+\@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{61}{subsection.4.5.2}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezos stacks of the motor Z3. }}{61}{figure.caption.80}\protected@file@percent }
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+\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{62}{\relax }{figure.caption.81}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{62}{\relax }{figure.caption.81}{}}
+\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{62}{\relax }{figure.caption.81}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{62}{\relax }{figure.caption.81}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.10}{\ignorespaces Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding.}}{62}{figure.caption.81}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs}{{4.10}{62}{Left (\subref {fig:Feedthrough_Repairs_left}) and right (\subref {fig:Feedthrough_Repairs_right}) side of Mask Aligner flange. \textcolor {tab_red}{Red} circles mark the changes made to the grounding}{figure.caption.81}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {4.1}{\ignorespaces The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII.}}{63}{table.caption.82}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{63}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables. The values agree within $1$ $\sigma $ and show no measurable improvement. Values were measured at $0.3$ mm sample distance. Optically determined with Bresser MicroCam II and MikroCamLabII}{table.caption.82}{}}
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-\newlabel{fig:calibration_after_repair}{{4.11}{63}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.84}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.11}{\ignorespaces The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions.}}{63}{figure.caption.83}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{63}{The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions}{figure.caption.83}{}}
\@setckpt{chap04}{
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diff --git a/chap04.tex b/chap04.tex
index 77ae2b5000fd7d5cb96301ef0d09eb27aeb6a410..90a29417fc189aa7ce3fdd38a738b05a6175ee36 100644
--- a/chap04.tex
+++ b/chap04.tex
@@ -169,8 +169,6 @@ The cause of this was determined to be the front plate of the Z3 motor, as switc
\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. \\
-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. \\
-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. \\
\begin{figure}[H]
\centering
@@ -179,18 +177,29 @@ Since the plate is separate from the rest of the Mask Aligner, the plate could b
\label{fig:Z3_screw_rot_after_rep}
\end{figure}
-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 could potentially negatively affect the performance of the new front 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.
+The piezo stacks were taken off the front plate, and it was decided, that $2$ of the $10$ replacement piezos would be glued to the surface of the plate in order to function as the new plate. In order for the gluing to give good alignment, an alignment tool was produced by the workshop. An Solidworks image of the alignment tool can be seen in Figure \ref{fig:Front_plate_repair_tool} \\
+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.
\begin{figure}[H]
\centering
\begin{subfigure}{0.495\linewidth}
- \includegraphics[width=0.95\linewidth]{img/Repairs/GlueAid.png}
- \caption{}
+ \centering
+ \includegraphics[width=0.55\linewidth, angle=90]{img/Repairs/GlueAid.png}
+ \caption{}
+ \label{fig:Front_plate_repair_tool}
\end{subfigure}
- \caption{}
+ \begin{subfigure}{0.495\linewidth}
+ \centering
+ \includegraphics[width=0.55\linewidth, angle=90]{img/Repairs/NewFrontPlate.png}
+ \caption{}
+ \label{fig:Front_plate_repair_plate}
+ \end{subfigure}
+ \caption{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.}
\label{fig:Front_plate_repair}
\end{figure}
diff --git a/chap05.aux b/chap05.aux
index 530411a087918db84a00f718c62fb5bb21d81095..95b411d5ea5861aebe22c28a5d04c6ff22ca1acb 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -1,93 +1,96 @@
\relax
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+\newlabel{fig:evaporation_measured_penumbra}{{5.7}{72}{Data obtained from the previously described method for each of the 5 evaporations, from evaporated dot each from the center of the field, the left, the right, the bottom and the top. The dot chosen depended on measurement condition such as contamination and phase characteristics of the dot. The data shows the smaller penumbra $\sigma _s$ (\subref {fig:evaporation_measured_penumbra_sigs}) the larger penumbra $\sigma _l$ (\subref {fig:evaporation_measured_penumbra_sigl}), the height of the dot (\subref {fig:evaporation_measured_penumbra_height}) and the diameter of the circle (\subref {fig:evaporation_measured_penumbra_circle_r})}{figure.caption.91}{}}
+\@writefile{tdo}{\contentsline {todo}{Check if script can fit negative penumbra}{72}{section*.92}\protected@file@percent }
\@writefile{toc}{\contentsline {section}{\numberline {5.4}Tilt}{74}{section.5.4}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces Image of the reconstruction of the tilt angle for Field 3 as an example (a) and the data given by all fields (b). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}}{74}{figure.caption.95}\protected@file@percent }
-\newlabel{fig:evaporation_tilts}{{5.8}{74}{Image of the reconstruction of the tilt angle for Field 3 as an example (a) and the data given by all fields (b). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case}{figure.caption.95}{}}
-\newlabel{fig:evaporation_SEM_sample}{{5.9a}{75}{\relax }{figure.caption.96}{}}
-\newlabel{sub@fig:evaporation_SEM_sample}{{a}{75}{\relax }{figure.caption.96}{}}
-\newlabel{fig:evaporation_SEM_mask}{{5.9b}{75}{\relax }{figure.caption.96}{}}
-\newlabel{sub@fig:evaporation_SEM_mask}{{b}{75}{\relax }{figure.caption.96}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. The \textcolor {tab_red}{red} lines show a line drawn approximately through the center of the holes. The outer red line shows curvature, while the inner one is completely straight. This shows some deformation due to bending.}}{75}{figure.caption.96}\protected@file@percent }
-\newlabel{fig:evaporation_SEM}{{5.9}{75}{SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. The \textcolor {tab_red}{red} lines show a line drawn approximately through the center of the holes. The outer red line shows curvature, while the inner one is completely straight. This shows some deformation due to bending}{figure.caption.96}{}}
-\newlabel{fig:evaporation_SEM_analysis_clog}{{5.10a}{76}{\relax }{figure.caption.97}{}}
-\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{76}{\relax }{figure.caption.97}{}}
-\newlabel{fig:evaporation_SEM_analysis_clog_overlay}{{5.10b}{76}{\relax }{figure.caption.97}{}}
-\newlabel{sub@fig:evaporation_SEM_analysis_clog_overlay}{{b}{76}{\relax }{figure.caption.97}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{76}{figure.caption.97}\protected@file@percent }
-\newlabel{fig:evaporation_SEM_analysis}{{5.10}{76}{An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields}{figure.caption.97}{}}
+\newlabel{fig:evaporation_tilts_example}{{5.8a}{74}{\relax }{figure.caption.93}{}}
+\newlabel{sub@fig:evaporation_tilts_example}{{a}{74}{\relax }{figure.caption.93}{}}
+\newlabel{fig:evaporation_tilts_all}{{5.8b}{74}{\relax }{figure.caption.93}{}}
+\newlabel{sub@fig:evaporation_tilts_all}{{b}{74}{\relax }{figure.caption.93}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces Image of the reconstruction of the tilt angle for Field 3 as an example (\subref {fig:evaporation_tilts_example}) and the data given by all fields (\subref {fig:evaporation_tilts_all}). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}}{74}{figure.caption.93}\protected@file@percent }
+\newlabel{fig:evaporation_tilts}{{5.8}{74}{Image of the reconstruction of the tilt angle for Field 3 as an example (\subref {fig:evaporation_tilts_example}) and the data given by all fields (\subref {fig:evaporation_tilts_all}). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case}{figure.caption.93}{}}
+\newlabel{fig:evaporation_SEM_sample}{{5.9a}{75}{\relax }{figure.caption.94}{}}
+\newlabel{sub@fig:evaporation_SEM_sample}{{a}{75}{\relax }{figure.caption.94}{}}
+\newlabel{fig:evaporation_SEM_mask}{{5.9b}{75}{\relax }{figure.caption.94}{}}
+\newlabel{sub@fig:evaporation_SEM_mask}{{b}{75}{\relax }{figure.caption.94}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. The \textcolor {tab_red}{red} lines show a line drawn approximately through the center of the holes. The outer red line shows curvature, while the inner one is completely straight. This shows some deformation due to bending.}}{75}{figure.caption.94}\protected@file@percent }
+\newlabel{fig:evaporation_SEM}{{5.9}{75}{SEM images of field 2 on the sample (\subref {fig:evaporation_SEM_sample}) and the mask (\subref {fig:evaporation_SEM_mask}) the inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects. The \textcolor {tab_red}{red} lines show a line drawn approximately through the center of the holes. The outer red line shows curvature, while the inner one is completely straight. This shows some deformation due to bending}{figure.caption.94}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog}{{5.10a}{76}{\relax }{figure.caption.95}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{76}{\relax }{figure.caption.95}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog_overlay}{{5.10b}{76}{\relax }{figure.caption.95}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog_overlay}{{b}{76}{\relax }{figure.caption.95}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{76}{figure.caption.95}\protected@file@percent }
+\newlabel{fig:evaporation_SEM_analysis}{{5.10}{76}{An example of the clogging noticed on $4$ of the mask holes (\subref {fig:evaporation_SEM_analysis_clog}) and the tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields}{figure.caption.95}{}}
\@writefile{toc}{\contentsline {section}{\numberline {5.5}Simulation}{76}{section.5.5}\protected@file@percent }
-\@writefile{tdo}{\contentsline {todo}{place image of Godot transform thing here}{77}{section*.98}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{place image of Godot transform thing here}{77}{section*.96}\protected@file@percent }
\citation{Bhaskar}
-\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.11a}{78}{\relax }{figure.caption.99}{}}
-\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{78}{\relax }{figure.caption.99}{}}
-\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.11b}{78}{\relax }{figure.caption.99}{}}
-\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{78}{\relax }{figure.caption.99}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $.}}{78}{figure.caption.99}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_first_compare}{{5.11}{78}{Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $}{figure.caption.99}{}}
-\@writefile{tdo}{\contentsline {todo}{you use tilt and deformation of mask very interchangably. Please distinguish tilt as a stiff mask with an angle to the mask. Deformation/bending in the mask is not same as tilt. If you want to talk about local angle on the deformed mask, that is a separate third thing}{78}{section*.100}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.12a}{79}{\relax }{figure.caption.101}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{79}{\relax }{figure.caption.101}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.12b}{79}{\relax }{figure.caption.101}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{79}{\relax }{figure.caption.101}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.12c}{79}{\relax }{figure.caption.101}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{79}{\relax }{figure.caption.101}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{79}{figure.caption.101}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness}{{5.12}{79}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.101}{}}
-\newlabel{fig:evaporation_simulation_rejection_prev}{{5.13a}{80}{\relax }{figure.caption.102}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{80}{\relax }{figure.caption.102}{}}
-\newlabel{fig:evaporation_simulation_rejection_after}{{5.13b}{80}{\relax }{figure.caption.102}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{80}{\relax }{figure.caption.102}{}}
-\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.13c}{80}{\relax }{figure.caption.102}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{80}{\relax }{figure.caption.102}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{80}{figure.caption.102}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_rejection}{{5.13}{80}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.102}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$.}}{81}{figure.caption.103}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_progression}{{5.14}{81}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$}{figure.caption.103}{}}
-\@writefile{toc}{\contentsline {paragraph}{Software improvements}{81}{section*.104}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.11a}{78}{\relax }{figure.caption.97}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{78}{\relax }{figure.caption.97}{}}
+\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.11b}{78}{\relax }{figure.caption.97}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{78}{\relax }{figure.caption.97}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $.}}{78}{figure.caption.97}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare}{{5.11}{78}{Comparison of a recorded AFM image, colors are for easier identification, (a) (grains were removed using interpolation during post-processing) and a simulated evaporation (b) with parameters obtained from measurement in the AFM image. Vibrations were assumed to be harmonic during the deposition and different sticking factors of \ce {Pb}-\ce {Si} and \ce {Pb}-\ce {Pb} were not considered. The oscillation was modeled with a displacement of $0.143$ $\mu $m in x and $-0.358$ $\mu $m in z direction and a tilt of $-41.12^\circ $ in $\alpha $, $10^\circ $ in $\beta $ and $31^\circ $ in $\gamma $}{figure.caption.97}{}}
+\@writefile{tdo}{\contentsline {todo}{you use tilt and deformation of mask very interchangably. Please distinguish tilt as a stiff mask with an angle to the mask. Deformation/bending in the mask is not same as tilt. If you want to talk about local angle on the deformed mask, that is a separate third thing}{78}{section*.98}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.12a}{79}{\relax }{figure.caption.99}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{79}{\relax }{figure.caption.99}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.12b}{79}{\relax }{figure.caption.99}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{79}{\relax }{figure.caption.99}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.12c}{79}{\relax }{figure.caption.99}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{79}{\relax }{figure.caption.99}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{79}{figure.caption.99}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness}{{5.12}{79}{Comparison of the evaporation with harmonic oscillation (\subref {fig:evaporation_simulation_sharpness_stick_simple}), an initial phase with no elliptical oscillation and then drift to the elliptical shape (\subref {fig:evaporation_simulation_sharpness_stick_initial}) and an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ (\subref {fig:evaporation_simulation_sharpness_stick_power}). The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.99}{}}
+\newlabel{fig:evaporation_simulation_rejection_prev}{{5.13a}{80}{\relax }{figure.caption.100}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{80}{\relax }{figure.caption.100}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{5.13b}{80}{\relax }{figure.caption.100}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{80}{\relax }{figure.caption.100}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.13c}{80}{\relax }{figure.caption.100}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{80}{\relax }{figure.caption.100}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{80}{figure.caption.100}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{5.13}{80}{Simulated evaporation dots without (\subref {fig:evaporation_simulation_rejection_prev}) and with (\subref {fig:evaporation_simulation_rejection_after}) $90$ \% probability to reject a deposition, when no previous deposition happened on the target pixel. (\subref {fig:evaporation_simulation_rejection_comparison}) shows the AFM image parameters for simulation were obtained from for comparison. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.100}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$.}}{81}{figure.caption.101}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_progression}{{5.14}{81}{Image of final simulation with parameters given in Figure \ref {fig:evaporation_simulation_first_compare} and an anharmonic oscillation with a power of $20$}{figure.caption.101}{}}
+\@writefile{toc}{\contentsline {paragraph}{Software improvements}{81}{section*.102}\protected@file@percent }
\@setckpt{chap05}{
\setcounter{page}{83}
\setcounter{equation}{1}
@@ -118,7 +121,7 @@
\setcounter{subfigure}{0}
\setcounter{subtable}{0}
\setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{19}
+\setcounter{@todonotes@numberoftodonotes}{17}
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diff --git a/chap05.tex b/chap05.tex
index b79b48672c762e43351ae35555e749340321cd38..17159e73d120230f427f2d6cf44307b19c2915fc 100644
--- a/chap05.tex
+++ b/chap05.tex
@@ -74,15 +74,15 @@ The entire sample's surface is contaminated with small particles, which are abou
\begin{figure}[H]
\centering
- \begin{subfigure}{0.45\linewidth}
+ \begin{subfigure}{0.495\linewidth}
\centering
- \includegraphics[width=0.9\linewidth]{img/Evaporation/Contamination.png}
+ \includegraphics[width=0.95\linewidth]{img/Evaporation/Contamination.png}
\caption{}
\label{fig:evaporation_contamination_img}
\end{subfigure}
- \begin{subfigure}{0.45\linewidth}
+ \begin{subfigure}{0.495\linewidth}
\centering
- \includegraphics[width=0.95\linewidth]{img/Evaporation/Contamination.pdf}
+ \includegraphics[width=\linewidth]{img/Evaporation/Contamination.pdf}
\caption{}
\label{fig:evaporation_contamination_anal}
\end{subfigure}
@@ -92,7 +92,8 @@ The entire sample's surface is contaminated with small particles, which are abou
The data in Figure \ref{fig:evaporation_contamination} 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. The distribution of particles across the sample surface appears approximately isotropic across the surface.
-In addition, the sample was contaminated with larger particles possibly from long exposure at atmospheric conditions as well as being inside the Mask Aligner Chamber during vacuum bakeout, where the system is heated to $>100$°C on $2$ separate occasions. The size of these larger particles was approximately determined to be in the order of $\mathcal{O}(100 \text{nm})$ using SEM and on the order of $\mathit{O}(10)$ $\mu$m in diameter. \\ \todo{Probably bad preparation UHV unlikely}Since the sample was checked only optically before insertion into UHV and due to this a large amount of contamination was overlooked. It is suggested that in future before the sample is inserted into UHV eventual contamination should be quantified in an AFM measurement.
+In addition, the sample was contaminated with larger particles possibly from long exposure at atmospheric conditions as well as being inside the Mask Aligner Chamber during vacuum bakeout, where the system is heated to $>100$°C on $2$ separate occasions. The size of these larger particles was approximately determined to be in the order of $\mathcal{O}(100 \text{nm})$ using SEM and on the order of $\mathit{O}(10)$ $\mu$m in diameter. \\
+Since the sample was checked only optically before insertion into UHV the small particle contamination might have been overlooked. It is suggested that in future before the sample is inserted into UHV eventual contamination should be quantified in an AFM measurement.
\section{Penumbra}
@@ -197,12 +198,14 @@ The larger penumbra data (Figure \ref{fig:evaporation_measured_penumbra_sigl}) i
\begin{subfigure}{0.495\linewidth}
\includegraphics[width=0.95\linewidth]{img/Evaporation/Field3Angle.pdf}
\caption{}
+ \label{fig:evaporation_tilts_example}
\end{subfigure}
\begin{subfigure}{0.495\linewidth}
\includegraphics[width=0.95\linewidth]{img/Evaporation/FieldsAngle.pdf}
\caption{}
+ \label{fig:evaporation_tilts_all}
\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.}
+ \caption{Image of the reconstruction of the tilt angle for Field 3 as an example (\subref{fig:evaporation_tilts_example}) and the data given by all fields (\subref{fig:evaporation_tilts_all}). For fields 1, 4, 5 the full field scans were performed at low resolution and due to this the direction of the tilt could not be determined from the images. The only dots drawn are the high resolution AFM scans of single dots, in this case.}
\label{fig:evaporation_tilts}
\end{figure}
diff --git a/conclusion.aux b/conclusion.aux
index da62a1c9ce6743e6cd7f910d9cb66b6cf39f0adf..2cfde423db74cd3b3223f8366e6fdac74720b620 100644
--- a/conclusion.aux
+++ b/conclusion.aux
@@ -1,6 +1,6 @@
\relax
\providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{83}{chapter*.105}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{83}{chapter*.103}\protected@file@percent }
\@setckpt{conclusion}{
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@@ -31,7 +31,7 @@
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+\setcounter{@todonotes@numberoftodonotes}{17}
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diff --git a/img/Evaporation/Contamination.png b/img/Evaporation/Contamination.png
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diff --git a/thesis.toc b/thesis.toc
index be68f5b5f167d1e951ddb27af163e6a33e390979..103978ec2cdc67379fdd8597ade50237526facfa 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -6,35 +6,35 @@
\contentsline {subsubsection}{Penumbra}{7}{section*.5}%
\contentsline {subsubsection}{Tilt induced penumbra}{9}{section*.7}%
\contentsline {section}{\numberline {1.3}Measurement techniques}{10}{section.1.3}%
-\contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{11}{subsection.1.3.1}%
+\contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{10}{subsection.1.3.1}%
\contentsline {subsubsection}{Modes}{11}{section*.10}%
-\contentsline {paragraph}{Contact}{12}{section*.11}%
-\contentsline {paragraph}{Non-Contact}{12}{section*.12}%
-\contentsline {paragraph}{Tapping}{13}{section*.13}%
+\contentsline {paragraph}{Contact}{11}{section*.11}%
+\contentsline {paragraph}{Non-Contact}{11}{section*.12}%
+\contentsline {paragraph}{Tapping}{12}{section*.13}%
\contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{13}{subsection.1.3.2}%
\contentsline {chapter}{\numberline {2}Mask Aligner}{16}{chapter.2}%
\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 {2.2.1}Motor calibration}{19}{subsection.2.2.1}%
\contentsline {subsection}{\numberline {2.2.2}Optical alignment}{25}{subsection.2.2.2}%
\contentsline {subsection}{\numberline {2.2.3}Approach curves}{26}{subsection.2.2.3}%
\contentsline {subsection}{\numberline {2.2.4}Reproducibility}{30}{subsection.2.2.4}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.35}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.34}%
\contentsline {subsection}{\numberline {2.2.5}Cross capacitances}{32}{subsection.2.2.5}%
-\contentsline {paragraph}{Leakage current}{37}{section*.45}%
-\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.46}%
+\contentsline {paragraph}{Leakage current}{37}{section*.44}%
+\contentsline {paragraph}{Improved gold pin fitting}{37}{section*.45}%
\contentsline {subsection}{\numberline {2.2.6}Stop Conditions}{37}{subsection.2.2.6}%
-\contentsline {paragraph}{High correlation between capacitance curves}{38}{section*.47}%
-\contentsline {paragraph}{Low correlation between capacitance curves}{38}{section*.49}%
+\contentsline {paragraph}{High correlation between capacitance curves}{38}{section*.46}%
+\contentsline {paragraph}{Low correlation between capacitance curves}{38}{section*.48}%
\contentsline {section}{\numberline {2.3}Mask Aligner operation}{38}{section.2.3}%
\contentsline {subsection}{\numberline {2.3.1}Sample preparation}{38}{subsection.2.3.1}%
\contentsline {chapter}{\numberline {3}Electronics}{40}{chapter.3}%
\contentsline {section}{\numberline {3.1}Slip stick principle}{40}{section.3.1}%
\contentsline {section}{\numberline {3.2}RHK}{41}{section.3.2}%
\contentsline {subsection}{\numberline {3.2.1}Overview}{41}{subsection.3.2.1}%
-\contentsline {paragraph}{amplitude}{41}{section*.51}%
-\contentsline {paragraph}{sweep period}{41}{section*.52}%
-\contentsline {paragraph}{time between sweeps}{41}{section*.53}%
+\contentsline {paragraph}{amplitude}{41}{section*.50}%
+\contentsline {paragraph}{sweep period}{41}{section*.51}%
+\contentsline {paragraph}{time between sweeps}{41}{section*.52}%
\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{41}{subsection.3.2.2}%
\contentsline {section}{\numberline {3.3}KIM001}{42}{section.3.3}%
\contentsline {subsection}{\numberline {3.3.1}Overview}{42}{subsection.3.3.1}%
@@ -46,11 +46,11 @@
\contentsline {subsection}{\numberline {3.4.3}Fast flank}{46}{subsection.3.4.3}%
\contentsline {subsection}{\numberline {3.4.4}Amplification}{47}{subsection.3.4.4}%
\contentsline {subsection}{\numberline {3.4.5}Parameters}{47}{subsection.3.4.5}%
-\contentsline {paragraph}{Amplitude (amp)}{47}{section*.64}%
-\contentsline {paragraph}{Voltage (volt)}{48}{section*.65}%
-\contentsline {paragraph}{Channel}{48}{section*.66}%
-\contentsline {paragraph}{Max Step}{48}{section*.67}%
-\contentsline {paragraph}{Polarity}{48}{section*.68}%
+\contentsline {paragraph}{Amplitude (amp)}{47}{section*.63}%
+\contentsline {paragraph}{Voltage (volt)}{48}{section*.64}%
+\contentsline {paragraph}{Channel}{48}{section*.65}%
+\contentsline {paragraph}{Max Step}{48}{section*.66}%
+\contentsline {paragraph}{Polarity}{48}{section*.67}%
\contentsline {subsection}{\numberline {3.4.6}Measured pulse shape}{48}{subsection.3.4.6}%
\contentsline {subsection}{\numberline {3.4.7}Driving the Mask Aligner}{50}{subsection.3.4.7}%
\contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{51}{chapter.4}%
@@ -62,53 +62,53 @@
\contentsline {section}{\numberline {4.4}Piezo re-gluing}{55}{section.4.4}%
\contentsline {section}{\numberline {4.5}Z3 motor}{57}{section.4.5}%
\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{58}{subsection.4.5.1}%
-\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{60}{subsection.4.5.2}%
-\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{61}{section.4.6}%
+\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{61}{subsection.4.5.2}%
+\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{62}{section.4.6}%
\contentsline {section}{\numberline {4.7}Final test}{63}{section.4.7}%
-\contentsline {chapter}{\numberline {5}Evaporations and measurement}{64}{chapter.5}%
-\contentsline {section}{\numberline {5.1}Evaporation configuration}{64}{section.5.1}%
+\contentsline {chapter}{\numberline {5}Evaporations and measurement}{65}{chapter.5}%
+\contentsline {section}{\numberline {5.1}Evaporation configuration}{65}{section.5.1}%
\contentsline {section}{\numberline {5.2}Contamination}{67}{section.5.2}%
\contentsline {section}{\numberline {5.3}Penumbra}{68}{section.5.3}%
\contentsline {section}{\numberline {5.4}Tilt}{74}{section.5.4}%
\contentsline {section}{\numberline {5.5}Simulation}{76}{section.5.5}%
-\contentsline {paragraph}{Software improvements}{81}{section*.104}%
-\contentsline {chapter}{Conclusions and Outlook}{83}{chapter*.105}%
-\contentsline {chapter}{Bibliography}{84}{chapter*.106}%
-\contentsline {chapter}{List of Abbreviations}{86}{chapter*.107}%
+\contentsline {paragraph}{Software improvements}{81}{section*.102}%
+\contentsline {chapter}{Conclusions and Outlook}{83}{chapter*.103}%
+\contentsline {chapter}{Bibliography}{84}{chapter*.104}%
+\contentsline {chapter}{List of Abbreviations}{86}{chapter*.105}%
\contentsline {chapter}{\numberline {6}Appendix}{i}{chapter.6}%
\contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.6.1}%
\contentsline {section}{\numberline {B}Walker circuit diagrams}{i}{section.6.2}%
\contentsline {section}{\numberline {C}New driver electronics}{v}{section.6.3}%
-\contentsline {paragraph}{pulse?}{v}{section*.108}%
-\contentsline {paragraph}{pol x}{v}{section*.109}%
-\contentsline {paragraph}{amp x}{v}{section*.110}%
-\contentsline {paragraph}{volt x}{v}{section*.111}%
-\contentsline {paragraph}{channel x}{v}{section*.112}%
-\contentsline {paragraph}{maxmstep x}{v}{section*.113}%
-\contentsline {paragraph}{step x}{v}{section*.114}%
-\contentsline {paragraph}{mstep x}{v}{section*.115}%
-\contentsline {paragraph}{cancel}{vi}{section*.116}%
-\contentsline {paragraph}{help}{vi}{section*.117}%
+\contentsline {paragraph}{pulse?}{v}{section*.106}%
+\contentsline {paragraph}{pol x}{v}{section*.107}%
+\contentsline {paragraph}{amp x}{v}{section*.108}%
+\contentsline {paragraph}{volt x}{v}{section*.109}%
+\contentsline {paragraph}{channel x}{v}{section*.110}%
+\contentsline {paragraph}{maxmstep x}{v}{section*.111}%
+\contentsline {paragraph}{step x}{v}{section*.112}%
+\contentsline {paragraph}{mstep x}{v}{section*.113}%
+\contentsline {paragraph}{cancel}{vi}{section*.114}%
+\contentsline {paragraph}{help}{vi}{section*.115}%
\contentsline {section}{\numberline {D}Raycast Simulation}{vi}{section.6.4}%
-\contentsline {paragraph}{radius\_1}{vi}{section*.118}%
-\contentsline {paragraph}{angle}{vi}{section*.119}%
-\contentsline {paragraph}{radius\_mask}{vi}{section*.120}%
-\contentsline {paragraph}{distance\_circle\_mask}{vi}{section*.121}%
-\contentsline {paragraph}{distance\_sample}{vi}{section*.122}%
-\contentsline {paragraph}{rays\_per\_frame}{vi}{section*.123}%
-\contentsline {paragraph}{running\_time}{vi}{section*.124}%
-\contentsline {paragraph}{deposition\_gain}{vi}{section*.125}%
-\contentsline {paragraph}{penalize\_deposition}{vi}{section*.126}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vi}{section*.127}%
-\contentsline {paragraph}{oscillation\_period}{vi}{section*.128}%
-\contentsline {paragraph}{delay\_oscill\_time}{vii}{section*.129}%
-\contentsline {paragraph}{save\_in\_progress\_images}{vii}{section*.130}%
-\contentsline {paragraph}{save\_intervall}{vii}{section*.131}%
-\contentsline {paragraph}{oscillation\_dir}{vii}{section*.132}%
-\contentsline {paragraph}{oscillation\_rot\_s}{vii}{section*.133}%
-\contentsline {paragraph}{oscillation\_rot\_e}{vii}{section*.134}%
-\contentsline {paragraph}{random\_seed}{vii}{section*.135}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{vii}{section*.136}%
-\contentsline {paragraph}{resolution}{vii}{section*.137}%
-\contentsline {paragraph}{path}{vii}{section*.138}%
-\contentsline {chapter}{Acknowledgments}{viii}{chapter*.139}%
+\contentsline {paragraph}{radius\_1}{vi}{section*.116}%
+\contentsline {paragraph}{angle}{vi}{section*.117}%
+\contentsline {paragraph}{radius\_mask}{vi}{section*.118}%
+\contentsline {paragraph}{distance\_circle\_mask}{vi}{section*.119}%
+\contentsline {paragraph}{distance\_sample}{vi}{section*.120}%
+\contentsline {paragraph}{rays\_per\_frame}{vi}{section*.121}%
+\contentsline {paragraph}{running\_time}{vi}{section*.122}%
+\contentsline {paragraph}{deposition\_gain}{vi}{section*.123}%
+\contentsline {paragraph}{penalize\_deposition}{vi}{section*.124}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{vi}{section*.125}%
+\contentsline {paragraph}{oscillation\_period}{vi}{section*.126}%
+\contentsline {paragraph}{delay\_oscill\_time}{vii}{section*.127}%
+\contentsline {paragraph}{save\_in\_progress\_images}{vii}{section*.128}%
+\contentsline {paragraph}{save\_intervall}{vii}{section*.129}%
+\contentsline {paragraph}{oscillation\_dir}{vii}{section*.130}%
+\contentsline {paragraph}{oscillation\_rot\_s}{vii}{section*.131}%
+\contentsline {paragraph}{oscillation\_rot\_e}{vii}{section*.132}%
+\contentsline {paragraph}{random\_seed}{vii}{section*.133}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{vii}{section*.134}%
+\contentsline {paragraph}{resolution}{vii}{section*.135}%
+\contentsline {paragraph}{path}{vii}{section*.136}%
+\contentsline {chapter}{Acknowledgments}{viii}{chapter*.137}%