diff --git a/acknowledgments.aux b/acknowledgments.aux
index b947653c9aed6032be1e6fc92ed6d2bb2cba2b1b..a232ecf347388b7ac8c7462a73f4942775de259a 100644
--- a/acknowledgments.aux
+++ b/acknowledgments.aux
@@ -1,6 +1,6 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{Acknowledgments}{ix}{chapter*.115}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Acknowledgments}{ix}{chapter*.118}\protected@file@percent }
 \@setckpt{acknowledgments}{
 \setcounter{page}{10}
 \setcounter{equation}{1}
@@ -31,7 +31,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/appendix.aux b/appendix.aux
index b439b109f1ebf2349babeaf123c8f85aee2de099..35be637e33c13a03637b5c409915fb1c3c3cbf5c 100644
--- a/appendix.aux
+++ b/appendix.aux
@@ -1,51 +1,51 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
-\@writefile{toc}{\contentsline {chapter}{Appendix}{i}{chapter*.81}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Appendix}{i}{chapter*.84}\protected@file@percent }
 \@writefile{toc}{\contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}\protected@file@percent }
 \newlabel{app:lock_in}{{A}{i}{LockIn amplifier settings}{section.5.1}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {5.2}{\ignorespaces Settings used for the Lock-in amplifier in the experiment. Sensitivity is increased a step at a time until the Lock-in is no longer in overload. Source is chosen as internal. Ground is set to grounded.}}{i}{table.caption.82}\protected@file@percent }
-\newlabel{fig:app_lock_in}{{5.2}{i}{Settings used for the Lock-in amplifier in the experiment. Sensitivity is increased a step at a time until the Lock-in is no longer in overload. Source is chosen as internal. Ground is set to grounded}{table.caption.82}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {5.2}{\ignorespaces Settings used for the Lock-in amplifier in the experiment. Sensitivity is increased a step at a time until the Lock-in is no longer in overload. Source is chosen as internal. Ground is set to grounded.}}{i}{table.caption.85}\protected@file@percent }
+\newlabel{fig:app_lock_in}{{5.2}{i}{Settings used for the Lock-in amplifier in the experiment. Sensitivity is increased a step at a time until the Lock-in is no longer in overload. Source is chosen as internal. Ground is set to grounded}{table.caption.85}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}\protected@file@percent }
 \newlabel{app:walker_diagram}{{B}{ii}{Walker principle diagram}{section.5.2}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Overview of the entire signal generation and amplification process of the new Mask Aligner controller.}}{ii}{figure.caption.83}\protected@file@percent }
-\newlabel{fig:electronics_diagramm}{{5.14}{ii}{Overview of the entire signal generation and amplification process of the new Mask Aligner controller}{figure.caption.83}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.14}{\ignorespaces Overview of the entire signal generation and amplification process of the new Mask Aligner controller.}}{ii}{figure.caption.86}\protected@file@percent }
+\newlabel{fig:electronics_diagramm}{{5.14}{ii}{Overview of the entire signal generation and amplification process of the new Mask Aligner controller}{figure.caption.86}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}\protected@file@percent }
 \newlabel{app:circuit_electronics}{{C}{ii}{Walker circuit diagrams}{section.5.3}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}\protected@file@percent }
 \newlabel{sec:appendix_walker}{{D}{vi}{New driver electronics}{section.5.4}{}}
-\@writefile{toc}{\contentsline {paragraph}{pulse?}{vi}{section*.84}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{pol x}{vi}{section*.85}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{amp x}{vi}{section*.86}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{volt x}{vi}{section*.87}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{channel x}{vi}{section*.88}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{maxmstep x}{vi}{section*.89}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{step x}{vi}{section*.90}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{mstep x}{vi}{section*.91}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{cancel}{vii}{section*.92}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{help}{vii}{section*.93}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{pulse?}{vi}{section*.87}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{pol x}{vi}{section*.88}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{amp x}{vi}{section*.89}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{volt x}{vi}{section*.90}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{channel x}{vi}{section*.91}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{maxmstep x}{vi}{section*.92}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{step x}{vi}{section*.93}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{mstep x}{vi}{section*.94}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{cancel}{vii}{section*.95}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{help}{vii}{section*.96}\protected@file@percent }
 \@writefile{toc}{\contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}\protected@file@percent }
 \newlabel{sec:appendix_raycast}{{E}{vii}{Raycast Simulation}{section.5.5}{}}
-\@writefile{toc}{\contentsline {paragraph}{radius\_1}{vii}{section*.94}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{angle}{vii}{section*.95}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{radius\_mask}{vii}{section*.96}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.97}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{distance\_sample}{vii}{section*.98}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.99}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{running\_time}{vii}{section*.100}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{deposition\_gain}{vii}{section*.101}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{penalize\_deposition}{vii}{section*.102}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.103}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{oscillation\_period}{vii}{section*.104}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.105}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.106}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{save\_intervall}{viii}{section*.107}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{oscillation\_dir}{viii}{section*.108}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.109}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.110}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{random\_seed}{viii}{section*.111}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.112}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{resolution}{viii}{section*.113}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{path}{viii}{section*.114}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{radius\_1}{vii}{section*.97}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{angle}{vii}{section*.98}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{radius\_mask}{vii}{section*.99}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.100}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{distance\_sample}{vii}{section*.101}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.102}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{running\_time}{vii}{section*.103}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{deposition\_gain}{vii}{section*.104}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{penalize\_deposition}{vii}{section*.105}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.106}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{oscillation\_period}{vii}{section*.107}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.108}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.109}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{save\_intervall}{viii}{section*.110}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{oscillation\_dir}{viii}{section*.111}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.112}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.113}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{random\_seed}{viii}{section*.114}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.115}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{resolution}{viii}{section*.116}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{path}{viii}{section*.117}\protected@file@percent }
 \@setckpt{appendix}{
 \setcounter{page}{9}
 \setcounter{equation}{1}
@@ -76,7 +76,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/bibliography.aux b/bibliography.aux
index cea12aa246ae6c616330d7847d66df4f73881a09..e756489aa09c939ba9b292c9b5fc860b919f0c33 100644
--- a/bibliography.aux
+++ b/bibliography.aux
@@ -14,7 +14,7 @@
 \bibcite{tungsten_evaporation}{{10}{}{{}}{{}}}
 \bibcite{afm_physics}{{11}{}{{}}{{}}}
 \bibcite{afm_bio}{{12}{}{{}}{{}}}
-\@writefile{toc}{\contentsline {chapter}{Bibliography}{74}{chapter*.79}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Bibliography}{74}{chapter*.82}\protected@file@percent }
 \bibcite{SEM_image_01}{{13}{}{{}}{{}}}
 \bibcite{SEM_image_02}{{14}{}{{}}{{}}}
 \bibcite{SEM_book}{{15}{}{{}}{{}}}
@@ -57,7 +57,7 @@
 \setcounter{subfigure}{3}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap01.aux b/chap01.aux
index aadbce4ee7e9d1575620a2c20e9554f748cc921f..291f03014d6ce5084309aeea4b27014730aa7b8e 100644
--- a/chap01.aux
+++ b/chap01.aux
@@ -5,52 +5,53 @@
 \@writefile{lot}{\addvspace {10\p@ }}
 \newlabel{ch:background}{{1}{5}{Mask Aligner background}{chapter.1}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {1.1}Electron beam evaporation}{5}{section.1.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam. }}{5}{figure.caption.3}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{Cut chapter?}{5}{section*.3}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {1.1}{\ignorespaces Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam. }}{5}{figure.caption.4}\protected@file@percent }
 \providecommand*\caption@xref[2]{\@setref\relax\@undefined{#1}}
-\newlabel{fig:e-beam_evap}{{1.1}{5}{Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam}{figure.caption.3}{}}
+\newlabel{fig:e-beam_evap}{{1.1}{5}{Schematic of a general electron beam evaporation chamber. The B-field is used to focus the beam onto the source. The shutter can interrupt the beam directed to the sample. The funnel is used to focus the vapor beam}{figure.caption.4}{}}
 \citation{knudsen}
 \citation{Vapor_depo_princ}
 \citation{sputter_damage}
 \citation{tungsten_evaporation}
 \newlabel{eq:hertz_knudsen}{{1.1}{6}{Electron beam evaporation}{equation.1.1.1}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {1.2}Stencil lithography}{6}{section.1.2}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsubsection}{Penumbra}{7}{section*.4}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsubsection}{Penumbra}{7}{section*.5}\protected@file@percent }
 \citation{Bhaskar}
-\@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces Diagram to determine the size of the penumbra $p$. The crucible is placed at distance $l$ from the mask, and beams emit from either side of the crucible to both edges of a hole in the mask. The area where only beams from one side of the crucible hit the sample is called penumbra.}}{8}{figure.caption.5}\protected@file@percent }
-\newlabel{fig:penumbra_explanation}{{1.2}{8}{Diagram to determine the size of the penumbra $p$. The crucible is placed at distance $l$ from the mask, and beams emit from either side of the crucible to both edges of a hole in the mask. The area where only beams from one side of the crucible hit the sample is called penumbra}{figure.caption.5}{}}
-\@writefile{toc}{\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.6}\protected@file@percent }
-\newlabel{fig:penumbra_explanation_tilt_2d}{{1.3a}{9}{\relax }{figure.caption.7}{}}
-\newlabel{sub@fig:penumbra_explanation_tilt_2d}{{a}{9}{\relax }{figure.caption.7}{}}
-\newlabel{fig:penumbra_explanation_tilt_sim}{{1.3b}{9}{\relax }{figure.caption.7}{}}
-\newlabel{sub@fig:penumbra_explanation_tilt_sim}{{b}{9}{\relax }{figure.caption.7}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {1.3}{\ignorespaces A diagram of the evaporation rays for a tilted mask with only one hole (\subref  {fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral widths $p_{\text  {i}}$ that appear in a cross-section. (\subref  {fig:penumbra_explanation_tilt_sim}) Simulated evaporation with large penumbra for a tilt angle of $45^\circ $ the penumbra, is wider on one side than on the other. The penumbra in the simulation is for a mask sample distance of $200$ $\mu $m and a hole diameter of $3$ $\mu $m. Program used for simulation is described in Section \ref {sec:simulation}}}{9}{figure.caption.7}\protected@file@percent }
-\newlabel{fig:penumbra_explanation_tilt}{{1.3}{9}{A diagram of the evaporation rays for a tilted mask with only one hole (\subref {fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral widths $p_{\text {i}}$ that appear in a cross-section. (\subref {fig:penumbra_explanation_tilt_sim}) Simulated evaporation with large penumbra for a tilt angle of $45^\circ $ the penumbra, is wider on one side than on the other. The penumbra in the simulation is for a mask sample distance of $200$ $\mu $m and a hole diameter of $3$ $\mu $m. Program used for simulation is described in Section \ref {sec:simulation}}{figure.caption.7}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {1.2}{\ignorespaces Diagram to determine the size of the penumbra $p$. The crucible is placed at distance $l$ from the mask, and beams emit from either side of the crucible to both edges of a hole in the mask. The area where only beams from one side of the crucible hit the sample is called penumbra.}}{8}{figure.caption.6}\protected@file@percent }
+\newlabel{fig:penumbra_explanation}{{1.2}{8}{Diagram to determine the size of the penumbra $p$. The crucible is placed at distance $l$ from the mask, and beams emit from either side of the crucible to both edges of a hole in the mask. The area where only beams from one side of the crucible hit the sample is called penumbra}{figure.caption.6}{}}
+\@writefile{toc}{\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.7}\protected@file@percent }
+\newlabel{fig:penumbra_explanation_tilt_2d}{{1.3a}{9}{\relax }{figure.caption.8}{}}
+\newlabel{sub@fig:penumbra_explanation_tilt_2d}{{a}{9}{\relax }{figure.caption.8}{}}
+\newlabel{fig:penumbra_explanation_tilt_sim}{{1.3b}{9}{\relax }{figure.caption.8}{}}
+\newlabel{sub@fig:penumbra_explanation_tilt_sim}{{b}{9}{\relax }{figure.caption.8}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {1.3}{\ignorespaces A diagram of the evaporation rays for a tilted mask with only one hole (\subref  {fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral widths $p_{\text  {i}}$ that appear in a cross-section. (\subref  {fig:penumbra_explanation_tilt_sim}) Simulated evaporation with large penumbra for a tilt angle of $45^\circ $ the penumbra, is wider on one side than on the other. The penumbra in the simulation is for a mask sample distance of $200$ $\mu $m and a hole diameter of $3$ $\mu $m. Program used for simulation is described in Section \ref {sec:simulation}}}{9}{figure.caption.8}\protected@file@percent }
+\newlabel{fig:penumbra_explanation_tilt}{{1.3}{9}{A diagram of the evaporation rays for a tilted mask with only one hole (\subref {fig:penumbra_explanation_tilt_2d}) showing the 2 different penumbral widths $p_{\text {i}}$ that appear in a cross-section. (\subref {fig:penumbra_explanation_tilt_sim}) Simulated evaporation with large penumbra for a tilt angle of $45^\circ $ the penumbra, is wider on one side than on the other. The penumbra in the simulation is for a mask sample distance of $200$ $\mu $m and a hole diameter of $3$ $\mu $m. Program used for simulation is described in Section \ref {sec:simulation}}{figure.caption.8}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {1.3}Measurement techniques}{9}{section.1.3}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{9}{subsection.1.3.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {1.4}{\ignorespaces Diagram showing the configuration of an AFM with the tip in contact with the sample. Arrows indicate movement directions.}}{10}{figure.caption.8}\protected@file@percent }
-\newlabel{fig:afm_principle}{{1.4}{10}{Diagram showing the configuration of an AFM with the tip in contact with the sample. Arrows indicate movement directions}{figure.caption.8}{}}
-\@writefile{toc}{\contentsline {subsubsection}{Modes}{10}{section*.9}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {1.5}{\ignorespaces Schematic diagram of the Lennart Jones potential governing the interaction between tip and sample in an AFM. The 3 areas of the AFM Modes are marked \textcolor {tab_green}{contact}, \textcolor {tab_blue}{tapping} and \textcolor {tab_red}{non-contact}. These regions are approximate. Units on both axes are arbitrary.}}{11}{figure.caption.10}\protected@file@percent }
-\newlabel{fig:afm_potential}{{1.5}{11}{Schematic diagram of the Lennart Jones potential governing the interaction between tip and sample in an AFM. The 3 areas of the AFM Modes are marked \textcolor {tab_green}{contact}, \textcolor {tab_blue}{tapping} and \textcolor {tab_red}{non-contact}. These regions are approximate. Units on both axes are arbitrary}{figure.caption.10}{}}
-\@writefile{toc}{\contentsline {paragraph}{Contact}{11}{section*.11}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Non-Contact}{11}{section*.12}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {1.4}{\ignorespaces Diagram showing the configuration of an AFM with the tip in contact with the sample. Arrows indicate movement directions.}}{10}{figure.caption.9}\protected@file@percent }
+\newlabel{fig:afm_principle}{{1.4}{10}{Diagram showing the configuration of an AFM with the tip in contact with the sample. Arrows indicate movement directions}{figure.caption.9}{}}
+\@writefile{toc}{\contentsline {subsubsection}{Modes}{10}{section*.10}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {1.5}{\ignorespaces Schematic diagram of the Lennart Jones potential governing the interaction between tip and sample in an AFM. The 3 areas of the AFM Modes are marked \textcolor {tab_green}{contact}, \textcolor {tab_blue}{tapping} and \textcolor {tab_red}{non-contact}. These regions are approximate. Units on both axes are arbitrary.}}{11}{figure.caption.11}\protected@file@percent }
+\newlabel{fig:afm_potential}{{1.5}{11}{Schematic diagram of the Lennart Jones potential governing the interaction between tip and sample in an AFM. The 3 areas of the AFM Modes are marked \textcolor {tab_green}{contact}, \textcolor {tab_blue}{tapping} and \textcolor {tab_red}{non-contact}. These regions are approximate. Units on both axes are arbitrary}{figure.caption.11}{}}
+\@writefile{toc}{\contentsline {paragraph}{Contact}{11}{section*.12}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Non-Contact}{11}{section*.13}\protected@file@percent }
 \citation{afm_physics,afm_bio}
 \citation{SEM_image_01}
 \citation{SEM_image_02}
 \citation{SEM_image_01}
 \citation{SEM_image_02}
-\@writefile{toc}{\contentsline {paragraph}{Tapping}{12}{section*.13}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Tapping}{12}{section*.14}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{12}{subsection.1.3.2}\protected@file@percent }
 \citation{SEM_book}
 \citation{SEM_book}
 \citation{SEM_book}
 \citation{SEM_book}
-\newlabel{fig:sem_setup_beam}{{1.6a}{13}{\relax }{figure.caption.14}{}}
-\newlabel{sub@fig:sem_setup_beam}{{a}{13}{\relax }{figure.caption.14}{}}
-\newlabel{fig:sem_setup_interaction}{{1.6b}{13}{\relax }{figure.caption.14}{}}
-\newlabel{sub@fig:sem_setup_interaction}{{b}{13}{\relax }{figure.caption.14}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {1.6}{\ignorespaces The beam path for an SEM (\subref  {fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref  {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite  {SEM_image_01} and ~\cite  {SEM_image_02}.}}{13}{figure.caption.14}\protected@file@percent }
-\newlabel{fig:sem_setup}{{1.6}{13}{The beam path for an SEM (\subref {fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite {SEM_image_01} and ~\cite {SEM_image_02}}{figure.caption.14}{}}
+\newlabel{fig:sem_setup_beam}{{1.6a}{13}{\relax }{figure.caption.15}{}}
+\newlabel{sub@fig:sem_setup_beam}{{a}{13}{\relax }{figure.caption.15}{}}
+\newlabel{fig:sem_setup_interaction}{{1.6b}{13}{\relax }{figure.caption.15}{}}
+\newlabel{sub@fig:sem_setup_interaction}{{b}{13}{\relax }{figure.caption.15}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {1.6}{\ignorespaces The beam path for an SEM (\subref  {fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref  {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite  {SEM_image_01} and ~\cite  {SEM_image_02}.}}{13}{figure.caption.15}\protected@file@percent }
+\newlabel{fig:sem_setup}{{1.6}{13}{The beam path for an SEM (\subref {fig:sem_setup_beam}). The $3$ detectors used in an SEM are shown near the bottom of the image. The secondary electron detector (Everhard-Thornley) and the back scattering and X-ray detector. A diagram showing electron matter interactions (\subref {fig:sem_setup_interaction}). The green area represents the penetration depth into the sample at which the different signals can be detected. Images were taken from~\cite {SEM_image_01} and ~\cite {SEM_image_02}}{figure.caption.15}{}}
 \citation{self_epitaxy}
 \@setckpt{chap01}{
 \setcounter{page}{15}
@@ -82,7 +83,7 @@
 \setcounter{subfigure}{2}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{0}
+\setcounter{@todonotes@numberoftodonotes}{1}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap01.tex b/chap01.tex
index 1126834178a3c4f75d084e02cb0298d0cd3dfb89..f46455ab03439859610d25af87b23e4d6a4fcc75 100644
--- a/chap01.tex
+++ b/chap01.tex
@@ -3,6 +3,7 @@
 The Mask Aligner is used to create thin patterned films on samples with high accuracy. This chapter will introduce the required background behind the evaporation and explain the basic evaporation and alignment setup.
 
 \section{Electron beam evaporation}
+\todo{Cut chapter?}
 Electron beam evaporation, also known as \textbf{E}lectron-\textbf{b}eam \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (EBPVD) is a \textbf{P}hysical \textbf{V}apor \textbf{D}eposition (PVD) technique that in \textbf{U}ltra \textbf{H}igh \textbf{V}acuum (UHV) deposits material onto a substrates surface.
 
 \begin{figure}[H]
diff --git a/chap02.aux b/chap02.aux
index 5bf3cc7b1f1a7b06d221d3e5e98177da32c0331e..20415045f1d3663d4b8b90c31547ae1576f90fb1 100644
--- a/chap02.aux
+++ b/chap02.aux
@@ -5,96 +5,98 @@
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
 \@writefile{toc}{\contentsline {section}{\numberline {2.1}Molecular beam evaporation chamber}{15}{section.2.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {2.1}{\ignorespaces Circuit diagram of the mask aligner and its associated vacuum system. It consists of the mask aligner (MA) chamber, the main chamber, the Pb evaporator and the \ce {Au} evaporator. The \ce {Au} evaporator is attached to the same vacuum system, but is unrelated to the Mask Aligner. The configuration depicted is used for evaporation. The \textcolor {tab_green}{green} line shows the sample/mask extraction and insertion path with the wobble stick. The black arrow shows the molecular beam path from the \ce {Pb} evaporator. BA stands for Bayard-Alpert pressure gauge. This diagram is accurate for the setup on 01.08.24.}}{15}{figure.caption.15}\protected@file@percent }
-\newlabel{fig:mask_aligner_chamber}{{2.1}{15}{Circuit diagram of the mask aligner and its associated vacuum system. It consists of the mask aligner (MA) chamber, the main chamber, the Pb evaporator and the \ce {Au} evaporator. The \ce {Au} evaporator is attached to the same vacuum system, but is unrelated to the Mask Aligner. The configuration depicted is used for evaporation. The \textcolor {tab_green}{green} line shows the sample/mask extraction and insertion path with the wobble stick. The black arrow shows the molecular beam path from the \ce {Pb} evaporator. BA stands for Bayard-Alpert pressure gauge. This diagram is accurate for the setup on 01.08.24}{figure.caption.15}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.1}{\ignorespaces Circuit diagram of the mask aligner and its associated vacuum system. It consists of the mask aligner (MA) chamber, the main chamber, the Pb evaporator and the \ce {Au} evaporator. The \ce {Au} evaporator is attached to the same vacuum system, but is unrelated to the Mask Aligner. The configuration depicted is used for evaporation. The \textcolor {tab_green}{green} line shows the sample/mask extraction and insertion path with the wobble stick. The black arrow shows the molecular beam path from the \ce {Pb} evaporator. BA stands for Bayard-Alpert pressure gauge. This diagram is accurate for the setup on 01.08.24.}}{15}{figure.caption.16}\protected@file@percent }
+\newlabel{fig:mask_aligner_chamber}{{2.1}{15}{Circuit diagram of the mask aligner and its associated vacuum system. It consists of the mask aligner (MA) chamber, the main chamber, the Pb evaporator and the \ce {Au} evaporator. The \ce {Au} evaporator is attached to the same vacuum system, but is unrelated to the Mask Aligner. The configuration depicted is used for evaporation. The \textcolor {tab_green}{green} line shows the sample/mask extraction and insertion path with the wobble stick. The black arrow shows the molecular beam path from the \ce {Pb} evaporator. BA stands for Bayard-Alpert pressure gauge. This diagram is accurate for the setup on 01.08.24}{figure.caption.16}{}}
 \citation{florian_forster}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.1.1}Lead evaporator}{16}{subsection.2.1.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {2.2}{\ignorespaces Solidworks diagram of the evaporator used on the Mask Aligner.}}{17}{figure.caption.16}\protected@file@percent }
-\newlabel{fig:ma_evap}{{2.2}{17}{Solidworks diagram of the evaporator used on the Mask Aligner}{figure.caption.16}{}}
-\newlabel{fig:mask_aligner_nomenclature_motors}{{2.3a}{18}{\relax }{figure.caption.17}{}}
-\newlabel{sub@fig:mask_aligner_nomenclature_motors}{{a}{18}{\relax }{figure.caption.17}{}}
-\newlabel{fig:mask_aligner_nomenclature_components}{{2.3b}{18}{\relax }{figure.caption.17}{}}
-\newlabel{sub@fig:mask_aligner_nomenclature_components}{{b}{18}{\relax }{figure.caption.17}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.3}{\ignorespaces (\subref  {fig:mask_aligner_nomenclature_motors}) shows the nomenclature for the motors of Mask Aligner. (\subref  {fig:mask_aligner_nomenclature_components}) shows the components of the Mask Aligner \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 stage, \textbf  {J} Mask, \textbf  {K} mask shuttle, \textbf  {L} neodymium magnet, \textbf  {M} \ce {Al2O3} plate, \textbf  {N} \ce {CuBe} spring, \textbf  {O} piezo motor front plate, \textbf  {P} sapphire prism, \textbf  {Q} lower body. In \textcolor {tab_red}{red} the molecular beam path to the mask is displayed.}}{18}{figure.caption.17}\protected@file@percent }
-\newlabel{fig:mask_aligner_nomenclature}{{2.3}{18}{(\subref {fig:mask_aligner_nomenclature_motors}) shows the nomenclature for the motors of Mask Aligner. (\subref {fig:mask_aligner_nomenclature_components}) shows the components of the Mask Aligner \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 stage, \textbf {J} Mask, \textbf {K} mask shuttle, \textbf {L} neodymium magnet, \textbf {M} \ce {Al2O3} plate, \textbf {N} \ce {CuBe} spring, \textbf {O} piezo motor front plate, \textbf {P} sapphire prism, \textbf {Q} lower body. In \textcolor {tab_red}{red} the molecular beam path to the mask is displayed}{figure.caption.17}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.2}{\ignorespaces Solidworks diagram of the evaporator used on the Mask Aligner.}}{17}{figure.caption.17}\protected@file@percent }
+\newlabel{fig:ma_evap}{{2.2}{17}{Solidworks diagram of the evaporator used on the Mask Aligner}{figure.caption.17}{}}
+\newlabel{fig:mask_aligner_nomenclature_motors}{{2.3a}{18}{\relax }{figure.caption.18}{}}
+\newlabel{sub@fig:mask_aligner_nomenclature_motors}{{a}{18}{\relax }{figure.caption.18}{}}
+\newlabel{fig:mask_aligner_nomenclature_components}{{2.3b}{18}{\relax }{figure.caption.18}{}}
+\newlabel{sub@fig:mask_aligner_nomenclature_components}{{b}{18}{\relax }{figure.caption.18}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.3}{\ignorespaces (\subref  {fig:mask_aligner_nomenclature_motors}) shows the nomenclature for the motors of Mask Aligner. (\subref  {fig:mask_aligner_nomenclature_components}) shows the components of the Mask Aligner \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 stage, \textbf  {J} mask, \textbf  {K} mask shuttle, \textbf  {L} neodymium magnet, \textbf  {M} \ce {Al2O3} plate, \textbf  {N} \ce {CuBe} spring, \textbf  {O} piezo motor front plate, \textbf  {P} sapphire prism, \textbf  {Q} lower body. In \textcolor {tab_red}{red} the molecular beam path to the mask is displayed.}}{18}{figure.caption.18}\protected@file@percent }
+\newlabel{fig:mask_aligner_nomenclature}{{2.3}{18}{(\subref {fig:mask_aligner_nomenclature_motors}) shows the nomenclature for the motors of Mask Aligner. (\subref {fig:mask_aligner_nomenclature_components}) shows the components of the Mask Aligner \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 stage, \textbf {J} mask, \textbf {K} mask shuttle, \textbf {L} neodymium magnet, \textbf {M} \ce {Al2O3} plate, \textbf {N} \ce {CuBe} spring, \textbf {O} piezo motor front plate, \textbf {P} sapphire prism, \textbf {Q} lower body. In \textcolor {tab_red}{red} the molecular beam path to the mask is displayed}{figure.caption.18}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {2.2}Slip stick principle}{19}{section.2.2}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {2.4}{\ignorespaces Image showing the slip-stick principle. On the right an example signal is shown.}}{20}{figure.caption.18}\protected@file@percent }
-\newlabel{fig:slip_stick_diagram}{{2.4}{20}{Image showing the slip-stick principle. On the right an example signal is shown}{figure.caption.18}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.4}{\ignorespaces Image showing the slip-stick principle. On the right an example signal is shown.}}{20}{figure.caption.19}\protected@file@percent }
+\newlabel{fig:slip_stick_diagram}{{2.4}{20}{Image showing the slip-stick principle. On the right an example signal is shown}{figure.caption.19}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {2.3}Shadow mask alignment}{20}{section.2.3}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.1}Motor screw configuration}{20}{subsection.2.3.1}\protected@file@percent }
-\newlabel{fig:screw_firmness_screw_image}{{2.5a}{21}{\relax }{figure.caption.19}{}}
-\newlabel{sub@fig:screw_firmness_screw_image}{{a}{21}{\relax }{figure.caption.19}{}}
-\newlabel{fig:screw_firmness_plot}{{2.5b}{21}{\relax }{figure.caption.19}{}}
-\newlabel{sub@fig:screw_firmness_plot}{{b}{21}{\relax }{figure.caption.19}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.5}{\ignorespaces (\subref  {fig:screw_firmness_screw_image}) shows a frontal view of the motor Z2 marked in red is the screw used for calibration of the motors on the Mask Aligner. (\subref  {fig:screw_firmness_plot}) shows example curves of how the screws of Z2 and Z3 affect the given motor's step size. The $0.0$ screw rotation is arbitrary. $+$ means retraction and $-$ means approach (Fig. \ref {fig:mask_aligner_nomenclature_motors}). The jumps in signal result from the \ce {CuBe} plate slipping across the winding of the screw. }}{21}{figure.caption.19}\protected@file@percent }
-\newlabel{fig:screw_firmness}{{2.5}{21}{(\subref {fig:screw_firmness_screw_image}) shows a frontal view of the motor Z2 marked in red is the screw used for calibration of the motors on the Mask Aligner. (\subref {fig:screw_firmness_plot}) shows example curves of how the screws of Z2 and Z3 affect the given motor's step size. The $0.0$ screw rotation is arbitrary. $+$ means retraction and $-$ means approach (Fig. \ref {fig:mask_aligner_nomenclature_motors}). The jumps in signal result from the \ce {CuBe} plate slipping across the winding of the screw}{figure.caption.19}{}}
+\newlabel{fig:screw_firmness_screw_image}{{2.5a}{21}{\relax }{figure.caption.20}{}}
+\newlabel{sub@fig:screw_firmness_screw_image}{{a}{21}{\relax }{figure.caption.20}{}}
+\newlabel{fig:screw_firmness_plot}{{2.5b}{21}{\relax }{figure.caption.20}{}}
+\newlabel{sub@fig:screw_firmness_plot}{{b}{21}{\relax }{figure.caption.20}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.5}{\ignorespaces (\subref  {fig:screw_firmness_screw_image}) shows a frontal view of the motor Z2 marked in red is the screw used for calibration of the motors on the Mask Aligner. (\subref  {fig:screw_firmness_plot}) shows example curves of how the screws of Z2 and Z3 affect the given motor's step size. The $0.0$ screw rotation is arbitrary. $+$ means retraction and $-$ means approach (Fig. \ref {fig:mask_aligner_nomenclature_motors}). The jumps in signal result from the \ce {CuBe} plate slipping across the winding of the screw. }}{21}{figure.caption.20}\protected@file@percent }
+\newlabel{fig:screw_firmness}{{2.5}{21}{(\subref {fig:screw_firmness_screw_image}) shows a frontal view of the motor Z2 marked in red is the screw used for calibration of the motors on the Mask Aligner. (\subref {fig:screw_firmness_plot}) shows example curves of how the screws of Z2 and Z3 affect the given motor's step size. The $0.0$ screw rotation is arbitrary. $+$ means retraction and $-$ means approach (Fig. \ref {fig:mask_aligner_nomenclature_motors}). The jumps in signal result from the \ce {CuBe} plate slipping across the winding of the screw}{figure.caption.20}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.2}Motor calibration}{21}{subsection.2.3.2}\protected@file@percent }
-\newlabel{fig:calibration_uhv_points_of_interest_z1}{{2.6a}{22}{\relax }{figure.caption.20}{}}
-\newlabel{sub@fig:calibration_uhv_points_of_interest_z1}{{a}{22}{\relax }{figure.caption.20}{}}
-\newlabel{fig:calibration_uhv_points_of_interest_z2z3}{{2.6b}{22}{\relax }{figure.caption.20}{}}
-\newlabel{sub@fig:calibration_uhv_points_of_interest_z2z3}{{b}{22}{\relax }{figure.caption.20}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.6}{\ignorespaces Points of interest for the calibration of the step size of the 3 piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination.}}{22}{figure.caption.20}\protected@file@percent }
-\newlabel{fig:calibration_uhv_points_of_interest}{{2.6}{22}{Points of interest for the calibration of the step size of the 3 piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination}{figure.caption.20}{}}
-\newlabel{fig:calibration_uhv_example_driving_z1}{{2.7a}{23}{\relax }{figure.caption.21}{}}
-\newlabel{sub@fig:calibration_uhv_example_driving_z1}{{a}{23}{\relax }{figure.caption.21}{}}
-\newlabel{fig:calibration_uhv_example_driving_z2}{{2.7b}{23}{\relax }{figure.caption.21}{}}
-\newlabel{sub@fig:calibration_uhv_example_driving_z2}{{b}{23}{\relax }{figure.caption.21}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.7}{\ignorespaces Comparison of photographs recorded prior and after $1000$ steps were driven. (\subref  {fig:calibration_uhv_example_driving_z1}) top of motor Z1, inset shows a zoom in of the top plate. The image after driving $1000$ approach steps superimposed. \textcolor {tab_red}{Red} lines show the top edge difference and resulting travel length. (\subref  {fig:calibration_uhv_example_driving_z2}) shows the same as (\subref  {fig:calibration_uhv_example_driving_z1}) for the screw used to determine step size for motor Z2. Inset shows both approach and retract for $1000$ steps.}}{23}{figure.caption.21}\protected@file@percent }
-\newlabel{fig:calibration_uhv_example_driving}{{2.7}{23}{Comparison of photographs recorded prior and after $1000$ steps were driven. (\subref {fig:calibration_uhv_example_driving_z1}) top of motor Z1, inset shows a zoom in of the top plate. The image after driving $1000$ approach steps superimposed. \textcolor {tab_red}{Red} lines show the top edge difference and resulting travel length. (\subref {fig:calibration_uhv_example_driving_z2}) shows the same as (\subref {fig:calibration_uhv_example_driving_z1}) for the screw used to determine step size for motor Z2. Inset shows both approach and retract for $1000$ steps}{figure.caption.21}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.8}{\ignorespaces Top view of the Mask Aligner with the motors Z1-Z3 and the screws on the mask frame displayed. The triangle and line construction shows the derivation for the motor movement from screw movement.}}{24}{figure.caption.22}\protected@file@percent }
-\newlabel{fig:calibration_screw_diff_explain}{{2.8}{24}{Top view of the Mask Aligner with the motors Z1-Z3 and the screws on the mask frame displayed. The triangle and line construction shows the derivation for the motor movement from screw movement}{figure.caption.22}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref {fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}}{24}{figure.caption.23}\protected@file@percent }
-\newlabel{fig:calibration_example}{{2.9}{24}{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref {fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit}{figure.caption.23}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.10}{\ignorespaces Step size as a function of voltage (DC peak) with linear fit and resulting slopes marked.}}{25}{figure.caption.24}\protected@file@percent }
-\newlabel{fig:calibration_voltage}{{2.10}{25}{Step size as a function of voltage (DC peak) with linear fit and resulting slopes marked}{figure.caption.24}{}}
+\newlabel{fig:calibration_uhv_points_of_interest_z1}{{2.6a}{22}{\relax }{figure.caption.21}{}}
+\newlabel{sub@fig:calibration_uhv_points_of_interest_z1}{{a}{22}{\relax }{figure.caption.21}{}}
+\newlabel{fig:calibration_uhv_points_of_interest_z2z3}{{2.6b}{22}{\relax }{figure.caption.21}{}}
+\newlabel{sub@fig:calibration_uhv_points_of_interest_z2z3}{{b}{22}{\relax }{figure.caption.21}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.6}{\ignorespaces Points of interest for the calibration of the step size of the 3 piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination.}}{22}{figure.caption.21}\protected@file@percent }
+\newlabel{fig:calibration_uhv_points_of_interest}{{2.6}{22}{Points of interest for the calibration of the step size of the 3 piezo motors in UHV. (a) motor Z1, \textcolor {tab_red}{red:} top of sapphire prism, \textcolor {tab_green}{green:} end of top plate used for step size determination (b) motors Z2/Z3, \textcolor {tab_red}{red:} screws on the motor plate that are close to motor Z2 and Z3 respectively, \textcolor {tab_green}{green:} lines used for step size determination}{figure.caption.21}{}}
+\newlabel{fig:calibration_uhv_example_driving_z1}{{2.7a}{23}{\relax }{figure.caption.22}{}}
+\newlabel{sub@fig:calibration_uhv_example_driving_z1}{{a}{23}{\relax }{figure.caption.22}{}}
+\newlabel{fig:calibration_uhv_example_driving_z2}{{2.7b}{23}{\relax }{figure.caption.22}{}}
+\newlabel{sub@fig:calibration_uhv_example_driving_z2}{{b}{23}{\relax }{figure.caption.22}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.7}{\ignorespaces Comparison of photographs recorded prior and after $1000$ steps were driven. (\subref  {fig:calibration_uhv_example_driving_z1}) top of motor Z1, inset shows a zoom in of the top plate. The image after driving $1000$ approach steps superimposed. \textcolor {tab_red}{Red} lines show the top edge difference and resulting travel length. (\subref  {fig:calibration_uhv_example_driving_z2}) shows the same as (\subref  {fig:calibration_uhv_example_driving_z1}) for the screw used to determine step size for motor Z2. Inset shows both approach and retract for $1000$ steps.}}{23}{figure.caption.22}\protected@file@percent }
+\newlabel{fig:calibration_uhv_example_driving}{{2.7}{23}{Comparison of photographs recorded prior and after $1000$ steps were driven. (\subref {fig:calibration_uhv_example_driving_z1}) top of motor Z1, inset shows a zoom in of the top plate. The image after driving $1000$ approach steps superimposed. \textcolor {tab_red}{Red} lines show the top edge difference and resulting travel length. (\subref {fig:calibration_uhv_example_driving_z2}) shows the same as (\subref {fig:calibration_uhv_example_driving_z1}) for the screw used to determine step size for motor Z2. Inset shows both approach and retract for $1000$ steps}{figure.caption.22}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.8}{\ignorespaces Top view of the Mask Aligner with the motors Z1-Z3 and the screws on the mask frame displayed. The triangle and line construction shows the derivation for the motor movement from screw movement.}}{24}{figure.caption.23}\protected@file@percent }
+\newlabel{fig:calibration_screw_diff_explain}{{2.8}{24}{Top view of the Mask Aligner with the motors Z1-Z3 and the screws on the mask frame displayed. The triangle and line construction shows the derivation for the motor movement from screw movement}{figure.caption.23}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.9}{\ignorespaces Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref {fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}}{24}{figure.caption.24}\protected@file@percent }
+\newlabel{fig:calibration_example}{{2.9}{24}{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref {fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit}{figure.caption.24}{}}
+\@writefile{tdo}{\contentsline {todo}{This graphic necessary?}{24}{section*.25}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.10}{\ignorespaces Step size as a function of voltage (DC peak) with linear fit and resulting slopes marked.}}{25}{figure.caption.26}\protected@file@percent }
+\newlabel{fig:calibration_voltage}{{2.10}{25}{Step size as a function of voltage (DC peak) with linear fit and resulting slopes marked}{figure.caption.26}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.3}Optical alignment}{25}{subsection.2.3.3}\protected@file@percent }
-\newlabel{fig:camera_alignment_example_low}{{2.11a}{26}{\relax }{figure.caption.25}{}}
-\newlabel{sub@fig:camera_alignment_example_low}{{a}{26}{\relax }{figure.caption.25}{}}
-\newlabel{fig:camera_alignment_example_high}{{2.11b}{26}{\relax }{figure.caption.25}{}}
-\newlabel{sub@fig:camera_alignment_example_high}{{b}{26}{\relax }{figure.caption.25}{}}
-\newlabel{fig:camera_alignment_example_good}{{2.11c}{26}{\relax }{figure.caption.25}{}}
-\newlabel{sub@fig:camera_alignment_example_good}{{c}{26}{\relax }{figure.caption.25}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment. }}{26}{figure.caption.25}\protected@file@percent }
-\newlabel{fig:camera_alignment_example}{{2.11}{26}{Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment}{figure.caption.25}{}}
-\newlabel{fig:optical_approach_a}{{2.12a}{26}{\relax }{figure.caption.26}{}}
-\newlabel{sub@fig:optical_approach_a}{{a}{26}{\relax }{figure.caption.26}{}}
-\newlabel{fig:optical_approach_b}{{2.12b}{26}{\relax }{figure.caption.26}{}}
-\newlabel{sub@fig:optical_approach_b}{{b}{26}{\relax }{figure.caption.26}{}}
-\newlabel{fig:optical_approach_c}{{2.12c}{26}{\relax }{figure.caption.26}{}}
-\newlabel{sub@fig:optical_approach_c}{{c}{26}{\relax }{figure.caption.26}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\ignorespaces The progression of optical alignment up from $65 \pm 5$ $\mu $m (a) to $25 \pm 5$ $\mu $m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length.}}{26}{figure.caption.26}\protected@file@percent }
-\newlabel{fig:optical_approach}{{2.12}{26}{The progression of optical alignment up from $65 \pm 5$ $\mu $m (a) to $25 \pm 5$ $\mu $m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length}{figure.caption.26}{}}
+\newlabel{fig:camera_alignment_example_low}{{2.11a}{26}{\relax }{figure.caption.27}{}}
+\newlabel{sub@fig:camera_alignment_example_low}{{a}{26}{\relax }{figure.caption.27}{}}
+\newlabel{fig:camera_alignment_example_high}{{2.11b}{26}{\relax }{figure.caption.27}{}}
+\newlabel{sub@fig:camera_alignment_example_high}{{b}{26}{\relax }{figure.caption.27}{}}
+\newlabel{fig:camera_alignment_example_good}{{2.11c}{26}{\relax }{figure.caption.27}{}}
+\newlabel{sub@fig:camera_alignment_example_good}{{c}{26}{\relax }{figure.caption.27}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.11}{\ignorespaces Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment. }}{26}{figure.caption.27}\protected@file@percent }
+\newlabel{fig:camera_alignment_example}{{2.11}{26}{Examples of camera views for different alignment situations. (a) camera placed or angled too low, (b) too high and (c) placed in good alignment}{figure.caption.27}{}}
+\newlabel{fig:optical_approach_a}{{2.12a}{26}{\relax }{figure.caption.28}{}}
+\newlabel{sub@fig:optical_approach_a}{{a}{26}{\relax }{figure.caption.28}{}}
+\newlabel{fig:optical_approach_b}{{2.12b}{26}{\relax }{figure.caption.28}{}}
+\newlabel{sub@fig:optical_approach_b}{{b}{26}{\relax }{figure.caption.28}{}}
+\newlabel{fig:optical_approach_c}{{2.12c}{26}{\relax }{figure.caption.28}{}}
+\newlabel{sub@fig:optical_approach_c}{{c}{26}{\relax }{figure.caption.28}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.12}{\ignorespaces The progression of optical alignment up from $65 \pm 5$ $\mu $m (a) to $25 \pm 5$ $\mu $m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length.}}{26}{figure.caption.28}\protected@file@percent }
+\newlabel{fig:optical_approach}{{2.12}{26}{The progression of optical alignment up from $65 \pm 5$ $\mu $m (a) to $25 \pm 5$ $\mu $m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length}{figure.caption.28}{}}
+\@writefile{tdo}{\contentsline {todo}{Is this image clear? How do I make it more clear?}{26}{section*.29}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.4}Capacitive distance measurements}{27}{subsection.2.3.4}\protected@file@percent }
-\newlabel{fig:mask_aligner_nomenclature_capacitances_motors}{{2.13a}{27}{\relax }{figure.caption.27}{}}
-\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_motors}{{a}{27}{\relax }{figure.caption.27}{}}
-\newlabel{fig:mask_aligner_nomenclature_capacitances_mask}{{2.13b}{27}{\relax }{figure.caption.27}{}}
-\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_mask}{{b}{27}{\relax }{figure.caption.27}{}}
-\newlabel{fig:mask_aligner_nomenclature_capacitances}{{\caption@xref {fig:mask_aligner_nomenclature_capacitances}{ on input line 279}}{27}{Capacitive distance measurements}{figure.caption.27}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces (\subref  {fig:mask_aligner_nomenclature_capacitances_motors}) shows a cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor {tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref  {fig:mask_aligner_nomenclature_capacitances_mask}) shows a diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is used to create patterns. Below is a cross section of the materials used.}}{27}{figure.caption.27}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven.}}{28}{figure.caption.28}\protected@file@percent }
-\newlabel{fig:diagram_MA_circ}{{2.14}{28}{Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven}{figure.caption.28}{}}
+\newlabel{fig:mask_aligner_nomenclature_capacitances_motors}{{2.13a}{27}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_motors}{{a}{27}{\relax }{figure.caption.30}{}}
+\newlabel{fig:mask_aligner_nomenclature_capacitances_mask}{{2.13b}{27}{\relax }{figure.caption.30}{}}
+\newlabel{sub@fig:mask_aligner_nomenclature_capacitances_mask}{{b}{27}{\relax }{figure.caption.30}{}}
+\newlabel{fig:mask_aligner_nomenclature_capacitances}{{\caption@xref {fig:mask_aligner_nomenclature_capacitances}{ on input line 282}}{27}{Capacitive distance measurements}{figure.caption.30}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.13}{\ignorespaces (\subref  {fig:mask_aligner_nomenclature_capacitances_motors}) shows a cross-section of the Mask Aligner showing the labeling and rough positioning of the capacitance sensors on the mask (inner \textcolor {tab_red}{red} triangle) in relation to the $3$ piezo motor stacks. (\subref  {fig:mask_aligner_nomenclature_capacitances_mask}) shows a diagram of the mask's dimensions as well as labeling of the mask's sensors. The inset shows the dimensions of the holey part of the mask, which is used to create patterns. Below is a cross section of the materials used.}}{27}{figure.caption.30}\protected@file@percent }
+\@writefile{lof}{\contentsline {figure}{\numberline {2.14}{\ignorespaces Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven.}}{28}{figure.caption.31}\protected@file@percent }
+\newlabel{fig:diagram_MA_circ}{{2.14}{28}{Diagram showing how communication with the RHK and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ one after another. The RHK relay controls, which motor is currently driven}{figure.caption.31}{}}
 \newlabel{eq:plate_capacitor}{{2.1}{28}{Capacitive distance measurements}{equation.2.3.1}{}}
-\newlabel{fig:approach_curve_example_cap}{{2.15a}{29}{\relax }{figure.caption.29}{}}
-\newlabel{sub@fig:approach_curve_example_cap}{{a}{29}{\relax }{figure.caption.29}{}}
-\newlabel{fig:approach_curve_example_cap_diff}{{2.15b}{29}{\relax }{figure.caption.29}{}}
-\newlabel{sub@fig:approach_curve_example_cap_diff}{{b}{29}{\relax }{figure.caption.29}{}}
-\newlabel{fig:approach_curve_example_first}{{2.15c}{29}{\relax }{figure.caption.29}{}}
-\newlabel{sub@fig:approach_curve_example_first}{{c}{29}{\relax }{figure.caption.29}{}}
-\newlabel{fig:approach_curve_example_second}{{2.15d}{29}{\relax }{figure.caption.29}{}}
-\newlabel{sub@fig:approach_curve_example_second}{{d}{29}{\relax }{figure.caption.29}{}}
-\newlabel{fig:approach_curve_example_full}{{2.15e}{29}{\relax }{figure.caption.29}{}}
-\newlabel{sub@fig:approach_curve_example_full}{{e}{29}{\relax }{figure.caption.29}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces (a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac  {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample.}}{29}{figure.caption.29}\protected@file@percent }
-\newlabel{fig:approach_curve_example}{{2.15}{29}{(a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample}{figure.caption.29}{}}
+\newlabel{fig:approach_curve_example_cap}{{2.15a}{29}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_curve_example_cap}{{a}{29}{\relax }{figure.caption.32}{}}
+\newlabel{fig:approach_curve_example_cap_diff}{{2.15b}{29}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_curve_example_cap_diff}{{b}{29}{\relax }{figure.caption.32}{}}
+\newlabel{fig:approach_curve_example_first}{{2.15c}{29}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_curve_example_first}{{c}{29}{\relax }{figure.caption.32}{}}
+\newlabel{fig:approach_curve_example_second}{{2.15d}{29}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_curve_example_second}{{d}{29}{\relax }{figure.caption.32}{}}
+\newlabel{fig:approach_curve_example_full}{{2.15e}{29}{\relax }{figure.caption.32}{}}
+\newlabel{sub@fig:approach_curve_example_full}{{e}{29}{\relax }{figure.caption.32}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.15}{\ignorespaces (a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac  {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample.}}{29}{figure.caption.32}\protected@file@percent }
+\newlabel{fig:approach_curve_example}{{2.15}{29}{(a) capacitance (approach) curve. (b) difference of each capacitance value. Only one sensor is shown. Marked with blue dashed lines are the important points where the slope of the $\frac {1}{r}$ curve changes. Below are images of the geometry between mask and sample at First (c), Second (d) and Full contact (e). Red lines or points indicate where the mask is touching the sample}{figure.caption.32}{}}
 \citation{Beeker}
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.3.5}Reproducibility}{30}{subsection.2.3.5}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.30}\protected@file@percent }
-\newlabel{fig:approach_replicability_cap}{{2.16a}{30}{\relax }{figure.caption.31}{}}
-\newlabel{sub@fig:approach_replicability_cap}{{a}{30}{\relax }{figure.caption.31}{}}
-\newlabel{fig:approach_replicability_cap_diff}{{2.16b}{30}{\relax }{figure.caption.31}{}}
-\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{30}{\relax }{figure.caption.31}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces (\subref  {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref  {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \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.}}{30}{figure.caption.31}\protected@file@percent }
-\newlabel{fig:approach_replicability}{{2.16}{30}{(\subref {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \textcolor {tab_red}{red} curve the mask was removed and reinserted. Larger fluctuations in the signal visible on the \textcolor {tab_blue}{Blue} curve are due to an accidental change in time constant of the LockIn Amplifier}{figure.caption.31}{}}
+\@writefile{toc}{\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.33}\protected@file@percent }
+\newlabel{fig:approach_replicability_cap}{{2.16a}{30}{\relax }{figure.caption.34}{}}
+\newlabel{sub@fig:approach_replicability_cap}{{a}{30}{\relax }{figure.caption.34}{}}
+\newlabel{fig:approach_replicability_cap_diff}{{2.16b}{30}{\relax }{figure.caption.34}{}}
+\newlabel{sub@fig:approach_replicability_cap_diff}{{b}{30}{\relax }{figure.caption.34}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {2.16}{\ignorespaces (\subref  {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref  {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \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.}}{30}{figure.caption.34}\protected@file@percent }
+\newlabel{fig:approach_replicability}{{2.16}{30}{(\subref {fig:approach_replicability_cap}) 3 subsequent approach curves. (\subref {fig:approach_replicability_cap_diff}) corresponding differences in capacitance. \textcolor {tab_green}{Green} is the initial curve. The \textcolor {tab_blue}{blue} curve is after sample has been carefully removed and reinserted. For the \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.34}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {2.4}Mask Aligner operation}{31}{section.2.4}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {2.4.1}Sample preparation}{31}{subsection.2.4.1}\protected@file@percent }
 \newlabel{sec:sample_prep}{{2.4.1}{31}{Sample preparation}{subsection.2.4.1}{}}
@@ -128,7 +130,7 @@
 \setcounter{subfigure}{2}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{0}
+\setcounter{@todonotes@numberoftodonotes}{3}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap02.tex b/chap02.tex
index 73c9d46199108b0793b9273cf7c211679f40c00b..44155d03fc2082aaefa02cff151350145434adad 100644
--- a/chap02.tex
+++ b/chap02.tex
@@ -46,7 +46,7 @@ In order to control the molecular flux, one can change the current applied to th
 	\label{fig:mask_aligner_nomenclature_components}
 	\end{subfigure}
 	\caption{(\subref{fig:mask_aligner_nomenclature_motors}) shows the nomenclature for the motors of Mask Aligner. (\subref{fig:mask_aligner_nomenclature_components}) shows the components of the Mask Aligner  \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 stage, \textbf{J} Mask, \textbf{K} mask shuttle,
+sample holder, \textbf{H} mask frame, \textbf{I} mask stage, \textbf{J} mask, \textbf{K} mask shuttle,
 \textbf{L} neodymium magnet, \textbf{M} \ce{Al2O3} plate, \textbf{N} \ce{CuBe}
 spring, \textbf{O} piezo motor front plate, \textbf{P} sapphire prism,
 \textbf{Q} lower body. In \textcolor{tab_red}{red} the molecular
@@ -173,6 +173,7 @@ With this one gets that for each unit of distance the motor moves, the screws mo
 	\caption{Upper curves: Measured distance of motors traveled as a function of steps driven with linear fit and marked results step size. $+$ is retract $-$ is approach (see Fig. \ref{fig:mask_aligner_nomenclature_motors}). Lower curves: deviation of the data points from fit.}
 	\label{fig:calibration_example}
 \end{figure}
+\todo{This graphic necessary?}
 
 A linear fit is performed for the given data. The slope gives the step size. Results are shown in Figure \ref{fig:calibration_example}. After each set of steps it has to be ensured, that the mask frame is not tilted. Excessive tilt will affect the step size. It should also be taken care that the movement range of the piezos is not exceeded. The \ce{Nd} magnets should not detach from the frame. Moreover, the sapphire prism can fall out of the motor if it is driven too far down. The measurement has to be done for both driving directions separately, since the step sizes will be different. Indeed, in Fig. \ref{fig:calibration_example} shows that the positive retract direction has consistently larger step sizes. The Z3 motor also shows a larger difference in step size for approach and retract than the other $2$ motors.
 
@@ -254,6 +255,8 @@ achievable optical accuracy.
 	\caption{The progression of optical alignment up from $65 \pm 5$ $\mu$m (a) to $25 \pm 5$ $\mu$m (c) mask sample distance. Measurement was obtained optically using measurement software and the sample's edge as a reference length.}
     \label{fig:optical_approach}
 \end{figure}
+\todo{Is this image clear? How do I make it more clear?}
+
 
 \newpage
 \subsection{Capacitive distance measurements}
diff --git a/chap03.aux b/chap03.aux
index 876a5e9c74446c00d4b2b40d666845edadbd7ddd..4e3041d87b5e6a11751f16e2861eb2187d96c53c 100644
--- a/chap03.aux
+++ b/chap03.aux
@@ -5,71 +5,71 @@
 \@writefile{lot}{\addvspace {10\p@ }}
 \@writefile{toc}{\contentsline {section}{\numberline {3.1}RHK piezo motor controller}{33}{section.3.1}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.1.1}Overview}{33}{subsection.3.1.1}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{amplitude}{33}{section*.32}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{sweep period}{33}{section*.33}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{time between sweeps}{33}{section*.34}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{amplitude}{33}{section*.35}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{sweep period}{33}{section*.36}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{time between sweeps}{33}{section*.37}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.1.2}Pulse shape}{33}{subsection.3.1.2}\protected@file@percent }
-\newlabel{fig:RHK_pulse_shape_approach}{{3.1a}{33}{\relax }{figure.caption.35}{}}
-\newlabel{sub@fig:RHK_pulse_shape_approach}{{a}{33}{\relax }{figure.caption.35}{}}
-\newlabel{fig:RHK_pulse_shape_retract}{{3.1b}{33}{\relax }{figure.caption.35}{}}
-\newlabel{sub@fig:RHK_pulse_shape_retract}{{b}{33}{\relax }{figure.caption.35}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.1}{\ignorespaces Oscilloscope data showing both an approach step (\subref  {fig:RHK_pulse_shape_approach}) and a retract step (\subref  {fig:RHK_pulse_shape_retract}) for the RHK Piezo motor controller given at a voltage of $80$ V, as specified per setting. }}{33}{figure.caption.35}\protected@file@percent }
-\newlabel{fig:RHK_pulse_shape}{{3.1}{33}{Oscilloscope data showing both an approach step (\subref {fig:RHK_pulse_shape_approach}) and a retract step (\subref {fig:RHK_pulse_shape_retract}) for the RHK Piezo motor controller given at a voltage of $80$ V, as specified per setting}{figure.caption.35}{}}
-\newlabel{fig:RHK_pulse_shape_fast_flank_z1}{{3.2a}{34}{\relax }{figure.caption.36}{}}
-\newlabel{sub@fig:RHK_pulse_shape_fast_flank_z1}{{a}{34}{\relax }{figure.caption.36}{}}
-\newlabel{fig:RHK_pulse_shape_fast_flank_z2}{{3.2b}{34}{\relax }{figure.caption.36}{}}
-\newlabel{sub@fig:RHK_pulse_shape_fast_flank_z2}{{b}{34}{\relax }{figure.caption.36}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.2}{\ignorespaces Plots showing the fast flank of the RHK signal, set to 80 V. (\subref  {fig:RHK_pulse_shape_fast_flank_z1}) shows larger timescale of the same signal than (\subref  {fig:RHK_pulse_shape_fast_flank_z2}).}}{34}{figure.caption.36}\protected@file@percent }
-\newlabel{fig:RHK_pulse_shape_fast_flank}{{3.2}{34}{Plots showing the fast flank of the RHK signal, set to 80 V. (\subref {fig:RHK_pulse_shape_fast_flank_z1}) shows larger timescale of the same signal than (\subref {fig:RHK_pulse_shape_fast_flank_z2})}{figure.caption.36}{}}
+\newlabel{fig:RHK_pulse_shape_approach}{{3.1a}{33}{\relax }{figure.caption.38}{}}
+\newlabel{sub@fig:RHK_pulse_shape_approach}{{a}{33}{\relax }{figure.caption.38}{}}
+\newlabel{fig:RHK_pulse_shape_retract}{{3.1b}{33}{\relax }{figure.caption.38}{}}
+\newlabel{sub@fig:RHK_pulse_shape_retract}{{b}{33}{\relax }{figure.caption.38}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.1}{\ignorespaces Oscilloscope data showing both an approach step (\subref  {fig:RHK_pulse_shape_approach}) and a retract step (\subref  {fig:RHK_pulse_shape_retract}) for the RHK Piezo motor controller given at a voltage of $80$ V, as specified per setting. }}{33}{figure.caption.38}\protected@file@percent }
+\newlabel{fig:RHK_pulse_shape}{{3.1}{33}{Oscilloscope data showing both an approach step (\subref {fig:RHK_pulse_shape_approach}) and a retract step (\subref {fig:RHK_pulse_shape_retract}) for the RHK Piezo motor controller given at a voltage of $80$ V, as specified per setting}{figure.caption.38}{}}
+\newlabel{fig:RHK_pulse_shape_fast_flank_z1}{{3.2a}{34}{\relax }{figure.caption.39}{}}
+\newlabel{sub@fig:RHK_pulse_shape_fast_flank_z1}{{a}{34}{\relax }{figure.caption.39}{}}
+\newlabel{fig:RHK_pulse_shape_fast_flank_z2}{{3.2b}{34}{\relax }{figure.caption.39}{}}
+\newlabel{sub@fig:RHK_pulse_shape_fast_flank_z2}{{b}{34}{\relax }{figure.caption.39}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.2}{\ignorespaces Plots showing the fast flank of the RHK signal, set to 80 V. (\subref  {fig:RHK_pulse_shape_fast_flank_z1}) shows larger timescale of the same signal than (\subref  {fig:RHK_pulse_shape_fast_flank_z2}).}}{34}{figure.caption.39}\protected@file@percent }
+\newlabel{fig:RHK_pulse_shape_fast_flank}{{3.2}{34}{Plots showing the fast flank of the RHK signal, set to 80 V. (\subref {fig:RHK_pulse_shape_fast_flank_z1}) shows larger timescale of the same signal than (\subref {fig:RHK_pulse_shape_fast_flank_z2})}{figure.caption.39}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {3.2}KIM001}{34}{section.3.2}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.2.1}Overview}{34}{subsection.3.2.1}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.2.2}Pulse shape}{34}{subsection.3.2.2}\protected@file@percent }
-\newlabel{fig:kim0001_pulse_shape_approach}{{3.3a}{35}{\relax }{figure.caption.37}{}}
-\newlabel{sub@fig:kim0001_pulse_shape_approach}{{a}{35}{\relax }{figure.caption.37}{}}
-\newlabel{fig:kim0001_pulse_shape_retract}{{3.3b}{35}{\relax }{figure.caption.37}{}}
-\newlabel{sub@fig:kim0001_pulse_shape_retract}{{b}{35}{\relax }{figure.caption.37}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.3}{\ignorespaces Plots showing both an approach step (\subref  {fig:kim0001_pulse_shape_approach}) and a retract step (\subref  {fig:kim0001_pulse_shape_retract}) for the KIM001 device.}}{35}{figure.caption.37}\protected@file@percent }
-\newlabel{fig:kim0001_pulse_shape}{{3.3}{35}{Plots showing both an approach step (\subref {fig:kim0001_pulse_shape_approach}) and a retract step (\subref {fig:kim0001_pulse_shape_retract}) for the KIM001 device}{figure.caption.37}{}}
+\newlabel{fig:kim0001_pulse_shape_approach}{{3.3a}{35}{\relax }{figure.caption.40}{}}
+\newlabel{sub@fig:kim0001_pulse_shape_approach}{{a}{35}{\relax }{figure.caption.40}{}}
+\newlabel{fig:kim0001_pulse_shape_retract}{{3.3b}{35}{\relax }{figure.caption.40}{}}
+\newlabel{sub@fig:kim0001_pulse_shape_retract}{{b}{35}{\relax }{figure.caption.40}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.3}{\ignorespaces Approach step (\subref  {fig:kim0001_pulse_shape_approach}) and a retract step (\subref  {fig:kim0001_pulse_shape_retract}) for the KIM001 device. Flatness of curve is not due to oscilloscope saturation. }}{35}{figure.caption.40}\protected@file@percent }
+\newlabel{fig:kim0001_pulse_shape}{{3.3}{35}{Approach step (\subref {fig:kim0001_pulse_shape_approach}) and a retract step (\subref {fig:kim0001_pulse_shape_retract}) for the KIM001 device. Flatness of curve is not due to oscilloscope saturation}{figure.caption.40}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.2.3}Voltage behavior}{35}{subsection.3.2.3}\protected@file@percent }
 \citation{arduino_datasheet}
 \citation{arduino_cpu_datasheet}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.4}{\ignorespaces Retract steps of the KIM0001 for a set Voltage of $125$ after different amount of steps. The voltage spikes beyond the desired voltage at the start and after $200$ steps settles on a voltage of ~$118$ V. }}{36}{figure.caption.38}\protected@file@percent }
-\newlabel{fig:kim0001_voltage_behaviour}{{3.4}{36}{Retract steps of the KIM0001 for a set Voltage of $125$ after different amount of steps. The voltage spikes beyond the desired voltage at the start and after $200$ steps settles on a voltage of ~$118$ V}{figure.caption.38}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.4}{\ignorespaces Retract steps of the KIM0001 for a set Voltage of $125$ after different amount of steps. The voltage spikes beyond the desired voltage at the start and after $200$ steps settles on a voltage of ~$118$ V. }}{36}{figure.caption.41}\protected@file@percent }
+\newlabel{fig:kim0001_voltage_behaviour}{{3.4}{36}{Retract steps of the KIM0001 for a set Voltage of $125$ after different amount of steps. The voltage spikes beyond the desired voltage at the start and after $200$ steps settles on a voltage of ~$118$ V}{figure.caption.41}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {3.3}Mask Aligner controller "Walker"}{36}{section.3.3}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.1}Overview}{36}{subsection.3.3.1}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.2}Signal generation}{36}{subsection.3.3.2}\protected@file@percent }
 \citation{switch_datasheet}
-\newlabel{fig:bessel_filter_unfiltered}{{3.5a}{37}{\relax }{figure.caption.39}{}}
-\newlabel{sub@fig:bessel_filter_unfiltered}{{a}{37}{\relax }{figure.caption.39}{}}
-\newlabel{fig:bessel_filter_filter}{{3.5b}{37}{\relax }{figure.caption.39}{}}
-\newlabel{sub@fig:bessel_filter_filter}{{b}{37}{\relax }{figure.caption.39}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.5}{\ignorespaces (a) aliased simulated signal. (b) 8th order Bessel filtered simulated signal. The amount of aliasing is exaggerated to make the effect more clear. }}{37}{figure.caption.39}\protected@file@percent }
-\newlabel{fig:bessel_filter}{{3.5}{37}{(a) aliased simulated signal. (b) 8th order Bessel filtered simulated signal. The amount of aliasing is exaggerated to make the effect more clear}{figure.caption.39}{}}
-\@writefile{tdo}{\contentsline {todo}{Aliases Signal}{37}{section*.40}\protected@file@percent }
+\newlabel{fig:bessel_filter_unfiltered}{{3.5a}{37}{\relax }{figure.caption.42}{}}
+\newlabel{sub@fig:bessel_filter_unfiltered}{{a}{37}{\relax }{figure.caption.42}{}}
+\newlabel{fig:bessel_filter_filter}{{3.5b}{37}{\relax }{figure.caption.42}{}}
+\newlabel{sub@fig:bessel_filter_filter}{{b}{37}{\relax }{figure.caption.42}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.5}{\ignorespaces (a) aliased simulated signal. (b) 8th order Bessel filtered simulated signal. The amount of aliasing is exaggerated to make the effect more clear. }}{37}{figure.caption.42}\protected@file@percent }
+\newlabel{fig:bessel_filter}{{3.5}{37}{(a) aliased simulated signal. (b) 8th order Bessel filtered simulated signal. The amount of aliasing is exaggerated to make the effect more clear}{figure.caption.42}{}}
+\@writefile{tdo}{\contentsline {todo}{Aliases Signal}{37}{section*.43}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.3}Fast flank}{37}{subsection.3.3.3}\protected@file@percent }
-\newlabel{fig:signal_switch_entry}{{3.6a}{38}{\relax }{figure.caption.41}{}}
-\newlabel{sub@fig:signal_switch_entry}{{a}{38}{\relax }{figure.caption.41}{}}
-\newlabel{fig:signal_switch_switched}{{3.6b}{38}{\relax }{figure.caption.41}{}}
-\newlabel{sub@fig:signal_switch_switched}{{b}{38}{\relax }{figure.caption.41}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.6}{\ignorespaces (a) normal and the inverted signal. (b) the signal achieved by switching between normal and inverted. }}{38}{figure.caption.41}\protected@file@percent }
-\newlabel{fig:signal_switch}{{3.6}{38}{(a) normal and the inverted signal. (b) the signal achieved by switching between normal and inverted}{figure.caption.41}{}}
+\newlabel{fig:signal_switch_entry}{{3.6a}{38}{\relax }{figure.caption.44}{}}
+\newlabel{sub@fig:signal_switch_entry}{{a}{38}{\relax }{figure.caption.44}{}}
+\newlabel{fig:signal_switch_switched}{{3.6b}{38}{\relax }{figure.caption.44}{}}
+\newlabel{sub@fig:signal_switch_switched}{{b}{38}{\relax }{figure.caption.44}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.6}{\ignorespaces (a) normal and the inverted signal. (b) the signal achieved by switching between normal and inverted. }}{38}{figure.caption.44}\protected@file@percent }
+\newlabel{fig:signal_switch}{{3.6}{38}{(a) normal and the inverted signal. (b) the signal achieved by switching between normal and inverted}{figure.caption.44}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.4}Amplification}{38}{subsection.3.3.4}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.5}Programming}{39}{subsection.3.3.5}\protected@file@percent }
-\@writefile{tdo}{\contentsline {todo}{What to write}{39}{section*.42}\protected@file@percent }
-\@writefile{toc}{\contentsline {subsubsection}{Parameters}{39}{section*.43}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Amplitude (amp)}{39}{section*.44}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Voltage (volt)}{39}{section*.45}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Channel}{39}{section*.46}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Max Step}{39}{section*.47}\protected@file@percent }
-\@writefile{toc}{\contentsline {paragraph}{Polarity}{39}{section*.48}\protected@file@percent }
+\@writefile{tdo}{\contentsline {todo}{What should I write with regard to the programming?}{39}{section*.45}\protected@file@percent }
+\@writefile{toc}{\contentsline {subsubsection}{Parameters}{39}{section*.46}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Amplitude (amp)}{39}{section*.47}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Voltage (volt)}{39}{section*.48}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Channel}{39}{section*.49}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Max Step}{39}{section*.50}\protected@file@percent }
+\@writefile{toc}{\contentsline {paragraph}{Polarity}{39}{section*.51}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{39}{subsection.3.3.6}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {3.7}{\ignorespaces (a) approach step and a (b) retract step for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly.}}{40}{figure.caption.49}\protected@file@percent }
-\newlabel{fig:walker_pulse_shape_slow}{{3.7}{40}{(a) approach step and a (b) retract step for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly}{figure.caption.49}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {3.8}{\ignorespaces Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both (a) approach and (b) retract, for a nominal voltage of 80 V (without load). }}{41}{figure.caption.50}\protected@file@percent }
-\newlabel{fig:walker_pulse_shape_fast}{{3.8}{41}{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both (a) approach and (b) retract, for a nominal voltage of 80 V (without load)}{figure.caption.50}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.7}{\ignorespaces (a) approach step and a (b) retract step for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly.}}{40}{figure.caption.52}\protected@file@percent }
+\newlabel{fig:walker_pulse_shape_slow}{{3.7}{40}{(a) approach step and a (b) retract step for the new Walker device \textcolor {tab_red}{(red)} and for comparison the RHK in \textcolor {tab_blue}{(blue)} in an unloaded state for a nominal voltage of 80 V. The dashed \textcolor {tab_green}{green} lines show a timeframe of 1000 $\mu $s around the fast flank, which should be the length of 1 pulse exactly}{figure.caption.52}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.8}{\ignorespaces Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both (a) approach and (b) retract, for a nominal voltage of 80 V (without load). }}{41}{figure.caption.53}\protected@file@percent }
+\newlabel{fig:walker_pulse_shape_fast}{{3.8}{41}{Plots showing the fast Flank of the Walker Signal and the fast flank of the RHK Signal, for both (a) approach and (b) retract, for a nominal voltage of 80 V (without load)}{figure.caption.53}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {3.3.7}Operation with the Mask Aligner}{41}{subsection.3.3.7}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {3.9}{\ignorespaces Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order. }}{42}{figure.caption.51}\protected@file@percent }
-\newlabel{fig:diagram_MA_circ_walker}{{3.9}{42}{Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order}{figure.caption.51}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {3.9}{\ignorespaces Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order. }}{42}{figure.caption.54}\protected@file@percent }
+\newlabel{fig:diagram_MA_circ_walker}{{3.9}{42}{Diagram showing how communication with the Walker and the Lock-in amplifier is done and how they interact with elements in vacuum. Red lines are input, black lines are output lines. The capacitance relay is used to measure $C_i$ in order}{figure.caption.54}{}}
 \@setckpt{chap03}{
 \setcounter{page}{43}
 \setcounter{equation}{1}
@@ -100,7 +100,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap03.tex b/chap03.tex
index 1d45a9bd3064b97f1ba3a06e453081995738e1f5..d3b00118addfc50757eb51429c808a4e4933294a 100644
--- a/chap03.tex
+++ b/chap03.tex
@@ -67,7 +67,7 @@ Both approach and retract show heavy aliasing artifacts, which could lead to the
     \caption{}
 	\label{fig:kim0001_pulse_shape_retract}
     \end{subfigure}
-    \caption{Plots showing both an approach step (\subref{fig:kim0001_pulse_shape_approach}) and a retract step  (\subref{fig:kim0001_pulse_shape_retract}) for the KIM001 device.}
+    \caption{Approach step (\subref{fig:kim0001_pulse_shape_approach}) and a retract step  (\subref{fig:kim0001_pulse_shape_retract}) for the KIM001 device. Flatness of curve is not due to oscilloscope saturation. }
     \label{fig:kim0001_pulse_shape}
 \end{figure}
 
@@ -143,7 +143,7 @@ The Arduino digital output pins $22$, $24$, $26$ and $28$ control, which channel
 Afterward there are $4$ relays, one for each channel that can be shut to prevent any current from being on the output leads, this is mainly a safety measure. The $4$ relays are also controlled by the Arduino from the digital outputs $53$, $51$, $49$ and $47$ for the channels Z1, Z2, Z3 and X respectively. The relays are switched off after a waiting period of $2$ seconds after no signal is supplied to the given channel. 
 
 \subsection{Programming}
-The software used by the Arduino to generate the signal was written in the course of this thesis. It is written in the Arduino's programming language. The software is controlled via commands send over a serial interface. \todo{What to write}
+The software used by the Arduino to generate the signal was written in the course of this thesis. It is written in the Arduino's programming language. The software is controlled via commands send over a serial interface. \todo{What should I write with regard to the programming?}
 
 \subsubsection{Parameters}
 The following parameters can be controlled via the new software:
diff --git a/chap04.aux b/chap04.aux
index 98146e2b9ad3d9c8d7409954a91dc966562821da..bfbd6eee04bf73e9da2903228b5008b91b188a44 100644
--- a/chap04.aux
+++ b/chap04.aux
@@ -5,80 +5,80 @@
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
 \@writefile{toc}{\contentsline {section}{\numberline {4.1}Overview}{43}{section.4.1}\protected@file@percent }
-\newlabel{fig:Repair_Diagram_diagram}{{4.1a}{43}{\relax }{figure.caption.52}{}}
-\newlabel{sub@fig:Repair_Diagram_diagram}{{a}{43}{\relax }{figure.caption.52}{}}
-\newlabel{fig:Repair_Diagram_image}{{4.1b}{43}{\relax }{figure.caption.52}{}}
-\newlabel{sub@fig:Repair_Diagram_image}{{b}{43}{\relax }{figure.caption.52}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.1}{\ignorespaces (\subref  {fig:Repair_Diagram_diagram}) diagram of front view of a single piezo motor with associated nomenclature. Front plate is turned around and moved to the side. (\subref  {fig:Repair_Diagram_image}) shows a roughly corresponding image as a photo of the Mask Aligner. The lower right solder anchor is detached in the image and the lower left solder anchor is bridged with a technique discussed in Section \ref {ch:solder_anchors}}}{43}{figure.caption.52}\protected@file@percent }
-\newlabel{fig:Repair_Diagram}{{4.1}{43}{(\subref {fig:Repair_Diagram_diagram}) diagram of front view of a single piezo motor with associated nomenclature. Front plate is turned around and moved to the side. (\subref {fig:Repair_Diagram_image}) shows a roughly corresponding image as a photo of the Mask Aligner. The lower right solder anchor is detached in the image and the lower left solder anchor is bridged with a technique discussed in Section \ref {ch:solder_anchors}}{figure.caption.52}{}}
+\newlabel{fig:Repair_Diagram_diagram}{{4.1a}{43}{\relax }{figure.caption.55}{}}
+\newlabel{sub@fig:Repair_Diagram_diagram}{{a}{43}{\relax }{figure.caption.55}{}}
+\newlabel{fig:Repair_Diagram_image}{{4.1b}{43}{\relax }{figure.caption.55}{}}
+\newlabel{sub@fig:Repair_Diagram_image}{{b}{43}{\relax }{figure.caption.55}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.1}{\ignorespaces (\subref  {fig:Repair_Diagram_diagram}) diagram of front view of a single piezo motor with associated nomenclature. Front plate is turned around and moved to the side. (\subref  {fig:Repair_Diagram_image}) shows a roughly corresponding image as a photo of the Mask Aligner. The lower right solder anchor is detached in the image and the lower left solder anchor is bridged with a technique discussed in Section \ref {ch:solder_anchors}}}{43}{figure.caption.55}\protected@file@percent }
+\newlabel{fig:Repair_Diagram}{{4.1}{43}{(\subref {fig:Repair_Diagram_diagram}) diagram of front view of a single piezo motor with associated nomenclature. Front plate is turned around and moved to the side. (\subref {fig:Repair_Diagram_image}) shows a roughly corresponding image as a photo of the Mask Aligner. The lower right solder anchor is detached in the image and the lower left solder anchor is bridged with a technique discussed in Section \ref {ch:solder_anchors}}{figure.caption.55}{}}
 \citation{torr_seal}
 \@writefile{toc}{\contentsline {section}{\numberline {4.2}General UHV device preparation}{44}{section.4.2}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {4.2.1}UHV compatible Soldering}{44}{subsection.4.2.1}\protected@file@percent }
 \@writefile{toc}{\contentsline {section}{\numberline {4.3}Soldering anchors}{44}{section.4.3}\protected@file@percent }
 \newlabel{ch:solder_anchors}{{4.3}{44}{Soldering anchors}{section.4.3}{}}
-\newlabel{fig:solder_anchors_diagram_base}{{4.2a}{45}{\relax }{figure.caption.53}{}}
-\newlabel{sub@fig:solder_anchors_diagram_base}{{a}{45}{\relax }{figure.caption.53}{}}
-\newlabel{fig:solder_anchors_diagram_SmallerDot}{{4.2b}{45}{\relax }{figure.caption.53}{}}
-\newlabel{sub@fig:solder_anchors_diagram_SmallerDot}{{b}{45}{\relax }{figure.caption.53}{}}
-\newlabel{fig:solder_anchors_diagram_AlO}{{4.2c}{45}{\relax }{figure.caption.53}{}}
-\newlabel{sub@fig:solder_anchors_diagram_AlO}{{c}{45}{\relax }{figure.caption.53}{}}
-\newlabel{fig:solder_anchors_diagram_GlueTop}{{4.2d}{45}{\relax }{figure.caption.53}{}}
-\newlabel{sub@fig:solder_anchors_diagram_GlueTop}{{d}{45}{\relax }{figure.caption.53}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces (\subref  {fig:solder_anchors_diagram_base}) solder anchor interfering with the prism due to deterioration over time. (\subref  {fig:solder_anchors_diagram_SmallerDot}) making the solder dot smaller. (\subref  {fig:solder_anchors_diagram_AlO}) replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate. (\subref  {fig:solder_anchors_diagram_GlueTop}) putting the anchor with glue on the top/bottom of the solder ceramic. The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray.}}{45}{figure.caption.53}\protected@file@percent }
-\newlabel{fig:solder_anchors_diagram}{{4.2}{45}{(\subref {fig:solder_anchors_diagram_base}) solder anchor interfering with the prism due to deterioration over time. (\subref {fig:solder_anchors_diagram_SmallerDot}) making the solder dot smaller. (\subref {fig:solder_anchors_diagram_AlO}) replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate. (\subref {fig:solder_anchors_diagram_GlueTop}) putting the anchor with glue on the top/bottom of the solder ceramic. The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray}{figure.caption.53}{}}
-\newlabel{fig:solder_anchors_examples_shear_01}{{4.3a}{46}{\relax }{figure.caption.54}{}}
-\newlabel{sub@fig:solder_anchors_examples_shear_01}{{a}{46}{\relax }{figure.caption.54}{}}
-\newlabel{fig:solder_anchors_examples_shear_02}{{4.3b}{46}{\relax }{figure.caption.54}{}}
-\newlabel{sub@fig:solder_anchors_examples_shear_02}{{b}{46}{\relax }{figure.caption.54}{}}
-\newlabel{fig:solder_anchors_examples_glue_bottom}{{4.3c}{46}{\relax }{figure.caption.54}{}}
-\newlabel{sub@fig:solder_anchors_examples_glue_bottom}{{c}{46}{\relax }{figure.caption.54}{}}
-\newlabel{fig:solder_anchors_examples_AlO}{{4.3d}{46}{\relax }{figure.caption.54}{}}
-\newlabel{sub@fig:solder_anchors_examples_AlO}{{d}{46}{\relax }{figure.caption.54}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.3}{\ignorespaces Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref  {fig:solder_anchors_examples_shear_01}) initial state of a solder ceramic interfering with the prism. (\subref  {fig:solder_anchors_examples_shear_02}) solder ceramic from before after some of the solder was carefully taken off. (\subref  {fig:solder_anchors_examples_glue_bottom}) a solder anchor attached to the bottom of a previously used solder ceramic. (\subref  {fig:solder_anchors_examples_AlO}) replacement of a solder ceramic with a thinner \ce {Al2O3} plate. }}{46}{figure.caption.54}\protected@file@percent }
-\newlabel{fig:solder_anchors_examples}{{4.3}{46}{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_shear_01}) initial state of a solder ceramic interfering with the prism. (\subref {fig:solder_anchors_examples_shear_02}) solder ceramic from before after some of the solder was carefully taken off. (\subref {fig:solder_anchors_examples_glue_bottom}) a solder anchor attached to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) replacement of a solder ceramic with a thinner \ce {Al2O3} plate}{figure.caption.54}{}}
+\newlabel{fig:solder_anchors_diagram_base}{{4.2a}{45}{\relax }{figure.caption.56}{}}
+\newlabel{sub@fig:solder_anchors_diagram_base}{{a}{45}{\relax }{figure.caption.56}{}}
+\newlabel{fig:solder_anchors_diagram_SmallerDot}{{4.2b}{45}{\relax }{figure.caption.56}{}}
+\newlabel{sub@fig:solder_anchors_diagram_SmallerDot}{{b}{45}{\relax }{figure.caption.56}{}}
+\newlabel{fig:solder_anchors_diagram_AlO}{{4.2c}{45}{\relax }{figure.caption.56}{}}
+\newlabel{sub@fig:solder_anchors_diagram_AlO}{{c}{45}{\relax }{figure.caption.56}{}}
+\newlabel{fig:solder_anchors_diagram_GlueTop}{{4.2d}{45}{\relax }{figure.caption.56}{}}
+\newlabel{sub@fig:solder_anchors_diagram_GlueTop}{{d}{45}{\relax }{figure.caption.56}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.2}{\ignorespaces (\subref  {fig:solder_anchors_diagram_base}) solder anchor interfering with the prism due to deterioration over time. (\subref  {fig:solder_anchors_diagram_SmallerDot}) making the solder dot smaller. (\subref  {fig:solder_anchors_diagram_AlO}) replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate. (\subref  {fig:solder_anchors_diagram_GlueTop}) putting the anchor with glue on the top/bottom of the solder ceramic. The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray.}}{45}{figure.caption.56}\protected@file@percent }
+\newlabel{fig:solder_anchors_diagram}{{4.2}{45}{(\subref {fig:solder_anchors_diagram_base}) solder anchor interfering with the prism due to deterioration over time. (\subref {fig:solder_anchors_diagram_SmallerDot}) making the solder dot smaller. (\subref {fig:solder_anchors_diagram_AlO}) replacing the solder anchor ceramic with a much smaller \ce {Al2O3} plate. (\subref {fig:solder_anchors_diagram_GlueTop}) putting the anchor with glue on the top/bottom of the solder ceramic. The prism is depicted in blue, the cable in brown, black represents the Mask Aligner body, solder ceramic in yellow and solder in gray}{figure.caption.56}{}}
+\newlabel{fig:solder_anchors_examples_shear_01}{{4.3a}{46}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:solder_anchors_examples_shear_01}{{a}{46}{\relax }{figure.caption.57}{}}
+\newlabel{fig:solder_anchors_examples_shear_02}{{4.3b}{46}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:solder_anchors_examples_shear_02}{{b}{46}{\relax }{figure.caption.57}{}}
+\newlabel{fig:solder_anchors_examples_glue_bottom}{{4.3c}{46}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:solder_anchors_examples_glue_bottom}{{c}{46}{\relax }{figure.caption.57}{}}
+\newlabel{fig:solder_anchors_examples_AlO}{{4.3d}{46}{\relax }{figure.caption.57}{}}
+\newlabel{sub@fig:solder_anchors_examples_AlO}{{d}{46}{\relax }{figure.caption.57}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.3}{\ignorespaces Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref  {fig:solder_anchors_examples_shear_01}) initial state of a solder ceramic interfering with the prism. (\subref  {fig:solder_anchors_examples_shear_02}) solder ceramic from before after some of the solder was carefully taken off. (\subref  {fig:solder_anchors_examples_glue_bottom}) a solder anchor attached to the bottom of a previously used solder ceramic. (\subref  {fig:solder_anchors_examples_AlO}) replacement of a solder ceramic with a thinner \ce {Al2O3} plate. }}{46}{figure.caption.57}\protected@file@percent }
+\newlabel{fig:solder_anchors_examples}{{4.3}{46}{Examples of the different approaches taken to solve the issues with the solder anchor points. (\subref {fig:solder_anchors_examples_shear_01}) initial state of a solder ceramic interfering with the prism. (\subref {fig:solder_anchors_examples_shear_02}) solder ceramic from before after some of the solder was carefully taken off. (\subref {fig:solder_anchors_examples_glue_bottom}) a solder anchor attached to the bottom of a previously used solder ceramic. (\subref {fig:solder_anchors_examples_AlO}) replacement of a solder ceramic with a thinner \ce {Al2O3} plate}{figure.caption.57}{}}
 \citation{Olschewski}
 \@writefile{toc}{\contentsline {section}{\numberline {4.4}Piezo regluing}{47}{section.4.4}\protected@file@percent }
 \newlabel{sec:piezo_reglue}{{4.4}{47}{Piezo regluing}{section.4.4}{}}
-\newlabel{fig:Z3_reglue_process_off}{{4.4a}{47}{\relax }{figure.caption.55}{}}
-\newlabel{sub@fig:Z3_reglue_process_off}{{a}{47}{\relax }{figure.caption.55}{}}
-\newlabel{fig:Z3_reglue_process_scratched}{{4.4b}{47}{\relax }{figure.caption.55}{}}
-\newlabel{sub@fig:Z3_reglue_process_scratched}{{b}{47}{\relax }{figure.caption.55}{}}
-\newlabel{fig:Z3_reglue_process_dot}{{4.4c}{47}{\relax }{figure.caption.55}{}}
-\newlabel{sub@fig:Z3_reglue_process_dot}{{c}{47}{\relax }{figure.caption.55}{}}
-\newlabel{fig:Z3_reglue_process_down}{{4.4d}{47}{\relax }{figure.caption.55}{}}
-\newlabel{sub@fig:Z3_reglue_process_down}{{d}{47}{\relax }{figure.caption.55}{}}
-\@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) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing.}}{47}{figure.caption.55}\protected@file@percent }
-\newlabel{fig:Z3_reglue_process}{{4.4}{47}{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing}{figure.caption.55}{}}
-\@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 $.}}{48}{figure.caption.56}\protected@file@percent }
-\newlabel{fig:Z3_after reglue}{{4.5}{48}{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.56}{}}
+\newlabel{fig:Z3_reglue_process_off}{{4.4a}{47}{\relax }{figure.caption.58}{}}
+\newlabel{sub@fig:Z3_reglue_process_off}{{a}{47}{\relax }{figure.caption.58}{}}
+\newlabel{fig:Z3_reglue_process_scratched}{{4.4b}{47}{\relax }{figure.caption.58}{}}
+\newlabel{sub@fig:Z3_reglue_process_scratched}{{b}{47}{\relax }{figure.caption.58}{}}
+\newlabel{fig:Z3_reglue_process_dot}{{4.4c}{47}{\relax }{figure.caption.58}{}}
+\newlabel{sub@fig:Z3_reglue_process_dot}{{c}{47}{\relax }{figure.caption.58}{}}
+\newlabel{fig:Z3_reglue_process_down}{{4.4d}{47}{\relax }{figure.caption.58}{}}
+\newlabel{sub@fig:Z3_reglue_process_down}{{d}{47}{\relax }{figure.caption.58}{}}
+\@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) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing.}}{47}{figure.caption.58}\protected@file@percent }
+\newlabel{fig:Z3_reglue_process}{{4.4}{47}{The re-gluing process shown for the upper left piezo on Z3 that was no longer attached to the Mask Aligner Body. (a) detached piezo. Remains of the EPO-TEK H70E epoxy glue are visible as brown stains on both the Mask Aligner Body and the piezo stack. (b) remains of glue were scratched off carefully. (c) shows the applied dot of Torr Seal epoxy glue. (d) two nuts and the prism used as weights and alignment tools during curing}{figure.caption.58}{}}
+\@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 $.}}{48}{figure.caption.59}\protected@file@percent }
+\newlabel{fig:Z3_after reglue}{{4.5}{48}{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.59}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {4.5}Z3 motor}{48}{section.4.5}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.6}{\ignorespaces Step size against screw rotation data obtained to calibrate the screw firmness for Z2 and Z3. Larger x-axis values means less firm screw. \textcolor {tab_blue}{Blue} and \textcolor {tab_orange}{orange} show Z3 before swapping front plate with Z1, \textcolor {tab_green}{green} and \textcolor {tab_red}{red} show after.}}{49}{figure.caption.57}\protected@file@percent }
-\newlabel{fig:Z3_screw_rot}{{4.6}{49}{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.57}{}}
+\@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.}}{49}{figure.caption.60}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot}{{4.6}{49}{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.60}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {4.5.1}Front plate repair}{49}{subsection.4.5.1}\protected@file@percent }
 \citation{Olschewski}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces Screw rotation calibration data for Z2 and Z3 after front plate repairs.}}{50}{figure.caption.58}\protected@file@percent }
-\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{50}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.58}{}}
-\newlabel{fig:Front_plate_repair_tool}{{4.8a}{51}{\relax }{figure.caption.59}{}}
-\newlabel{sub@fig:Front_plate_repair_tool}{{a}{51}{\relax }{figure.caption.59}{}}
-\newlabel{fig:Front_plate_repair_plate}{{4.8b}{51}{\relax }{figure.caption.59}{}}
-\newlabel{sub@fig:Front_plate_repair_plate}{{b}{51}{\relax }{figure.caption.59}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces (\subref  {fig:Front_plate_repair_tool}) Solidworks explosive diagram of the Z3 front plate with the alignment tool. (\subref  {fig:Front_plate_repair_plate}) final front plate assembled.}}{51}{figure.caption.59}\protected@file@percent }
-\newlabel{fig:Front_plate_repair}{{4.8}{51}{(\subref {fig:Front_plate_repair_tool}) Solidworks explosive diagram of the Z3 front plate with the alignment tool. (\subref {fig:Front_plate_repair_plate}) final front plate assembled}{figure.caption.59}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.7}{\ignorespaces Screw rotation calibration data for Z2 and Z3 after front plate repairs.}}{50}{figure.caption.61}\protected@file@percent }
+\newlabel{fig:Z3_screw_rot_after_rep}{{4.7}{50}{Screw rotation calibration data for Z2 and Z3 after front plate repairs}{figure.caption.61}{}}
+\newlabel{fig:Front_plate_repair_tool}{{4.8a}{51}{\relax }{figure.caption.62}{}}
+\newlabel{sub@fig:Front_plate_repair_tool}{{a}{51}{\relax }{figure.caption.62}{}}
+\newlabel{fig:Front_plate_repair_plate}{{4.8b}{51}{\relax }{figure.caption.62}{}}
+\newlabel{sub@fig:Front_plate_repair_plate}{{b}{51}{\relax }{figure.caption.62}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.8}{\ignorespaces (\subref  {fig:Front_plate_repair_tool}) Solidworks explosive diagram of the Z3 front plate with the alignment tool. (\subref  {fig:Front_plate_repair_plate}) final front plate assembled.}}{51}{figure.caption.62}\protected@file@percent }
+\newlabel{fig:Front_plate_repair}{{4.8}{51}{(\subref {fig:Front_plate_repair_tool}) Solidworks explosive diagram of the Z3 front plate with the alignment tool. (\subref {fig:Front_plate_repair_plate}) final front plate assembled}{figure.caption.62}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {4.5.2}Small capacitance stack}{51}{subsection.4.5.2}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezo stacks of the motor Z3. }}{52}{figure.caption.60}\protected@file@percent }
-\newlabel{fig:Z3_weaker_stack}{{4.9}{52}{The measured capacitance values for the piezo stacks of the motor Z3}{figure.caption.60}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {4.9}{\ignorespaces The measured capacitance values for the piezo stacks of the motor Z3. }}{52}{figure.caption.63}\protected@file@percent }
+\newlabel{fig:Z3_weaker_stack}{{4.9}{52}{The measured capacitance values for the piezo stacks of the motor Z3}{figure.caption.63}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {4.6}Feed through cabling optimizations}{52}{section.4.6}\protected@file@percent }
-\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{53}{\relax }{figure.caption.61}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{53}{\relax }{figure.caption.61}{}}
-\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{53}{\relax }{figure.caption.61}{}}
-\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{53}{\relax }{figure.caption.61}{}}
-\@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.}}{53}{figure.caption.61}\protected@file@percent }
-\newlabel{fig:Feedthrough_Repairs}{{4.10}{53}{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.61}{}}
-\@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.}}{53}{table.caption.62}\protected@file@percent }
-\newlabel{tab:cross_cap_after_repair}{{4.1}{53}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables}{table.caption.62}{}}
+\newlabel{fig:Feedthrough_Repairs_left}{{4.10a}{53}{\relax }{figure.caption.64}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_left}{{a}{53}{\relax }{figure.caption.64}{}}
+\newlabel{fig:Feedthrough_Repairs_right}{{4.10b}{53}{\relax }{figure.caption.64}{}}
+\newlabel{sub@fig:Feedthrough_Repairs_right}{{b}{53}{\relax }{figure.caption.64}{}}
+\@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.}}{53}{figure.caption.64}\protected@file@percent }
+\newlabel{fig:Feedthrough_Repairs}{{4.10}{53}{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.64}{}}
+\@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.}}{53}{table.caption.65}\protected@file@percent }
+\newlabel{tab:cross_cap_after_repair}{{4.1}{53}{The cross capacitance values of mask 1 before and after the optimizations of the feedthrough and capacitance sensor cables}{table.caption.65}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {4.7}Final test}{53}{section.4.7}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {4.11}{\ignorespaces The final calibration that was performed, after all the optimizations were done. Driving of the motors was done in 2000, 4000, 6000, 8000 and 10000 steps under ambient conditions.}}{54}{figure.caption.63}\protected@file@percent }
-\newlabel{fig:calibration_after_repair}{{4.11}{54}{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.63}{}}
+\@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.}}{54}{figure.caption.66}\protected@file@percent }
+\newlabel{fig:calibration_after_repair}{{4.11}{54}{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.66}{}}
 \@setckpt{chap04}{
 \setcounter{page}{55}
 \setcounter{equation}{0}
@@ -109,7 +109,7 @@
 \setcounter{subfigure}{0}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/chap05.aux b/chap05.aux
index 4117ae739f6cd2646eacf1cf53ee8de597b9ec0e..0b1e645c707cc6859088865c240d40c1145f176f 100644
--- a/chap05.aux
+++ b/chap05.aux
@@ -4,91 +4,91 @@
 \@writefile{lof}{\addvspace {10\p@ }}
 \@writefile{lot}{\addvspace {10\p@ }}
 \@writefile{toc}{\contentsline {section}{\numberline {5.1}Evaporation configuration}{55}{section.5.1}\protected@file@percent }
-\@writefile{lof}{\contentsline {figure}{\numberline {5.1}{\ignorespaces The approach curve measured for field 1 until full contact.}}{55}{figure.caption.64}\protected@file@percent }
-\newlabel{fig:evaporation_approach_curve}{{5.1}{55}{The approach curve measured for field 1 until full contact}{figure.caption.64}{}}
-\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}}{56}{table.caption.65}\protected@file@percent }
-\newlabel{tab:evaporation_settings}{{5.1}{56}{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}{table.caption.65}{}}
-\newlabel{fig:Evaporation_diagramm_sample_img}{{5.2a}{57}{\relax }{figure.caption.66}{}}
-\newlabel{sub@fig:Evaporation_diagramm_sample_img}{{a}{57}{\relax }{figure.caption.66}{}}
-\newlabel{fig:Evaporation_diagramm_mask_img}{{5.2b}{57}{\relax }{figure.caption.66}{}}
-\newlabel{sub@fig:Evaporation_diagramm_mask_img}{{b}{57}{\relax }{figure.caption.66}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.2}{\ignorespaces (\subref  {fig:Evaporation_diagramm_sample_img}) diagram showing the Evaporation performed on the sample. Red squares represent the positions of the evaporated fields. The number shows the order of evaporations. Distances are measured using an optical microscope. Fields are at a $10^\circ $ angle with respect to the sample holder. (\subref  {fig:Evaporation_diagramm_mask_img}) microscope image of the mask taken before evaporation. The mask holder is placed straight in the microscope. The mask itself is angled on the mask holder.}}{57}{figure.caption.66}\protected@file@percent }
-\newlabel{fig:Evaporation_diagramm}{{5.2}{57}{(\subref {fig:Evaporation_diagramm_sample_img}) diagram showing the Evaporation performed on the sample. Red squares represent the positions of the evaporated fields. The number shows the order of evaporations. Distances are measured using an optical microscope. Fields are at a $10^\circ $ angle with respect to the sample holder. (\subref {fig:Evaporation_diagramm_mask_img}) microscope image of the mask taken before evaporation. The mask holder is placed straight in the microscope. The mask itself is angled on the mask holder}{figure.caption.66}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.1}{\ignorespaces The approach curve measured for field 1 until full contact.}}{55}{figure.caption.67}\protected@file@percent }
+\newlabel{fig:evaporation_approach_curve}{{5.1}{55}{The approach curve measured for field 1 until full contact}{figure.caption.67}{}}
+\@writefile{lot}{\contentsline {table}{\numberline {5.1}{\ignorespaces Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}}{56}{table.caption.68}\protected@file@percent }
+\newlabel{tab:evaporation_settings}{{5.1}{56}{Table with all the evaporation parameters. FIL stands for the current applied to the heating Filament, EMIS stands for the emission current, FLUX is the measured molecular flux. Press is the maximum pressure in the chamber during the evaporation, and T is the maximal temperature the crucible reached during the evaporation. The voltage was changed to ensure FLUX was in the desired range between $450-520$}{table.caption.68}{}}
+\newlabel{fig:Evaporation_diagramm_sample_img}{{5.2a}{57}{\relax }{figure.caption.69}{}}
+\newlabel{sub@fig:Evaporation_diagramm_sample_img}{{a}{57}{\relax }{figure.caption.69}{}}
+\newlabel{fig:Evaporation_diagramm_mask_img}{{5.2b}{57}{\relax }{figure.caption.69}{}}
+\newlabel{sub@fig:Evaporation_diagramm_mask_img}{{b}{57}{\relax }{figure.caption.69}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.2}{\ignorespaces (\subref  {fig:Evaporation_diagramm_sample_img}) diagram showing the Evaporation performed on the sample. Red squares represent the positions of the evaporated fields. The number shows the order of evaporations. Distances are measured using an optical microscope. Fields are at a $10^\circ $ angle with respect to the sample holder. (\subref  {fig:Evaporation_diagramm_mask_img}) microscope image of the mask taken before evaporation. The mask holder is placed straight in the microscope. The mask itself is angled on the mask holder.}}{57}{figure.caption.69}\protected@file@percent }
+\newlabel{fig:Evaporation_diagramm}{{5.2}{57}{(\subref {fig:Evaporation_diagramm_sample_img}) diagram showing the Evaporation performed on the sample. Red squares represent the positions of the evaporated fields. The number shows the order of evaporations. Distances are measured using an optical microscope. Fields are at a $10^\circ $ angle with respect to the sample holder. (\subref {fig:Evaporation_diagramm_mask_img}) microscope image of the mask taken before evaporation. The mask holder is placed straight in the microscope. The mask itself is angled on the mask holder}{figure.caption.69}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {5.2}Contamination}{57}{section.5.2}\protected@file@percent }
-\newlabel{fig:evaporation_contamination_img}{{5.3a}{58}{\relax }{figure.caption.67}{}}
-\newlabel{sub@fig:evaporation_contamination_img}{{a}{58}{\relax }{figure.caption.67}{}}
-\newlabel{fig:evaporation_contamination_anal}{{5.3b}{58}{\relax }{figure.caption.67}{}}
-\newlabel{sub@fig:evaporation_contamination_anal}{{b}{58}{\relax }{figure.caption.67}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.3}{\ignorespaces (\subref  {fig:evaporation_contamination_img}) AFM image of field $3$ without any grain removal applied. Data was obtained on multiple different spots on the sample. (\subref  {fig:evaporation_contamination_anal}) line cuts obtained from contamination particles. \textcolor {tab_red}{Red} and \textcolor {tab_green}{green} lines show the average height and width of the contamination particles obtained from peak fits.}}{58}{figure.caption.67}\protected@file@percent }
-\newlabel{fig:evaporation_contamination}{{5.3}{58}{(\subref {fig:evaporation_contamination_img}) AFM image of field $3$ without any grain removal applied. Data was obtained on multiple different spots on the sample. (\subref {fig:evaporation_contamination_anal}) line cuts obtained from contamination particles. \textcolor {tab_red}{Red} and \textcolor {tab_green}{green} lines show the average height and width of the contamination particles obtained from peak fits}{figure.caption.67}{}}
+\newlabel{fig:evaporation_contamination_img}{{5.3a}{58}{\relax }{figure.caption.70}{}}
+\newlabel{sub@fig:evaporation_contamination_img}{{a}{58}{\relax }{figure.caption.70}{}}
+\newlabel{fig:evaporation_contamination_anal}{{5.3b}{58}{\relax }{figure.caption.70}{}}
+\newlabel{sub@fig:evaporation_contamination_anal}{{b}{58}{\relax }{figure.caption.70}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.3}{\ignorespaces (\subref  {fig:evaporation_contamination_img}) AFM image of field $3$ without any grain removal applied. Data was obtained on multiple different spots on the sample. (\subref  {fig:evaporation_contamination_anal}) line cuts obtained from contamination particles. \textcolor {tab_red}{Red} and \textcolor {tab_green}{green} lines show the average height and width of the contamination particles obtained from peak fits.}}{58}{figure.caption.70}\protected@file@percent }
+\newlabel{fig:evaporation_contamination}{{5.3}{58}{(\subref {fig:evaporation_contamination_img}) AFM image of field $3$ without any grain removal applied. Data was obtained on multiple different spots on the sample. (\subref {fig:evaporation_contamination_anal}) line cuts obtained from contamination particles. \textcolor {tab_red}{Red} and \textcolor {tab_green}{green} lines show the average height and width of the contamination particles obtained from peak fits}{figure.caption.70}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {5.3}Penumbra}{58}{section.5.3}\protected@file@percent }
-\newlabel{fig:penumbra_tilt_sigmas}{{5.4a}{59}{\relax }{figure.caption.68}{}}
-\newlabel{sub@fig:penumbra_tilt_sigmas}{{a}{59}{\relax }{figure.caption.68}{}}
-\newlabel{fig:Evaporation_diagramm_field}{{5.4b}{59}{\relax }{figure.caption.68}{}}
-\newlabel{sub@fig:Evaporation_diagramm_field}{{b}{59}{\relax }{figure.caption.68}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.4}{\ignorespaces (\subref  {fig:penumbra_tilt_sigmas}) AFM image of evaporated \ce {Pb} dot illustrating the penumbral widths used for evaporation analysis $\sigma _s$ and $\sigma _l$, depicted in \textcolor {tab_red}{red}, and the major axis of the tilt \textcolor {tab_green}{(green)}. $\sigma _s$ is drawn larger than actually measured, to aid visibility. The \textcolor {tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data is from Evaporation 5. (\subref  {fig:Evaporation_diagramm_field}) AFM image of the top right part of field $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field.}}{59}{figure.caption.68}\protected@file@percent }
-\newlabel{fig:penumbra_tilt_sigmas_and_field_show}{{5.4}{59}{(\subref {fig:penumbra_tilt_sigmas}) AFM image of evaporated \ce {Pb} dot illustrating the penumbral widths used for evaporation analysis $\sigma _s$ and $\sigma _l$, depicted in \textcolor {tab_red}{red}, and the major axis of the tilt \textcolor {tab_green}{(green)}. $\sigma _s$ is drawn larger than actually measured, to aid visibility. The \textcolor {tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data is from Evaporation 5. (\subref {fig:Evaporation_diagramm_field}) AFM image of the top right part of field $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field}{figure.caption.68}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.5}{\ignorespaces Example of the analysis conducted on each of the recorded dots for a single line cut. (a) raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) cleaned image. The black lines in (b) show how multiple line cuts were obtained on a single image to obtain values for $\sigma _s$ and $\sigma _l$. The fit parameters are the two different penumbra widths induced by the tilt $\sigma _s$ and $\sigma _l$ for a single line cut. (c) line cut data from one line as an example. This line cut was obtained from \textcolor {tab_green}{(green)} line in (b). }}{61}{figure.caption.69}\protected@file@percent }
-\newlabel{fig:evaporation_analysis}{{5.5}{61}{Example of the analysis conducted on each of the recorded dots for a single line cut. (a) raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) cleaned image. The black lines in (b) show how multiple line cuts were obtained on a single image to obtain values for $\sigma _s$ and $\sigma _l$. The fit parameters are the two different penumbra widths induced by the tilt $\sigma _s$ and $\sigma _l$ for a single line cut. (c) line cut data from one line as an example. This line cut was obtained from \textcolor {tab_green}{(green)} line in (b)}{figure.caption.69}{}}
-\newlabel{fig:evaporation_measured_penumbra_sigs}{{5.6a}{62}{\relax }{figure.caption.70}{}}
-\newlabel{sub@fig:evaporation_measured_penumbra_sigs}{{a}{62}{\relax }{figure.caption.70}{}}
-\newlabel{fig:evaporation_measured_penumbra_sigl}{{5.6b}{62}{\relax }{figure.caption.70}{}}
-\newlabel{sub@fig:evaporation_measured_penumbra_sigl}{{b}{62}{\relax }{figure.caption.70}{}}
-\newlabel{fig:evaporation_measured_penumbra_height}{{5.6c}{62}{\relax }{figure.caption.70}{}}
-\newlabel{sub@fig:evaporation_measured_penumbra_height}{{c}{62}{\relax }{figure.caption.70}{}}
-\newlabel{fig:evaporation_measured_penumbra_circle_r}{{5.6d}{62}{\relax }{figure.caption.70}{}}
-\newlabel{sub@fig:evaporation_measured_penumbra_circle_r}{{d}{62}{\relax }{figure.caption.70}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.6}{\ignorespaces Data obtained from the previously described method for each of the 5 evaporations, one dot each from the center, the left, the right, the bottom and the top. (\subref  {fig:evaporation_measured_penumbra_sigs})smaller penumbra $\sigma _s$. (\subref  {fig:evaporation_measured_penumbra_sigl}) larger penumbra $\sigma _l$. (\subref  {fig:evaporation_measured_penumbra_height}) height of the dot. (\subref  {fig:evaporation_measured_penumbra_circle_r}) diameter of the circle.}}{62}{figure.caption.70}\protected@file@percent }
-\newlabel{fig:evaporation_measured_penumbra}{{5.6}{62}{Data obtained from the previously described method for each of the 5 evaporations, one dot each from the center, the left, the right, the bottom and the top. (\subref {fig:evaporation_measured_penumbra_sigs})smaller penumbra $\sigma _s$. (\subref {fig:evaporation_measured_penumbra_sigl}) larger penumbra $\sigma _l$. (\subref {fig:evaporation_measured_penumbra_height}) height of the dot. (\subref {fig:evaporation_measured_penumbra_circle_r}) diameter of the circle}{figure.caption.70}{}}
+\newlabel{fig:penumbra_tilt_sigmas}{{5.4a}{59}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:penumbra_tilt_sigmas}{{a}{59}{\relax }{figure.caption.71}{}}
+\newlabel{fig:Evaporation_diagramm_field}{{5.4b}{59}{\relax }{figure.caption.71}{}}
+\newlabel{sub@fig:Evaporation_diagramm_field}{{b}{59}{\relax }{figure.caption.71}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.4}{\ignorespaces (\subref  {fig:penumbra_tilt_sigmas}) AFM image of evaporated \ce {Pb} dot illustrating the penumbral widths used for evaporation analysis $\sigma _s$ and $\sigma _l$, depicted in \textcolor {tab_red}{red}, and the major axis of the tilt \textcolor {tab_green}{(green)}. $\sigma _s$ is drawn larger than actually measured, to aid visibility. The \textcolor {tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data is from Evaporation 5. (\subref  {fig:Evaporation_diagramm_field}) AFM image of the top right part of field $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field.}}{59}{figure.caption.71}\protected@file@percent }
+\newlabel{fig:penumbra_tilt_sigmas_and_field_show}{{5.4}{59}{(\subref {fig:penumbra_tilt_sigmas}) AFM image of evaporated \ce {Pb} dot illustrating the penumbral widths used for evaporation analysis $\sigma _s$ and $\sigma _l$, depicted in \textcolor {tab_red}{red}, and the major axis of the tilt \textcolor {tab_green}{(green)}. $\sigma _s$ is drawn larger than actually measured, to aid visibility. The \textcolor {tab_blue}{blue} lines are the major $a$ and minor $b$ axis of the ellipse formed on the evaporated dot. Inset shows the same image in the phase data. The data is from Evaporation 5. (\subref {fig:Evaporation_diagramm_field}) AFM image of the top right part of field $3$. Grains were reduced using post-processing. Black circles show the dots chosen for further examination on this particular field}{figure.caption.71}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.5}{\ignorespaces Example of the analysis conducted on each of the recorded dots for a single line cut. (a) raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) cleaned image. The black lines in (b) show how multiple line cuts were obtained on a single image to obtain values for $\sigma _s$ and $\sigma _l$. The fit parameters are the two different penumbra widths induced by the tilt $\sigma _s$ and $\sigma _l$ for a single line cut. (c) line cut data from one line as an example. This line cut was obtained from \textcolor {tab_green}{(green)} line in (b). }}{61}{figure.caption.72}\protected@file@percent }
+\newlabel{fig:evaporation_analysis}{{5.5}{61}{Example of the analysis conducted on each of the recorded dots for a single line cut. (a) raw AFM data before cleaning with a large amount of very bright contaminant particles. (b) cleaned image. The black lines in (b) show how multiple line cuts were obtained on a single image to obtain values for $\sigma _s$ and $\sigma _l$. The fit parameters are the two different penumbra widths induced by the tilt $\sigma _s$ and $\sigma _l$ for a single line cut. (c) line cut data from one line as an example. This line cut was obtained from \textcolor {tab_green}{(green)} line in (b)}{figure.caption.72}{}}
+\newlabel{fig:evaporation_measured_penumbra_sigs}{{5.6a}{62}{\relax }{figure.caption.73}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_sigs}{{a}{62}{\relax }{figure.caption.73}{}}
+\newlabel{fig:evaporation_measured_penumbra_sigl}{{5.6b}{62}{\relax }{figure.caption.73}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_sigl}{{b}{62}{\relax }{figure.caption.73}{}}
+\newlabel{fig:evaporation_measured_penumbra_height}{{5.6c}{62}{\relax }{figure.caption.73}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_height}{{c}{62}{\relax }{figure.caption.73}{}}
+\newlabel{fig:evaporation_measured_penumbra_circle_r}{{5.6d}{62}{\relax }{figure.caption.73}{}}
+\newlabel{sub@fig:evaporation_measured_penumbra_circle_r}{{d}{62}{\relax }{figure.caption.73}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.6}{\ignorespaces Data obtained from the previously described method for each of the 5 evaporations, one dot each from the center, the left, the right, the bottom and the top. (\subref  {fig:evaporation_measured_penumbra_sigs})smaller penumbra $\sigma _s$. (\subref  {fig:evaporation_measured_penumbra_sigl}) larger penumbra $\sigma _l$. (\subref  {fig:evaporation_measured_penumbra_height}) height of the dot. (\subref  {fig:evaporation_measured_penumbra_circle_r}) diameter of the circle.}}{62}{figure.caption.73}\protected@file@percent }
+\newlabel{fig:evaporation_measured_penumbra}{{5.6}{62}{Data obtained from the previously described method for each of the 5 evaporations, one dot each from the center, the left, the right, the bottom and the top. (\subref {fig:evaporation_measured_penumbra_sigs})smaller penumbra $\sigma _s$. (\subref {fig:evaporation_measured_penumbra_sigl}) larger penumbra $\sigma _l$. (\subref {fig:evaporation_measured_penumbra_height}) height of the dot. (\subref {fig:evaporation_measured_penumbra_circle_r}) diameter of the circle}{figure.caption.73}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {5.4}Tilt and deformation}{63}{section.5.4}\protected@file@percent }
-\newlabel{fig:evaporation_tilts_example}{{5.7a}{64}{\relax }{figure.caption.71}{}}
-\newlabel{sub@fig:evaporation_tilts_example}{{a}{64}{\relax }{figure.caption.71}{}}
-\newlabel{fig:evaporation_tilts_all}{{5.7b}{64}{\relax }{figure.caption.71}{}}
-\newlabel{sub@fig:evaporation_tilts_all}{{b}{64}{\relax }{figure.caption.71}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.7}{\ignorespaces (\subref  {fig:evaporation_tilts_example}) image of the reconstruction of the tilt angle for Field 3. (\subref  {fig:evaporation_tilts_all}) the same for all fields. 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 in this case are the high resolution AFM scans of single dots.}}{64}{figure.caption.71}\protected@file@percent }
-\newlabel{fig:evaporation_tilts}{{5.7}{64}{(\subref {fig:evaporation_tilts_example}) image of the reconstruction of the tilt angle for Field 3. (\subref {fig:evaporation_tilts_all}) the same for all fields. 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 in this case are the high resolution AFM scans of single dots}{figure.caption.71}{}}
-\newlabel{fig:evaporation_SEM_sample}{{5.8a}{65}{\relax }{figure.caption.72}{}}
-\newlabel{sub@fig:evaporation_SEM_sample}{{a}{65}{\relax }{figure.caption.72}{}}
-\newlabel{fig:evaporation_SEM_mask}{{5.8b}{65}{\relax }{figure.caption.72}{}}
-\newlabel{sub@fig:evaporation_SEM_mask}{{b}{65}{\relax }{figure.caption.72}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces (\subref  {fig:evaporation_SEM_sample}) SEM images of field 2 on the sample. (\subref  {fig:evaporation_SEM_mask}) SEM image of the mask. The inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects.}}{65}{figure.caption.72}\protected@file@percent }
-\newlabel{fig:evaporation_SEM}{{5.8}{65}{(\subref {fig:evaporation_SEM_sample}) SEM images of field 2 on the sample. (\subref {fig:evaporation_SEM_mask}) SEM image of the mask. The inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects}{figure.caption.72}{}}
-\newlabel{fig:evaporation_SEM_analysis_clog}{{5.9a}{66}{\relax }{figure.caption.73}{}}
-\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{66}{\relax }{figure.caption.73}{}}
-\newlabel{fig:evaporation_SEM_analysis_clog_overlay}{{5.9b}{66}{\relax }{figure.caption.73}{}}
-\newlabel{sub@fig:evaporation_SEM_analysis_clog_overlay}{{b}{66}{\relax }{figure.caption.73}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces (\subref  {fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes. (\subref  {fig:evaporation_SEM_analysis_clog_overlay}) tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{66}{figure.caption.73}\protected@file@percent }
-\newlabel{fig:evaporation_SEM_analysis}{{5.9}{66}{(\subref {fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes. (\subref {fig:evaporation_SEM_analysis_clog_overlay}) 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.73}{}}
+\newlabel{fig:evaporation_tilts_example}{{5.7a}{64}{\relax }{figure.caption.74}{}}
+\newlabel{sub@fig:evaporation_tilts_example}{{a}{64}{\relax }{figure.caption.74}{}}
+\newlabel{fig:evaporation_tilts_all}{{5.7b}{64}{\relax }{figure.caption.74}{}}
+\newlabel{sub@fig:evaporation_tilts_all}{{b}{64}{\relax }{figure.caption.74}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.7}{\ignorespaces (\subref  {fig:evaporation_tilts_example}) image of the reconstruction of the tilt angle for Field 3. (\subref  {fig:evaporation_tilts_all}) the same for all fields. 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 in this case are the high resolution AFM scans of single dots.}}{64}{figure.caption.74}\protected@file@percent }
+\newlabel{fig:evaporation_tilts}{{5.7}{64}{(\subref {fig:evaporation_tilts_example}) image of the reconstruction of the tilt angle for Field 3. (\subref {fig:evaporation_tilts_all}) the same for all fields. 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 in this case are the high resolution AFM scans of single dots}{figure.caption.74}{}}
+\newlabel{fig:evaporation_SEM_sample}{{5.8a}{65}{\relax }{figure.caption.75}{}}
+\newlabel{sub@fig:evaporation_SEM_sample}{{a}{65}{\relax }{figure.caption.75}{}}
+\newlabel{fig:evaporation_SEM_mask}{{5.8b}{65}{\relax }{figure.caption.75}{}}
+\newlabel{sub@fig:evaporation_SEM_mask}{{b}{65}{\relax }{figure.caption.75}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.8}{\ignorespaces (\subref  {fig:evaporation_SEM_sample}) SEM images of field 2 on the sample. (\subref  {fig:evaporation_SEM_mask}) SEM image of the mask. The inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects.}}{65}{figure.caption.75}\protected@file@percent }
+\newlabel{fig:evaporation_SEM}{{5.8}{65}{(\subref {fig:evaporation_SEM_sample}) SEM images of field 2 on the sample. (\subref {fig:evaporation_SEM_mask}) SEM image of the mask. The inset shows another image of the same mask. The image of the mask was very unstable due to heavy charging effects}{figure.caption.75}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog}{{5.9a}{66}{\relax }{figure.caption.76}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog}{{a}{66}{\relax }{figure.caption.76}{}}
+\newlabel{fig:evaporation_SEM_analysis_clog_overlay}{{5.9b}{66}{\relax }{figure.caption.76}{}}
+\newlabel{sub@fig:evaporation_SEM_analysis_clog_overlay}{{b}{66}{\relax }{figure.caption.76}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.9}{\ignorespaces (\subref  {fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes. (\subref  {fig:evaporation_SEM_analysis_clog_overlay}) tilt direction from \ref {fig:evaporation_tilts} overlayed over the SEM image of the mask after it was rotated to match the fields.}}{66}{figure.caption.76}\protected@file@percent }
+\newlabel{fig:evaporation_SEM_analysis}{{5.9}{66}{(\subref {fig:evaporation_SEM_analysis_clog}) example of the clogging noticed on $4$ of the mask holes. (\subref {fig:evaporation_SEM_analysis_clog_overlay}) 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.76}{}}
 \@writefile{toc}{\contentsline {section}{\numberline {5.5}Simulation}{66}{section.5.5}\protected@file@percent }
 \newlabel{sec:simulation}{{5.5}{66}{Simulation}{section.5.5}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {5.5.1}Overview and principle}{66}{subsection.5.5.1}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {5.5.2}Results}{68}{subsection.5.5.2}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.10a}{68}{\relax }{figure.caption.74}{}}
-\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{68}{\relax }{figure.caption.74}{}}
-\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.10b}{68}{\relax }{figure.caption.74}{}}
-\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{68}{\relax }{figure.caption.74}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces (a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image. }}{68}{figure.caption.74}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_first_compare}{{5.10}{68}{(a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image}{figure.caption.74}{}}
+\newlabel{fig:evaporation_simulation_first_compare_AFM}{{5.10a}{68}{\relax }{figure.caption.77}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_AFM}{{a}{68}{\relax }{figure.caption.77}{}}
+\newlabel{fig:evaporation_simulation_first_compare_SIM}{{5.10b}{68}{\relax }{figure.caption.77}{}}
+\newlabel{sub@fig:evaporation_simulation_first_compare_SIM}{{b}{68}{\relax }{figure.caption.77}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.10}{\ignorespaces (a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image. }}{68}{figure.caption.77}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_first_compare}{{5.10}{68}{(a) a recorded AFM image, colors are for easier identification. (b) a simulated evaporation with parameters obtained from measurement in the AFM image}{figure.caption.77}{}}
 \citation{Bhaskar}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask. }}{69}{figure.caption.75}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_overlap}{{5.11}{69}{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask}{figure.caption.75}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.11}{\ignorespaces Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask. }}{69}{figure.caption.78}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_overlap}{{5.11}{69}{Simulation showing the effect of only x-y vibration on the resulting evaporation. White circles show the extreme positions of the circular mask}{figure.caption.78}{}}
 \citation{grain_growth}
-\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.12a}{70}{\relax }{figure.caption.76}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{70}{\relax }{figure.caption.76}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.12b}{70}{\relax }{figure.caption.76}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{70}{\relax }{figure.caption.76}{}}
-\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.12c}{70}{\relax }{figure.caption.76}{}}
-\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{70}{\relax }{figure.caption.76}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces (\subref  {fig:evaporation_simulation_sharpness_stick_simple}) Comparison of the evaporation with harmonic oscillation. (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) initial phase with no elliptical oscillation and then drift to the elliptical shape. (\subref  {fig:evaporation_simulation_sharpness_stick_power})an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ . The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{70}{figure.caption.76}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_sharpness}{{5.12}{70}{(\subref {fig:evaporation_simulation_sharpness_stick_simple}) Comparison of the evaporation with harmonic oscillation. (\subref {fig:evaporation_simulation_sharpness_stick_initial}) initial phase with no elliptical oscillation and then drift to the elliptical shape. (\subref {fig:evaporation_simulation_sharpness_stick_power})an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ . The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.76}{}}
-\newlabel{fig:evaporation_simulation_rejection_prev}{{5.13a}{71}{\relax }{figure.caption.77}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{71}{\relax }{figure.caption.77}{}}
-\newlabel{fig:evaporation_simulation_rejection_after}{{5.13b}{71}{\relax }{figure.caption.77}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{71}{\relax }{figure.caption.77}{}}
-\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.13c}{71}{\relax }{figure.caption.77}{}}
-\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{71}{\relax }{figure.caption.77}{}}
-\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces (\subref  {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref  {fig:evaporation_simulation_rejection_prev}) 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}) the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{71}{figure.caption.77}\protected@file@percent }
-\newlabel{fig:evaporation_simulation_rejection}{{5.13}{71}{(\subref {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref {fig:evaporation_simulation_rejection_prev}) 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}) the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.77}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_simple}{{5.12a}{70}{\relax }{figure.caption.79}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_simple}{{a}{70}{\relax }{figure.caption.79}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_initial}{{5.12b}{70}{\relax }{figure.caption.79}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_initial}{{b}{70}{\relax }{figure.caption.79}{}}
+\newlabel{fig:evaporation_simulation_sharpness_stick_power}{{5.12c}{70}{\relax }{figure.caption.79}{}}
+\newlabel{sub@fig:evaporation_simulation_sharpness_stick_power}{{c}{70}{\relax }{figure.caption.79}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.12}{\ignorespaces (\subref  {fig:evaporation_simulation_sharpness_stick_simple}) Comparison of the evaporation with harmonic oscillation. (\subref  {fig:evaporation_simulation_sharpness_stick_initial}) initial phase with no elliptical oscillation and then drift to the elliptical shape. (\subref  {fig:evaporation_simulation_sharpness_stick_power})an anharmonic oscillation with $\sin (\frac  {t}{T} + \phi )^{20}$ . The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{70}{figure.caption.79}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_sharpness}{{5.12}{70}{(\subref {fig:evaporation_simulation_sharpness_stick_simple}) Comparison of the evaporation with harmonic oscillation. (\subref {fig:evaporation_simulation_sharpness_stick_initial}) initial phase with no elliptical oscillation and then drift to the elliptical shape. (\subref {fig:evaporation_simulation_sharpness_stick_power})an anharmonic oscillation with $\sin (\frac {t}{T} + \phi )^{20}$ . The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.79}{}}
+\newlabel{fig:evaporation_simulation_rejection_prev}{{5.13a}{71}{\relax }{figure.caption.80}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_prev}{{a}{71}{\relax }{figure.caption.80}{}}
+\newlabel{fig:evaporation_simulation_rejection_after}{{5.13b}{71}{\relax }{figure.caption.80}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_after}{{b}{71}{\relax }{figure.caption.80}{}}
+\newlabel{fig:evaporation_simulation_rejection_comparison}{{5.13c}{71}{\relax }{figure.caption.80}{}}
+\newlabel{sub@fig:evaporation_simulation_rejection_comparison}{{c}{71}{\relax }{figure.caption.80}{}}
+\@writefile{lof}{\contentsline {figure}{\numberline {5.13}{\ignorespaces (\subref  {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref  {fig:evaporation_simulation_rejection_prev}) 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}) the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}.}}{71}{figure.caption.80}\protected@file@percent }
+\newlabel{fig:evaporation_simulation_rejection}{{5.13}{71}{(\subref {fig:evaporation_simulation_rejection_prev}) simulated evaporation dots without rejection. (\subref {fig:evaporation_simulation_rejection_prev}) 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}) the AFM image from which the parameters were obtained. The parameters of the ellipse are the same as in Figure \ref {fig:evaporation_simulation_first_compare}}{figure.caption.80}{}}
 \@writefile{toc}{\contentsline {subsection}{\numberline {5.5.3}Software improvements}{71}{subsection.5.5.3}\protected@file@percent }
 \@writefile{toc}{\contentsline {subsection}{\numberline {5.5.4}Final Remark}{72}{subsection.5.5.4}\protected@file@percent }
 \@setckpt{chap05}{
@@ -121,7 +121,7 @@
 \setcounter{subfigure}{3}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/conclusion.aux b/conclusion.aux
index 35cc92e0dced9b0ab9b0860e9784f8244044f776..0888a35ae355a25370f8e35f3b4924bee59bcb85 100644
--- a/conclusion.aux
+++ b/conclusion.aux
@@ -1,7 +1,7 @@
 \relax 
 \providecommand\hyper@newdestlabel[2]{}
 \citation{self_epitaxy}
-\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.78}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.81}\protected@file@percent }
 \@setckpt{conclusion}{
 \setcounter{page}{74}
 \setcounter{equation}{1}
@@ -32,7 +32,7 @@
 \setcounter{subfigure}{3}
 \setcounter{subtable}{0}
 \setcounter{lstnumber}{1}
-\setcounter{@todonotes@numberoftodonotes}{2}
+\setcounter{@todonotes@numberoftodonotes}{5}
 \setcounter{float@type}{8}
 \setcounter{AM@survey}{0}
 \setcounter{thm}{0}
diff --git a/pdfa.xmpi b/pdfa.xmpi
index 6e09b8423f7855dbf6eb486a5420dc44e40dc6ae..0bffbeeb7d38655606a8767b3bf5660e3f8e5bc9 100644
--- a/pdfa.xmpi
+++ b/pdfa.xmpi
@@ -73,15 +73,15 @@
   </rdf:Description> 
   <rdf:Description rdf:about="" xmlns:xmp="http://ns.adobe.com/xap/1.0/"> 
    <xmp:CreatorTool>LaTeX with hyperref</xmp:CreatorTool> 
-   <xmp:ModifyDate>2024-10-03T01:00:02+02:00</xmp:ModifyDate> 
-   <xmp:CreateDate>2024-10-03T01:00:02+02:00</xmp:CreateDate> 
-   <xmp:MetadataDate>2024-10-03T01:00:02+02:00</xmp:MetadataDate> 
+   <xmp:ModifyDate>2024-10-07T10:03:57+02:00</xmp:ModifyDate> 
+   <xmp:CreateDate>2024-10-07T10:03:57+02:00</xmp:CreateDate> 
+   <xmp:MetadataDate>2024-10-07T10:03:57+02:00</xmp:MetadataDate> 
   </rdf:Description> 
   <rdf:Description rdf:about="" xmlns:xmpRights = "http://ns.adobe.com/xap/1.0/rights/"> 
   </rdf:Description> 
   <rdf:Description rdf:about="" xmlns:xmpMM="http://ns.adobe.com/xap/1.0/mm/"> 
    <xmpMM:DocumentID>uuid:C8CFC28F-88E1-7995-E9AD-F6D12EAD346B</xmpMM:DocumentID> 
-   <xmpMM:InstanceID>uuid:96D507C5-D4CF-027E-6900-18B3564C2203</xmpMM:InstanceID> 
+   <xmpMM:InstanceID>uuid:C1E07DF5-D566-4779-C2BD-D497C9AE59B4</xmpMM:InstanceID> 
   </rdf:Description> 
  </rdf:RDF> 
 </x:xmpmeta> 
diff --git a/thesis.aux b/thesis.aux
index ee952b0f772fb31f59308d48f4cce1a8bb3e6b58..942e0264653002f6f42a2486c08a980452a51dc6 100644
--- a/thesis.aux
+++ b/thesis.aux
@@ -6,19 +6,28 @@
 \@input{title.aux}
 \@input{preface.aux}
 \@input{chap01.aux}
+\pgfsyspdfmark {pgfid1}{4736286}{42184011}
+\pgfsyspdfmark {pgfid4}{37433768}{42204785}
+\pgfsyspdfmark {pgfid5}{39282063}{41930059}
 \@input{chap02.aux}
+\pgfsyspdfmark {pgfid6}{4736286}{12310330}
+\pgfsyspdfmark {pgfid9}{37433768}{12331104}
+\pgfsyspdfmark {pgfid10}{39282063}{12056378}
+\pgfsyspdfmark {pgfid11}{4736286}{10200800}
+\pgfsyspdfmark {pgfid14}{37433768}{10221574}
+\pgfsyspdfmark {pgfid15}{39282063}{9946848}
 \@input{chap03.aux}
-\pgfsyspdfmark {pgfid1}{4736286}{14857764}
-\pgfsyspdfmark {pgfid4}{37433768}{14878538}
-\pgfsyspdfmark {pgfid5}{39282063}{14603812}
-\pgfsyspdfmark {pgfid6}{19294448}{46753504}
-\pgfsyspdfmark {pgfid9}{37433768}{46774278}
-\pgfsyspdfmark {pgfid10}{39282063}{46499552}
+\pgfsyspdfmark {pgfid16}{4736286}{14857764}
+\pgfsyspdfmark {pgfid19}{37433768}{14878538}
+\pgfsyspdfmark {pgfid20}{39282063}{14603812}
+\pgfsyspdfmark {pgfid21}{19294448}{46753504}
+\pgfsyspdfmark {pgfid24}{37433768}{46774278}
+\pgfsyspdfmark {pgfid25}{39282063}{46499552}
 \@input{chap04.aux}
 \@input{chap05.aux}
 \@input{conclusion.aux}
 \@input{bibliography.aux}
-\@writefile{toc}{\contentsline {chapter}{List of Abbreviations}{77}{chapter*.80}\protected@file@percent }
+\@writefile{toc}{\contentsline {chapter}{List of Abbreviations}{77}{chapter*.83}\protected@file@percent }
 \@input{appendix.aux}
 \@input{acknowledgments.aux}
 \providecommand\NAT@force@numbers{}\NAT@force@numbers
diff --git a/thesis.log b/thesis.log
index fe6f4d922cee5f78ca2c22086952e5dae44b8793..737d168a89e1bf058c696ccf4b04c56472948210 100644
--- a/thesis.log
+++ b/thesis.log
@@ -1,4 +1,4 @@
-This is pdfTeX, Version 3.141592653-2.6-1.40.25 (MiKTeX 24.1) (preloaded format=pdflatex 2024.9.29)  3 OCT 2024 01:00
+This is pdfTeX, Version 3.141592653-2.6-1.40.25 (MiKTeX 24.1) (preloaded format=pdflatex 2024.9.29)  7 OCT 2024 10:03
 entering extended mode
  restricted \write18 enabled.
  %&-line parsing enabled.
@@ -1635,13 +1635,15 @@ c}] [4]
 
  (chap01.tex
 Chapter 1.
+Package hyperref Info: bookmark level for unknown todo defaults to 0 on input l
+ine 6.
 <img/EBeamDep.pdf, id=372, 422.32782pt x 512.66531pt>
 File: img/EBeamDep.pdf Graphic file (type pdf)
 <use img/EBeamDep.pdf>
-Package pdftex.def Info: img/EBeamDep.pdf  used on input line 10.
+Package pdftex.def Info: img/EBeamDep.pdf  used on input line 11.
 (pdftex.def)             Requested size: 230.36061pt x 279.64346pt.
 
-Underfull \hbox (badness 10000) in paragraph at lines 19--20
+Underfull \hbox (badness 10000) in paragraph at lines 20--21
 
  []
 
@@ -1652,119 +1654,119 @@ Underfull \hbox (badness 10000) in paragraph at lines 19--20
 
 {C:/Users/Luzifer/AppData/Local/Programs/MiKTeX/fonts/enc/dvips/lm/lm-mathsy.en
 c} <./img/EBeamDep.pdf>]
-Underfull \hbox (badness 10000) in paragraph at lines 23--24
+Underfull \hbox (badness 10000) in paragraph at lines 24--25
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 40--46
+Underfull \hbox (badness 10000) in paragraph at lines 41--47
 
  []
 
 [6]
-Underfull \hbox (badness 10000) in paragraph at lines 50--51
+Underfull \hbox (badness 10000) in paragraph at lines 51--52
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 52--53
+Underfull \hbox (badness 10000) in paragraph at lines 53--54
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 54--55
+Underfull \hbox (badness 10000) in paragraph at lines 55--56
 
  []
 
-<img/Plots/Background/Penumbra_diagramm.pdf, id=452, 490.1206pt x 456.06708pt>
+<img/Plots/Background/Penumbra_diagramm.pdf, id=453, 490.1206pt x 456.06708pt>
 File: img/Plots/Background/Penumbra_diagramm.pdf Graphic file (type pdf)
 <use img/Plots/Background/Penumbra_diagramm.pdf>
 Package pdftex.def Info: img/Plots/Background/Penumbra_diagramm.pdf  used on in
-put line 62.
+put line 63.
 (pdftex.def)             Requested size: 230.36061pt x 214.3585pt.
 [7]
-Underfull \hbox (badness 10000) in paragraph at lines 67--68
+Underfull \hbox (badness 10000) in paragraph at lines 68--69
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 74--75
+Underfull \hbox (badness 10000) in paragraph at lines 75--76
 
  []
 
-<img/Plots/Background/Penumbra_diagramm_tilt.pdf, id=463, 316.68901pt x 226.646
+<img/Plots/Background/Penumbra_diagramm_tilt.pdf, id=464, 316.68901pt x 226.646
 1pt>
 File: img/Plots/Background/Penumbra_diagramm_tilt.pdf Graphic file (type pdf)
 <use img/Plots/Background/Penumbra_diagramm_tilt.pdf>
 Package pdftex.def Info: img/Plots/Background/Penumbra_diagramm_tilt.pdf  used 
-on input line 79.
+on input line 80.
 (pdftex.def)             Requested size: 207.32315pt x 148.373pt.
-<img/Plots/Background/Penumbra_ImageTilt.pdf, id=464, 371.04158pt x 280.97652pt
+<img/Plots/Background/Penumbra_ImageTilt.pdf, id=465, 371.04158pt x 280.97652pt
 >
 File: img/Plots/Background/Penumbra_ImageTilt.pdf Graphic file (type pdf)
 <use img/Plots/Background/Penumbra_ImageTilt.pdf>
 Package pdftex.def Info: img/Plots/Background/Penumbra_ImageTilt.pdf  used on i
-nput line 84.
+nput line 85.
 (pdftex.def)             Requested size: 207.32315pt x 156.99849pt.
 [8 <./img/Plots/Background/Penumbra_diagramm.pdf>]
-Underfull \hbox (badness 10000) in paragraph at lines 98--100
+Underfull \hbox (badness 10000) in paragraph at lines 99--101
 
  []
 
 [9 <./img/Plots/Background/Penumbra_diagramm_tilt.pdf> <./img/Plots/Background/
 Penumbra_ImageTilt.pdf>]
-<img/Plots/Background/AFMDiagram.pdf, id=557, 525.07625pt x 367.71567pt>
+<img/Plots/Background/AFMDiagram.pdf, id=558, 525.07625pt x 367.71567pt>
 File: img/Plots/Background/AFMDiagram.pdf Graphic file (type pdf)
 <use img/Plots/Background/AFMDiagram.pdf>
 Package pdftex.def Info: img/Plots/Background/AFMDiagram.pdf  used on input lin
-e 105.
+e 106.
 (pdftex.def)             Requested size: 322.50345pt x 225.85481pt.
-<img/Plots/AFMPotential.pdf, id=559, 433.62pt x 289.08pt>
+<img/Plots/AFMPotential.pdf, id=560, 433.62pt x 289.08pt>
 File: img/Plots/AFMPotential.pdf Graphic file (type pdf)
 <use img/Plots/AFMPotential.pdf>
-Package pdftex.def Info: img/Plots/AFMPotential.pdf  used on input line 115.
+Package pdftex.def Info: img/Plots/AFMPotential.pdf  used on input line 116.
 (pdftex.def)             Requested size: 322.50345pt x 215.01418pt.
  [10 <./img/Plots/Background/AFMDiagram.pdf>]
 LaTeX Font Info:    Trying to load font information for TS1+lmr on input line 1
-27.
+28.
 
 (C:\Users\Luzifer\AppData\Local\Programs\MiKTeX\tex/latex/lm\ts1lmr.fd
 File: ts1lmr.fd 2015/05/01 v1.6.1 Font defs for Latin Modern
 )
 [11{C:/Users/Luzifer/AppData/Local/Programs/MiKTeX/fonts/enc/dvips/lm/lm-ts1.en
 c} <./img/Plots/AFMPotential.pdf>]
-<img/Plots/Background/SEMSetup.png, id=692, 481.8pt x 642.4803pt>
+<img/Plots/Background/SEMSetup.png, id=693, 481.8pt x 642.4803pt>
 File: img/Plots/Background/SEMSetup.png Graphic file (type png)
 <use img/Plots/Background/SEMSetup.png>
 Package pdftex.def Info: img/Plots/Background/SEMSetup.png  used on input line 
-143.
+144.
 (pdftex.def)             Requested size: 186.58957pt x 248.8115pt.
-<img/Plots/Background/Electron_Beam_Matter_Interaction.pdf, id=694, 227.93503pt
+<img/Plots/Background/Electron_Beam_Matter_Interaction.pdf, id=695, 227.93503pt
  x 203.94936pt>
 File: img/Plots/Background/Electron_Beam_Matter_Interaction.pdf Graphic file (t
 ype pdf)
 <use img/Plots/Background/Electron_Beam_Matter_Interaction.pdf>
 Package pdftex.def Info: img/Plots/Background/Electron_Beam_Matter_Interaction.
-pdf  used on input line 148.
+pdf  used on input line 149.
 (pdftex.def)             Requested size: 186.58957pt x 166.96257pt.
  [12]
-Underfull \hbox (badness 10000) in paragraph at lines 156--157
+Underfull \hbox (badness 10000) in paragraph at lines 157--158
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 158--160
+Underfull \hbox (badness 10000) in paragraph at lines 159--161
 
  []
 
 [13 <./img/Plots/Background/SEMSetup.png> <./img/Plots/Background/Electron_Beam
 _Matter_Interaction.pdf>]
-Underfull \hbox (badness 10000) in paragraph at lines 161--163
+Underfull \hbox (badness 10000) in paragraph at lines 162--164
 
  []
 
 )
-Underfull \hbox (badness 10000) in paragraph at lines 164--130
+Underfull \hbox (badness 10000) in paragraph at lines 165--130
 
  []
 
@@ -1773,7 +1775,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 164--130
 
  (chap02.tex
 Chapter 2.
-<img/MaskAlignerChamber.pdf, id=770, 569.05513pt x 566.20984pt>
+<img/MaskAlignerChamber.pdf, id=771, 569.05513pt x 566.20984pt>
 File: img/MaskAlignerChamber.pdf Graphic file (type pdf)
 <use img/MaskAlignerChamber.pdf>
 Package pdftex.def Info: img/MaskAlignerChamber.pdf  used on input line 7.
@@ -1793,7 +1795,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 24--25
 
  []
 
-<img/MA/Evaporator.pdf, id=797, 735.31029pt x 663.98062pt>
+<img/MA/Evaporator.pdf, id=798, 735.31029pt x 663.98062pt>
 File: img/MA/Evaporator.pdf Graphic file (type pdf)
 <use img/MA/Evaporator.pdf>
 Package pdftex.def Info: img/MA/Evaporator.pdf  used on input line 28.
@@ -1803,13 +1805,13 @@ Underfull \hbox (badness 10000) in paragraph at lines 33--34
 
  []
 
-<img/MA/NomenclatureMaskAlignerFront.pdf, id=805, 466.6252pt x 859.27322pt>
+<img/MA/NomenclatureMaskAlignerFront.pdf, id=806, 466.6252pt x 859.27322pt>
 File: img/MA/NomenclatureMaskAlignerFront.pdf Graphic file (type pdf)
 <use img/MA/NomenclatureMaskAlignerFront.pdf>
 Package pdftex.def Info: img/MA/NomenclatureMaskAlignerFront.pdf  used on input
  line 38.
 (pdftex.def)             Requested size: 193.50208pt x 356.32951pt.
-<img/MA/NomenclatureMaskAlignerCrossSec.pdf, id=806, 478.00629pt x 808.05826pt>
+<img/MA/NomenclatureMaskAlignerCrossSec.pdf, id=807, 478.00629pt x 808.05826pt>
 
 File: img/MA/NomenclatureMaskAlignerCrossSec.pdf Graphic file (type pdf)
 <use img/MA/NomenclatureMaskAlignerCrossSec.pdf>
@@ -1836,19 +1838,19 @@ Underfull \hbox (badness 10000) in paragraph at lines 63--65
 
  []
 
-<img/SlipStickGrafix.pdf, id=889, 865.10777pt x 482.39015pt>
+<img/SlipStickGrafix.pdf, id=890, 865.10777pt x 482.39015pt>
 File: img/SlipStickGrafix.pdf Graphic file (type pdf)
 <use img/SlipStickGrafix.pdf>
 Package pdftex.def Info: img/SlipStickGrafix.pdf  used on input line 72.
 (pdftex.def)             Requested size: 414.6463pt x 231.20605pt.
 [19]
-<img/MA/Calibration_screw_image.pdf, id=897, 1220.64026pt x 1220.64026pt>
+<img/MA/Calibration_screw_image.pdf, id=898, 1220.64026pt x 1220.64026pt>
 File: img/MA/Calibration_screw_image.pdf Graphic file (type pdf)
 <use img/MA/Calibration_screw_image.pdf>
 Package pdftex.def Info: img/MA/Calibration_screw_image.pdf  used on input line
  91.
 (pdftex.def)             Requested size: 172.77046pt x 172.76964pt.
-<img/Plots/ScrewRot_SwappedPlate.pdf, id=898, 462.52798pt x 346.89601pt>
+<img/Plots/ScrewRot_SwappedPlate.pdf, id=899, 462.52798pt x 346.89601pt>
 File: img/Plots/ScrewRot_SwappedPlate.pdf Graphic file (type pdf)
 <use img/Plots/ScrewRot_SwappedPlate.pdf>
 Package pdftex.def Info: img/Plots/ScrewRot_SwappedPlate.pdf  used on input lin
@@ -1869,24 +1871,24 @@ Underfull \hbox (badness 10000) in paragraph at lines 113--116
 
  []
 
-<img/CalibrationUHV_Z1.pdf, id=993, 3661.68pt x 3178.48857pt>
+<img/CalibrationUHV_Z1.pdf, id=994, 3661.68pt x 3178.48857pt>
 File: img/CalibrationUHV_Z1.pdf Graphic file (type pdf)
 <use img/CalibrationUHV_Z1.pdf>
 Package pdftex.def Info: img/CalibrationUHV_Z1.pdf  used on input line 120.
 (pdftex.def)             Requested size: 193.50208pt x 167.9547pt.
-<img/CalibrationUHV_Z2_Z3.pdf, id=994, 3661.68pt x 3184.17902pt>
+<img/CalibrationUHV_Z2_Z3.pdf, id=995, 3661.68pt x 3184.17902pt>
 File: img/CalibrationUHV_Z2_Z3.pdf Graphic file (type pdf)
 <use img/CalibrationUHV_Z2_Z3.pdf>
 Package pdftex.def Info: img/CalibrationUHV_Z2_Z3.pdf  used on input line 125.
 (pdftex.def)             Requested size: 193.50208pt x 168.25539pt.
 [21 <./img/MA/Calibration_screw_image.pdf> <./img/Plots/ScrewRot_SwappedPlate.p
 df>]
-<img/MA/CalibrationZ1.pdf, id=1061, 1445.4pt x 1445.4pt>
+<img/MA/CalibrationZ1.pdf, id=1062, 1445.4pt x 1445.4pt>
 File: img/MA/CalibrationZ1.pdf Graphic file (type pdf)
 <use img/MA/CalibrationZ1.pdf>
 Package pdftex.def Info: img/MA/CalibrationZ1.pdf  used on input line 139.
 (pdftex.def)             Requested size: 228.05475pt x 228.04869pt.
-<img/MA/CalibrationZ2.pdf, id=1062, 1445.4pt x 1445.4pt>
+<img/MA/CalibrationZ2.pdf, id=1063, 1445.4pt x 1445.4pt>
 File: img/MA/CalibrationZ2.pdf Graphic file (type pdf)
 <use img/MA/CalibrationZ2.pdf>
 Package pdftex.def Info: img/MA/CalibrationZ2.pdf  used on input line 145.
@@ -1900,7 +1902,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 155--162
 
  []
 
-<img/Plots/Calibrations/screw_diff_explain.pdf, id=1095, 554.82875pt x 464.6079
+<img/Plots/Calibrations/screw_diff_explain.pdf, id=1096, 554.82875pt x 464.6079
 pt>
 File: img/Plots/Calibrations/screw_diff_explain.pdf Graphic file (type pdf)
 <use img/Plots/Calibrations/screw_diff_explain.pdf>
@@ -1912,7 +1914,7 @@ Package pdftex.def Info: img/Plots/Calibrations/screw_diff_explain.pdf  used on
 pdfTeX warning: pdflatex.exe (file ./img/MA/CalibrationZ2.pdf): PDF inclusion: 
 multiple pdfs with page group included in a single page
 >]
-<img/Plots/Calibrations/80V.pdf, id=1134, 578.16pt x 325.215pt>
+<img/Plots/Calibrations/80V.pdf, id=1135, 578.16pt x 325.215pt>
 File: img/Plots/Calibrations/80V.pdf Graphic file (type pdf)
 <use img/Plots/Calibrations/80V.pdf>
 Package pdftex.def Info: img/Plots/Calibrations/80V.pdf  used on input line 172
@@ -1920,159 +1922,159 @@ Package pdftex.def Info: img/Plots/Calibrations/80V.pdf  used on input line 172
 (pdftex.def)             Requested size: 368.57838pt x 207.32306pt.
  [24 <./img/Plots/Calibrations/screw_diff_explain.pdf> <./img/Plots/Calibration
 s/80V.pdf>]
-<img/Plots/Calibrations/VoltageBehaviour.pdf, id=1248, 867.24pt x 433.62pt>
+<img/Plots/Calibrations/VoltageBehaviour.pdf, id=1250, 867.24pt x 433.62pt>
 File: img/Plots/Calibrations/VoltageBehaviour.pdf Graphic file (type pdf)
 <use img/Plots/Calibrations/VoltageBehaviour.pdf>
 Package pdftex.def Info: img/Plots/Calibrations/VoltageBehaviour.pdf  used on i
-nput line 185.
+nput line 186.
 (pdftex.def)             Requested size: 414.6463pt x 207.3214pt.
 
-Underfull \hbox (badness 10000) in paragraph at lines 190--194
+Underfull \hbox (badness 10000) in paragraph at lines 191--195
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 196--202
+Underfull \hbox (badness 10000) in paragraph at lines 197--203
 
  []
 
 [25 <./img/Plots/Calibrations/VoltageBehaviour.pdf>]
-Underfull \hbox (badness 10000) in paragraph at lines 203--207
+Underfull \hbox (badness 10000) in paragraph at lines 204--208
 
  []
 
-<img/CameraAlignment_bad_low.pdf, id=1293, 2938.98pt x 1334.9875pt>
+<img/CameraAlignment_bad_low.pdf, id=1295, 2938.98pt x 1334.9875pt>
 File: img/CameraAlignment_bad_low.pdf Graphic file (type pdf)
 <use img/CameraAlignment_bad_low.pdf>
 Package pdftex.def Info: img/CameraAlignment_bad_low.pdf  used on input line 21
-1.
+2.
 (pdftex.def)             Requested size: 147.43416pt x 66.95699pt.
-<img/CameraAlignment_high.png, id=1294, 2938.98pt x 1334.9875pt>
+<img/CameraAlignment_high.png, id=1296, 2938.98pt x 1334.9875pt>
 File: img/CameraAlignment_high.png Graphic file (type png)
 <use img/CameraAlignment_high.png>
-Package pdftex.def Info: img/CameraAlignment_high.png  used on input line 216.
+Package pdftex.def Info: img/CameraAlignment_high.png  used on input line 217.
 (pdftex.def)             Requested size: 147.43416pt x 66.95699pt.
-<img/CameraAlignment_good.png, id=1295, 2938.98pt x 1334.9875pt>
+<img/CameraAlignment_good.png, id=1297, 2938.98pt x 1334.9875pt>
 File: img/CameraAlignment_good.png Graphic file (type png)
 <use img/CameraAlignment_good.png>
-Package pdftex.def Info: img/CameraAlignment_good.png  used on input line 221.
+Package pdftex.def Info: img/CameraAlignment_good.png  used on input line 222.
 (pdftex.def)             Requested size: 147.43416pt x 66.95699pt.
-<img/OpticalAlign01.png, id=1300, 977.6525pt x 977.6525pt>
+<img/OpticalAlign01.png, id=1302, 977.6525pt x 977.6525pt>
 File: img/OpticalAlign01.png Graphic file (type png)
 <use img/OpticalAlign01.png>
-Package pdftex.def Info: img/OpticalAlign01.png  used on input line 240.
+Package pdftex.def Info: img/OpticalAlign01.png  used on input line 241.
 (pdftex.def)             Requested size: 147.43416pt x 147.43219pt.
-<img/OpticalAlign02.png, id=1301, 977.6525pt x 977.6525pt>
+<img/OpticalAlign02.png, id=1303, 977.6525pt x 977.6525pt>
 File: img/OpticalAlign02.png Graphic file (type png)
 <use img/OpticalAlign02.png>
-Package pdftex.def Info: img/OpticalAlign02.png  used on input line 245.
+Package pdftex.def Info: img/OpticalAlign02.png  used on input line 246.
 (pdftex.def)             Requested size: 147.43416pt x 147.43219pt.
-<img/OpticalAlign03.png, id=1302, 977.6525pt x 977.6525pt>
+<img/OpticalAlign03.png, id=1304, 977.6525pt x 977.6525pt>
 File: img/OpticalAlign03.png Graphic file (type png)
 <use img/OpticalAlign03.png>
-Package pdftex.def Info: img/OpticalAlign03.png  used on input line 250.
+Package pdftex.def Info: img/OpticalAlign03.png  used on input line 251.
 (pdftex.def)             Requested size: 147.43416pt x 147.43219pt.
 [26 <./img/CameraAlignment_bad_low.pdf> <./img/CameraAlignment_high.png> <./img
 /CameraAlignment_good.png> <./img/OpticalAlign01.png> <./img/OpticalAlign02.png
 > <./img/OpticalAlign03.png>]
 LaTeX Font Info:    External font `lmex10' loaded for size
-(Font)              <5> on input line 263.
-<img/MA/NomeclatureMotorsAndCapacitance.pdf, id=1330, 597.50786pt x 597.50786pt
+(Font)              <5> on input line 266.
+<img/MA/NomeclatureMotorsAndCapacitance.pdf, id=1333, 597.50786pt x 597.50786pt
 >
 File: img/MA/NomeclatureMotorsAndCapacitance.pdf Graphic file (type pdf)
 <use img/MA/NomeclatureMotorsAndCapacitance.pdf>
 Package pdftex.def Info: img/MA/NomeclatureMotorsAndCapacitance.pdf  used on in
-put line 270.
+put line 273.
 (pdftex.def)             Requested size: 228.05475pt x 228.04912pt.
-<img/MA/Mask.pdf, id=1331, 477.04668pt x 674.3149pt>
+<img/MA/Mask.pdf, id=1334, 477.04668pt x 674.3149pt>
 File: img/MA/Mask.pdf Graphic file (type pdf)
 <use img/MA/Mask.pdf>
-Package pdftex.def Info: img/MA/Mask.pdf  used on input line 275.
+Package pdftex.def Info: img/MA/Mask.pdf  used on input line 278.
 (pdftex.def)             Requested size: 157.5676pt x 222.73038pt.
  [27 <./img/MA/NomeclatureMotorsAndCapacitance.pdf> <./img/MA/Mask.pdf
 
 pdfTeX warning: pdflatex.exe (file ./img/MA/Mask.pdf): PDF inclusion: multiple 
 pdfs with page group included in a single page
 >]
-<img/MA/SchaltDiagramRHK.pdf, id=1426, 544.13278pt x 385.4176pt>
+<img/MA/SchaltDiagramRHK.pdf, id=1429, 544.13278pt x 385.4176pt>
 File: img/MA/SchaltDiagramRHK.pdf Graphic file (type pdf)
 <use img/MA/SchaltDiagramRHK.pdf>
-Package pdftex.def Info: img/MA/SchaltDiagramRHK.pdf  used on input line 287.
+Package pdftex.def Info: img/MA/SchaltDiagramRHK.pdf  used on input line 290.
 (pdftex.def)             Requested size: 345.54092pt x 244.7492pt.
 
-Underfull \hbox (badness 10000) in paragraph at lines 306--313
+Underfull \hbox (badness 10000) in paragraph at lines 309--316
 
  []
 
-<img/Diagram/ApproachExplanation.pdf, id=1428, 578.16pt x 433.62pt>
+<img/Diagram/ApproachExplanation.pdf, id=1431, 578.16pt x 433.62pt>
 File: img/Diagram/ApproachExplanation.pdf Graphic file (type pdf)
 <use img/Diagram/ApproachExplanation.pdf>
 Package pdftex.def Info: img/Diagram/ApproachExplanation.pdf  used on input lin
-e 317.
+e 320.
 (pdftex.def)             Requested size: 207.32315pt x 155.48775pt.
-<img/Diagram/ApproachExplanation_diff.pdf, id=1429, 578.16pt x 433.62pt>
+<img/Diagram/ApproachExplanation_diff.pdf, id=1432, 578.16pt x 433.62pt>
 File: img/Diagram/ApproachExplanation_diff.pdf Graphic file (type pdf)
 <use img/Diagram/ApproachExplanation_diff.pdf>
 Package pdftex.def Info: img/Diagram/ApproachExplanation_diff.pdf  used on inpu
-t line 322.
+t line 325.
 (pdftex.def)             Requested size: 207.32315pt x 155.48775pt.
-<img/Diagram/ApproachCurve_FirstContact.png, id=1430, 1084.05pt x 513.92pt>
+<img/Diagram/ApproachCurve_FirstContact.png, id=1433, 1084.05pt x 513.92pt>
 File: img/Diagram/ApproachCurve_FirstContact.png Graphic file (type png)
 <use img/Diagram/ApproachCurve_FirstContact.png>
 Package pdftex.def Info: img/Diagram/ApproachCurve_FirstContact.png  used on in
-put line 328.
+put line 331.
 (pdftex.def)             Requested size: 138.21777pt x 65.51805pt.
-<img/Diagram/ApproachCurve_SecondContact.png, id=1431, 1084.05pt x 513.92pt>
+<img/Diagram/ApproachCurve_SecondContact.png, id=1434, 1084.05pt x 513.92pt>
 File: img/Diagram/ApproachCurve_SecondContact.png Graphic file (type png)
 <use img/Diagram/ApproachCurve_SecondContact.png>
 Package pdftex.def Info: img/Diagram/ApproachCurve_SecondContact.png  used on i
-nput line 334.
+nput line 337.
 (pdftex.def)             Requested size: 138.21777pt x 65.51805pt.
-<img/Diagram/ApproachCurve_FullContact.png, id=1432, 1084.05pt x 513.92pt>
+<img/Diagram/ApproachCurve_FullContact.png, id=1435, 1084.05pt x 513.92pt>
 File: img/Diagram/ApproachCurve_FullContact.png Graphic file (type png)
 <use img/Diagram/ApproachCurve_FullContact.png>
 Package pdftex.def Info: img/Diagram/ApproachCurve_FullContact.png  used on inp
-ut line 340.
+ut line 343.
 (pdftex.def)             Requested size: 138.21777pt x 65.51805pt.
 [28 <./img/MA/SchaltDiagramRHK.pdf>]
-Underfull \hbox (badness 10000) in paragraph at lines 351--354
+Underfull \hbox (badness 10000) in paragraph at lines 354--357
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 355--368
+Underfull \hbox (badness 10000) in paragraph at lines 358--371
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 369--379
+Underfull \hbox (badness 10000) in paragraph at lines 372--382
 
  []
 
 [29 <./img/Diagram/ApproachExplanation.pdf> <./img/Diagram/ApproachExplanation_
 diff.pdf> <./img/Diagram/ApproachCurve_FirstContact.png> <./img/Diagram/Approac
 hCurve_SecondContact.png> <./img/Diagram/ApproachCurve_FullContact.png>]
-<img/MA/InsertionReproducibility.pdf, id=1661, 578.16pt x 361.35pt>
+<img/MA/InsertionReproducibility.pdf, id=1664, 578.16pt x 361.35pt>
 File: img/MA/InsertionReproducibility.pdf Graphic file (type pdf)
 <use img/MA/InsertionReproducibility.pdf>
 Package pdftex.def Info: img/MA/InsertionReproducibility.pdf  used on input lin
-e 410.
+e 413.
 (pdftex.def)             Requested size: 228.05475pt x 142.53043pt.
-<img/MA/InsertionReproducibility_diff.pdf, id=1662, 578.16pt x 361.35pt>
+<img/MA/InsertionReproducibility_diff.pdf, id=1665, 578.16pt x 361.35pt>
 File: img/MA/InsertionReproducibility_diff.pdf Graphic file (type pdf)
 <use img/MA/InsertionReproducibility_diff.pdf>
 Package pdftex.def Info: img/MA/InsertionReproducibility_diff.pdf  used on inpu
-t line 415.
+t line 418.
 (pdftex.def)             Requested size: 228.05475pt x 142.53043pt.
 
 [30 <./img/MA/InsertionReproducibility.pdf> <./img/MA/InsertionReproducibility_
 diff.pdf>]
-Underfull \hbox (badness 10000) in paragraph at lines 425--426
+Underfull \hbox (badness 10000) in paragraph at lines 428--429
 
  []
 
 
-Underfull \hbox (badness 10000) in paragraph at lines 427--428
+Underfull \hbox (badness 10000) in paragraph at lines 430--431
 
  []
 
@@ -2081,13 +2083,13 @@ Underfull \hbox (badness 10000) in paragraph at lines 427--428
 
  (chap03.tex
 Chapter 3.
-<img/Plots/RHK/F0002CH1.CSV.pdf, id=1762, 867.24pt x 650.43pt>
+<img/Plots/RHK/F0002CH1.CSV.pdf, id=1765, 867.24pt x 650.43pt>
 File: img/Plots/RHK/F0002CH1.CSV.pdf Graphic file (type pdf)
 <use img/Plots/RHK/F0002CH1.CSV.pdf>
 Package pdftex.def Info: img/Plots/RHK/F0002CH1.CSV.pdf  used on input line 18.
 
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
-<img/Plots/RHK/F0003CH1.CSV.pdf, id=1763, 867.24pt x 650.43pt>
+<img/Plots/RHK/F0003CH1.CSV.pdf, id=1766, 867.24pt x 650.43pt>
 File: img/Plots/RHK/F0003CH1.CSV.pdf Graphic file (type pdf)
 <use img/Plots/RHK/F0003CH1.CSV.pdf>
 Package pdftex.def Info: img/Plots/RHK/F0003CH1.CSV.pdf  used on input line 23.
@@ -2099,13 +2101,13 @@ Package pdftex.def Info: img/Plots/RHK/F0003CH1.CSV.pdf  used on input line 23.
 
 
  <./img/Plots/RHK/F0002CH1.CSV.pdf> <./img/Plots/RHK/F0003CH1.CSV.pdf>]
-<img/Plots/RHK/F0006CH1.CSV.pdf, id=1829, 867.24pt x 650.43pt>
+<img/Plots/RHK/F0006CH1.CSV.pdf, id=1832, 867.24pt x 650.43pt>
 File: img/Plots/RHK/F0006CH1.CSV.pdf Graphic file (type pdf)
 <use img/Plots/RHK/F0006CH1.CSV.pdf>
 Package pdftex.def Info: img/Plots/RHK/F0006CH1.CSV.pdf  used on input line 37.
 
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
-<img/Plots/RHK/F0008CH1.CSV.pdf, id=1830, 867.24pt x 650.43pt>
+<img/Plots/RHK/F0008CH1.CSV.pdf, id=1833, 867.24pt x 650.43pt>
 File: img/Plots/RHK/F0008CH1.CSV.pdf Graphic file (type pdf)
 <use img/Plots/RHK/F0008CH1.CSV.pdf>
 Package pdftex.def Info: img/Plots/RHK/F0008CH1.CSV.pdf  used on input line 42.
@@ -2116,12 +2118,12 @@ Underfull \hbox (badness 10000) in paragraph at lines 52--53
 
  []
 
-<img/Plots/KIM001/ALL0001.pdf, id=1836, 867.24pt x 650.43pt>
+<img/Plots/KIM001/ALL0001.pdf, id=1839, 867.24pt x 650.43pt>
 File: img/Plots/KIM001/ALL0001.pdf Graphic file (type pdf)
 <use img/Plots/KIM001/ALL0001.pdf>
 Package pdftex.def Info: img/Plots/KIM001/ALL0001.pdf  used on input line 61.
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
-<img/Plots/KIM001/ALL0002.pdf, id=1837, 867.24pt x 650.43pt>
+<img/Plots/KIM001/ALL0002.pdf, id=1840, 867.24pt x 650.43pt>
 File: img/Plots/KIM001/ALL0002.pdf Graphic file (type pdf)
 <use img/Plots/KIM001/ALL0002.pdf>
 Package pdftex.def Info: img/Plots/KIM001/ALL0002.pdf  used on input line 66.
@@ -2131,7 +2133,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 76--77
 
  []
 
-<img/Plots/KIM001/voltage_behavior.pdf, id=1899, 867.24pt x 650.43pt>
+<img/Plots/KIM001/voltage_behavior.pdf, id=1902, 867.24pt x 650.43pt>
 File: img/Plots/KIM001/voltage_behavior.pdf Graphic file (type pdf)
 <use img/Plots/KIM001/voltage_behavior.pdf>
 Package pdftex.def Info: img/Plots/KIM001/voltage_behavior.pdf  used on input l
@@ -2139,25 +2141,23 @@ ine 82.
 (pdftex.def)             Requested size: 276.43555pt x 207.32802pt.
 [35 <./img/Plots/KIM001/ALL0001.pdf> <./img/Plots/KIM001/ALL0002.pdf>] [36 <./i
 mg/Plots/KIM001/voltage_behavior.pdf>]
-<img/Plots/Filtering.pdf, id=1998, 433.62pt x 289.08pt>
+<img/Plots/Filtering.pdf, id=2001, 433.62pt x 289.08pt>
 File: img/Plots/Filtering.pdf Graphic file (type pdf)
 <use img/Plots/Filtering.pdf>
 Package pdftex.def Info: img/Plots/Filtering.pdf  used on input line 106.
 (pdftex.def)             Requested size: 225.75594pt x 150.50331pt.
-<img/Plots/FilteringDone.pdf, id=1999, 433.62pt x 289.08pt>
+<img/Plots/FilteringDone.pdf, id=2002, 433.62pt x 289.08pt>
 File: img/Plots/FilteringDone.pdf Graphic file (type pdf)
 <use img/Plots/FilteringDone.pdf>
 Package pdftex.def Info: img/Plots/FilteringDone.pdf  used on input line 111.
 (pdftex.def)             Requested size: 225.75594pt x 150.50331pt.
-Package hyperref Info: bookmark level for unknown todo defaults to 0 on input l
-ine 118.
  [37 <./img/Plots/Filtering.pdf> <./img/Plots/FilteringDone.pdf>]
-<img/Plots/InvertedSginal.pdf, id=2084, 433.62pt x 289.08pt>
+<img/Plots/InvertedSginal.pdf, id=2087, 433.62pt x 289.08pt>
 File: img/Plots/InvertedSginal.pdf Graphic file (type pdf)
 <use img/Plots/InvertedSginal.pdf>
 Package pdftex.def Info: img/Plots/InvertedSginal.pdf  used on input line 127.
 (pdftex.def)             Requested size: 225.75594pt x 150.50331pt.
-<img/Plots/Switching01.pdf, id=2085, 433.62pt x 289.08pt>
+<img/Plots/Switching01.pdf, id=2088, 433.62pt x 289.08pt>
 File: img/Plots/Switching01.pdf Graphic file (type pdf)
 <use img/Plots/Switching01.pdf>
 Package pdftex.def Info: img/Plots/Switching01.pdf  used on input line 132.
@@ -2168,13 +2168,13 @@ Underfull \hbox (badness 10000) in paragraph at lines 159--160
  []
 
 [39]
-<img/Plots/Walker/WalkerApproach.pdf, id=2188, 867.24pt x 650.43pt>
+<img/Plots/Walker/WalkerApproach.pdf, id=2191, 867.24pt x 650.43pt>
 File: img/Plots/Walker/WalkerApproach.pdf Graphic file (type pdf)
 <use img/Plots/Walker/WalkerApproach.pdf>
 Package pdftex.def Info: img/Plots/Walker/WalkerApproach.pdf  used on input lin
 e 170.
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
-<img/Plots/Walker/WalkerRetract.pdf, id=2189, 867.24pt x 650.43pt>
+<img/Plots/Walker/WalkerRetract.pdf, id=2192, 867.24pt x 650.43pt>
 File: img/Plots/Walker/WalkerRetract.pdf Graphic file (type pdf)
 <use img/Plots/Walker/WalkerRetract.pdf>
 Package pdftex.def Info: img/Plots/Walker/WalkerRetract.pdf  used on input line
@@ -2182,19 +2182,19 @@ Package pdftex.def Info: img/Plots/Walker/WalkerRetract.pdf  used on input line
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
  [40 <./img/Plots/Walker/WalkerApproach.pdf> <./img/Plots/Walker/WalkerRetract.
 pdf>]
-<img/Plots/Walker/WalkerApproach_ff.pdf, id=2265, 867.24pt x 650.43pt>
+<img/Plots/Walker/WalkerApproach_ff.pdf, id=2268, 867.24pt x 650.43pt>
 File: img/Plots/Walker/WalkerApproach_ff.pdf Graphic file (type pdf)
 <use img/Plots/Walker/WalkerApproach_ff.pdf>
 Package pdftex.def Info: img/Plots/Walker/WalkerApproach_ff.pdf  used on input 
 line 186.
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
-<img/Plots/Walker/WalkerRetract_ff.pdf, id=2266, 867.24pt x 650.43pt>
+<img/Plots/Walker/WalkerRetract_ff.pdf, id=2269, 867.24pt x 650.43pt>
 File: img/Plots/Walker/WalkerRetract_ff.pdf Graphic file (type pdf)
 <use img/Plots/Walker/WalkerRetract_ff.pdf>
 Package pdftex.def Info: img/Plots/Walker/WalkerRetract_ff.pdf  used on input l
 ine 190.
 (pdftex.def)             Requested size: 225.75594pt x 169.31622pt.
-<img/MA/SchaltDiagramWalker.pdf, id=2269, 544.13278pt x 385.4176pt>
+<img/MA/SchaltDiagramWalker.pdf, id=2272, 544.13278pt x 385.4176pt>
 File: img/MA/SchaltDiagramWalker.pdf Graphic file (type pdf)
 <use img/MA/SchaltDiagramWalker.pdf>
 Package pdftex.def Info: img/MA/SchaltDiagramWalker.pdf  used on input line 202
@@ -2206,13 +2206,13 @@ ct_ff.pdf>]) [42 <./img/MA/SchaltDiagramWalker.pdf>]
 
  (chap04.tex
 Chapter 4.
-<img/Repairs/NomeclatureDiagram.pdf, id=2449, 542.86818pt x 488.42506pt>
+<img/Repairs/NomeclatureDiagram.pdf, id=2452, 542.86818pt x 488.42506pt>
 File: img/Repairs/NomeclatureDiagram.pdf Graphic file (type pdf)
 <use img/Repairs/NomeclatureDiagram.pdf>
 Package pdftex.def Info: img/Repairs/NomeclatureDiagram.pdf  used on input line
  10.
 (pdftex.def)             Requested size: 216.53954pt x 194.82251pt.
-<img/Repairs/nomeclaturediagram_side.png, id=2450, 1053.6966pt x 1118.0169pt>
+<img/Repairs/nomeclaturediagram_side.png, id=2453, 1053.6966pt x 1118.0169pt>
 File: img/Repairs/nomeclaturediagram_side.png Graphic file (type png)
 <use img/Repairs/nomeclaturediagram_side.png>
 Package pdftex.def Info: img/Repairs/nomeclaturediagram_side.png  used on input
@@ -2234,25 +2234,25 @@ Underfull \hbox (badness 10000) in paragraph at lines 52--54
 
  []
 
-<img/Repairs/SolderAnchorsBase.pdf, id=2474, 467.37352pt x 406.31995pt>
+<img/Repairs/SolderAnchorsBase.pdf, id=2477, 467.37352pt x 406.31995pt>
 File: img/Repairs/SolderAnchorsBase.pdf Graphic file (type pdf)
 <use img/Repairs/SolderAnchorsBase.pdf>
 Package pdftex.def Info: img/Repairs/SolderAnchorsBase.pdf  used on input line 
 58.
 (pdftex.def)             Requested size: 110.57463pt x 96.12999pt.
-<img/Repairs/SolderAnchorsSmallerDot.pdf, id=2475, 467.37352pt x 406.31995pt>
+<img/Repairs/SolderAnchorsSmallerDot.pdf, id=2478, 467.37352pt x 406.31995pt>
 File: img/Repairs/SolderAnchorsSmallerDot.pdf Graphic file (type pdf)
 <use img/Repairs/SolderAnchorsSmallerDot.pdf>
 Package pdftex.def Info: img/Repairs/SolderAnchorsSmallerDot.pdf  used on input
  line 63.
 (pdftex.def)             Requested size: 110.57463pt x 96.12999pt.
-<img/Repairs/SolderAnchorsAlO.pdf, id=2476, 467.37352pt x 406.31995pt>
+<img/Repairs/SolderAnchorsAlO.pdf, id=2479, 467.37352pt x 406.31995pt>
 File: img/Repairs/SolderAnchorsAlO.pdf Graphic file (type pdf)
 <use img/Repairs/SolderAnchorsAlO.pdf>
 Package pdftex.def Info: img/Repairs/SolderAnchorsAlO.pdf  used on input line 6
 8.
 (pdftex.def)             Requested size: 110.57463pt x 96.12999pt.
-<img/Repairs/SolderAnchorsGlueTop.pdf, id=2477, 467.37352pt x 406.31995pt>
+<img/Repairs/SolderAnchorsGlueTop.pdf, id=2480, 467.37352pt x 406.31995pt>
 File: img/Repairs/SolderAnchorsGlueTop.pdf Graphic file (type pdf)
 <use img/Repairs/SolderAnchorsGlueTop.pdf>
 Package pdftex.def Info: img/Repairs/SolderAnchorsGlueTop.pdf  used on input li
@@ -2292,14 +2292,14 @@ lusion: multiple pdfs with page group included in a single page
 pdfTeX warning: pdflatex.exe (file ./img/Repairs/SolderAnchorsGlueTop.pdf): PDF
  inclusion: multiple pdfs with page group included in a single page
 >]
-<img/Repairs/SolderAnchors/Solder_shear_big.png, id=2509, 1575.8875pt x 1798.72
+<img/Repairs/SolderAnchors/Solder_shear_big.png, id=2512, 1575.8875pt x 1798.72
 pt>
 File: img/Repairs/SolderAnchors/Solder_shear_big.png Graphic file (type png)
 <use img/Repairs/SolderAnchors/Solder_shear_big.png>
 Package pdftex.def Info: img/Repairs/SolderAnchors/Solder_shear_big.png  used o
 n input line 95.
 (pdftex.def)             Requested size: 145.12872pt x 165.63794pt.
-<img/Repairs/SolderAnchors/Solder_shear_smaller.png, id=2510, 1575.8875pt x 179
+<img/Repairs/SolderAnchors/Solder_shear_smaller.png, id=2513, 1575.8875pt x 179
 8.72pt>
 File: img/Repairs/SolderAnchors/Solder_shear_smaller.png Graphic file (type png
 )
@@ -2307,13 +2307,13 @@ File: img/Repairs/SolderAnchors/Solder_shear_smaller.png Graphic file (type png
 Package pdftex.def Info: img/Repairs/SolderAnchors/Solder_shear_smaller.png  us
 ed on input line 101.
 (pdftex.def)             Requested size: 145.12872pt x 165.63794pt.
-<img/Repairs/SolderAnchors/GlueBelow.png, id=2511, 2457.18pt x 2055.68pt>
+<img/Repairs/SolderAnchors/GlueBelow.png, id=2514, 2457.18pt x 2055.68pt>
 File: img/Repairs/SolderAnchors/GlueBelow.png Graphic file (type png)
 <use img/Repairs/SolderAnchors/GlueBelow.png>
 Package pdftex.def Info: img/Repairs/SolderAnchors/GlueBelow.png  used on input
  line 107.
 (pdftex.def)             Requested size: 145.12872pt x 121.39072pt.
-<img/Repairs/SolderAnchors/AlO.png, id=2512, 2457.18pt x 2055.68pt>
+<img/Repairs/SolderAnchors/AlO.png, id=2515, 2457.18pt x 2055.68pt>
 File: img/Repairs/SolderAnchors/AlO.png Graphic file (type png)
 <use img/Repairs/SolderAnchors/AlO.png>
 Package pdftex.def Info: img/Repairs/SolderAnchors/AlO.png  used on input line 
@@ -2331,22 +2331,22 @@ Underfull \hbox (badness 10000) in paragraph at lines 126--127
 
  []
 
-<img/Repairs/Z3-PiezoOff.png, id=2534, 2055.68pt x 1399.2275pt>
+<img/Repairs/Z3-PiezoOff.png, id=2537, 2055.68pt x 1399.2275pt>
 File: img/Repairs/Z3-PiezoOff.png Graphic file (type png)
 <use img/Repairs/Z3-PiezoOff.png>
 Package pdftex.def Info: img/Repairs/Z3-PiezoOff.png  used on input line 132.
 (pdftex.def)             Requested size: 156.64394pt x 106.60286pt.
-<img/Repairs/Z3-scratched.png, id=2535, 2055.68pt x 1399.2275pt>
+<img/Repairs/Z3-scratched.png, id=2538, 2055.68pt x 1399.2275pt>
 File: img/Repairs/Z3-scratched.png Graphic file (type png)
 <use img/Repairs/Z3-scratched.png>
 Package pdftex.def Info: img/Repairs/Z3-scratched.png  used on input line 138.
 (pdftex.def)             Requested size: 156.64394pt x 106.60286pt.
-<img/Repairs/Z3-GlueDot.png, id=2536, 2055.68pt x 1399.2275pt>
+<img/Repairs/Z3-GlueDot.png, id=2539, 2055.68pt x 1399.2275pt>
 File: img/Repairs/Z3-GlueDot.png Graphic file (type png)
 <use img/Repairs/Z3-GlueDot.png>
 Package pdftex.def Info: img/Repairs/Z3-GlueDot.png  used on input line 144.
 (pdftex.def)             Requested size: 156.64394pt x 106.60286pt.
-<img/Repairs/Z3-WeightDown.png, id=2537, 2055.68pt x 1399.2275pt>
+<img/Repairs/Z3-WeightDown.png, id=2540, 2055.68pt x 1399.2275pt>
 File: img/Repairs/Z3-WeightDown.png Graphic file (type png)
 <use img/Repairs/Z3-WeightDown.png>
 Package pdftex.def Info: img/Repairs/Z3-WeightDown.png  used on input line 150.
@@ -2359,12 +2359,12 @@ Underfull \hbox (badness 10000) in paragraph at lines 158--159
 
 [47 <./img/Repairs/Z3-PiezoOff.png> <./img/Repairs/Z3-scratched.png> <./img/Rep
 airs/Z3-GlueDot.png> <./img/Repairs/Z3-WeightDown.png>]
-<img/Repairs/Z3-afterglue.pdf, id=2551, 2055.68pt x 1399.22762pt>
+<img/Repairs/Z3-afterglue.pdf, id=2554, 2055.68pt x 1399.22762pt>
 File: img/Repairs/Z3-afterglue.pdf Graphic file (type pdf)
 <use img/Repairs/Z3-afterglue.pdf>
 Package pdftex.def Info: img/Repairs/Z3-afterglue.pdf  used on input line 165.
 (pdftex.def)             Requested size: 322.50345pt x 219.50415pt.
-<img/Repairs/ScrewRot_CompareSwappedPlate.pdf, id=2553, 462.52798pt x 346.89601
+<img/Repairs/ScrewRot_CompareSwappedPlate.pdf, id=2556, 462.52798pt x 346.89601
 pt>
 File: img/Repairs/ScrewRot_CompareSwappedPlate.pdf Graphic file (type pdf)
 <use img/Repairs/ScrewRot_CompareSwappedPlate.pdf>
@@ -2387,7 +2387,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 188--189
  []
 
 [49 <./img/Repairs/ScrewRot_CompareSwappedPlate.pdf>]
-<img/Repairs/ScrewRot_SwappedPlate.pdf, id=2636, 462.52798pt x 346.89601pt>
+<img/Repairs/ScrewRot_SwappedPlate.pdf, id=2639, 462.52798pt x 346.89601pt>
 File: img/Repairs/ScrewRot_SwappedPlate.pdf Graphic file (type pdf)
 <use img/Repairs/ScrewRot_SwappedPlate.pdf>
 Package pdftex.def Info: img/Repairs/ScrewRot_SwappedPlate.pdf  used on input l
@@ -2409,12 +2409,12 @@ Underfull \hbox (badness 10000) in paragraph at lines 202--203
  []
 
 [50 <./img/Repairs/ScrewRot_SwappedPlate.pdf>]
-<img/Repairs/GlueAid.png, id=2695, 302.0886pt x 542.7477pt>
+<img/Repairs/GlueAid.png, id=2698, 302.0886pt x 542.7477pt>
 File: img/Repairs/GlueAid.png Graphic file (type png)
 <use img/Repairs/GlueAid.png>
 Package pdftex.def Info: img/Repairs/GlueAid.png  used on input line 210.
 (pdftex.def)             Requested size: 125.4308pt x 225.35204pt.
-<img/Repairs/NewFrontPlate.png, id=2696, 1507.6325pt x 1969.3575pt>
+<img/Repairs/NewFrontPlate.png, id=2699, 1507.6325pt x 1969.3575pt>
 File: img/Repairs/NewFrontPlate.png Graphic file (type png)
 <use img/Repairs/NewFrontPlate.png>
 Package pdftex.def Info: img/Repairs/NewFrontPlate.png  used on input line 216.
@@ -2425,20 +2425,20 @@ Underfull \hbox (badness 10000) in paragraph at lines 227--228
 
  []
 
-<img/Repairs/WeakerCapacitor.pdf, id=2703, 597.50786pt x 597.50786pt>
+<img/Repairs/WeakerCapacitor.pdf, id=2706, 597.50786pt x 597.50786pt>
 File: img/Repairs/WeakerCapacitor.pdf Graphic file (type pdf)
 <use img/Repairs/WeakerCapacitor.pdf>
 Package pdftex.def Info: img/Repairs/WeakerCapacitor.pdf  used on input line 23
 3.
 (pdftex.def)             Requested size: 207.32315pt x 207.31654pt.
 [51 <./img/Repairs/GlueAid.png> <./img/Repairs/NewFrontPlate.png>]
-<img/Repairs/FeedThroughtLeft.pdf, id=2711, 2663.9525pt x 2465.21pt>
+<img/Repairs/FeedThroughtLeft.pdf, id=2714, 2663.9525pt x 2465.21pt>
 File: img/Repairs/FeedThroughtLeft.pdf Graphic file (type pdf)
 <use img/Repairs/FeedThroughtLeft.pdf>
 Package pdftex.def Info: img/Repairs/FeedThroughtLeft.pdf  used on input line 2
 44.
 (pdftex.def)             Requested size: 216.6513pt x 200.45581pt.
-<img/Repairs/FeedThroughtRight.pdf, id=2712, 2663.9525pt x 2465.21pt>
+<img/Repairs/FeedThroughtRight.pdf, id=2715, 2663.9525pt x 2465.21pt>
 File: img/Repairs/FeedThroughtRight.pdf Graphic file (type pdf)
 <use img/Repairs/FeedThroughtRight.pdf>
 Package pdftex.def Info: img/Repairs/FeedThroughtRight.pdf  used on input line 
@@ -2449,7 +2449,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 257--258
 
  []
 
-<img/Repairs/80.0V.pdf, id=2736, 578.16pt x 324.92592pt>
+<img/Repairs/80.0V.pdf, id=2739, 578.16pt x 324.92592pt>
 File: img/Repairs/80.0V.pdf Graphic file (type pdf)
 <use img/Repairs/80.0V.pdf>
 Package pdftex.def Info: img/Repairs/80.0V.pdf  used on input line 280.
@@ -2468,7 +2468,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 285--133
 
  (chap05.tex
 Chapter 5.
-<img/Evaporation/Approach_Curve_Field01.pdf, id=2838, 1156.32pt x 650.43pt>
+<img/Evaporation/Approach_Curve_Field01.pdf, id=2841, 1156.32pt x 650.43pt>
 File: img/Evaporation/Approach_Curve_Field01.pdf Graphic file (type pdf)
 <use img/Evaporation/Approach_Curve_Field01.pdf>
 Package pdftex.def Info: img/Evaporation/Approach_Curve_Field01.pdf  used on in
@@ -2485,26 +2485,26 @@ Underfull \hbox (badness 10000) in paragraph at lines 16--17
 
 
  <./img/Evaporation/Approach_Curve_Field01.pdf>]
-<img/Evaporation/SampleImage.pdf, id=2901, 299.74013pt x 380.17047pt>
+<img/Evaporation/SampleImage.pdf, id=2904, 299.74013pt x 380.17047pt>
 File: img/Evaporation/SampleImage.pdf Graphic file (type pdf)
 <use img/Evaporation/SampleImage.pdf>
 Package pdftex.def Info: img/Evaporation/SampleImage.pdf  used on input line 57
 .
 (pdftex.def)             Requested size: 186.58957pt x 236.6604pt.
-<img/Evaporation/Mask01_Aspect.png, id=2902, 367.3725pt x 462.528pt>
+<img/Evaporation/Mask01_Aspect.png, id=2905, 367.3725pt x 462.528pt>
 File: img/Evaporation/Mask01_Aspect.png Graphic file (type png)
 <use img/Evaporation/Mask01_Aspect.png>
 Package pdftex.def Info: img/Evaporation/Mask01_Aspect.png  used on input line 
 63.
 (pdftex.def)             Requested size: 186.58957pt x 234.92632pt.
  [56]
-<img/Evaporation/Contamination.png, id=2914, 1325.95375pt x 1097.09875pt>
+<img/Evaporation/Contamination.png, id=2917, 1325.95375pt x 1097.09875pt>
 File: img/Evaporation/Contamination.png Graphic file (type png)
 <use img/Evaporation/Contamination.png>
 Package pdftex.def Info: img/Evaporation/Contamination.png  used on input line 
 81.
 (pdftex.def)             Requested size: 216.6513pt x 179.25574pt.
-<img/Evaporation/Contamination.pdf, id=2915, 433.62pt x 361.35pt>
+<img/Evaporation/Contamination.pdf, id=2918, 433.62pt x 361.35pt>
 File: img/Evaporation/Contamination.pdf Graphic file (type pdf)
 <use img/Evaporation/Contamination.pdf>
 Package pdftex.def Info: img/Evaporation/Contamination.pdf  used on input line 
@@ -2516,14 +2516,14 @@ Underfull \hbox (badness 10000) in paragraph at lines 102--103
 
  []
 
-<img/Plots/Background/IllustrationSigmas.pdf, id=2938, 944.027pt x 810.77919pt>
+<img/Plots/Background/IllustrationSigmas.pdf, id=2941, 944.027pt x 810.77919pt>
 
 File: img/Plots/Background/IllustrationSigmas.pdf Graphic file (type pdf)
 <use img/Plots/Background/IllustrationSigmas.pdf>
 Package pdftex.def Info: img/Plots/Background/IllustrationSigmas.pdf  used on i
 nput line 107.
 (pdftex.def)             Requested size: 214.46744pt x 184.18657pt.
-<img/Evaporation/Field3_TR.pdf, id=2939, 957.5775pt x 812.28468pt>
+<img/Evaporation/Field3_TR.pdf, id=2942, 957.5775pt x 812.28468pt>
 File: img/Evaporation/Field3_TR.pdf Graphic file (type pdf)
 <use img/Evaporation/Field3_TR.pdf>
 Package pdftex.def Info: img/Evaporation/Field3_TR.pdf  used on input line 112.
@@ -2541,19 +2541,19 @@ R.pdf
 pdfTeX warning: pdflatex.exe (file ./img/Evaporation/Field3_TR.pdf): PDF inclus
 ion: multiple pdfs with page group included in a single page
 >]
-<img/Evaporation/Field5_top_demo01.png, id=3015, 1337.99875pt x 1097.09875pt>
+<img/Evaporation/Field5_top_demo01.png, id=3018, 1337.99875pt x 1097.09875pt>
 File: img/Evaporation/Field5_top_demo01.png Graphic file (type png)
 <use img/Evaporation/Field5_top_demo01.png>
 Package pdftex.def Info: img/Evaporation/Field5_top_demo01.png  used on input l
 ine 142.
 (pdftex.def)             Requested size: 196.95636pt x 161.49422pt.
-<img/Evaporation/Field5_top_demo02.png, id=3016, 1335.99126pt x 1089.06876pt>
+<img/Evaporation/Field5_top_demo02.png, id=3019, 1335.99126pt x 1089.06876pt>
 File: img/Evaporation/Field5_top_demo02.png Graphic file (type png)
 <use img/Evaporation/Field5_top_demo02.png>
 Package pdftex.def Info: img/Evaporation/Field5_top_demo02.png  used on input l
 ine 147.
 (pdftex.def)             Requested size: 196.95636pt x 160.54485pt.
-<img/Evaporation/TopField5Fit.pdf, id=3017, 462.52798pt x 346.89601pt>
+<img/Evaporation/TopField5Fit.pdf, id=3020, 462.52798pt x 346.89601pt>
 File: img/Evaporation/TopField5Fit.pdf Graphic file (type pdf)
 <use img/Evaporation/TopField5Fit.pdf>
 Package pdftex.def Info: img/Evaporation/TopField5Fit.pdf  used on input line 1
@@ -2561,25 +2561,25 @@ Package pdftex.def Info: img/Evaporation/TopField5Fit.pdf  used on input line 1
 (pdftex.def)             Requested size: 262.61292pt x 196.97055pt.
  [60{C:/Users/Luzifer/AppData/Local/Programs/MiKTeX/fonts/enc/dvips/lm/lm-mathe
 x.enc}]
-<img/Evaporation/sigmas_summary.pdf, id=3028, 433.62pt x 289.08pt>
+<img/Evaporation/sigmas_summary.pdf, id=3031, 433.62pt x 289.08pt>
 File: img/Evaporation/sigmas_summary.pdf Graphic file (type pdf)
 <use img/Evaporation/sigmas_summary.pdf>
 Package pdftex.def Info: img/Evaporation/sigmas_summary.pdf  used on input line
  164.
 (pdftex.def)             Requested size: 228.05475pt x 152.03833pt.
-<img/Evaporation/sigmal_summary.pdf, id=3029, 433.62pt x 289.08pt>
+<img/Evaporation/sigmal_summary.pdf, id=3032, 433.62pt x 289.08pt>
 File: img/Evaporation/sigmal_summary.pdf Graphic file (type pdf)
 <use img/Evaporation/sigmal_summary.pdf>
 Package pdftex.def Info: img/Evaporation/sigmal_summary.pdf  used on input line
  169.
 (pdftex.def)             Requested size: 228.05475pt x 152.03833pt.
-<img/Evaporation/heights_summary.pdf, id=3030, 433.62pt x 289.08pt>
+<img/Evaporation/heights_summary.pdf, id=3033, 433.62pt x 289.08pt>
 File: img/Evaporation/heights_summary.pdf Graphic file (type pdf)
 <use img/Evaporation/heights_summary.pdf>
 Package pdftex.def Info: img/Evaporation/heights_summary.pdf  used on input lin
 e 174.
 (pdftex.def)             Requested size: 228.05475pt x 152.03833pt.
-<img/Evaporation/umbra_summary.pdf, id=3031, 433.62pt x 289.08pt>
+<img/Evaporation/umbra_summary.pdf, id=3034, 433.62pt x 289.08pt>
 File: img/Evaporation/umbra_summary.pdf Graphic file (type pdf)
 <use img/Evaporation/umbra_summary.pdf>
 Package pdftex.def Info: img/Evaporation/umbra_summary.pdf  used on input line 
@@ -2618,13 +2618,13 @@ Underfull \hbox (badness 10000) in paragraph at lines 199--200
 
  []
 
-<img/Evaporation/Field3Angle.pdf, id=3237, 543.44762pt x 657.25867pt>
+<img/Evaporation/Field3Angle.pdf, id=3240, 543.44762pt x 657.25867pt>
 File: img/Evaporation/Field3Angle.pdf Graphic file (type pdf)
 <use img/Evaporation/Field3Angle.pdf>
 Package pdftex.def Info: img/Evaporation/Field3Angle.pdf  used on input line 20
 4.
 (pdftex.def)             Requested size: 216.6513pt x 262.02629pt.
-<img/Evaporation/FieldsAngle.pdf, id=3238, 543.44762pt x 657.25867pt>
+<img/Evaporation/FieldsAngle.pdf, id=3241, 543.44762pt x 657.25867pt>
 File: img/Evaporation/FieldsAngle.pdf Graphic file (type pdf)
 <use img/Evaporation/FieldsAngle.pdf>
 Package pdftex.def Info: img/Evaporation/FieldsAngle.pdf  used on input line 20
@@ -2635,14 +2635,14 @@ Underfull \hbox (badness 10000) in paragraph at lines 217--218
 
  []
 
-<img/Evaporation/SEM/SEM_Probe_01_cropped.png, id=3248, 692.5875pt x 692.5875pt
+<img/Evaporation/SEM/SEM_Probe_01_cropped.png, id=3251, 692.5875pt x 692.5875pt
 >
 File: img/Evaporation/SEM/SEM_Probe_01_cropped.png Graphic file (type png)
 <use img/Evaporation/SEM/SEM_Probe_01_cropped.png>
 Package pdftex.def Info: img/Evaporation/SEM/SEM_Probe_01_cropped.png  used on 
 input line 223.
 (pdftex.def)             Requested size: 214.46744pt x 214.4674pt.
-<img/Evaporation/SEM/SEM_Mask_cropped.pdf, id=3249, 692.5875pt x 692.5875pt>
+<img/Evaporation/SEM/SEM_Mask_cropped.pdf, id=3252, 692.5875pt x 692.5875pt>
 File: img/Evaporation/SEM/SEM_Mask_cropped.pdf Graphic file (type pdf)
 <use img/Evaporation/SEM/SEM_Mask_cropped.pdf>
 Package pdftex.def Info: img/Evaporation/SEM/SEM_Mask_cropped.pdf  used on inpu
@@ -2653,13 +2653,13 @@ t line 229.
 pdfTeX warning: pdflatex.exe (file ./img/Evaporation/FieldsAngle.pdf): PDF incl
 usion: multiple pdfs with page group included in a single page
 >]
-<img/Evaporation/SEM/ShowingClog.pdf, id=3284, 359.41805pt x 360.5994pt>
+<img/Evaporation/SEM/ShowingClog.pdf, id=3287, 359.41805pt x 360.5994pt>
 File: img/Evaporation/SEM/ShowingClog.pdf Graphic file (type pdf)
 <use img/Evaporation/SEM/ShowingClog.pdf>
 Package pdftex.def Info: img/Evaporation/SEM/ShowingClog.pdf  used on input lin
 e 244.
 (pdftex.def)             Requested size: 203.17896pt x 203.84908pt.
-<img/Evaporation/SEM/SEM_CloggingOverlay.png, id=3285, 609.2361pt x 569.4876pt>
+<img/Evaporation/SEM/SEM_CloggingOverlay.png, id=3288, 609.2361pt x 569.4876pt>
 
 File: img/Evaporation/SEM/SEM_CloggingOverlay.png Graphic file (type png)
 <use img/Evaporation/SEM/SEM_CloggingOverlay.png>
@@ -2693,13 +2693,13 @@ Underfull \hbox (badness 10000) in paragraph at lines 282--283
 
  []
 
-<img/Evaporation/Sim/Field3_right.pdf, id=3330, 1003.49907pt x 822.82407pt>
+<img/Evaporation/Sim/Field3_right.pdf, id=3333, 1003.49907pt x 822.82407pt>
 File: img/Evaporation/Sim/Field3_right.pdf Graphic file (type pdf)
 <use img/Evaporation/Sim/Field3_right.pdf>
 Package pdftex.def Info: img/Evaporation/Sim/Field3_right.pdf  used on input li
 ne 289.
 (pdftex.def)             Requested size: 196.95636pt x 161.48586pt.
-<img/Evaporation/Sim/Field3_right_sim_simple.pdf, id=3331, 364.9783pt x 280.976
+<img/Evaporation/Sim/Field3_right_sim_simple.pdf, id=3334, 364.9783pt x 280.976
 52pt>
 File: img/Evaporation/Sim/Field3_right_sim_simple.pdf Graphic file (type pdf)
 <use img/Evaporation/Sim/Field3_right_sim_simple.pdf>
@@ -2711,7 +2711,7 @@ Underfull \hbox (badness 10000) in paragraph at lines 302--303
 
  []
 
-<img/Evaporation/Sim/OverlapCircles.pdf, id=3339, 364.36125pt x 280.04625pt>
+<img/Evaporation/Sim/OverlapCircles.pdf, id=3342, 364.36125pt x 280.04625pt>
 File: img/Evaporation/Sim/OverlapCircles.pdf Graphic file (type pdf)
 <use img/Evaporation/Sim/OverlapCircles.pdf>
 Package pdftex.def Info: img/Evaporation/Sim/OverlapCircles.pdf  used on input 
@@ -2733,7 +2733,7 @@ File: img/Evaporation/Sim/Field3_right_sim_simple.pdf Graphic file (type pdf)
 Package pdftex.def Info: img/Evaporation/Sim/Field3_right_sim_simple.pdf  used 
 on input line 320.
 (pdftex.def)             Requested size: 149.73299pt x 115.2697pt.
-<img/Evaporation/Sim/Field3_right_sim_simple_initial.pdf, id=3396, 364.9783pt x
+<img/Evaporation/Sim/Field3_right_sim_simple_initial.pdf, id=3399, 364.9783pt x
  280.97652pt>
 File: img/Evaporation/Sim/Field3_right_sim_simple_initial.pdf Graphic file (typ
 e pdf)
@@ -2741,7 +2741,7 @@ e pdf)
 Package pdftex.def Info: img/Evaporation/Sim/Field3_right_sim_simple_initial.pd
 f  used on input line 325.
 (pdftex.def)             Requested size: 149.73299pt x 115.2697pt.
-<img/Evaporation/Sim/Field3_right_sim_simple_power.pdf, id=3397, 364.9783pt x 2
+<img/Evaporation/Sim/Field3_right_sim_simple_power.pdf, id=3400, 364.9783pt x 2
 80.97652pt>
 File: img/Evaporation/Sim/Field3_right_sim_simple_power.pdf Graphic file (type 
 pdf)
@@ -2765,7 +2765,7 @@ pdf)
 Package pdftex.def Info: img/Evaporation/Sim/Field3_right_sim_simple_power.pdf 
  used on input line 348.
 (pdftex.def)             Requested size: 149.73299pt x 115.2697pt.
-<img/Evaporation/Sim/Field3_right_sim_simple_rejection.pdf, id=3432, 364.9783pt
+<img/Evaporation/Sim/Field3_right_sim_simple_rejection.pdf, id=3435, 364.9783pt
  x 280.97652pt>
 File: img/Evaporation/Sim/Field3_right_sim_simple_rejection.pdf Graphic file (t
 ype pdf)
@@ -2773,7 +2773,7 @@ ype pdf)
 Package pdftex.def Info: img/Evaporation/Sim/Field3_right_sim_simple_rejection.
 pdf  used on input line 353.
 (pdftex.def)             Requested size: 149.73299pt x 115.2697pt.
-<img/Evaporation/Sim/Field3_right.png, id=3433, 1231.60126pt x 1083.04625pt>
+<img/Evaporation/Sim/Field3_right.png, id=3436, 1231.60126pt x 1083.04625pt>
 File: img/Evaporation/Sim/Field3_right.png Graphic file (type png)
 <use img/Evaporation/Sim/Field3_right.png>
 Package pdftex.def Info: img/Evaporation/Sim/Field3_right.png  used on input li
@@ -2903,7 +2903,7 @@ pdfTeX warning (ext4): destination with the same identifier (name{section.5.2})
                    \relax 
 l.28 \section{Walker principle diagram}
                                        \label{app:walker_diagram}
-<img/ElectronicsDiagramm.pdf, id=3600, 778.32848pt x 492.10774pt>
+<img/ElectronicsDiagramm.pdf, id=3603, 778.32848pt x 492.10774pt>
 File: img/ElectronicsDiagramm.pdf Graphic file (type pdf)
 <use img/ElectronicsDiagramm.pdf>
 Package pdftex.def Info: img/ElectronicsDiagramm.pdf  used on input line 31.
@@ -2922,7 +2922,7 @@ l.36 \section{Walker circuit diagrams}
 pdfTeX warning: pdflatex.exe (file ./img/Plots/Walker/MaskAlign Walker Signalel
 ektronik 1.0.pdf): PDF inclusion: found PDF version <1.7>, but at most version 
 <1.5> allowed
-<img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf, id=3607, 845.07724
+<img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf, id=3610, 845.07724
 pt x 597.55246pt>
 File: img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf Graphic file (
 type pdf)
@@ -2951,7 +2951,7 @@ ektronik 1.0.pdf): PDF inclusion: found PDF version <1.7>, but at most version
 pdfTeX warning: pdflatex.exe (file ./img/Plots/Walker/MaskAlign Walker Signalel
 ektronik 1.0.pdf): PDF inclusion: found PDF version <1.7>, but at most version 
 <1.5> allowed
-<img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf, id=3610, page=1, 8
+<img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf, id=3613, page=1, 8
 45.07724pt x 597.55246pt>
 File: img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf Graphic file (
 type pdf)
@@ -2991,7 +2991,7 @@ Package pdftex.def Info: img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0
 pdfTeX warning: pdflatex.exe (file ./img/Plots/Walker/MaskAlign Walker Signalel
 ektronik 1.0.pdf): PDF inclusion: found PDF version <1.7>, but at most version 
 <1.5> allowed
-<img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf, id=3683, page=2, 8
+<img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf, id=3686, page=2, 8
 45.07724pt x 597.55246pt>
 File: img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0.pdf Graphic file (
 type pdf)
@@ -3018,7 +3018,7 @@ Package pdftex.def Info: img/Plots/Walker/MaskAlign Walker Signalelektronik 1.0
 pdfTeX warning: pdflatex.exe (file ./img/Plots/Walker/MaskAlign Walker Netzteil
  modifiziert 24-05-2024.pdf): PDF inclusion: found PDF version <1.7>, but at mo
 st version <1.5> allowed
-<img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf, id=3688
+<img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf, id=3691
 , 1194.98447pt x 845.07724pt>
 File: img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf Gra
 phic file (type pdf)
@@ -3047,7 +3047,7 @@ st version <1.5> allowed
 pdfTeX warning: pdflatex.exe (file ./img/Plots/Walker/MaskAlign Walker Netzteil
  modifiziert 24-05-2024.pdf): PDF inclusion: found PDF version <1.7>, but at mo
 st version <1.5> allowed
-<img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf, id=3691
+<img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf, id=3694
 , page=1, 1194.98447pt x 845.07724pt>
 File: img/Plots/Walker/MaskAlign Walker Netzteil modifiziert 24-05-2024.pdf Gra
 phic file (type pdf)
@@ -3115,13 +3115,13 @@ LaTeX2e <2023-11-01> patch level 1
 L3 programming layer <2024-01-04>
  ***********
 Package rerunfilecheck Info: File `thesis.out' has not changed.
-(rerunfilecheck)             Checksum: 282D30D82A5087D522B94106BB389632;10079.
+(rerunfilecheck)             Checksum: 24E723D9DB1608DC0B4875BAAA19F41D;10079.
  ) 
 Here is how much of TeX's memory you used:
- 32171 strings out of 474485
- 610850 string characters out of 5742790
- 1942542 words of memory out of 5000000
- 53490 multiletter control sequences out of 15000+600000
+ 32200 strings out of 474485
+ 611493 string characters out of 5742790
+ 1945542 words of memory out of 5000000
+ 53516 multiletter control sequences out of 15000+600000
  645576 words of font info for 105 fonts, out of 8000000 for 9000
  1141 hyphenation exceptions out of 8191
  99i,19n,101p,1765b,2326s stack positions out of 10000i,1000n,20000p,200000b,200000s
@@ -3141,9 +3141,9 @@ lm/lmr17.pfb><C:/Users/Luzifer/AppData/Local/Programs/MiKTeX/fonts/type1/public
 ic/lm/lmri8.pfb><C:/Users/Luzifer/AppData/Local/Programs/MiKTeX/fonts/type1/pub
 lic/lm/lmsy10.pfb><C:/Users/Luzifer/AppData/Local/Programs/MiKTeX/fonts/type1/p
 ublic/lm/lmsy8.pfb>
-Output written on thesis.pdf (87 pages, 253284789 bytes).
+Output written on thesis.pdf (87 pages, 253286280 bytes).
 PDF statistics:
- 3898 PDF objects out of 4296 (max. 8388607)
- 301 named destinations out of 1000 (max. 500000)
+ 3901 PDF objects out of 4296 (max. 8388607)
+ 304 named destinations out of 1000 (max. 500000)
  1123 words of extra memory for PDF output out of 10000 (max. 10000000)
 
diff --git a/thesis.out b/thesis.out
index 02c7a0aa98f0fbe1a62c6f8633be817bee3e3f8c..46894df50ac8c5de162558ce909f33404ad0679a 100644
--- a/thesis.out
+++ b/thesis.out
@@ -54,13 +54,13 @@
 \BOOKMARK [2][-]{subsection.5.5.2}{\376\377\000R\000e\000s\000u\000l\000t\000s}{section.5.5}% 54
 \BOOKMARK [2][-]{subsection.5.5.3}{\376\377\000S\000o\000f\000t\000w\000a\000r\000e\000\040\000i\000m\000p\000r\000o\000v\000e\000m\000e\000n\000t\000s}{section.5.5}% 55
 \BOOKMARK [2][-]{subsection.5.5.4}{\376\377\000F\000i\000n\000a\000l\000\040\000R\000e\000m\000a\000r\000k}{section.5.5}% 56
-\BOOKMARK [0][-]{chapter*.78}{\376\377\000C\000o\000n\000c\000l\000u\000s\000i\000o\000n\000s\000\040\000a\000n\000d\000\040\000O\000u\000t\000l\000o\000o\000k}{}% 57
-\BOOKMARK [0][-]{chapter*.79}{\376\377\000B\000i\000b\000l\000i\000o\000g\000r\000a\000p\000h\000y}{}% 58
-\BOOKMARK [0][-]{chapter*.80}{\376\377\000L\000i\000s\000t\000\040\000o\000f\000\040\000A\000b\000b\000r\000e\000v\000i\000a\000t\000i\000o\000n\000s}{}% 59
-\BOOKMARK [0][-]{chapter*.81}{\376\377\000A\000p\000p\000e\000n\000d\000i\000x}{}% 60
-\BOOKMARK [1][-]{section.5.1}{\376\377\000L\000o\000c\000k\000I\000n\000\040\000a\000m\000p\000l\000i\000f\000i\000e\000r\000\040\000s\000e\000t\000t\000i\000n\000g\000s}{chapter*.81}% 61
-\BOOKMARK [1][-]{section.5.2}{\376\377\000W\000a\000l\000k\000e\000r\000\040\000p\000r\000i\000n\000c\000i\000p\000l\000e\000\040\000d\000i\000a\000g\000r\000a\000m}{chapter*.81}% 62
-\BOOKMARK [1][-]{section.5.3}{\376\377\000W\000a\000l\000k\000e\000r\000\040\000c\000i\000r\000c\000u\000i\000t\000\040\000d\000i\000a\000g\000r\000a\000m\000s}{chapter*.81}% 63
-\BOOKMARK [1][-]{section.5.4}{\376\377\000N\000e\000w\000\040\000d\000r\000i\000v\000e\000r\000\040\000e\000l\000e\000c\000t\000r\000o\000n\000i\000c\000s}{chapter*.81}% 64
-\BOOKMARK [1][-]{section.5.5}{\376\377\000R\000a\000y\000c\000a\000s\000t\000\040\000S\000i\000m\000u\000l\000a\000t\000i\000o\000n}{chapter*.81}% 65
-\BOOKMARK [0][-]{chapter*.115}{\376\377\000A\000c\000k\000n\000o\000w\000l\000e\000d\000g\000m\000e\000n\000t\000s}{}% 66
+\BOOKMARK [0][-]{chapter*.81}{\376\377\000C\000o\000n\000c\000l\000u\000s\000i\000o\000n\000s\000\040\000a\000n\000d\000\040\000O\000u\000t\000l\000o\000o\000k}{}% 57
+\BOOKMARK [0][-]{chapter*.82}{\376\377\000B\000i\000b\000l\000i\000o\000g\000r\000a\000p\000h\000y}{}% 58
+\BOOKMARK [0][-]{chapter*.83}{\376\377\000L\000i\000s\000t\000\040\000o\000f\000\040\000A\000b\000b\000r\000e\000v\000i\000a\000t\000i\000o\000n\000s}{}% 59
+\BOOKMARK [0][-]{chapter*.84}{\376\377\000A\000p\000p\000e\000n\000d\000i\000x}{}% 60
+\BOOKMARK [1][-]{section.5.1}{\376\377\000L\000o\000c\000k\000I\000n\000\040\000a\000m\000p\000l\000i\000f\000i\000e\000r\000\040\000s\000e\000t\000t\000i\000n\000g\000s}{chapter*.84}% 61
+\BOOKMARK [1][-]{section.5.2}{\376\377\000W\000a\000l\000k\000e\000r\000\040\000p\000r\000i\000n\000c\000i\000p\000l\000e\000\040\000d\000i\000a\000g\000r\000a\000m}{chapter*.84}% 62
+\BOOKMARK [1][-]{section.5.3}{\376\377\000W\000a\000l\000k\000e\000r\000\040\000c\000i\000r\000c\000u\000i\000t\000\040\000d\000i\000a\000g\000r\000a\000m\000s}{chapter*.84}% 63
+\BOOKMARK [1][-]{section.5.4}{\376\377\000N\000e\000w\000\040\000d\000r\000i\000v\000e\000r\000\040\000e\000l\000e\000c\000t\000r\000o\000n\000i\000c\000s}{chapter*.84}% 64
+\BOOKMARK [1][-]{section.5.5}{\376\377\000R\000a\000y\000c\000a\000s\000t\000\040\000S\000i\000m\000u\000l\000a\000t\000i\000o\000n}{chapter*.84}% 65
+\BOOKMARK [0][-]{chapter*.118}{\376\377\000A\000c\000k\000n\000o\000w\000l\000e\000d\000g\000m\000e\000n\000t\000s}{}% 66
diff --git a/thesis.pdf b/thesis.pdf
index b0aa58924b24866ebc96282910cf75ddf9aeb913..9f5cb875e471da1be3fc0a80ed57df609f302272 100644
Binary files a/thesis.pdf and b/thesis.pdf differ
diff --git a/thesis.synctex.gz b/thesis.synctex.gz
index 7746af7a8fd765558e8617ebb98160e29c03d695..b6b612fc0ba1de1242980a3d7dd5883853b7d815 100644
Binary files a/thesis.synctex.gz and b/thesis.synctex.gz differ
diff --git a/thesis.toc b/thesis.toc
index 26f0eb05391820d4779051268207e57f16ef5f8f..89cf4d3aab50af33bc8e30e469639257ff7443ee 100644
--- a/thesis.toc
+++ b/thesis.toc
@@ -2,14 +2,14 @@
 \contentsline {chapter}{\numberline {1}Mask Aligner background}{5}{chapter.1}%
 \contentsline {section}{\numberline {1.1}Electron beam evaporation}{5}{section.1.1}%
 \contentsline {section}{\numberline {1.2}Stencil lithography}{6}{section.1.2}%
-\contentsline {subsubsection}{Penumbra}{7}{section*.4}%
-\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.6}%
+\contentsline {subsubsection}{Penumbra}{7}{section*.5}%
+\contentsline {subsubsection}{Tilt induced penumbra}{8}{section*.7}%
 \contentsline {section}{\numberline {1.3}Measurement techniques}{9}{section.1.3}%
 \contentsline {subsection}{\numberline {1.3.1}Atomic Force Microscopy}{9}{subsection.1.3.1}%
-\contentsline {subsubsection}{Modes}{10}{section*.9}%
-\contentsline {paragraph}{Contact}{11}{section*.11}%
-\contentsline {paragraph}{Non-Contact}{11}{section*.12}%
-\contentsline {paragraph}{Tapping}{12}{section*.13}%
+\contentsline {subsubsection}{Modes}{10}{section*.10}%
+\contentsline {paragraph}{Contact}{11}{section*.12}%
+\contentsline {paragraph}{Non-Contact}{11}{section*.13}%
+\contentsline {paragraph}{Tapping}{12}{section*.14}%
 \contentsline {subsection}{\numberline {1.3.2}Scanning Electron Microscopy}{12}{subsection.1.3.2}%
 \contentsline {chapter}{\numberline {2}Mask Aligner}{15}{chapter.2}%
 \contentsline {section}{\numberline {2.1}Molecular beam evaporation chamber}{15}{section.2.1}%
@@ -21,15 +21,15 @@
 \contentsline {subsection}{\numberline {2.3.3}Optical alignment}{25}{subsection.2.3.3}%
 \contentsline {subsection}{\numberline {2.3.4}Capacitive distance measurements}{27}{subsection.2.3.4}%
 \contentsline {subsection}{\numberline {2.3.5}Reproducibility}{30}{subsection.2.3.5}%
-\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.30}%
+\contentsline {subsubsection}{Reproducibility when removing sample/mask}{30}{section*.33}%
 \contentsline {section}{\numberline {2.4}Mask Aligner operation}{31}{section.2.4}%
 \contentsline {subsection}{\numberline {2.4.1}Sample preparation}{31}{subsection.2.4.1}%
 \contentsline {chapter}{\numberline {3}Electronics}{33}{chapter.3}%
 \contentsline {section}{\numberline {3.1}RHK piezo motor controller}{33}{section.3.1}%
 \contentsline {subsection}{\numberline {3.1.1}Overview}{33}{subsection.3.1.1}%
-\contentsline {paragraph}{amplitude}{33}{section*.32}%
-\contentsline {paragraph}{sweep period}{33}{section*.33}%
-\contentsline {paragraph}{time between sweeps}{33}{section*.34}%
+\contentsline {paragraph}{amplitude}{33}{section*.35}%
+\contentsline {paragraph}{sweep period}{33}{section*.36}%
+\contentsline {paragraph}{time between sweeps}{33}{section*.37}%
 \contentsline {subsection}{\numberline {3.1.2}Pulse shape}{33}{subsection.3.1.2}%
 \contentsline {section}{\numberline {3.2}KIM001}{34}{section.3.2}%
 \contentsline {subsection}{\numberline {3.2.1}Overview}{34}{subsection.3.2.1}%
@@ -41,12 +41,12 @@
 \contentsline {subsection}{\numberline {3.3.3}Fast flank}{37}{subsection.3.3.3}%
 \contentsline {subsection}{\numberline {3.3.4}Amplification}{38}{subsection.3.3.4}%
 \contentsline {subsection}{\numberline {3.3.5}Programming}{39}{subsection.3.3.5}%
-\contentsline {subsubsection}{Parameters}{39}{section*.43}%
-\contentsline {paragraph}{Amplitude (amp)}{39}{section*.44}%
-\contentsline {paragraph}{Voltage (volt)}{39}{section*.45}%
-\contentsline {paragraph}{Channel}{39}{section*.46}%
-\contentsline {paragraph}{Max Step}{39}{section*.47}%
-\contentsline {paragraph}{Polarity}{39}{section*.48}%
+\contentsline {subsubsection}{Parameters}{39}{section*.46}%
+\contentsline {paragraph}{Amplitude (amp)}{39}{section*.47}%
+\contentsline {paragraph}{Voltage (volt)}{39}{section*.48}%
+\contentsline {paragraph}{Channel}{39}{section*.49}%
+\contentsline {paragraph}{Max Step}{39}{section*.50}%
+\contentsline {paragraph}{Polarity}{39}{section*.51}%
 \contentsline {subsection}{\numberline {3.3.6}Measured pulse shape}{39}{subsection.3.3.6}%
 \contentsline {subsection}{\numberline {3.3.7}Operation with the Mask Aligner}{41}{subsection.3.3.7}%
 \contentsline {chapter}{\numberline {4}Mask Aligner repairs and optimizations}{43}{chapter.4}%
@@ -70,44 +70,44 @@
 \contentsline {subsection}{\numberline {5.5.2}Results}{68}{subsection.5.5.2}%
 \contentsline {subsection}{\numberline {5.5.3}Software improvements}{71}{subsection.5.5.3}%
 \contentsline {subsection}{\numberline {5.5.4}Final Remark}{72}{subsection.5.5.4}%
-\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.78}%
-\contentsline {chapter}{Bibliography}{74}{chapter*.79}%
-\contentsline {chapter}{List of Abbreviations}{77}{chapter*.80}%
-\contentsline {chapter}{Appendix}{i}{chapter*.81}%
+\contentsline {chapter}{Conclusions and Outlook}{73}{chapter*.81}%
+\contentsline {chapter}{Bibliography}{74}{chapter*.82}%
+\contentsline {chapter}{List of Abbreviations}{77}{chapter*.83}%
+\contentsline {chapter}{Appendix}{i}{chapter*.84}%
 \contentsline {section}{\numberline {A}LockIn amplifier settings}{i}{section.5.1}%
 \contentsline {section}{\numberline {B}Walker principle diagram}{ii}{section.5.2}%
 \contentsline {section}{\numberline {C}Walker circuit diagrams}{ii}{section.5.3}%
 \contentsline {section}{\numberline {D}New driver electronics}{vi}{section.5.4}%
-\contentsline {paragraph}{pulse?}{vi}{section*.84}%
-\contentsline {paragraph}{pol x}{vi}{section*.85}%
-\contentsline {paragraph}{amp x}{vi}{section*.86}%
-\contentsline {paragraph}{volt x}{vi}{section*.87}%
-\contentsline {paragraph}{channel x}{vi}{section*.88}%
-\contentsline {paragraph}{maxmstep x}{vi}{section*.89}%
-\contentsline {paragraph}{step x}{vi}{section*.90}%
-\contentsline {paragraph}{mstep x}{vi}{section*.91}%
-\contentsline {paragraph}{cancel}{vii}{section*.92}%
-\contentsline {paragraph}{help}{vii}{section*.93}%
+\contentsline {paragraph}{pulse?}{vi}{section*.87}%
+\contentsline {paragraph}{pol x}{vi}{section*.88}%
+\contentsline {paragraph}{amp x}{vi}{section*.89}%
+\contentsline {paragraph}{volt x}{vi}{section*.90}%
+\contentsline {paragraph}{channel x}{vi}{section*.91}%
+\contentsline {paragraph}{maxmstep x}{vi}{section*.92}%
+\contentsline {paragraph}{step x}{vi}{section*.93}%
+\contentsline {paragraph}{mstep x}{vi}{section*.94}%
+\contentsline {paragraph}{cancel}{vii}{section*.95}%
+\contentsline {paragraph}{help}{vii}{section*.96}%
 \contentsline {section}{\numberline {E}Raycast Simulation}{vii}{section.5.5}%
-\contentsline {paragraph}{radius\_1}{vii}{section*.94}%
-\contentsline {paragraph}{angle}{vii}{section*.95}%
-\contentsline {paragraph}{radius\_mask}{vii}{section*.96}%
-\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.97}%
-\contentsline {paragraph}{distance\_sample}{vii}{section*.98}%
-\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.99}%
-\contentsline {paragraph}{running\_time}{vii}{section*.100}%
-\contentsline {paragraph}{deposition\_gain}{vii}{section*.101}%
-\contentsline {paragraph}{penalize\_deposition}{vii}{section*.102}%
-\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.103}%
-\contentsline {paragraph}{oscillation\_period}{vii}{section*.104}%
-\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.105}%
-\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.106}%
-\contentsline {paragraph}{save\_intervall}{viii}{section*.107}%
-\contentsline {paragraph}{oscillation\_dir}{viii}{section*.108}%
-\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.109}%
-\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.110}%
-\contentsline {paragraph}{random\_seed}{viii}{section*.111}%
-\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.112}%
-\contentsline {paragraph}{resolution}{viii}{section*.113}%
-\contentsline {paragraph}{path}{viii}{section*.114}%
-\contentsline {chapter}{Acknowledgments}{ix}{chapter*.115}%
+\contentsline {paragraph}{radius\_1}{vii}{section*.97}%
+\contentsline {paragraph}{angle}{vii}{section*.98}%
+\contentsline {paragraph}{radius\_mask}{vii}{section*.99}%
+\contentsline {paragraph}{distance\_circle\_mask}{vii}{section*.100}%
+\contentsline {paragraph}{distance\_sample}{vii}{section*.101}%
+\contentsline {paragraph}{rays\_per\_frame}{vii}{section*.102}%
+\contentsline {paragraph}{running\_time}{vii}{section*.103}%
+\contentsline {paragraph}{deposition\_gain}{vii}{section*.104}%
+\contentsline {paragraph}{penalize\_deposition}{vii}{section*.105}%
+\contentsline {paragraph}{first\_layer\_deposition\_prob}{vii}{section*.106}%
+\contentsline {paragraph}{oscillation\_period}{vii}{section*.107}%
+\contentsline {paragraph}{delay\_oscill\_time}{viii}{section*.108}%
+\contentsline {paragraph}{save\_in\_progress\_images}{viii}{section*.109}%
+\contentsline {paragraph}{save\_intervall}{viii}{section*.110}%
+\contentsline {paragraph}{oscillation\_dir}{viii}{section*.111}%
+\contentsline {paragraph}{oscillation\_rot\_s}{viii}{section*.112}%
+\contentsline {paragraph}{oscillation\_rot\_e}{viii}{section*.113}%
+\contentsline {paragraph}{random\_seed}{viii}{section*.114}%
+\contentsline {paragraph}{x\_min, x\_max, y\_min, y\_max}{viii}{section*.115}%
+\contentsline {paragraph}{resolution}{viii}{section*.116}%
+\contentsline {paragraph}{path}{viii}{section*.117}%
+\contentsline {chapter}{Acknowledgments}{ix}{chapter*.118}%