+\subsection{Ag-Bright on Si substrate}
+
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth, angle=0]{figures/ellipsometer/ag_on_si/psi_final_model.png}
+ \label{psi_final_model.png}
+\end{figure}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth, angle=0]{figures/ellipsometer/ag_on_si/delta_final_model.png}
+ \label{delta_final_model.png}
+\end{figure}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth, angle=0]{figures/ellipsometer/ag_on_si/ag_fit_vs_bulk_opticalconstants.png}
+ \label{ag_fit_vs_bulk_opticalconstants.png}
+\end{figure}
+
+The plots show the measured and fitted ellipsometric parameters for a thin film of Ag on a Si substrate. The model was constructed to include an $\text{SiO}^2$ oxide layer on the Si, and a surface roughness Effective Medium Approximation (EMA) (Bruggeman). A fit was first performed for the thickness of the Ag film assuming bulk optical constants; this fit was then improved by allowing the software to adjust the Ag film's optical constants. Final model:
+
+\begin{center}
+ \begin{tabular}{lll}
+ {\bf Layer} & {\bf Thickness} \\
+ Ag (fit for $n$ and $k$) & $16.092 \pm 2.7$ nm \\
+ Intermix (Ag/$\text{SiO}^2$) & $0.267 \pm 0.03$ nm \\
+ $\text{SiO}^2$ & $4.02 \pm 0.57$ nm \\
+ Si & (substrate)
+ \end{tabular}
+ \captionof{table}{Model for thin Ag on Si}
+\end{center}
+
+\subsection{Black Ag on Si}
+
+
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth, angle=0]{figures/ellipsometer/blackag_on_si/psi.png}
+ \label{psi_final_model.png}
+\end{figure}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth, angle=0]{figures/ellipsometer/blackag_on_si/delta.png}
+ \label{delta_final_model.png}
+\end{figure}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth, angle=0]{figures/ellipsometer/blackag_on_si/blackag_opticalconstants_comparison.png}
+ \label{ag_fit_vs_bulk_opticalconstants.png}
+\end{figure}
+
+\begin{center}
+ \begin{tabular}{lll}
+ {\bf Layer} & {\bf Thickness} \\
+ Surface roughness EMA (75.8\% void) & 2.708 nm \\
+ Black Ag (fit for $n$ and $k$) & 3.726 nm \\
+ $\text{SiO}^2$ & 8.00 nm \\
+ Si & (substrate)
+ \end{tabular}
+ \captionof{table}{Model for thin Ag on Si}
+\end{center}
+
+\pagebreak
+
+\section{Optical Reflection Spectroscopy using the VASE}
+
+\subsection{Au on Si}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth]{figures/ellipsometer/au_and_blackau/au_on_si.png}
+ \caption{figure}{Reflection measurements for Au layers on Si}
+\end{figure}
+
+
+\subsection{Au on Au-Black on Au on Si}
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth]{figures/ellipsometer/au_and_blackau/au_on_blackau_si.png}
+ \caption{figure}{Reflection measurements for an Au layer on Au-Black on Au layers on Si}
+\end{figure}
+
+\subsection{Comparison with model of 50nm Au on Si}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.8\textwidth]{figures/ellipsometer/au_and_blackau/generated_au_on_si_reflection.png}
+ \caption{Generated 50nm on Si}
+\end{figure}
+
+\pagebreak
+
+\section{Optical Transmission Spectroscopy using OceanOptics Spectrometer}
+
+\subsection{Dark Spectrum}
+
+{\bf NOTE: Probably won't include in the final thesis}
+
+Figure \ref{dark_comparison.eps} shows the spectrum of the background (taken at different times on the same day), without the light source.
+The room lights were off, the experiment was covered with a cardboard box and layers of black plastic sheeting; but the spectra still changed for different times of the day.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.5\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/dark_comparison.eps}
+ \caption{Dark spectra}
+ \label{dark_comparison.eps}
+\end{figure}
+
+In all subsequent experiments, the dark intensity has been subtracted from measured intensity counts:
+\begin{align*}
+ I(\lambda) = I_{\text{measured}}(\lambda) - I_{\text{dark}}(\lambda)
+\end{align*}
+
+\pagebreak
+\subsection{Reference Spectrum}
+
+{\bf Note: Also don't include in final thesis? Or at least, remove the time dependence; just show one curve.}
+
+The Ellipsometer's Xe Arc Lamp was used as a light source. It's spectrum $I_0(\lambda)$ is shown in Figure \ref{reference.eps}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.5\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/reference.eps}
+ \caption{Xe Lamp reference spectra}
+ \label{reference.eps}
+\end{figure}
+
+Because the dark spectra changed over time scales comparable to the length of measurement, some features in the processed spectra are due to the reference spectra of the Xe lamp.
+
+\pagebreak
+\subsection{Testing the Spectrometer}
+
+{\bf Note: Also don't include?}
+
+The spectrometer was tested using a 653nm filter. \ref{653nm_filter.eps}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.5\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/653nm_filter.eps}
+ \caption{Tested Spectrometer with 653nm Filter}
+ \label{653nm_filter.eps}
+\end{figure}
+
+The transmission was calculated as:
+\begin{align}
+ t(\lambda) &= \frac{I(\lambda)}{I_0{\lambda}} \label{transmission1}
+\end{align}
+Where $I_0(\lambda)$ was the intensity (arbitrary units) of the Xe Arc Lamp at wavelength $\lambda$, and $I(\lambda)$ was the measured intensity.
+
+\subsection{Transmission Spectra of Glass}
+
+{\bf Note: Should probably include this, as the substrate is important to the final transmission}
+
+All films were prepared on microscope glass; the transmission of the glass must be known to determine the transmission of the films.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.5\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/glass_transmission.eps}
+ \caption{Glass reference transmission spectrum}
+ \label{glass_transmission.eps}
+\end{figure}
+
+{\bf NOTE:} The reason that the glass has transmission $> 1$ is (probably) because the background level has increased between the reference measurement and the measurement of glass. I should probably normalise the glass transmission spectrum to its maximum value.
+
+Transmission was calculated using \eqref{transmission1}.
+
+\subsection{Transmission Spectra of Au and Au-Black on Glass}
+
+Figure \ref{blackau_vs_au.eps} shows all measured transmission spectra for Au vs Au-Black (pressure 1e-6 is for the Au-bright films, all others are Au-Black) {\bf NOTE: Need to relabel plot}
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.7\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/blackau_vs_au.eps}
+ \caption{Transmission Spectra for various Au films}
+ \label{blackau_vs_au.eps}
+\end{figure}
+
+Transmission is calculated as:
+\begin{align*}
+ t &= \frac{I(\lambda)}{I_0(\lambda)} \times \frac{I_\text{glass}(\lambda)}{I_0(\lambda)}
+\end{align*}
+Where $t_{\text{glass}} = \frac{I_\text{glass}}{I_0}$ is the transmission spectrum of the microscope slide glass.
+
+{\bf Note: I should select just 2 or 3 of these spectra to use in the final report}
+
+The general trends:
+\begin{enumerate}
+ \item Thin films (low current or short evaporation time) show similar shape regardless of pressure (1e-6 or 1e-2 mbar)
+ \item Thicker layers all show peak near 500nm, followed by minima at 600-700nm
+ \item All curves show fine structure at same wavelengths above 800nm. This may be due to the Xe lamp spectrum; if the background level has increased, then Xe lamp spectral features will show up in the final spectrum.
+ \item Thick layers of Au-Black show much lower transmission to 700nm, but a much faster increase at longer $\lambda$
+ \item At least one of the Au-Black samples shows a similar spectrum to a (thick) Au-Bright sample.
+\end{enumerate}
+
+\subsubsection{Effect of Atmosphere on Transmission Spectra of Au-Black}
+
+A paper \cite{} has found differences between Au-Black prepared in Air or an inert gas. The Au-Black prepared in Air contains traces of Tungsten Oxides; the Au-Black prepared in an inert gas does not. This was the motivation for making a comparison between samples prepared in Air and He.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.7\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/he_blackau_vs_air_blackau.eps}
+ \caption{Transmission Spectra for Black Au films prepared in different atmospheres}
+ \label{he_blackau_vs_air_blackau.eps}
+\end{figure}
+
+\subsection{Transmission Spectra of Ag}
+
+A pre-existing Ag sample (unknown preparation conditions), on glass.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.7\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/silver_transmission.eps}
+ \caption{Transmission Spectra for a Silver film on glass}
+ \label{silver_transmission.eps}
+\end{figure}
+
+
+\subsection{Transmission Spectra of Ag and Ag-Black on Glass}
+
+The Ag sample compared with Ag-Black.
+Notice fine structure not in original Ag sample. Probably due to dark spectrum changing.
+
+A pre-existing Ag sample (unknown preparation conditions), on glass.
+
+\begin{figure}[H]
+ \centering
+ \includegraphics[width=0.7\textwidth, angle=270]{/home/sam/Documents/University/honours/thesis/figures/transmission_spectroscopy/blackag_vs_ag.eps}
+ \caption{Transmission Spectra for a Silver film on glass}
+ \label{blackag_vs_ag.eps}
+\end{figure}
+
+{\bf Note:} The Ag-Black is much thinner than the Ag-Bright sample; by eye it appears to be a thin grey layer. Also, the Ag-Bright sample was not uniformly thick; part of the film had been scratched or wiped off.
+