2018-03-24 16:45

14 files changed, 127 insertions, 176 deletions

diff --git a/.gitignore b/.gitignore
index 8e9e032..32a97ad 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,6 +11,9 @@
 *.cb
 *.cb2
 *.listing
+*.syg
+
+dissertation.pdf
 
 ## Intermediate documents:
 *.dvi
diff --git a/MX2/chapter.tex b/MX2/chapter.tex
index 6c59f86..60aa0eb 100644
--- a/MX2/chapter.tex
+++ b/MX2/chapter.tex
@@ -28,7 +28,7 @@ important when the excitation pulses are temporally overlapped.  %
 In this region, the coherent dynamics create diagonal features involving both the excitonic states
 and continuum states, while the partially coherent pathways contribute to cross-peak features.  %
 
-\section{Introduction}  % -------------------------------------------------------------------------
+\section{Introduction}  % =========================================================================
 
 Transition metal dichalcogenides (TMDCs), such as MoS\textsubscript{2}, are layered semiconductors
 with strong spin-orbit coupling, high charge mobility, and an indirect band gap that becomes direct
@@ -82,9 +82,7 @@ vector for each beam and the subscripts label the excitation frequencies.  %
 Multidimensional spectra result from measuring the output intensity dependence on frequency and
 delay times.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=0.5\textwidth]{MX2/01}
   \caption[CMDS tutorial]{
     (a) Example delays of the $\omega_1$, $\omega_2$, and $\omega_{2^\prime}$ excitation pulses.
@@ -98,7 +96,6 @@ delay times.  %
     labeling two diagonal and cross-peak features for the A and B excitons.}
   \label{fig:Czech01}
 \end{figure}
-\clearpage}
 
 \autoref{fig:Czech01} introduces our conventions for representing multidimensional spectra.  %
 \autoref{fig:Czech01}b,d are simulated data.  %
@@ -144,16 +141,13 @@ The intensity of the cross-peaks depends on the importance of state filling and
 relaxation of hot A excitons as well as the presence of interband population trnasfer of the A and
 B exciton states.  %
 
-\section{Methods}  % ------------------------------------------------------------------------------
+\section{Methods}  % ==============================================================================
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/S1}
   \caption{Schemiatic of the synthetic setup used for Mo thin film sulfidation reactions.}
   \label{fig:CzechS1}
 \end{figure}
-\clearpage}
 
 MoS\textsubscript{2} thin films were prepared \textit{via} a Mo film sulfidation reaction, similar
 to methods reported by \textcite{LaskarMasihhurR2013a}.  %
@@ -185,9 +179,7 @@ with DI water, and transferred to a Cu-mesh TEM grid.  %
 TEM experiments were performed on a FEI Titan aberration corrected (S)TEM under 200 kV accelerating
 voltage.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/10}
   \caption[Mask and epi vs transmissive.]{
     (a) Mask.
@@ -198,7 +190,6 @@ voltage.  %
     representative of the pure MoS\textsubscript{2} response.}
   \label{fig:Czech10}
 \end{figure}
-\clearpage}
 
 The coherent multidimensional spectroscopy system used a 35 fs seed pulse, centered at 800 nm and
 generated by a 1 kHz Tsunami Ti-sapphire oscillator.  %
@@ -211,14 +202,11 @@ Signal and idler were not filtered out, but played no role due to their low phot
 Pulse $\omega_2$ was split into pulses labeled $\omega_2$ and $\omega_{2^\prime}$ to create a total
 of three excitation pulses.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/S4}
   \caption{OPA outputs at each color explored.}
   \label{fig:CzechS4}
 \end{figure}
-\clearpage}
 
 In this experiment we use motorized OPAs which allow us to set the output color in software.  %
 OPA1 and OPA2 were used to create the $\omega_1$ and $\omega_2$ frequencies, respectively.  %
@@ -235,14 +223,11 @@ focused onto the sample surface by a 1 meter focal length spherical mirror in a
 geometry to form a 630, 580, and 580 $\mu$m FWHM spot sizes for $\omega_1$, $\omega_2$, and
 $\omega_{2^\prime}$, respectively.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/S5}
   \caption{Spectral delay correction.}
   \label{fig:CzechS5}
 \end{figure}
-\clearpage}
 
 \autoref{fig:CzechS5} represents delay corrections applied for each OPA.  %
 The corrections were experimentally determined using driven FWM output from fused silica.  %
@@ -277,9 +262,7 @@ signal id is the geometry chosen for this experiment.  %
 This discrimination between a film and the substrate was also seen in reflective and transmissive
 CARS microscopy experiments. \cite{VolkmerAndreas2001a}  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/11}
   \caption[MoS\textsubscript{2} post processing.]{
     Visualization of data collection and processing.
@@ -305,7 +288,6 @@ CARS microscopy experiments. \cite{VolkmerAndreas2001a}  %
     Note that the color bar's range is different than in \autoref{fig:Czech03}.}
   \label{fig:Czech11}
 \end{figure}
-\clearpage}
 
 Once measured, the FWM signal was sent through a four-stage workup process to create the data set
 shown here.  %
@@ -326,11 +308,9 @@ signal.  %
 IPython \cite{PerezFernando2007a} and matplotlib \cite{HunterJohnD2007a} were important for data
 processing and plotting in this work.
 
-\section{Results and discussion}  % ---------------------------------------------------------------
+\section{Results and discussion}  % ===============================================================
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=0.75\textwidth]{MX2/02}
   \caption[Few-layer MoS\textsubscript{2} thin film characterization.]{
     Characterization of the few-layer MoS\textsubscript{2} film studied in this work.
@@ -344,7 +324,6 @@ processing and plotting in this work.
     and representative excitation pulse shape (red).}
   \label{fig:Czech02}
 \end{figure}
-\clearpage}
 
 The few-layer MoS\textsubscript{2} thin film sample studied in this work was prepared on a
 transparent fused silica substrate by a simple sufidation reaction of a Mo thin film using a
@@ -363,9 +342,7 @@ corresponds to approximately four monolayers.  %
 and B excitonic line shapes that were extracted from the absorption spectrum. A representative
 excitation pulse profile is also shown in red for comparison.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/S3}
   \caption[MoS\textsubscript{2} absorbance.]{Extraction of excitonic features from absorbance
     spectrum. (a) Second derivative spectra of absorbance (black) and fit second derivative
@@ -373,7 +350,6 @@ excitation pulse profile is also shown in red for comparison.  %
     (black), Gaussian fits (blue and red), and remainder (black dotted).}
   \label{fig:CzechS3}
 \end{figure}
-\clearpage}
 
 Extracting the exciton absorbance spectrum is complicated by the large ``rising background'' signal
 from other MoS\textsubscript{2} bands.  %
@@ -397,9 +373,7 @@ In order to compare the FWM spectra with the absorption spectrum, the signal has
 the square root of the measured FWM signal since FWM depends quadratically on the sample
 concentration and path length.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/03}
   \caption[MoS\textsubscript{2} frequency-frequency slices.]{2D frequency-frequency spectra of the
     MoS\textsubscript{2} sample in the epi configuration. In all spectra $\tau_{22^\prime}=0$ fs,
@@ -412,7 +386,6 @@ concentration and path length.  %
     of the A and B excitons, as designated from the absorption spectrum.}
   \label{fig:Czech03}
 \end{figure}
-\clearpage}
 
 The main set of data presented in this work is an $\omega_1\omega_2\tau_{21}$ ``movie'' with
 $\tau_{22\prime}=0$. 
@@ -426,9 +399,7 @@ In contrast, we see no well-defined excitonic peaks along the $\omega_2$ ``pump'
 Instead, the signal amplitude increases toward bluer $\omega_2$ values.  %
 The decrease in FWM above 2.05 eV is caused by a drop in the $\omega_2$ OPA power.
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=0.75\textwidth]{MX2/04}
   \caption[MoS\textsubscript{2} $\omega_1$ Wigner progression.]{Mixed $\omega_1$---$\tau_{21}$
     time---frequency representations of the 3D data set at five ascending $\omega_2$ excitation
@@ -437,11 +408,8 @@ The decrease in FWM above 2.05 eV is caused by a drop in the $\omega_2$ OPA powe
     marked as dashed lines within each spectrum.}
   \label{fig:Czech04}
 \end{figure}
-\clearpage}
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=0.75\textwidth]{MX2/05}
   \caption[MoS\textsubscript{2} $\omega_2$ Wigner progression.]{Mixed $\omega_2$---$\tau_{21}$
     time---frequency representations of the 3D data set at five ascending $\omega_1$ probe
@@ -450,7 +418,6 @@ The decrease in FWM above 2.05 eV is caused by a drop in the $\omega_2$ OPA powe
     marked as dashed lines within each spectrum.}
   \label{fig:Czech05}
 \end{figure}
-\clearpage}
 
 Figures \ref{fig:Czech04} and \ref{fig:Czech05} show representative 2D frequency-delay slices from
 this movie, where the absicissa is the $\omega_1$ or $\omega_2$ frequency, respectively, the
@@ -477,9 +444,7 @@ Both the line shapes and the dynamics of the spectral features are very similar.
 \autoref{fig:Czech05} is an excitation spectrum that shows that the dynamics of the spectral
 features do not depend strongly on the $\omega_1$ frequency.
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=0.5\textwidth]{MX2/06}
   \caption[Pathway V, VI liouville pathways.]{Liouville pathways for \autoref{fig:Czech04}. gg and
     ee designate ground- and excited-state populations, the eg, 2e,e, and e$^\prime$+e,e represent
@@ -488,7 +453,6 @@ features do not depend strongly on the $\omega_1$ frequency.
     either A or B excitonic states.}
   \label{fig:Czech06}
 \end{figure}
-\clearpage}
 
 The spectral features in Figures \ref{fig:Czech03}, \ref{fig:Czech04} and \ref{fig:Czech05} depend
 on the quantum mechanical interference effects caused by the different pathways.  %
@@ -580,9 +544,7 @@ $\omega_2$ is lower than the A exciton frequency (the top subplot).  %
 If population transfer of holes from the B to A valence bands occurred during temporal overlap, the
 B/A ratio would be independent of pump frequency at $\tau_21<0$.
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/07}
   \caption[MoS\textsubscript{2} transients.]{
     Transients taken at the different $\omega_1$ and $\omega_2$ frequencies indicated by the
@@ -591,7 +553,6 @@ B/A ratio would be independent of pump frequency at $\tau_21<0$.
     constant represented as an unchanging offset over this timescale (black dashed line).}
   \label{fig:Czech07}
 \end{figure}
-\clearpage}
 
 \autoref{fig:Czech07} shows the delay transients at the different frequencies shown in the 2D
 spectrum.  %
@@ -607,16 +568,13 @@ offset that represents the long time decay.  %
 The 680 fs decay is similar to previously published pump-probe and transient absorption
 experiments. \cite{NieZhaogang2014a, SunDezheng2014a, DochertyCallumJ2014a}  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=\textwidth]{MX2/08}
   \caption[MoS\textsubscript{2} frequency-frequency slices near pulse overlap.]{2D
     frequency-frquency spectra near zero $\tau_{21}$ delay times. The signal amplitude is
     normalized to the brightest features in each spectrum.}
   \label{fig:Czech08}
 \end{figure}
-\clearpage}
 
 The spectral features change quantitatively for delay times near temporal overlap.  %
 \autoref{fig:Czech08} shows a series of 2D spectra for both positive and negative $\tau_{21}$ delay
@@ -628,16 +586,13 @@ The spectra also develop more diagonal character as the delay time moves from ne
 values.  %
 The AB cross-peak is also a strong feature in the spectrum at early times.  %
 
-\afterpage{
 \begin{figure}
-  \centering
   \includegraphics[width=0.5\textwidth]{MX2/09}
   \caption[Pathways I, III Liouville pathways.]{Liouville pathways for the $\omega_1$, $\omega_2$,
     and $\omega_{2^\prime}$ time ordering of pulse interactions. e and e$^\prime$ represent either
     A or B excitonic states.}
   \label{fig:Czech09}
 \end{figure}
-\clearpage}
 
 The pulse overlap region is complicated by the multiple Liouville pathways that must be
 considered.  %
@@ -665,7 +620,7 @@ More positie values of $\tau_{21}$ emphasize the \autoref{fig:Czech09} pathways
 \autoref{fig:Czech06} pathways, accounting for the increasing percentage of diagonal character at
 increasingly positive delays.  %
 
-\section{Conclusions}  % --------------------------------------------------------------------------
+\section{Conclusions}  % ==========================================================================
 
 This paper presents the first coherent multidimensional spectroscopy of MoS\textsubscript{2} thin
 films.  %
diff --git a/PEDOT:PSS/chapter.tex b/PEDOT:PSS/chapter.tex
index 8bb1510..1e26434 100644
--- a/PEDOT:PSS/chapter.tex
+++ b/PEDOT:PSS/chapter.tex
@@ -71,7 +71,7 @@ processing.  %
 thin film used in this work.  %
 
 \clearpage
-\begin{dfigure}
+\begin{figure}
   \centering
 	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/linear"}
 	\caption[PEDOT:PSS transmission and reflectance spectra.]{
@@ -80,7 +80,7 @@ thin film used in this work.  %
     Extinction is $\log_{10}{\mathsf{(transmission)}}$.  %
   }
 	\label{fig:PEDOTPSS_linear}
-\end{dfigure}
+\end{figure}
 \clearpage
 
 \section{Three-pulse echo spectroscopy}  % --------------------------------------------------------
@@ -98,7 +98,7 @@ that all three excitation pulse powers were equal within measurement error.  %
 
 \autoref{fig:PEDOTPSS_mask} diagrams the phase matching mask used in this set of experiments.  %
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=0.5\linewidth]{"PEDOT:PSS/mask"}
 	\caption[PEDOT:PSS 3PE phase matching mask.]{
     Phase matching mask used in this experiment.
@@ -107,19 +107,19 @@ that all three excitation pulse powers were equal within measurement error.  %
     The two stars mark the two output poyntings detected in this work.
   }
 	\label{fig:PEDOTPSS_mask}
-\end{dfigure}
+\end{figure}
 
 \autoref{fig:PEDOTPSS_raw} shows the ten raw 2D delay-delay scans that comprise the primary dataset
 described in this section.  %
 The rows correspond to the two phase matching conditions, as labeled.  %
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/raw"}
 	\caption[PEDOT:PSS 3PE raw data.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_raw}
-\end{dfigure}
+\end{figure}
 
 \subsection{Assignment of zero delay}  % ----------------------------------------------------------
 
@@ -161,37 +161,37 @@ These pulse-overlap effects cause the 3PEPS at small $T$ even without inhomogene
 [CITE]  %
 At long $T$, the average static 3PEPS is 2.5 fs.  %
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/delay space"}
 	\caption[PEDOT:PSS 3PE delay space.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_delay_space}
-\end{dfigure}
+\end{figure}
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/processed"}
 	\caption[PEDOT:PSS 3PE processed data.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_processed}
-\end{dfigure}
+\end{figure}
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/overtraces"}
 	\caption[PEDOT:PSS 3PE traces.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_overtraces}
-\end{dfigure}
+\end{figure}
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/traces"}
 	\caption[PEDOT:PSS 3PE traces.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_traces}
-\end{dfigure}
+\end{figure}
 
 There is a deviation of the TO \RomanNumeral{1}-\RomanNumeral{3} 3PEPS* trace (green line) from the
 other traces.  %
@@ -238,13 +238,13 @@ Taken together, it is clear that both pure dephasing and ensemble dephasing infl
 shift so it is important to find valuse of $T_2^*$ and $\Delta_{\mathsf{inhom}}$ that uniquely
 constrain the measured response.  %
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/parametric"}
 	\caption[PEDOT:PSS 3PE traces.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_parametric}
-\end{dfigure}
+\end{figure}
 
 We simulated the $\tau$ trance for a variety of $\Delta_{\mathsf{inhom}}$ and $T_2$ values.  %
 The results for $\Delta_t = 40$ fs are summarized in \autoref{fig:PEDOTPSS_parametric}.  %
@@ -264,7 +264,7 @@ fs.  %
 Clearly, there is no upper limit that can provide an upper limit for the inhomogeneous
 broadening.  %
 
-\begin{dtable}
+\begin{table}
  \begin{tabular}{ c | c c c }
   $\Delta_t$ (fs) & $T_2$ (fs) & $\hbar T_2^{-1}$ (meV) & $\Delta_{\mathsf{inhom}}$ (meV) \\ \hline
   45 & --- & --- & --- \\
@@ -274,15 +274,15 @@ broadening.  %
    CAPTION TODO
  }
  \label{tab:PEDOTPSS_table}
-\end{dtable}
+\end{table}
 
-\begin{dfigure}
+\begin{figure}
 	\includegraphics[width=\linewidth]{"PEDOT:PSS/agreement"}
 	\caption[PEDOT:PSS 3PE traces.]{
     CAPTION TODO
   }
 	\label{fig:PEDOTPSS_agreement}
-\end{dfigure}
+\end{figure}
 
 Our model system does ans excellent job of reproducing the entire 2D transient within measurement
 error (\autoref{fig:PEDOTPSS_agreement}).  %
diff --git a/acquisition/.#chapter.tex b/acquisition/.#chapter.tex
deleted file mode 120000
index 469b4f1..0000000
--- a/acquisition/.#chapter.tex
+++ /dev/null
@@ -1 +0,0 @@
-blaise@rooibos.28849:1520978912
\ No newline at end of file
diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex
index 7fe8760..e3035a0 100644
--- a/acquisition/chapter.tex
+++ b/acquisition/chapter.tex
@@ -121,11 +121,11 @@ S_n &=& (1-c)\left(\frac{N}{n}\right)^{-\frac{\tau_{\mathrm{step}}}{\tau_{\mathr
 S_n &=& (1-c)\left(\frac{n}{N}\right)^{\frac{\tau_{\mathrm{step}}}{\tau_{\mathrm{actual}}}} + c

 \end{eqnarray}

 

-\begin{dfigure}[p!]

+\begin{figure}

 	\includegraphics[scale=0.5]{"processing/PyCMDS/ideal axis positions/exponential"}

 	\caption[TODO]{TODO}

   \label{fig:exponential_steps}

-\end{dfigure}

+\end{figure}

 

 \subsubsection{Gaussian}

 

diff --git a/active_correction/chapter.tex b/active_correction/chapter.tex
index 6d429a0..fbbc26c 100644
--- a/active_correction/chapter.tex
+++ b/active_correction/chapter.tex
@@ -56,7 +56,7 @@ parameterization of delay space chosen.  %
 First I focus on the interference patterns in 2D delay space where all excitation fields and the

 detection field are at the same frequency.  %

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[scale=0.5]{"active_correction/scatter/scatter interference in TrEE old"}

 	\caption[Simulated interference paterns in old delay parameterization.]{Numerically simulated

     interference patterns between scatter and TrEE for the old delay parametrization. Each column

@@ -64,7 +64,7 @@ detection field are at the same frequency.  %
     bottom row shows the 2D Fourier transform, with the colorbar's dynamic range chosen to show the

     cross peaks.}

   label{fig:scatterinterferenceinTrEEold}

-\end{dfigure}

+\end{figure}

 

 Here I derive the slopes of constant phase for the old delay space, where

 $\mathrm{d1}=\tau_{2^\prime1}$ and $\mathrm{d2}=\tau_{21}$.  %

@@ -89,7 +89,7 @@ The cross term between scatter and signal is the product of $\Phi_\mathrm{sig}$
 Figure \ref{fig:scatterinterferenceinTrEEold} presents numerical simulations of scatter interference as a visual aid. See Yurs 2011 \cite{YursLenaA2011a}.

 % TODO: Yurs 2011 Data

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=7in]{"active_correction/scatter/scatter interference in TrEE current"}

 	\caption[Simulated interference paterns in current delay parameterization.]{Numerically simulated

     interference patterns between scatter and TrEE for the current delay parametrization. Each

@@ -97,7 +97,7 @@ Figure \ref{fig:scatterinterferenceinTrEEold} presents numerical simulations of
     the bottom row shows the 2D Fourier transform, with the colorbar's dynamic range chosen to show

     the cross peaks.}

   \label{fig:scatterinterferenceinTrEEcurrent}

-\end{dfigure}

+\end{figure}

 

 Here I derive the slopes of constant phase for the current delay space, where $\mathrm{d1}=\tau_{22^\prime}$ and $\mathrm{d2}=\tau_{21}$. I take $\tau_2$ to be $0$, so that $\tau_{22^\prime}\rightarrow\tau_{2^\prime}$ and $\tau_{21}\rightarrow\tau_1$. The phase of the signal is then

 \begin{equation}

@@ -181,7 +181,7 @@ this technique was used prior to May 2016 in the Wright Group...  %
 `leveling' and single-chopping is also used in some early 2DES work...

 \cite{BrixnerTobias2004a}.  %

 

-\begin{dfigure} 

+\begin{figure} 

 	\includegraphics[scale=0.5]{"active_correction/scatter/TA chopping comparison"}

 	\caption[Comparison of single, dual chopping.]{Comparison of single and dual chopping in a

     MoS\textsubscript{2} transient absorption experiment. Note that this data has not been

@@ -189,7 +189,7 @@ this technique was used prior to May 2016 in the Wright Group...  %
     grey line near 2 eV represents the pump energy. The inset labels are the number of laser shots

     taken and the chopping strategy used.}

   \label{fig:ta-chopping-comparison}

-\end{dfigure}

+\end{figure}

 

 Figure \ref{fig:ta-chopping-comparison} shows the effects of dual chopping for some representative

 MoS\textsubscript{2} TA data.  %

diff --git a/build.sh b/build.sh
index 7abca57..649b522 100755
--- a/build.sh
+++ b/build.sh
@@ -49,7 +49,7 @@ if [[ "$1" = "all" ]] || [[ "$1" = "dissertation" ]] ; then
   printLine
   printColor documents
   pdflatex --interaction=nonstopmode --shell-escape dissertation
-  bibtex dissertation
+  biber dissertation
   pdflatex --interaction=nonstopmode --shell-escape dissertation
   pdflatex --interaction=nonstopmode --shell-escape dissertation
 fi
diff --git a/dissertation.cls b/dissertation.cls
index 6397be2..bf2e6f6 100644
--- a/dissertation.cls
+++ b/dissertation.cls
@@ -13,21 +13,30 @@
 \RequirePackage{xcolor}
 \RequirePackage{array} 
 
+% --- floats --------------------------------------------------------------------------------------
+
+
+% force all floats to center (see https://tex.stackexchange.com/a/53383)
+\makeatletter
+\g@addto@macro\@floatboxreset{\centering}
+\makeatother
+
+
 % --- headers -------------------------------------------------------------------------------------
 
 % required: page number in upper right, nothing else
 
 \RequirePackage{fancyhdr}
 \fancypagestyle{plain}{
-	\fancyhf{}
-	\fancyhead[R]{\thepage}
-	\fancyfoot{}
+  \fancyhf{}
+  \fancyhead[R]{\thepage}
+  \fancyfoot{}
 	\renewcommand{\headrulewidth}{0pt}
 	\renewcommand{\footrulewidth}{0pt}
 }
 \pagestyle{plain}{\rhead{\thepage}}
 
-\setlength{\headheight}{11pt}
+\setlength{\headheight}{14pt}
 
 % --- text ----------------------------------------------------------------------------------------
 
@@ -119,19 +128,6 @@
 
 \newcommand{\includepython}[1]{\inputminted[bgcolor=bg]{python}{#1}}
 
-% --- tables --------------------------------------------------------------------------------------
-
-\newenvironment{dtable}
-  {
-  \clearpage
-  \begin{table}
-  \centering
-  }
-  {
-  \end{table}
-  \clearpage
-  }
-
 % --- graphics ------------------------------------------------------------------------------------
 
 \RequirePackage{graphics}
@@ -141,15 +137,8 @@
 \RequirePackage{etoc}
 \RequirePackage{tikz}
 
-\newenvironment{dfigure}
-  {
-  \clearpage
-  \begin{figure}
-  \centering
-  }
-  {
-  \end{figure}
-  \clearpage}
+\BeforeBeginEnvironment{figure}{\clearpage}
+\AfterEndEnvironment{figure}{\clearpage}
 
 % --- math ----------------------------------------------------------------------------------------
 
@@ -179,30 +168,29 @@ anchorcolor=black]{hyperref}
 
 % --- glossary ------------------------------------------------------------------------------------
 
-\RequirePackage[acronym, nopostdot, nogroupskip]{glossaries}
-\newcommand{\comma}{,\penalty \exhyphenpenalty}
-\newlength\glsnamewidth
-\setlength{\glsnamewidth}{0.3\hsize}
-\setlength{\glsdescwidth}{1\hsize}
-\newglossarystyle{myglossarystyle}{
-	\setglossarystyle{super}
-	\renewenvironment{theglossary}{
-		\tablehead{}
-		\tabletail{}
-		\begin{supertabular}{p{\glsnamewidth}p{\glsdescwidth}}}{\end{supertabular}}
-	\renewcommand{\glossentry}[2]{
-		\raggedleft
-		\glsentryitem{##1}\glstarget{##1}{\glossentryname{##1}} &
-		\glossentrydesc{##1}\glspostdescription\space ##2\tabularnewline}}
-\renewcommand{\arraystretch}{1}
-\setglossarystyle{myglossarystyle}
-\newglossary[slg]{symbolslist}{syi}{syg}{Symbols}
-\makeglossaries
-\include{glossary}
-
-\RequirePackage{tocloft}
+%\RequirePackage[acronym, nopostdot, nogroupskip]{glossaries}
+%\newcommand{\comma}{,\penalty \exhyphenpenalty}
+%\newlength\glsnamewidth
+%\setlength{\glsnamewidth}{0.3\hsize}
+%\setlength{\glsdescwidth}{1\hsize}
+%\newglossarystyle{myglossarystyle}{
+%	\setglossarystyle{super}
+%	\renewenvironment{theglossary}{
+%		\tablehead{}
+%		\tabletail{}
+%		\begin{supertabular}{p{\glsnamewidth}p{\glsdescwidth}}}{\end{supertabular}}
+%	\renewcommand{\glossentry}[2]{
+%		\raggedleft
+%		\glsentryitem{##1}\glstarget{##1}{\glossentryname{##1}} &
+%		\glossentrydesc{##1}\glspostdescription\space ##2\tabularnewline}}
+%\renewcommand{\arraystretch}{1}
+%\setglossarystyle{myglossarystyle}
+%\newglossary[slg]{symbolslist}{syi}{syg}{Symbols}
+%\makeglossaries
+
+%\RequirePackage{tocloft}
  
-\setlength\cftparskip{0pt}
-\setlength\cftbeforechapskip{-5pt}
-\setlength\cftbeforesecskip{-7pt}
-\setlength\cftbeforesubsecskip{-10pt}
\ No newline at end of file
+%\setlength\cftparskip{0pt}
+%\setlength\cftbeforechapskip{-5pt}
+%\setlength\cftbeforesecskip{-7pt}
+%\setlength\cftbeforesubsecskip{-10pt}
\ No newline at end of file
diff --git a/dissertation.pdf b/dissertation.pdf
deleted file mode 100644
index 141ab65..0000000
--- a/dissertation.pdf
+++ /dev/null
diff --git a/dissertation.syg b/dissertation.syg
deleted file mode 100644
index 3d211de..0000000
--- a/dissertation.syg
+++ /dev/null
@@ -1,2 +0,0 @@
-\glossaryentry{\ensuremath {N}?\glossentry{N}|setentrycounter[]{page}\glsnumberformat}{10}
-\glossaryentry{\ensuremath {N}?\glossentry{N}|setentrycounter[]{page}\glsnumberformat}{10}
diff --git a/dissertation.tex b/dissertation.tex
index 22e0383..c5c1a1a 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -1,7 +1,12 @@
 \documentclass{dissertation}

 

+%\include{glossary}

+

+

 \begin{document}

 

+

+

 % --- preamble ------------------------------------------------------------------------------------

 

 \begin{centering}

@@ -41,9 +46,12 @@ This dissertation is approved by the following members of the Final Oral Committ
 \pagenumbering{roman}  % must use roman page numbering in preamble

 

 % CONTENTS

+\renewcommand{\baselinestretch}{0.5}\normalsize

 \tableofcontents

+% TODO: consider adding chapter headings to list of figures / list of tables

 \listoffigures

 \listoftables

+\renewcommand{\baselinestretch}{1}\normalsize

 

 % ACKNOWLEDGEMENTS

 \cleardoublepage

@@ -59,16 +67,16 @@ This dissertation is approved by the following members of the Final Oral Committ
 

 % chapters ----------------------------------------------------------------------------------------

 

-\include{introduction/chapter}

+%\include{introduction/chapter}

 

 \part{Background}

-\include{spectroscopy/chapter}

-\include{materials/chapter}

-\include{software/chapter}

+%\include{spectroscopy/chapter}

+%\include{materials/chapter}

+%\include{software/chapter}

 

 \part{Development}

-\include{processing/chapter}

-\include{acquisition/chapter}

+%\include{processing/chapter}

+%\include{acquisition/chapter}

 %\include{active_correction/chapter}

 %\include{opa/chapter}

 %\include{mixed_domain/chapter}

@@ -99,9 +107,9 @@ This dissertation is approved by the following members of the Final Oral Committ
 

 \pagenumbering{gobble}

 

-\singlespacing

-\renewcommand{\arraystretch}{2}  % there is probably a better way...

-\printglossaries

+%\singlespacing

+%\renewcommand{\arraystretch}{2}  % there is probably a better way...

+%\printglossaries

 \printbibliography

 

 \end{document}
\ No newline at end of file
diff --git a/mixed_domain/chapter.tex b/mixed_domain/chapter.tex
index 12b0278..18af8d1 100644
--- a/mixed_domain/chapter.tex
+++ b/mixed_domain/chapter.tex
@@ -146,7 +146,7 @@ from these measurement artifacts.  %
 

 \section{Theory}  % -------------------------------------------------------------------------------

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=0.5\linewidth]{"mixed_domain/WMELs"}

 	\caption[Sixteen triply-resonant Liouville pathways.]{

 		The sixteen triply-resonant Liouville pathways for the third-order response of the system used

@@ -156,7 +156,7 @@ from these measurement artifacts.  %
     are yellow, excitations with $\omega_2=\omega_{2'}$ are purple, and the final emission is gray.

 	}

 	\label{fig:WMELs}

-\end{dfigure}

+\end{figure}

 

 We consider a simple three-level system (states $n=0,1,2$) that highlights the multidimensional

 line shape changes resulting from choices of the relative dephasing and detuning of the system and

@@ -240,7 +240,7 @@ this paper.  %
 The steady state and impulsive limits of Equation \ref{eq:rho_f_int} are discussed in TODO

 % Appendix \ref{sec:cw_imp}.  %

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{"mixed_domain/simulation overview"}

 	\caption[Overview of the MR-CMDS simulation.]{

 		Overview of the MR-CMDS simulation. 

@@ -258,7 +258,7 @@ The steady state and impulsive limits of Equation \ref{eq:rho_f_int} are discuss
     help introduce our delay convention.  

 	}

 	\label{fig:overview}

-\end{dfigure}

+\end{figure}

 

 Fig. \ref{fig:overview} gives an overview of the simulations done in this work.  %

 Fig. \ref{fig:overview}a shows an excitation pulse (gray-shaded) and examples of a coherent

@@ -494,7 +494,7 @@ The driven limit holds for large detunings, regardless of delay.  %
 

 \subsection{Convolution Technique for Inhomogeneous Broadening} \label{sec:mixed_convolution}  % --

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{mixed_domain/convolve}

   \caption[Convolution overview.]

   {Overview of the convolution.

@@ -503,7 +503,7 @@ The driven limit holds for large detunings, regardless of delay.  %
     (c) The resulting ensemble line shape computed from the convolution.

     The thick black line represents the FWHM of the distribution function.}

 	\label{fig:convolution}

-\end{dfigure}

+\end{figure}

 

 Here we describe how to transform the data of a single reference oscillator signal to that of an

 inhomogeneous distribution.  %

@@ -589,7 +589,7 @@ pulse delay times, and inhomogeneous broadening.  %
 

 \subsection{Evolution of single coherence}\label{sec:evolution_SQC}

 

-\begin{dfigure}

+\begin{figure}

   \centering

 	\includegraphics[width=0.5\linewidth]{"mixed_domain/fid vs dpr"}

 	\caption[Relative importance of FID and driven response for a single quantum coherence.]{

@@ -601,7 +601,7 @@ pulse delay times, and inhomogeneous broadening.  %
     slightly detuned (relative detuning, $\Omega_{fx}/\Delta_{\omega}=0.1$).

 	}

 	\label{fig:fid_dpr}

-\end{dfigure}

+\end{figure}

 

 It is illustrative to first consider the evolution of single coherences, $\rho_0 \xrightarrow{x}

 \rho_1$, under various excitation conditions.  %

@@ -638,7 +638,7 @@ We note that our choices of $\Gamma_{10}\Delta_t=2.0, 1.0,$ and $0.5$ give coher
 mainly driven, roughly equal driven and FID parts, and mainly FID components, respectively.  %

 FID character is difficult to isolate when $\Gamma_{10}\Delta_t=2.0$.  %

 

-\begin{dfigure}

+\begin{figure}

   \centering

 	\includegraphics[width=0.5\linewidth]{"mixed_domain/fid vs detuning"}

 	\caption[Pulsed excitation of a single quantum coherence and its dependance on pulse detuning.]{

@@ -659,7 +659,7 @@ FID character is difficult to isolate when $\Gamma_{10}\Delta_t=2.0$.  %
 		In all plots, the gray line is the electric field amplitude. 

 	}

 	\label{fig:fid_detuning}

-\end{dfigure}

+\end{figure}

 

 Fig. \ref{fig:fid_detuning}a shows the temporal evolution of $\rho_1$ at several values of

 $\Omega_{1x}/\Delta_{\omega}$ with $\Gamma_{10}\Delta_t=1$.

@@ -728,7 +728,7 @@ $\Gamma_{10}\Delta_t=1$.  %
 

 \subsection{Evolution of single Liouville pathway}

 

-\begin{dfigure}

+\begin{figure}

   \centering

 	\includegraphics[width=\linewidth]{"mixed_domain/pw1 lineshapes"}

 	\caption[2D frequency response of a single Liouville pathway at different delay values.]{

@@ -741,7 +741,7 @@ $\Gamma_{10}\Delta_t=1$.  %
     compare 2D spectrum frame color with dot color on 2D delay plot.

 		}

 	\label{fig:pw1}

-\end{dfigure}

+\end{figure}

 

 We now consider the multidimensional response of a single Liouville pathway involving three pulse

 interactions.  %

@@ -779,7 +779,7 @@ the changing resonance conditions for each of the four delay coordinates studied
 Since $E_1$ is not the last pulse in pathway I$\gamma$, the tracking monochromator must also be

 considered.  %

 

-\begin{dtable}

+\begin{table}

 	\caption{\label{tab:table2} Conditions for peak intensity at different pulse delays for pathway

     I$\gamma$.}

 	\begin{tabular}{c c | c c c c}

@@ -796,7 +796,7 @@ considered.  %
 		2.4 & -2.4 & $\omega_1=\omega_{10}$ & $\omega_2=\omega_{10}$ & $\omega_2=\omega_{10}$ &

     $\omega_1=\omega_2$ \\

 	\end{tabular}

-\end{dtable}

+\end{table}

 

 When the pulses are all overlapped ($\tau_{21}=\tau_{22^\prime}=0$, lower right, orange), all

 transitions in the Liouville pathway are simultaneously driven by the incident fields.  %

@@ -870,7 +870,7 @@ in unexpected ways.  %
 

 \subsection{Temporal pathway discrimination}  % ---------------------------------------------------

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{"mixed_domain/delay space ratios"}

 	\caption[2D delay response for different relative dephasing rates.]{

 		Comparison of the 2D delay response for different relative dephasing rates (labeled atop each

@@ -885,7 +885,7 @@ in unexpected ways.  %
     (purple), and III or I (teal).

 	}

 	\label{fig:delay_purity}

-\end{dfigure}

+\end{figure}

 

 In the last section we showed how a single pathway's spectra can evolve with delay due to pulse

 effects and time gating.  %

@@ -935,7 +935,7 @@ vanishing signal intensities; the contour of $P=0.99$ across our systems highlig
 

 \subsection{Multidimensional line shape dependence on pulse delay time}

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{"mixed_domain/spectral evolution"}

 	\caption[Evolution of the 2D frequency response.]{

 		Evolution of the 2D frequency response as a function of $\tau_{21}$ (labeled inset) and the

@@ -950,7 +950,7 @@ vanishing signal intensities; the contour of $P=0.99$ across our systems highlig
     $\tau_{22^\prime}=0$.

 	}

 	\label{fig:hom_2d_spectra}

-\end{dfigure}

+\end{figure}

 

 In the previous sections we showed how pathway spectra and weights evolve with delay.  %

 This section ties the two concepts together by exploring the evolution of the spectral line shape

@@ -1025,14 +1025,14 @@ only the absorptive line shape along $\omega_2$.  %
 This narrowing, however, is unresolvable when the pulse bandwidth becomes broader than that of the

 resonance, which gives rise to a vertically elongated signal when $\Gamma_{10}\Delta_t=0.5$.  %

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{"mixed_domain/wigners"}

 	\caption[Wigners.]{

 		Transient ($\omega_1$) line shapes and their dependence on $\omega_2$ frequency.  

 		The relative dephasing rate is $\Gamma_{10}\Delta_t=1$ and $\tau_{22^\prime}=0$.  

 		For each plot, the corresponding $\omega_2$ value is shown as a light gray vertical line.}

 	\label{fig:wigners}

-\end{dfigure}

+\end{figure}

 

 It is also common to represent data as ``Wigner plots,'' where one axis is delay and the other is

 frequency. \cite{KohlerDanielDavid2014a, AubockGerald2012a, CzechKyleJonathan2015a,

@@ -1051,7 +1051,7 @@ Again, these features can resemble spectral diffusion even though our system is
 

 \subsection{Inhomogeneous broadening} \label{sec:res_inhom}  % ------------------------------------

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=0.5\linewidth]{"mixed_domain/inhom delay space ratios"}

 	\caption[2D delay response with inhomogeneity.]{

 		2D delay response for $\Gamma_{10}\Delta_t=1$ with sample inhomogeneity.  %

@@ -1066,7 +1066,7 @@ Again, these features can resemble spectral diffusion even though our system is
     (purple), III (teal, dashed), and I (teal, solid).  %

 	}

 	\label{fig:delay_inhom}

-\end{dfigure}

+\end{figure}

 

 With the homogeneous system characterized, we can now consider the effect of inhomogeneity.  %

 For inhomogeneous systems, time-orderings III and V are enhanced because their final coherence will

@@ -1118,7 +1118,7 @@ distortion has not been investigated previously.  %
 Peak-shifting due to pulse overlap is less important when $\omega_1\neq\omega_2$ because

 time-ordering III is decoupled by detuning.  %

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{"mixed_domain/inhom spectral evolution"}

 	\caption[Spectral evolution of an inhomogenious system.]{

 		Same as Fig. \ref{fig:hom_2d_spectra}, but each system has inhomogeneity

@@ -1135,7 +1135,7 @@ time-ordering III is decoupled by detuning.  %
     time-orderings V and VI unequal.

 	}

 	\label{fig:inhom_2d_spectra}

-\end{dfigure}

+\end{figure}

 

 In frequency space, spectral elongation along the diagonal is the signature of inhomogeneous

 broadening.  %

@@ -1218,7 +1218,7 @@ Only time-orderings V and VI are relevant.  %
 The intermediate population resonance is still impulsive but it depends on

 $\omega_{2^\prime}-\omega_2$ which is not explored in our 2D frequency space.  %

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\linewidth]{"mixed_domain/steady state"}

 	\caption[Conditional validity of the driven limit.]{

 		Comparing approximate expressions of the 2D frequency response with the directly integrated

@@ -1231,11 +1231,11 @@ $\omega_{2^\prime}-\omega_2$ which is not explored in our 2D frequency space.  %
 		Third column:  The directly integrated response.  %

 	}

 	\label{fig:steady_state}

-\end{dfigure}

+\end{figure}

 

 \subsection{Extracting true material correlation}  % ----------------------------------------------

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=0.5\linewidth]{"mixed_domain/metrics"}

 	\caption[Metrics of correlation.]{

 		Temporal (3PEPS) and spectral (ellipticity) metrics of correlation and their relation to the

@@ -1252,7 +1252,7 @@ $\omega_{2^\prime}-\omega_2$ which is not explored in our 2D frequency space.  %
     area are connected).  %

 }

 	\label{fig:metrics}

-\end{dfigure}

+\end{figure}

 

 We have shown that pulse effects mimic the qualitative signatures of inhomogeneity.  %

 Here we address how one can extract true system inhomogeneity in light of these effects.  %

diff --git a/processing/chapter.tex b/processing/chapter.tex
index fa449fe..28d1858 100644
--- a/processing/chapter.tex
+++ b/processing/chapter.tex
@@ -421,21 +421,21 @@ In the future, other libraries (e.g. mayavi), may be incorporated.  %
 

 \subsubsection{1D}

 

-\begin{dfigure}

+\begin{figure}

   \includegraphics[width=0.5\textwidth]{"processing/quick1D 000"}

   \includepython{"processing/quick1D.py"}

   \caption[CAPTION TODO]

     {CAPTION TODO}

-\end{dfigure}

+\end{figure}

 

 \subsubsection{2D}

 

-\begin{dfigure}

+\begin{figure}

   \includegraphics[width=0.5\textwidth]{"processing/quick2D 000"}

   \includepython{"processing/quick2D.py"}

   \caption[CAPTION TODO]

     {CAPTION TODO}

-\end{dfigure}

+\end{figure}

 

 \subsection{Specialty}  % -------------------------------------------------------------------------

 

diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex
index a301117..fe10f60 100644
--- a/spectroscopy/chapter.tex
+++ b/spectroscopy/chapter.tex
@@ -176,11 +176,11 @@ Transient absorbance (TA) spectroscopy is a self-heterodyned technique.  %
 Through chopping you can measure nonlinearities quantitatively much easier than with homodyne

 detected (or explicitly heterodyned) experiments.

 

-\begin{dfigure}

+\begin{figure}

 	\includegraphics[width=\textwidth]{"spectroscopy/TA setup"}

 	\label{fig:ta_and_tr_setup}

 	\caption{CAPTION TODO}

-\end{dfigure}

+\end{figure}

 

 \autoref{fig:ta_and_tr_setup} diagrams the TA measurement for a generic sample.  %

 Here I show measurement of both the reflected and transmitted probe beam \dots not important in