2018-04-15 00:16

8 files changed, 86 insertions, 73 deletions

diff --git a/OPA_interferometry.wt5 b/OPA_interferometry.wt5
new file mode 100644
index 0000000..82daee0
--- /dev/null
+++ b/OPA_interferometry.wt5
diff --git a/PEDOT_PSS/chapter.tex b/PEDOT_PSS/chapter.tex
index b7fba1f..10a7472 100644
--- a/PEDOT_PSS/chapter.tex
+++ b/PEDOT_PSS/chapter.tex
@@ -1,6 +1,5 @@
 \chapter{PEDOT:PSS}  \label{cha:pps}
 
-
 \textit{This Chapter presents content first published in \textcite{HorakErikH2018a}.
   The authors are:
   \begin{denumerate}
diff --git a/dissertation.tex b/dissertation.tex
index 9c0d90a..9d40288 100644
--- a/dissertation.tex
+++ b/dissertation.tex
@@ -90,7 +90,7 @@ This dissertation is approved by the following members of the Final Oral Committ
 \begin{appendix}

 % AFTER DEFENSE \include{public/chapter}

 \include{procedures/chapter}  % prc

-\include{hardware/chapter}  % hdw

+% AFTER DEFENSE \include{hardware/chapter}  % hdw

 \include{irf/chapter}  % irf

 \include{quantitative_ta/chapter}  % qta

 \include{opa_phase/chapter}  % rpa

diff --git a/irf/chapter.tex b/irf/chapter.tex
index 07cd561..3066d9e 100644
--- a/irf/chapter.tex
+++ b/irf/chapter.tex
@@ -4,7 +4,7 @@ The instrumental response function (IRF) is a classic concept in analytical scie
 Defining IRF becomes complex with instruments as complex as these, but it is still useful to
 attempt.  %
 
-It is particularly useful to define bandwidth.
+It is particularly useful to define bandwidth.  %
 
 \subsubsection{Time Domain}
 
@@ -63,7 +63,4 @@ A tune test contains this information.  %
 
 \subsubsection{Time-Bandwidth Product}
 
-For a Gaussian, approximately 0.441
-
-% TODO: find reference
-% TODO: number defined on INTENSITY level!
\ No newline at end of file
+For a Gaussian, approximately 0.441
\ No newline at end of file
diff --git a/opa_phase/chapter.tex b/opa_phase/chapter.tex
index 774ab45..ae1a9ea 100644
--- a/opa_phase/chapter.tex
+++ b/opa_phase/chapter.tex
@@ -1,35 +1,53 @@
 \chapter{Abandon the random phase approximation} \label{cha:rpa}
 
-Recently we've made some measurements that seem to imply phase stability between the fs OPAs.  %
-We've typically assumed that the OPAs have random phase on every shot, making coherent heterodyne
-processes average to zero.  %
-These measurements show that this is a very bad assumption.  %
-
-I've taken the interferogram of OPA1 vs OPA2, Clearly the OPAs remain phase locked for many shots.  %
-In 'over time' I show the spectral phase pattern (D = 500 fs) for 1000 single shot acquisitions
-over 430 seconds in lab time.  %
-The phase does drift, but it is certainly not quickly randomized.  %
+\clearpage
+
+Historically, we've assumed that OPAs have random phase on every shot.  %
+This makes interference processes quickly average to zero over many shots---we rarely take fewer
+than 100 shots per pixel.  %
+Here I demonstrate that this assumption is very poor, at least for the femtosecond OPAs.  %
+
+In these experiments, I simply send OPA1 and OPA2 simultaniously into the array detector.  %
+The crucial detail is that the beams are exactly collinear---overlaped in a beamsplitter.  %
+I then scan delay between them while collecting single shot spectra using the array detector.  %
 
-I have more data showing:
-How the spectral phase changes over the course of hours.
-How the phase evolves as we scan the OPAs against each-other in color.
-The reproducibility of phase as the OPA motors move away and then return to a given color.
+\autoref{rpa:fig:delay} shows the results of these experiments for OPA2 vs itself
+(``auto-interference'')  and vs OPA1 (``cross interference'').  %
+At zero delay all colors arise simultaniously, so there are no modulations along the array axis
+(vertical).  %
+As I scan further from zero modulations set in as each wavelength within the pulse has a different
+period in delay space.  %
+It is crucial to remember that the monochromator acts like a stretcher, so we see interference
+between the two pulses even when separated by 400 fs.  %
+
+The fringe pattern is expected in the case of auto-interference, but it is also quite stable in
+cross-interference. In the next experiment, I explore just how stable the cross-phase is.
+
+\autoref{rpa:fig:time} shows the same single-shot spectrum taken 1000 times at a fixed delay of 500
+fs.  %
+The phase does drift, but it is certainly not quickly randomized.  %
+In fact, the period shifts by 180 degrees in roughly one minute---much much longer than any single
+pixel that we have taken.  %
 
-I'll work this data up and send out another email with many more details and thoughts once I have
-time.  %
-This quick note is just to let the group know that we must abandon the 'random phase' assumption
-when thinking about what heterodyne processes can happen as coherent artifacts.  %
+This result forces us to reconsider our assumptions when identifying potential sources of artifact
+in our measurements.  %
 
 \begin{figure}
-  \includegraphics[width=\textwidth]{"opa_phase/cross interference"}
-  \caption[CAPTION TODO]{
-    CAPTION TODO
+  \includegraphics[width=\textwidth]{"opa_phase/auto_cross_interference"}
+  \caption[Auto-interference vs cross-interference.]{
+    Interference between OPA outputs as function of relative arrival time.
+    In the left hand plot, OPA2 interferes with itself.
+    In the right hand plot, OPA1 interferes with OPA2.
+    Signal is intensity level.
   }
+  \label{rpa:fig:delay}
 \end{figure}
 
 \begin{figure}
-  \includegraphics[width=\textwidth]{"opa_phase/430 seconds"}
-  \caption[CAPTION TODO]{
-    CAPTION TODO
+  \includegraphics[width=\textwidth]{"opa_phase/time_interference"}
+  \caption[Cross interference over 100 seconds.]{
+    Cross interference at fixed delay of 500 fs.
+    1000 single-shot acquisitions over a period of 100 seconds in lab time.
   }
+  \label{rpa:fig:time}
 \end{figure}
diff --git a/opa_phase/darien_playing.py b/opa_phase/darien_playing.py
index cc8ce39..b8bd5b7 100644
--- a/opa_phase/darien_playing.py
+++ b/opa_phase/darien_playing.py
@@ -93,8 +93,7 @@ if True:
        ax.set_xlabel('lab time (s)')
        ax.set_ylabel(col.auto.wa.label)
        ax.grid()
-       
-    #d.array.clip(.3)
+    d.array.clip(.3)
     fig, gs = wt.artists.create_figure(width='double', cols=[1, 'cbar'], default_aspect=.5)
     # overtime
     ax = plt.subplot(gs[0,0])
diff --git a/procedures/chapter.tex b/procedures/chapter.tex
index fd04bc3..8c8d0b2 100644
--- a/procedures/chapter.tex
+++ b/procedures/chapter.tex
@@ -1,7 +1,17 @@
 \chapter{Procedures}
 
-\clearpage
-\section{``Six-month'' maintenance}  % ------------------------------------------------------------
+\begin{dquote}
+  These are the vegetables we must eat before we can have our pixels of ice cream.
+
+  \dsignature{Wright Group saying}.
+\end{dquote}
+
+\vfill
+
+In this chapter I document the various procedures that I have performed to maintain the MR-CMDS
+instruments.  %
+
+\section{``Six-month'' maintenance}  % ============================================================
 
 The laser system that the Wright Group's MR-CMDS instruments use requires regular maintenance.  %
 Each component is sensitive to lab conditions such as temperature, humidity, and vibrations.  %
@@ -13,7 +23,6 @@ Historically, the Wright Group has engaged in reactive maintenance: a ``fix it i
 don't touch otherwise'' kind of approach.  %
 This approach makes a lot of sense for instruments that are quick to fix, and have few active
 users.  %
-
 I instituted a proactive, regular maintenance procedure (described below) that has improved the
 predictability of instrumental performance.  %
 Predictability is key for instruments with multiple users.  %
@@ -48,9 +57,9 @@ Procedure:
         \end{denumerate}
       \item Chiller maintenance.
         \begin{ditemize}
-          \item See x
-          \item See y
-          \item See z
+          \item See \autoref{prc:sec:lytron}
+          \item See \autoref{prc:sec:polyscience}
+          \item See \autoref{prc:sec:neslab}
         \end{ditemize}
       \item Lab cleaning.
         \begin{denumerate}
@@ -68,13 +77,9 @@ Procedure:
     \end{ditemize}
   \item Let lab sit overnight to allow dust to settle and the air to dehumidify.
   \item Start up system again.
-    \begin{denumerate}
-      \item TODO
-    \end{denumerate}
 \end{denumerate}
 
-\clearpage
-\section{Lytron Kodiak RC006}  % ------------------------------------------------------------------
+\section{Lytron Kodiak RC006} \label{prc:sec:lytron}  % ===========================================
 
 We have one Lytron Kodiak RC006: Model Number RC006G03BB1C002, Serial Number 739383-02.
 
@@ -107,10 +112,7 @@ These seem to have been fixed by adding a “high” flow loop connecting the ou
 chiller.  %
 Ideally the pressure drop across this loop is sufficient to still drive fluid through the laser.  %
 
-% TODO: figure
-
-\clearpage
-\section{PolyScience 6000 Series}  % --------------------------------------------------------------
+\section{PolyScience 6000 Series} \label{prc:sec:polyscience}  % ==================================
 
 We own two PolyScience chillers---different models but functionally equivalent.
 
@@ -142,8 +144,7 @@ Regular chiller maintenance:
     \end{denumerate}
 \end{denumerate}
 
-\clearpage
-\section{NesLab Merlin M33}  % ====================================================================
+\section{NesLab Merlin M33} \label{prc:sec:neslab}  % =============================================
 
 We have one NesLab Merlin M33 Chiller, Serial Number 106227049.  %
 
@@ -171,7 +172,6 @@ Regular chiller maintenance
 
 % TODO: figures
 
-\clearpage
 \section{Calibrating the 407A}  % =================================================================
 
 Calibrating the 407.A
@@ -180,11 +180,11 @@ You may sometimes notice that the zero position changes dramatically from sensit
 sensitivity with the 407A. If this happens, iterate through the following until zero stays
 consistent:
 
-Use the fine adjust (knob on side) to zero the 407A on the highest sensitivity
-
-Use the front adjust (flathead screwdriver needed) to zero on the lowest sensitivity
-
-\clearpage
+\begin{ditemize}
+  \item Use the fine adjust (knob on side) to zero the 407A on the highest sensitivity.
+  \item Use the front adjust (flathead screwdriver needed) to zero on the lowest sensitivity.
+\end{ditemize}
+    
 \section{Millenia}  % =============================================================================
 
 \subsection{Startup}  % ---------------------------------------------------------------------------
@@ -228,7 +228,6 @@ These allow us to record things like Diode hours.  %
 Service mode can be buggy, so it's best to leave the Millenia in normal Power mode during regular
 operation.  %
 
-\clearpage
 \section{Spitfire Pro}  % =========================================================================
 
 Only tune up the Spitfire if you need to, and do not treat it casually---set aside an entire
@@ -429,7 +428,6 @@ Since we have not messed with the stretcher frequently this guide cannot be trus
     square mirrors preceding the compressor.
 \end{denumerate}
   
-\clearpage
 \section{TOPAS-C}  % ==============================================================================
 
 % TODO: figure
@@ -668,7 +666,6 @@ Input poynting is adjusted to ensure good alignment through L1 and L2 into D1.
   \item Measure and record power---should be over 600 mW.
 \end{denumerate}
 
-\clearpage
 \section{MicroHR Monochromator}  % ================================================================
 
 Visible Grating.  %
diff --git a/quantitative_ta/chapter.tex b/quantitative_ta/chapter.tex
index c8b594d..099b606 100644
--- a/quantitative_ta/chapter.tex
+++ b/quantitative_ta/chapter.tex
@@ -1,32 +1,35 @@
-\chapter{Quantitative transient absorbance} \label{cha:qta}
+\chapter{Quantitative differential absorbance} \label{cha:qta}
 
-\subsubsection{Quantitative TA}
+\clearpage
 
 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.
+detected (or explicitly heterodyned) experiments.  %
 
-\begin{figure}
-	\includegraphics[width=\textwidth]{"spectroscopy/TA setup"}
-	\label{fig:ta_and_tr_setup}
-	\caption{CAPTION TODO}
-\end{figure}
+%\begin{figure}
+%	\includegraphics[width=\textwidth]{"spectroscopy/TA setup"}
+%	\label{fig:ta_and_tr_setup}
+%	\caption{CAPTION TODO}
+%\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
-opaque (pyrite) or non-reflective (quantum dot) samples \dots  %
+%\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
+%opaque (pyrite) or non-reflective (quantum dot) samples \dots  %
 
 Typically one attempts to calculate the change in absorbance $\Delta A$ \dots  %
 
 \begin{eqnarray}
 \Delta A &=& A_{\mathrm{on}} - A_{\mathrm{off}} \\
-&=& -\log_{10}\left(\frac{I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}} + I_{\Delta\mathrm{R}}}{I_0}\right) + \log\left(\frac{I_\mathrm{T}+I_\mathrm{R}}{I_0}\right) \\
-&=& -\left(\log_{10}(I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}}+ I_{\Delta\mathrm{R}})-\log_{10}(I_0)\right)+\left(\log_{10}(I_\mathrm{T}+I_\mathrm{R})-\log_{10}(I_0)\right) \\
+&=& -\log_{10}\left(\frac{I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}} +
+    I_{\Delta\mathrm{R}}}{I_0}\right) + \log\left(\frac{I_\mathrm{T}+I_\mathrm{R}}{I_0}\right) \\
+&=& -\left(\log_{10}(I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}}+
+    I_{\Delta\mathrm{R}})-\log_{10}(I_0)\right)+\left(\log_{10}(I_\mathrm{T}+I_\mathrm{R})-\log_{10}(I_0)\right)
+  \\ 
 &=& -\left(\log_{10}(I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}}+ I_{\Delta\mathrm{R}})-\log_{10}(I_\mathrm{T}+I_\mathrm{R})\right) \\
-&=& -\log_{10}\left(\frac{I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}}+ I_{\Delta\mathrm{R}}}{I_\mathrm{T}+I_\mathrm{R}}\right) \label{eq:ta_complete}
+&=& -\log_{10}\left(\frac{I_\mathrm{T}+I_\mathrm{R}+I_{\Delta\mathrm{T}}+ I_{\Delta\mathrm{R}}}{I_\mathrm{T}+I_\mathrm{R}}\right) \label{qta:eqn:ta_complete}
 \end{eqnarray}
 
-\autoref{eq:ta_complete} simplifies beautifully  if reflectivity is negligible \dots
+\autoref{qta:eqn:ta_complete} simplifies beautifully  if reflectivity is negligible \dots
 
 Now I define a variable for each experimental measurable:
 \begin{center}