From a556dba6d7b956ab6469916d886dfeea8dcc2932 Mon Sep 17 00:00:00 2001 From: John Wright Date: Wed, 4 Apr 2018 12:08:57 -0500 Subject: little warning fixes --- acquisition/chapter.tex | 4 ++-- dissertation.cls | 10 +++++----- opa/chapter.tex | 2 +- processing/chapter.tex | 2 +- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/acquisition/chapter.tex b/acquisition/chapter.tex index 0d3d1c5..0436028 100644 --- a/acquisition/chapter.tex +++ b/acquisition/chapter.tex @@ -36,7 +36,7 @@ for w2 in w2_points: set_d2(d2) measure_signal() \end{codefragment} -In this simple example, there are 5 \python{w1} destinations, 7 \phon{w2} destinations, and 12 +In this simple example, there are 5 \python{w1} destinations, 7 \python{w2} destinations, and 12 \python{d2} destinations, so there are a total of $5\times7\times12=420$ pixels in the three-dimensional scan. % The acquisition software must set the hardware to each of these points and acquire data at each of @@ -732,7 +732,7 @@ We can write the conjugate equation to \ref{eq:simple_exponential_decay}, asking need to get a cerain signal level?'': \begin{eqnarray} \log{(S)} &=& -\frac{t}{\tau} \\ -t &=& -\taulog{(S)}. +t &=& -\tau\log{(S)}. \end{eqnarray} So to step linearly in $t$, my step size has to go as $-\tau\log{(S)}$. diff --git a/dissertation.cls b/dissertation.cls index afb2dc9..aecaaad 100644 --- a/dissertation.cls +++ b/dissertation.cls @@ -118,17 +118,17 @@ colback=bg, boxrule=1pt, colframe=bg, - arc=0, + arc=0pt, shadow=false, - use counter=equation, + new/use counter=equation, boxsep=1ex, top=0pt, left=0pt, right=0pt, bottom=0pt, comment={\hfill(\arabic{chapter}.\arabic{equation})}, listing outside comment, - righthand width=2.5em, + righthand width=3em, sidebyside gap=0pt, minted language=#1, - before skip =-0.5\baselinestretch, - after skip=2\baselinestretch, + %before skip =-0.5\baselinestretch, + %after skip=2\baselinestretch, } \BeforeBeginEnvironment{codefragment}{\begin{singlespace}\stepcounter{equation}} diff --git a/opa/chapter.tex b/opa/chapter.tex index 75459b5..a57847a 100644 --- a/opa/chapter.tex +++ b/opa/chapter.tex @@ -129,7 +129,7 @@ are shown. % \end{figure} \begin{figure} - \includegraphics[width=\textwidth]{opa/c2}} + \includegraphics[width=\textwidth]{opa/c2} \caption{ CAPTION TODO } diff --git a/processing/chapter.tex b/processing/chapter.tex index 81886c2..baca84c 100644 --- a/processing/chapter.tex +++ b/processing/chapter.tex @@ -128,7 +128,7 @@ It contains a central data ``container'' that is capable of storing all of the i each multidimensional (or one-dimensional) spectra: the \python{Data} class. % It also defines a \python{Collection} class that contains data objects, collection objects, and other pieces of metadata in a hierarchical structure. % -Let's first discuss \mitinline{python}{Data}. +Let's first discuss \mintinline{python}{Data}. All spectra are stored within WrightTools as multidimensional arrays. % Arrays are containers that store many instances of the same data type, typically numerical -- cgit v1.2.3 From ba8235a76c56f6fba6eb9919f3a64054f17fe79d Mon Sep 17 00:00:00 2001 From: John Wright Date: Thu, 5 Apr 2018 07:41:09 -0500 Subject: JCW Summary of Changes --- abstract.tex | 7 ++++--- introduction/chapter.tex | 7 ++++--- spectroscopy/chapter.tex | 3 ++- 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/abstract.tex b/abstract.tex index dd08aa0..2c9b4ed 100644 --- a/abstract.tex +++ b/abstract.tex @@ -5,9 +5,10 @@ Coherent multidimensional spectroscopy (CMDS) encompasses a family of experimental strategies involving the nonlinear interaction between electric fields and a material under investigation. % -This approach has several unique capabilities: 1. resolving congested states [CITE KLUG], 2. -extracting spectra that would otherwise be selection-rule disslowed [CITE BOYLE], 3. resolving -fully coherent dyanmics [CITE], 4. measuring coupling [CITE], and 5. resolving ultrafast dynamics +This approach has several unique capabilities: 1. resolving congested states [CITE KLUG and % JCW Zhao and Wright-JACS], +2. extracting spectra that would otherwise be selection-rule disslowed [CITE BOYLE], 3. resolving +fully coherent dyanmics [CITE % JCW Pakoulev and Wright], +4. measuring coupling [CITE], and 5. resolving ultrafast dynamics [CITE]. % CMDS can be collected in the frequency or the time domain, and each approach has advantages and diff --git a/introduction/chapter.tex b/introduction/chapter.tex index be4572d..b8877e6 100644 --- a/introduction/chapter.tex +++ b/introduction/chapter.tex @@ -52,7 +52,7 @@ flexable in the kinds of experiments that they can perform. % This dissertation contains several projects undertaken to improve the reliability and accessibility of MR-CMDS. % While MR-CMDS will never be a single-shot experiment, there are many improvements that can improve -data collection speed. % +data collection speed. % JCW- NOT SO SURE IT CAN'T BE SINGLE SHOT Necessary calibration, especially OPA calibration, can be made robust and fully automatic. % Common artifacts can be addressed through relatively simple modifications in hardware and software. % @@ -64,11 +64,12 @@ frequency-domain coherent multidimensional spectroscopy. % Due to its diversity and dimensionality, MR-CMDS data is challenging to process and represent. % The data processing tools that a scientist develops to process one experiment may not work when she attempts to process an experiment where different experimental variables are explored. % -Historically, this has meant that MR-CMDS practitioners have used custom, one-off data processing +Historically, this % JCW- "THIS" SHOULDN'T BE A NOUN STANDING ALONE AS THE SUBJECT OF THE SENTENCE +has meant that MR-CMDS practitioners have used custom, one-off data processing workflows that need to be changed for each particular experiment. % These changes take time to implement, and can become stumbling blocks or opportunities for error. % -Even worse, the challenge of designing a new processing workflow may make dissuade scientist from +Even worse, the challenge of designing a new processing workflow may dissuade A scientist from creatively modifying their experimental strategy, or comparing their data with data taken from another group. % This limit to creativity and flexibility defeats one of the main advantages of the MR-CMDS diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex index 3bde7b4..030edd5 100644 --- a/spectroscopy/chapter.tex +++ b/spectroscopy/chapter.tex @@ -67,6 +67,7 @@ For simplicity, we consider a single transition dipole, $\mu$. % The Hamiltonian which controls the coupling of or simple system to the electric field described in ...: +% jcw- ISN'T IT JUST MU DOT E WHERE E IS A VECTOR THAT IS TIME DEPENDENT, NOT A TIME DERIVATIVE \begin{equation} H = H_{\circ} - \mu \dot E \end{equation} @@ -90,7 +91,7 @@ In Dirac notation \cite{DiracPaulAdrienMaurice1939a}., an observable (such as $\ \end{equation} The complex wavefunction is called a \emph{ket}, represented $|b>$. % The complex conjugate is called a \emph{bra}, represented $ + \left -- cgit v1.2.3