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DPhil thesis.

Perl 0.17% TeX 85.17% Python 14.67%

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use negative space in 1JCH in tables A.3 and A.6

re-enable tex ligatures for other optical weights

Table 0.1: Spectrometers used in this thesis. A more complete description may be accessed via the links in the `internal name' column

quotes aren't showing up properly after I removed tex ligatures from everything (see also #2)

Disable ligatures for mono font

thesis/preamble/fonts.tex

Lines 5 to 29 in e25af25

 \defaultfontfeatures{Ligatures=TeX} 

 % Main fonts used in the document 

 \setmainfont[ 

 Path={/Users/yongrenjie/Library/Fonts/}, 

 Extension=.otf, 

 UprightFont={*-regular}, 

 BoldFont={*-semibold}, 

 ItalicFont={*-italic}, 

 BoldItalicFont={*-semibolditalic}, 

 ]{minion3} 

 \setmonofont[ 

 Path={/Users/yongrenjie/Library/Fonts/}, 

 Extension=.ttf, 

 UprightFont={*-Regular}, 

 BoldFont={*-SemiBold}, 

 ItalicFont={*-Italic}, 

 BoldItalicFont={*-SemiBoldItalic}, 

 Scale=MatchLowercase 

 ]{RobotoMono} 

 \setmathfont[ 

 Path={./fonts/}, 

 Scale=MatchLowercase 

 ]{LibertinusMath-Regular.otf} 

 \mathitalicsmode=1

The use of \defaultfontfeatures{Ligatures=TeX} here is applied to all fonts, including the monospace font. For some reason, this leads to double quotes in code listings turning into curly quotes (I have no clue why it doesn't happen to single quotes).

Because TeX ligatures are by default applied to setmainfont (see fontspec documentation https://texdoc.org/serve/fontspec/0 Part II, section 1), commenting this out should ensure that TeX ligatures are still used for the text (in Minion) but not for the listings such as this one:

thesis/noah/parallel.tex

Lines 176 to 181 in e25af25

 \begin{mylisting}[!htbp] % lst:generalised_pp {{{1 

 \begin{tcbminted}{bruker} 

 "l0 = td1/2" ; TD1/NBL 

 "cnst53 = cnst51 - cnst52" ; automatically calculate m_2 = M - m_1 

 ; ...

That should fix the curly double quotes in the listings.

In principle I think I should re-add TeX ligatures for the math font because I really don't know if I've used them somewhere. It would be very odd for that to be the case, but anyway it can be done by just adding Ligatures=TeX as another option in \setmathfont.

typo software

Plots are generated using Python 3, using a number of packages (namely: numpy, scipy, matplotlib, seaborn, and penguins

missing closing parenthesis

conclusion chpt3

Springer thesis nomination

Create a title page that states only your name, the title of your work and the phrase “Doctoral Thesis accepted by the University of Oxford, UK”.
Please remove the “Declaration of Authorship”
(emailed Tim 16/7) Please provide a foreword written by your supervisor (Supervisor’s Foreword) and insert this into the frontmatter of your thesis. The foreword should comprise approximately one page explaining the significance of the research reported in a wider context and what makes the thesis outstanding, plus any other related information of interest to the reader e.g. the thesis results have already inspired further work in progress on xyz. It should end with the name of the supervisor and the date.
Please add a list of all your publications in the frontmatter, entitled: “Parts of this thesis have been published in the following journal articles:”. This should list all the articles that were published from your thesis work.
Please use the following structure in the frontmatter of your SpringerTheses manuscript: Title page – Supervisor’s Foreword – Abstract – Preface - “Parts of this thesis…” – Acknowledgments – Table of Contents – List of Figures – List of Tables – List of code listings – List of acronyms”
(see comment below) Please send a list of the figures which must be printed in color in order to make scientific sense.
Please send us a short bio text (max 200 words) with your main achievements and scientific interests. This text will be displayed on the book’s SpringerLink webpage.
(all figures are original, done by myself) We need your confirmation that you have permission to re-publish any figures and text identical to that in previous publications (authored by you and/or others). Usually the permissions are easily obtained via an online platform called RightsLink. You can find more information about the acquisition of permissions on our website: https://www.springer.com/gp/rights-permissions/obtaining-permissions/882 If you need help when applying for permission or encounter any difficulties in the process, please contact me. Even if you have gathered the permissions for your original publication, you need to obtain the permissions again for the publication with a commercial publisher as Springer. When reusing Figures published in your journal articles, please add a credit line in the figure’s caption as follows: “Reused/adapted with permission from [source]”.

ref 109 in noah chapter doesn't show up right

(109) Pérez-Trujillo, M.; Nolis, P.; Parella, T. CN-HMBC:� A Powerful NMR Technique for the Simultaneous Detection of Long-Range ¹H,¹³C and ¹H,¹⁵N Connectivities. Org. Lett. 2007, 9, 29–32,

note that the HTML tags also need to be removed, they appear correct in the github issue because it's interpreted

10.1021/ol062511h

Michaelmas Term 2022

Should be Trinity 2022.

Typos

Pi symbol not showing in figure caption using siunitx

thesis/theory/pulseacq.tex

Lines 71 to 82 in e25af25

 \begin{figure}[htbp] 

 \centering 

 \includegraphics[]{theory/lorentzians.png}% 

 {\phantomsubcaption\label{fig:lorentzians_absorption}}% 

 {\phantomsubcaption\label{fig:lorentzians_dispersion}}% 

 \caption[Absorption- and dispersion-mode Lorentzian lineshapes]{ 

 \textbf{(\subref*{fig:lorentzians_absorption})} Absorption-mode lineshape $A(\omega; \Omega = 0)$. 

 \textbf{(\subref*{fig:lorentzians_dispersion})} Dispersion-mode lineshape $D(\omega; \Omega = 0)$. 

 Both lines have been plotted using $k = \qty{\pi}{\radian\per\second}$. 

 } 

 \label{fig:lorentzians} 

 \end{figure}

There's probably a fix for this somewhere online...

	\defaultfontfeatures{Ligatures=TeX}

	% Main fonts used in the document
	\setmainfont[
	Path={/Users/yongrenjie/Library/Fonts/},
	Extension=.otf,
	UprightFont={*-regular},
	BoldFont={*-semibold},
	ItalicFont={*-italic},
	BoldItalicFont={*-semibolditalic},
	]{minion3}
	\setmonofont[
	Path={/Users/yongrenjie/Library/Fonts/},
	Extension=.ttf,
	UprightFont={*-Regular},
	BoldFont={*-SemiBold},
	ItalicFont={*-Italic},
	BoldItalicFont={*-SemiBoldItalic},
	Scale=MatchLowercase
	]{RobotoMono}
	\setmathfont[
	Path={./fonts/},
	Scale=MatchLowercase
	]{LibertinusMath-Regular.otf}
	\mathitalicsmode=1

	\begin{mylisting}[!htbp] % lst:generalised_pp {{{1
	\begin{tcbminted}{bruker}
	"l0 = td1/2" ; TD1/NBL
	"cnst53 = cnst51 - cnst52" ; automatically calculate m_2 = M - m_1
	; ...

	\begin{figure}[htbp]
	\centering
	\includegraphics[]{theory/lorentzians.png}%
	{\phantomsubcaption\label{fig:lorentzians_absorption}}%
	{\phantomsubcaption\label{fig:lorentzians_dispersion}}%
	\caption[Absorption- and dispersion-mode Lorentzian lineshapes]{
	\textbf{(\subref*{fig:lorentzians_absorption})} Absorption-mode lineshape $A(\omega; \Omega = 0)$.
	\textbf{(\subref*{fig:lorentzians_dispersion})} Dispersion-mode lineshape $D(\omega; \Omega = 0)$.
	Both lines have been plotted using $k = \qty{\pi}{\radian\per\second}$.
	}
	\label{fig:lorentzians}
	\end{figure}

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