diff --git a/.gitignore b/.gitignore index 13a4ea1..1652230 100644 --- a/.gitignore +++ b/.gitignore @@ -24,7 +24,11 @@ result # SyncTeX files *.synctex.gz *.synctex(busy) - +openspec +.claude +**/node_modules +**/dist +log.txt # PDF files *.pdf diff --git a/Chapters/Chapter1.tex b/Chapters/Chapter1.tex deleted file mode 100755 index 0ea6b9b..0000000 --- a/Chapters/Chapter1.tex +++ /dev/null @@ -1,603 +0,0 @@ -% Chapter 1 - -\chapter{Chapter Title Here} % Main chapter title - -\label{Chapter1} % For referencing the chapter elsewhere, use \ref{Chapter1} - -%---------------------------------------------------------------------------------------- - -% Define some commands to keep the formatting separated from the content -\newcommand{\keyword}[1]{\textbf{#1}} -\newcommand{\tabhead}[1]{\textbf{#1}} -\newcommand{\code}[1]{\texttt{#1}} -\newcommand{\file}[1]{\texttt{\bfseries#1}} -\newcommand{\option}[1]{\texttt{\itshape#1}} - -%---------------------------------------------------------------------------------------- - -\section{Welcome and Thank You} -Welcome to this \LaTeX{} Thesis Template, a beautiful and easy to use -template for writing a thesis using the \LaTeX{} typesetting system. - -If you are writing a thesis (or will be in the future) and its -subject is technical or mathematical (though it doesn't have to be), -then creating it in \LaTeX{} is highly recommended as a way to make -sure you can just get down to the essential writing without having to -worry over formatting or wasting time arguing with your word processor. - -\LaTeX{} is easily able to professionally typeset documents that run -to hundreds or thousands of pages long. With simple mark-up commands, -it automatically sets out the table of contents, margins, page -headers and footers and keeps the formatting consistent and -beautiful. One of its main strengths is the way it can easily typeset -mathematics, even \emph{heavy} mathematics. Even if those equations -are the most horribly twisted and most difficult mathematical -problems that can only be solved on a super-computer, you can at -least count on \LaTeX{} to make them look stunning. - -%---------------------------------------------------------------------------------------- - -\section{Learning \LaTeX{}} - -\LaTeX{} is not a \textsc{wysiwyg} (What You See is What You Get) -program, unlike word processors such as Microsoft Word or Apple's -Pages. Instead, a document written for \LaTeX{} is actually a simple, -plain text file that contains \emph{no formatting}. You tell \LaTeX{} -how you want the formatting in the finished document by writing in -simple commands amongst the text, for example, if I want to use -\emph{italic text for emphasis}, I write the \verb|\emph{text}| -command and put the text I want in italics in between the curly -braces. This means that \LaTeX{} is a \enquote{mark-up} language, -very much like HTML. - -\subsection{A (not so short) Introduction to \LaTeX{}} - -If you are new to \LaTeX{}, there is a very good eBook -- freely -available online as a PDF file -- called, \enquote{The Not So Short -Introduction to \LaTeX{}}. The book's title is typically shortened to -just \emph{lshort}. You can download the latest version (as it is -occasionally updated) from here: -\url{http://www.ctan.org/tex-archive/info/lshort/english/lshort.pdf} - -It is also available in several other languages. Find yours from the -list on this page: \url{http://www.ctan.org/tex-archive/info/lshort/} - -It is recommended to take a little time out to learn how to use -\LaTeX{} by creating several, small `test' documents, or having a -close look at several templates on:\\ -\url{http://www.LaTeXTemplates.com}\\ -Making the effort now means you're not stuck learning the system when -what you \emph{really} need to be doing is writing your thesis. - -\subsection{A Short Math Guide for \LaTeX{}} - -If you are writing a technical or mathematical thesis, then you may -want to read the document by the AMS (American Mathematical Society) -called, \enquote{A Short Math Guide for \LaTeX{}}. It can be found online here: -\url{http://www.ams.org/tex/amslatex.html} -under the \enquote{Additional Documentation} section towards the -bottom of the page. - -\subsection{Common \LaTeX{} Math Symbols} -There are a multitude of mathematical symbols available for \LaTeX{} -and it would take a great effort to learn the commands for them all. -The most common ones you are likely to use are shown on this page: -\url{http://www.sunilpatel.co.uk/latex-type/latex-math-symbols/} - -You can use this page as a reference or crib sheet, the symbols are -rendered as large, high quality images so you can quickly find the -\LaTeX{} command for the symbol you need. - -\subsection{\LaTeX{} on a Mac} - -The \LaTeX{} distribution is available for many systems including -Windows, Linux and Mac OS X. The package for OS X is called MacTeX -and it contains all the applications you need -- bundled together and -pre-customized -- for a fully working \LaTeX{} environment and work flow. - -MacTeX includes a custom dedicated \LaTeX{} editor called TeXShop for -writing your `\file{.tex}' files and BibDesk: a program to manage -your references and create your bibliography section just as easily -as managing songs and creating playlists in iTunes. - -%---------------------------------------------------------------------------------------- - -\section{Getting Started with this Template} - -If you are familiar with \LaTeX{}, then you should explore the -directory structure of the template and then proceed to place your -own information into the \emph{THESIS INFORMATION} block of the -\file{main.tex} file. You can then modify the rest of this file to -your unique specifications based on your degree/university. Section -\ref{FillingFile} on page \pageref{FillingFile} will help you do -this. Make sure you also read section \ref{ThesisConventions} about -thesis conventions to get the most out of this template. - -If you are new to \LaTeX{} it is recommended that you carry on -reading through the rest of the information in this document. - -Before you begin using this template you should ensure that its style -complies with the thesis style guidelines imposed by your -institution. In most cases this template style and layout will be -suitable. If it is not, it may only require a small change to bring -the template in line with your institution's recommendations. These -modifications will need to be done on the \file{MastersDoctoralThesis.cls} file. - -\subsection{About this Template} - -This \LaTeX{} Thesis Template is originally based and created around -a \LaTeX{} style file created by Steve R.\ Gunn from the University -of Southampton (UK), department of Electronics and Computer Science. -You can find his original thesis style file at his site, here: -\url{http://www.ecs.soton.ac.uk/~srg/softwaretools/document/templates/} - -Steve's \file{ecsthesis.cls} was then taken by Sunil Patel who -modified it by creating a skeleton framework and folder structure to -place the thesis files in. The resulting template can be found on -Sunil's site here: -\url{http://www.sunilpatel.co.uk/thesis-template} - -Sunil's template was made available through -\url{http://www.LaTeXTemplates.com} where it was modified many times -based on user requests and questions. Version 2.0 and onwards of this -template represents a major modification to Sunil's template and is, -in fact, hardly recognisable. The work to make version 2.0 possible -was carried out by \href{mailto:vel@latextemplates.com}{Vel} and -Johannes Böttcher. - -%---------------------------------------------------------------------------------------- - -\section{What this Template Includes} - -\subsection{Folders} - -This template comes as a single zip file that expands out to several -files and folders. The folder names are mostly self-explanatory: - -\keyword{Appendices} -- this is the folder where you put the -appendices. Each appendix should go into its own separate \file{.tex} -file. An example and template are included in the directory. - -\keyword{Chapters} -- this is the folder where you put the thesis -chapters. A thesis usually has about six chapters, though there is no -hard rule on this. Each chapter should go in its own separate -\file{.tex} file and they can be split as: -\begin{itemize} - \item Chapter 1: Introduction to the thesis topic - \item Chapter 2: Background information and theory - \item Chapter 3: (Laboratory) experimental setup - \item Chapter 4: Details of experiment 1 - \item Chapter 5: Details of experiment 2 - \item Chapter 6: Discussion of the experimental results - \item Chapter 7: Conclusion and future directions -\end{itemize} -This chapter layout is specialised for the experimental sciences, -your discipline may be different. - -\keyword{Figures} -- this folder contains all figures for the thesis. -These are the final images that will go into the thesis document. - -\subsection{Files} - -Included are also several files, most of them are plain text and you -can see their contents in a text editor. After initial compilation, -you will see that more auxiliary files are created by \LaTeX{} or -BibTeX and which you don't need to delete or worry about: - -\keyword{example.bib} -- this is an important file that contains all -the bibliographic information and references that you will be citing -in the thesis for use with BibTeX. You can write it manually, but -there are reference manager programs available that will create and -manage it for you. Bibliographies in \LaTeX{} are a large subject and -you may need to read about BibTeX before starting with this. Many -modern reference managers will allow you to export your references in -BibTeX format which greatly eases the amount of work you have to do. - -\keyword{MastersDoctoralThesis.cls} -- this is an important file. It -is the class file that tells \LaTeX{} how to format the thesis. - -\keyword{main.pdf} -- this is your beautifully typeset thesis (in the -PDF file format) created by \LaTeX{}. It is supplied in the PDF with -the template and after you compile the template you should get an -identical version. - -\keyword{main.tex} -- this is an important file. This is the file -that you tell \LaTeX{} to compile to produce your thesis as a PDF -file. It contains the framework and constructs that tell \LaTeX{} how -to layout the thesis. It is heavily commented so you can read exactly -what each line of code does and why it is there. After you put your -own information into the \emph{THESIS INFORMATION} block -- you have -now started your thesis! - -Files that are \emph{not} included, but are created by \LaTeX{} as -auxiliary files include: - -\keyword{main.aux} -- this is an auxiliary file generated by -\LaTeX{}, if it is deleted \LaTeX{} simply regenerates it when you -run the main \file{.tex} file. - -\keyword{main.bbl} -- this is an auxiliary file generated by BibTeX, -if it is deleted, BibTeX simply regenerates it when you run the -\file{main.aux} file. Whereas the \file{.bib} file contains all the -references you have, this \file{.bbl} file contains the references -you have actually cited in the thesis and is used to build the -bibliography section of the thesis. - -\keyword{main.blg} -- this is an auxiliary file generated by BibTeX, -if it is deleted BibTeX simply regenerates it when you run the main -\file{.aux} file. - -\keyword{main.lof} -- this is an auxiliary file generated by -\LaTeX{}, if it is deleted \LaTeX{} simply regenerates it when you -run the main \file{.tex} file. It tells \LaTeX{} how to build the -\emph{List of Figures} section. - -\keyword{main.log} -- this is an auxiliary file generated by -\LaTeX{}, if it is deleted \LaTeX{} simply regenerates it when you -run the main \file{.tex} file. It contains messages from \LaTeX{}, if -you receive errors and warnings from \LaTeX{}, they will be in this -\file{.log} file. - -\keyword{main.lot} -- this is an auxiliary file generated by -\LaTeX{}, if it is deleted \LaTeX{} simply regenerates it when you -run the main \file{.tex} file. It tells \LaTeX{} how to build the -\emph{List of Tables} section. - -\keyword{main.out} -- this is an auxiliary file generated by -\LaTeX{}, if it is deleted \LaTeX{} simply regenerates it when you -run the main \file{.tex} file. - -So from this long list, only the files with the \file{.bib}, -\file{.cls} and \file{.tex} extensions are the most important ones. -The other auxiliary files can be ignored or deleted as \LaTeX{} and -BibTeX will regenerate them. - -%---------------------------------------------------------------------------------------- - -\section{Filling in Your Information in the \file{main.tex} -File}\label{FillingFile} - -You will need to personalise the thesis template and make it your own -by filling in your own information. This is done by editing the -\file{main.tex} file in a text editor or your favourite LaTeX environment. - -Open the file and scroll down to the third large block titled -\emph{THESIS INFORMATION} where you can see the entries for -\emph{University Name}, \emph{Department Name}, etc \ldots - -Fill out the information about yourself, your group and institution. -You can also insert web links, if you do, make sure you use the full -URL, including the \code{http://} for this. If you don't want these -to be linked, simply remove the \verb|\href{url}{name}| and only leave the name. - -When you have done this, save the file and recompile \code{main.tex}. -All the information you filled in should now be in the PDF, complete -with web links. You can now begin your thesis proper! - -%---------------------------------------------------------------------------------------- - -\section{The \code{main.tex} File Explained} - -The \file{main.tex} file contains the structure of the thesis. There -are plenty of written comments that explain what pages, sections and -formatting the \LaTeX{} code is creating. Each major document element -is divided into commented blocks with titles in all capitals to make -it obvious what the following bit of code is doing. Initially there -seems to be a lot of \LaTeX{} code, but this is all formatting, and -it has all been taken care of so you don't have to do it. - -Begin by checking that your information on the title page is correct. -For the thesis declaration, your institution may insist on something -different than the text given. If this is the case, just replace what -you see with what is required in the \emph{DECLARATION PAGE} block. - -Then comes a page which contains a funny quote. You can put your own, -or quote your favourite scientist, author, person, and so on. Make -sure to put the name of the person who you took the quote from. - -Following this is the abstract page which summarises your work in a -condensed way and can almost be used as a standalone document to -describe what you have done. The text you write will cause the -heading to move up so don't worry about running out of space. - -Next come the acknowledgements. On this page, write about all the -people who you wish to thank (not forgetting parents, partners and -your advisor/supervisor). - -The contents pages, list of figures and tables are all taken care of -for you and do not need to be manually created or edited. The next -set of pages are more likely to be optional and can be deleted since -they are for a more technical thesis: insert a list of abbreviations -you have used in the thesis, then a list of the physical constants -and numbers you refer to and finally, a list of mathematical symbols -used in any formulae. Making the effort to fill these tables means -the reader has a one-stop place to refer to instead of searching the -internet and references to try and find out what you meant by certain -abbreviations or symbols. - -The list of symbols is split into the Roman and Greek alphabets. -Whereas the abbreviations and symbols ought to be listed in -alphabetical order (and this is \emph{not} done automatically for -you) the list of physical constants should be grouped into similar themes. - -The next page contains a one line dedication. Who will you dedicate -your thesis to? - -Finally, there is the block where the chapters are included. -Uncomment the lines (delete the \code{\%} character) as you write the -chapters. Each chapter should be written in its own file and put into -the \emph{Chapters} folder and named \file{Chapter1}, -\file{Chapter2}, etc\ldots Similarly for the appendices, uncomment -the lines as you need them. Each appendix should go into its own file -and placed in the \emph{Appendices} folder. - -After the preamble, chapters and appendices finally comes the -bibliography. The bibliography style (called \option{authoryear}) is -used for the bibliography and is a fully featured style that will -even include links to where the referenced paper can be found online. -Do not underestimate how grateful your reader will be to find that a -reference to a paper is just a click away. Of course, this relies on -you putting the URL information into the BibTeX file in the first place. - -%---------------------------------------------------------------------------------------- - -\section{Thesis Features and Conventions}\label{ThesisConventions} - -To get the best out of this template, there are a few conventions -that you may want to follow. - -One of the most important (and most difficult) things to keep track -of in such a long document as a thesis is consistency. Using certain -conventions and ways of doing things (such as using a Todo list) -makes the job easier. Of course, all of these are optional and you -can adopt your own method. - -\subsection{Printing Format} - -This thesis template is designed for double sided printing (i.e. -content on the front and back of pages) as most theses are printed -and bound this way. Switching to one sided printing is as simple as -uncommenting the \option{oneside} option of the \code{documentclass} -command at the top of the \file{main.tex} file. You may then wish to -adjust the margins to suit specifications from your institution. - -The headers for the pages contain the page number on the outer side -(so it is easy to flick through to the page you want) and the chapter -name on the inner side. - -The text is set to 11 point by default with single line spacing, -again, you can tune the text size and spacing should you want or need -to using the options at the very start of \file{main.tex}. The -spacing can be changed similarly by replacing the -\option{singlespacing} with \option{onehalfspacing} or \option{doublespacing}. - -\subsection{Using US Letter Paper} - -The paper size used in the template is A4, which is the standard size -in Europe. If you are using this thesis template elsewhere and -particularly in the United States, then you may have to change the A4 -paper size to the US Letter size. This can be done in the margins -settings section in \file{main.tex}. - -Due to the differences in the paper size, the resulting margins may -be different to what you like or require (as it is common for -institutions to dictate certain margin sizes). If this is the case, -then the margin sizes can be tweaked by modifying the values in the -same block as where you set the paper size. Now your document should -be set up for US Letter paper size with suitable margins. - -\subsection{References} - -The \code{biblatex} package is used to format the bibliography and -inserts references such as this one \parencite{Reference1}. The -options used in the \file{main.tex} file mean that the in-text -citations of references are formatted with the author(s) listed with -the date of the publication. Multiple references are separated by -semicolons (e.g. \parencite{Reference2, Reference1}) and references -with more than three authors only show the first author with \emph{et -al.} indicating there are more authors (e.g. \parencite{Reference3}). -This is done automatically for you. To see how you use references, -have a look at the \file{Chapter1.tex} source file. Many reference -managers allow you to simply drag the reference into the document as you type. - -Scientific references should come \emph{before} the punctuation mark -if there is one (such as a comma or period). The same goes for -footnotes\footnote{Such as this footnote, here down at the bottom of -the page.}. You can change this but the most important thing is to -keep the convention consistent throughout the thesis. Footnotes -themselves should be full, descriptive sentences (beginning with a -capital letter and ending with a full stop). The APA6 states: -\enquote{Footnote numbers should be superscripted, [...], following -any punctuation mark except a dash.} The Chicago manual of style -states: \enquote{A note number should be placed at the end of a - sentence or clause. The number follows any punctuation mark except -the dash, which it precedes. It follows a closing parenthesis.} - -The bibliography is typeset with references listed in alphabetical -order by the first author's last name. This is similar to the APA -referencing style. To see how \LaTeX{} typesets the bibliography, -have a look at the very end of this document (or just click on the -reference number links in in-text citations). - -\subsubsection{A Note on bibtex} - -The bibtex backend used in the template by default does not correctly -handle unicode character encoding (i.e. "international" characters). -You may see a warning about this in the compilation log and, if your -references contain unicode characters, they may not show up correctly -or at all. The solution to this is to use the biber backend instead -of the outdated bibtex backend. This is done by finding this in -\file{main.tex}: \option{backend=bibtex} and changing it to -\option{backend=biber}. You will then need to delete all auxiliary -BibTeX files and navigate to the template directory in your terminal -(command prompt). Once there, simply type \code{biber main} and biber -will compile your bibliography. You can then compile \file{main.tex} -as normal and your bibliography will be updated. An alternative is to -set up your LaTeX editor to compile with biber instead of bibtex, see -\href{http://tex.stackexchange.com/questions/154751/biblatex-with-biber-configuring-my-editor-to-avoid-undefined-citations/}{here} -for how to do this for various editors. - -\subsection{Tables} - -Tables are an important way of displaying your results, below is an -example table which was generated with this code: - -{\small - \begin{verbatim} -\begin{table} -\caption{The effects of treatments X and Y on the four groups studied.} -\label{tab:treatments} -\centering -\begin{tabular}{l l l} -\toprule -\tabhead{Groups} & \tabhead{Treatment X} & \tabhead{Treatment Y} \\ -\midrule -1 & 0.2 & 0.8\\ -2 & 0.17 & 0.7\\ -3 & 0.24 & 0.75\\ -4 & 0.68 & 0.3\\ -\bottomrule\\ -\end{tabular} -\end{table} - \end{verbatim} -} - -\begin{table} - \caption{The effects of treatments X and Y on the four groups studied.} - \label{tab:treatments} - \centering - \begin{tabular}{l l l} - \toprule - \tabhead{Groups} & \tabhead{Treatment X} & \tabhead{Treatment Y} \\ - \midrule - 1 & 0.2 & 0.8\\ - 2 & 0.17 & 0.7\\ - 3 & 0.24 & 0.75\\ - 4 & 0.68 & 0.3\\ - \bottomrule\\ - \end{tabular} -\end{table} - -You can reference tables with \verb|\ref{