migrate the customised thesis

old_thesis/.gitignore

@@ -1,3 +1,12 @@
+#Extra styles
+abhepexpt.sty 
+abhep.sty 
+abmath.sty 
+lineno.sty 
+siunitx.sty 
+SIunits.sty 
+varwidth.sty
+
 #Compilation byproducts
 *.aux
 *.bbl
@@ -11,7 +20,3 @@
 *.snm
 thesis.pdf
 comment.cut
-feyngraph.mp
-
-*.pdf
-refs/*

old_thesis/Makefile

@@ -0,0 +1,23 @@
+DOCNAME = thesis
+
+INPUT = $(DOCNAME).tex
+TARGET= $(DOCNAME).pdf
+
+THESIS_STY= mythesis.sty mythesismath.sty
+EXTRASTYS = abhepexpt.sty abhep.sty abmath.sty lineno.sty siunitx.sty SIunits.sty varwidth.sty
+
+default: $(TARGET)
+
+$(TARGET): $(INPUT) extrastyles.zip $(THESIS_STY) Makefile chapters/*.tex
+	@rm -f $(EXTRASTYS)
+	@unzip extrastyles.zip
+	@rm -f $(DOCNAME).{aux,toc,lof,lot}
+	pdflatex $< && bibtex $(DOCNAME) && pdflatex $< && pdflatex $<
+	@rm -f $(DOCNAME).{aux,toc,lof,lot}
+	@rm -f $(EXTRASTYS)
+
+clean:
+	@rm -f $(EXTRASTYS)
+	@rm -f *.{aux,toc,lof,lot}
+	@rm -f *.{aux,bbl,blg,log,nav,out,snm,toc,lot,lof} $(TARGET)
+	@rm -f comment.cut

old_thesis/chapters/backmatter.tex

@@ -1,6 +1,6 @@
-%\begin{colophon}
-  %This thesis was made in \LaTeXe{} using the ``hepthesis'' class~\cite{hepthesis}.
-%\end{colophon}
+\begin{colophon}
+  This thesis was made in \LaTeXe{} using the ``hepthesis'' class~\cite{hepthesis}.
+\end{colophon}
 
 %% You're recommended to use the eprint-aware biblio styles which
 %% can be obtained from e.g. www.arxiv.org. The file mythesis.bib
@@ -10,8 +10,8 @@
 
 %% I prefer to put these tables here rather than making the
 %% front matter seemingly interminable. No-one cares, anyway!
-%\listoffigures
-%\listoftables
+\listoffigures
+\listoftables
 
 %% If you have time and interest to generate a (decent) index,
 %% then you've clearly spent more time on the write-up than the 

old_thesis/chapters/frontmatter.tex

@@ -0,0 +1,54 @@
+%% Title
+\titlepage[of Graduate School of Science]%
+{A dissertation submitted to the Osaka University\\
+for the degree of Doctor of Philosophy}
+
+%% Abstract
+\begin{abstract}%[\smaller \thetitle\\ \vspace*{1cm} \smaller {\theauthor}]
+	%\thispagestyle{empty}
+	\LHCb is a \bphysics detector experiment which will take data at
+	the \unit{14}{\TeV} \LHC accelerator at \CERN from 2007 onward\dots
+\end{abstract}
+
+
+%% Declaration
+\begin{declaration}
+	This dissertation is the result of my own work, except where explicit
+	reference is made to the work of others, and has not been submitted
+	for another qualification to this or any other university. This
+	dissertation does not exceed the word limit for the respective Degree
+	Committee.
+	\vspace*{1cm}
+	\begin{flushright}
+		Andy Buckley
+	\end{flushright}
+\end{declaration}
+
+
+%% Acknowledgements
+\begin{acknowledgements}
+	Of the many people who deserve thanks, some are particularly prominent,
+	such as my supervisor\dots
+\end{acknowledgements}
+
+
+%% Preface
+\begin{preface}
+	This thesis describes my research on various aspects of the \LHCb
+	particle physics program, centred around the \LHCb detector and \LHC
+	accelerator at \CERN in Geneva.
+
+	\noindent
+	For this example, I'll just mention \ChapterRef{chap:SomeStuff}
+	and \ChapterRef{chap:MoreStuff}.
+\end{preface}
+
+%% ToC
+\tableofcontents
+
+
+%% Strictly optional!
+\frontquote{%
+	Writing in English is the most ingenious torture\\
+ever devised for sins committed in previous lives.}%
+{James Joyce}

old_thesis/custom_macro.tex

@@ -0,0 +1,10 @@
+
+\newcommand{\lagr}{\cal{L}}
+\newcommand{\mueg}{$\mu^{+} \rightarrow e^{+}\gamma$}
+\newcommand{\meee}{$\mu \rightarrow eee$}
+\newcommand{\muenn}{$\mu \rightarrow e \nu \overline{\nu}$}
+\newcommand{\muenng}{$\mu \rightarrow e \nu \overline{\nu} \gamma$}
+\newcommand{\muec}{$\mu^{-} N \rightarrow e^{-} N$}
+\newcommand{\muecaz}{$\mu^{-} + N(A,Z) \rightarrow e^{-} + N(A,Z)$}
+\newcommand{\sindrumlimit}
+{$\mathcal{B} (\mu^- + Au \rightarrow e^- +Au) < 7\times 10^{-13}$}

old_thesis/h-physrev.bst

@@ -219,9 +219,9 @@ if$
 }
 FUNCTION {format.title}
 { title empty$
-  { "" }
-  { title "t" change.case$ }
-  if$
+{ "" }
+{ title "t" change.case$ }
+if$
 }
 FUNCTION {n.dashify}
 { 't :=
@@ -435,84 +435,19 @@ if$
 }
 FUNCTION {format.inst.tr.num.date}
 { institution empty$
-  { "" "empty institution in " cite$ * warning$ }
-  { institution }
-  if$
-  " Report No." *
-  number empty$
-  { "" }
-  { number tie.or.space.connect }
-  if$
-  year empty$
-  { "empty year in " cite$ * warning$ }
-  { ", " * year * " (unpublished)" * }
-  if$
+{ "" "empty institution in " cite$ * warning$ }
+{ institution }
+if$
+" Report No." *
+number empty$
+{ "" }
+{ number tie.or.space.connect }
+if$
+year empty$
+{ "empty year in " cite$ * warning$ }
+{ ", " * year * " (unpublished)" * }
+if$
 }
-
-FUNCTION {format.inst.tr.num.prop}
-{ institution empty$
-  { "" "empty institution in " cite$ * warning$ }
-  { institution }
-  if$
-
-  type empty$
-  {" Report"}
-  {" " * type *}
-  if$
-
-  number empty$
-  { "" }
-  { number tie.or.space.connect embolden}
-  if$
-}
-
-FUNCTION {format.inst.tr.num}
-{ institution empty$
-  { "" "empty institution in " cite$ * warning$ }
-  { institution }
-  if$
-
-  type empty$
-  {" Report"}
-  {" " * type *}
-  if$
-
-  number empty$
-  { "" }
-  { number tie.or.space.connect embolden}
-  if$
-}
-
-FUNCTION {format.inst.tr.num.year}
-{ institution empty$
-  { "" "empty institution in " cite$ * warning$ }
-  { institution }
-  if$
-
-  type empty$
-  {" Report" *}
-  {" " * type *}
-  if$
-
-  number empty$
-  { "" tie.or.space.connect embolden}
-  { number tie.or.space.connect embolden}
-  if$
-
-  year empty$
-  {"" "empty year in " cite$ * warning$ }
-  { " (" * year * ")" * }
-  if$
-}
-
-FUNCTION {format.inst.tr.title}
-{ title empty$
-  { "" }
-  { title emphasize "t" change.case$ }
-  if$
-
-}
-
 FUNCTION {format.article.crossref}
 { key empty$
 { journal empty$
@@ -863,16 +798,14 @@ fin.entry
 }
 FUNCTION {techreport}
 { output.bibitem
-  collaboration output
-  format.authors "author" output.check
-  new.block
-  format.inst.tr.title "title" output.check
-  new.block
-  format.inst.tr.num.year output.nonnull
-  eprint output
-  new.block
-  note output
-  fin.entry
+collaboration output
+format.authors "author" output.check
+new.block
+format.inst.tr.num.date output.nonnull
+eprint output
+new.block
+note output
+fin.entry
 }
 FUNCTION {unpublished}
 { output.bibitem

old_thesis/mythesis.sty

@@ -0,0 +1,66 @@
+\ProvidesPackage{mythesis}[2005/07/28]
+%\RequirePackage{timing}
+\RequirePackage{hepnicenames,abhep}
+% \RequirePackage{siunitx}
+
+%% Citation spacing hack to bring the citation
+%% number a little closer to the referring text
+\let\@OldCite\cite
+\renewcommand{\cite}[1]{\mbox{\!\!\!\@OldCite{#1}}}
+
+%% Maths
+\DeclareRobustCommand{\thesismath}[1]{\ensuremath{\maybebmsf{#1}}}
+\DeclareRobustCommand{\parenths}[1]{\mymath{\left({#1}\right)}}
+\DeclareRobustCommand{\braces}[1]{\mymath{\left\{{#1}\right\}}}
+\DeclareRobustCommand{\angles}[1]{\mymath{\left\langle{#1}\right\rangle}}
+\DeclareRobustCommand{\sqbracs}[1]{\mymath{\left[{#1}\right]}}
+\DeclareRobustCommand{\mods}[1]{\mymath{\left\lvert{#1}\right\rvert}}
+\DeclareRobustCommand{\modsq}[1]{\mymath{\mods{#1}^2}}
+\DeclareRobustCommand{\dblmods}[1]{\mymath{\left\lVert{#1}\right\rVert}}
+\DeclareRobustCommand{\expOf}[1]{\mymath{\exp{\!\parenths{#1}}}}
+\DeclareRobustCommand{\eexp}[1]{\mymath{e^{#1}}}
+\DeclareRobustCommand{\plusquad}{\mymath{\oplus}}
+\DeclareRobustCommand{\logOf}[1]{\log\!\parenths{#1}}
+\DeclareRobustCommand{\lnOf}[1]{\ln\!\parenths{#1}}
+\DeclareRobustCommand{\ofOrder}[1]{\mymath{ \mathcal{O}\parenths{#1} }}
+
+%% General utility defns
+\DeclareRobustCommand{\arXivCode}[1]{arXiv:#1}
+\DeclareRobustCommand{\CPviolation}{\CP-violation\xspace}
+\DeclareRobustCommand{\CPv}{\CPviolation}
+\DeclareRobustCommand{\LHCb}{LHCb\xspace}
+\DeclareRobustCommand{\LHC}{LHC\xspace}
+\DeclareRobustCommand{\LEP}{LEP\xspace}
+\DeclareRobustCommand{\CERN}{CERN\xspace}
+
+%% Basic rate formalisms
+\DeclareRobustCommand{\Rate}{\thesismath{\Gamma}\xspace}
+\DeclareRobustCommand{\RateOf}[1]{\thesismath{\Gamma}\parenths{#1}\xspace}
+
+%% Phrases to be consistent about (with b/B)
+\DeclareRobustCommand{\bphysics}{\Pbottom-physics\xspace}
+\DeclareRobustCommand{\bhadron}{\Pbottom-hadron\xspace}
+\DeclareRobustCommand{\Bmeson}{\PB-meson\xspace}
+\DeclareRobustCommand{\bbaryon}{\Pbottom-baryon\xspace}
+\DeclareRobustCommand{\Bdecay}{\PB-decay\xspace}
+\DeclareRobustCommand{\bdecay}{\Pbottom-decay\xspace}
+
+%% Processes
+\DeclareRobustCommand{\BToKPi}{\HepProcess{ \PB \to \PK \, \Ppi }\xspace}
+\DeclareRobustCommand{\BToPiPi}{\HepProcess{ \PB \to \Ppi \, \Ppi }\xspace}
+\DeclareRobustCommand{\BToKK}{\HepProcess{\PB \to \PK \, \PK}\xspace}
+\DeclareRobustCommand{\BToRhoPi}{\HepProcess{ \PB \to \Prho \, \Ppi }\xspace}
+\DeclareRobustCommand{\BToRhoRho}{\HepProcess{ \PB \to \Prho \Prho }\xspace}
+\DeclareRobustCommand{\X}{\thesismath{X}\xspace}
+\DeclareRobustCommand{\Xbar}{\thesismath{\overline{X}}\xspace}
+\DeclareRobustCommand{\Xzero}{\HepGenParticle{X}{}{0}\xspace}
+\DeclareRobustCommand{\Xzerobar}{\HepGenAntiParticle{X}{}{0}\xspace}
+\DeclareRobustCommand{\epluseminus}{\Pelectron\Ppositron\xspace}
+
+% Fix hyperref labels in PDFTeX
+\@ifpackageloaded{hyperref}{%
+  \pdfstringdefDisableCommands{%
+      \def\pi{pi}%
+      \def\gamma{gamma}%
+  }%
+}{}

old_thesis/thesis.bib

@@ -0,0 +1,51 @@
+%% Obtained via the getNewBibTeX script and the SPIRES biblio service
+
+@Article{Phys.Rev.Lett.19.1264,
+     author    = "Weinberg, Steven",
+     title     = "A MODEL OF LEPTONS",
+     journal   = "Phys. Rev. Lett.",
+     volume    = "19",
+     year      = "1967",
+     pages     = "1264-1266",
+     SLACcitation  = "%%CITATION = PRLTA,19,1264;%%"
+}
+
+@Article{Phys.Rev.D2.1285,
+     author    = "Glashow, S. L. and Iliopoulos, J. and Maiani, L.",
+     title     = "WEAK INTERACTIONS WITH LEPTON - HADRON SYMMETRY",
+     journal   = "Phys. Rev.",
+     volume    = "D2",
+     year      = "1970",
+     pages     = "1285-1292",
+     SLACcitation  = "%%CITATION = PHRVA,D2,1285;%%"
+}
+
+@Article{hep-ph/0410370,
+     author    = "Willenbrock, Scott",
+     title     = "Symmetries of the standard model",
+     year      = "2004",
+     eprint    = "hep-ph/0410370",
+     SLACcitation  = "%%CITATION = HEP-PH 0410370;%%"
+}
+
+@Article{Brianti:2004qq,
+     author    = "Brianti, G.",
+     title     = "The Large Hadron Collider project: Historical account",
+     journal   = "Phys. Rept.",
+     volume    = "403-404",
+     year      = "2004",
+     pages     = "349-364",
+     SLACcitation  = "%%CITATION = PRPLC,403-404,349;%%"
+}
+
+@Article{Amato:1998xt,
+     author    = "Amato, S. and others",
+ collaboration = "LHCb",
+     title     = "LHCb technical proposal",
+     note     = "CERN-LHCC-98-4"
+}
+
+@Misc{hepthesis,
+     author = "Buckley, Andy",
+     title  = "The hepthesis {\LaTeX} class"
+}

old_thesis/thesis.tex

@@ -0,0 +1,65 @@
+\documentclass{mythesis}
+\usepackage{mythesis}
+\usepackage{hyperref}
+\usepackage{booktabs}
+\usepackage{tabularx}
+\usepackage{color}
+
+\input{custom_macro.tex}
+%% You can set the line spacing this way
+%\setallspacing{double}
+%% or a section at a time like this
+%\setfrontmatterspacing{double}
+
+%% PDF metadata
+\makeatletter
+\@ifpackageloaded{hyperref}{%
+\hypersetup{%
+	pdftitle = {A Study of Muon Capture for Muon to Electron Conversion
+	Experiments},
+	pdfsubject = {Nam H Tran's PhD thesis},
+	pdfkeywords = {muon capture, muon to electron conversion, COMET},
+	pdfauthor = {\textcopyright\ Nam Hoai Tran}
+}
+}{}
+\makeatother
+
+%% Define the thesis title and author
+\title{A Study of Muon Capture for \\Muon to Electron Conversion Experiments}
+\author{Nam Hoai Tran}
+
+%% Start the document
+\begin{document}
+
+%% Define the un-numbered front matter (cover pages, rubrik and table of contents)
+\begin{frontmatter}
+  \input{chapters/frontmatter}
+\end{frontmatter}
+
+%% Start the content body of the thesis
+\begin{mainmatter}
+  %% Actually, more semantic chapter filenames are better, like "chap-bgtheory.tex"
+  \input{chapters/chap1}
+  %\input{chapters/chap2}
+  %\input{chapters/chap3}
+  %\input{chapters/chap4}
+  %\input{chapters/chap5}
+  %\input{chapters/chap6}
+  %% To ignore a specific chapter while working on another,
+  %% making the build faster, comment it out like this:
+  %\input{chapters/chap4}
+\end{mainmatter}
+
+%% Produce the appendices
+\begin{appendices}
+  %\input{chapters/appendices}
+\end{appendices}
+
+%% Produce the un-numbered back matter (e.g. colophon,
+%% bibliography, tables of figures etc., index...)
+\begin{backmatter}
+  \input{chapters/backmatter}
+\end{backmatter}
+
+%% Close
+\end{document}

thesis/.gitignore

@@ -1,12 +1,3 @@
-#Extra styles
-abhepexpt.sty 
-abhep.sty 
-abmath.sty 
-lineno.sty 
-siunitx.sty 
-SIunits.sty 
-varwidth.sty
-
 #Compilation byproducts
 *.aux
 *.bbl
@@ -20,3 +11,7 @@ varwidth.sty
 *.snm
 thesis.pdf
 comment.cut
+feyngraph.mp
+
+*.pdf
+refs/*

thesis/Makefile

@@ -3,21 +3,13 @@ DOCNAME = thesis
 INPUT = $(DOCNAME).tex
 TARGET= $(DOCNAME).pdf
 
-THESIS_STY= mythesis.sty mythesismath.sty
-EXTRASTYS = abhepexpt.sty abhep.sty abmath.sty lineno.sty siunitx.sty SIunits.sty varwidth.sty
-
 default: $(TARGET)
 
-$(TARGET): $(INPUT) extrastyles.zip $(THESIS_STY) Makefile chapters/*.tex
-	@rm -f $(EXTRASTYS)
-	@unzip extrastyles.zip
+$(TARGET): $(INPUT) Makefile chapters/*.tex custom_macro.tex mythesis.sty
 	@rm -f $(DOCNAME).{aux,toc,lof,lot}
 	pdflatex $< && bibtex $(DOCNAME) && pdflatex $< && pdflatex $<
-	@rm -f $(DOCNAME).{aux,toc,lof,lot}
-	@rm -f $(EXTRASTYS)
 
 clean:
-	@rm -f $(EXTRASTYS)
 	@rm -f *.{aux,toc,lof,lot}
 	@rm -f *.{aux,bbl,blg,log,nav,out,snm,toc,lot,lof} $(TARGET)
 	@rm -f comment.cut

thesis/chapters/backmatter.tex

@@ -1,6 +1,6 @@
-\begin{colophon}
-  This thesis was made in \LaTeXe{} using the ``hepthesis'' class~\cite{hepthesis}.
-\end{colophon}
+%\begin{colophon}
+  %This thesis was made in \LaTeXe{} using the ``hepthesis'' class~\cite{hepthesis}.
+%\end{colophon}
 
 %% You're recommended to use the eprint-aware biblio styles which
 %% can be obtained from e.g. www.arxiv.org. The file mythesis.bib
@@ -10,8 +10,8 @@
 
 %% I prefer to put these tables here rather than making the
 %% front matter seemingly interminable. No-one cares, anyway!
-\listoffigures
-\listoftables
+%\listoffigures
+%\listoftables
 
 %% If you have time and interest to generate a (decent) index,
 %% then you've clearly spent more time on the write-up than the 

thesis/chapters/frontmatter.tex

@@ -1,54 +1,74 @@
 %% Title
-\titlepage[of Graduate School of Science]%
-{A dissertation submitted to the Osaka University\\
-for the degree of Doctor of Philosophy}
+%\titlepage[\vspace{5mm}Department of Physics,\\
+%Graduate School of Science]%
+%{A dissertation submitted to the Osaka University\\
+%for the degree of Doctor of Philosophy}
+\titlepage[]{\vspace{5mm}Department of Physics, Graduate School of Science\\
+Osaka University}
 
 %% Abstract
-\begin{abstract}%[\smaller \thetitle\\ \vspace*{1cm} \smaller {\theauthor}]
-	%\thispagestyle{empty}
-	\LHCb is a \bphysics detector experiment which will take data at
-	the \unit{14}{\TeV} \LHC accelerator at \CERN from 2007 onward\dots
+\begin{abstract}
+  %[\smaller \thetitle\\ \vspace*{1cm} \smaller {\theauthor}]
+  \thispagestyle{empty}
+COMET [1] is an experiment that aims to search for a charged lepton flavor
+violation (CLFV) process, the muon-to-electron conversion in the presence of
+a nucleus,
+\muec. The process is forbidden in the Standard Model (SM), however is
+predicted to occur in various extensions of SM, such as . Current experimental
+upper limit of the branching ratio is $BR(\mu^{-} + Au \rightarrow e^{-} + Au)
+< 7 \times 10^{-13}$, set by the SINDRUM II experiment [2].
+
+Using the J-PARC proton beam and the pion capture by
+a solenoidal field, COMET will have a single event sensitivity  10,000 times
+better than the current limit. The COMET collaboration has taken a phased
+approach in which the first phase, COMET Phase-I [3], starts in 2013 and
+initial data taking in around 2017. 
+
+In order to optimize detector design for the Phase-I, backgrounds from nuclear
+muon capture are crucial. We have proposed a dedicated experiment , namely
+AlCap, at PSI, Switzerland to study the backgrounds, including: heavy charged
+particles, neutrons and photons. The measurements of heavy charged particles
+have been carried out in the 2013 run and the preliminary analysis results are
+presented in this thesis.
 \end{abstract}
 
 
 %% Declaration
 \begin{declaration}
-	This dissertation is the result of my own work, except where explicit
-	reference is made to the work of others, and has not been submitted
-	for another qualification to this or any other university. This
-	dissertation does not exceed the word limit for the respective Degree
-	Committee.
-	\vspace*{1cm}
-	\begin{flushright}
-		Andy Buckley
-	\end{flushright}
+  \thispagestyle{empty}
+  This dissertation is the result of my own work, except where explicit
+  reference is made to the work of others, and has not been submitted
+  for another qualification to this or any other university. 
+  \vspace*{1cm}
+  \begin{flushright}
+    Nam Hoai Tran
+  \end{flushright}
 \end{declaration}
 
 
-%% Acknowledgements
-\begin{acknowledgements}
-	Of the many people who deserve thanks, some are particularly prominent,
-	such as my supervisor\dots
-\end{acknowledgements}
+% Acknowledgements
+%\begin{acknowledgements}
+  %\thispagestyle{empty}
+  %Of the many people who deserve thanks, some are particularly prominent,
+  %such as my supervisor Professor Yoshitaka Kuno.
+%\end{acknowledgements}
 
 
 %% Preface
-\begin{preface}
-	This thesis describes my research on various aspects of the \LHCb
-	particle physics program, centred around the \LHCb detector and \LHC
-	accelerator at \CERN in Geneva.
-
-	\noindent
-	For this example, I'll just mention \ChapterRef{chap:SomeStuff}
-	and \ChapterRef{chap:MoreStuff}.
-\end{preface}
+%\begin{preface}
+  %\thispagestyle{empty}
+  %The thesis is about measurements of products of nuclear muon capture on an
+  %aluminum target, which is important for optimization of a tracking detector
+  %of a search for muon to electron conversion, the E21 experiment - so called
+  %COMET - at Japan Proton Accelerator Complex (J-PARC).
+%\end{preface}
 
 %% ToC
 \tableofcontents
 
 
 %% Strictly optional!
-\frontquote{%
-	Writing in English is the most ingenious torture\\
-ever devised for sins committed in previous lives.}%
-{James Joyce}
+%\frontquote{%
+	%Writing in English is the most ingenious torture\\
+%ever devised for sins committed in previous lives.}%
+%{James Joyce}

thesis/custom_macro.tex

@@ -1,10 +1,56 @@
-
+\usepackage[]{xspace}
 \newcommand{\lagr}{\cal{L}}
-\newcommand{\mueg}{$\mu^{+} \rightarrow e^{+}\gamma$}
-\newcommand{\meee}{$\mu \rightarrow eee$}
-\newcommand{\muenn}{$\mu \rightarrow e \nu \overline{\nu}$}
-\newcommand{\muenng}{$\mu \rightarrow e \nu \overline{\nu} \gamma$}
-\newcommand{\muec}{$\mu^{-} N \rightarrow e^{-} N$}
-\newcommand{\muecaz}{$\mu^{-} + N(A,Z) \rightarrow e^{-} + N(A,Z)$}
+%%% muon decays
+\newcommand{\mueg}{$\mu^{+} \rightarrow e^{+}\gamma$\xspace}
+%\newcommand{\mueg}{\APmuon $\rightarrow$ \APelectron\Pphoton}
+
+%\newcommand{\mueee}{$\mu \rightarrow eee$}
+\newcommand{\mueee}{$\mu^+ \rightarrow e^+e^+e^+$\xspace}
+%\newcommand{\meee}{\Pmuon $\rightarrow$ \Pelectron\Pelectron\Pelectron}
+
+\newcommand{\muenn}{$\mu \rightarrow e \nu \overline{\nu}$\xspace}
+%\newcommand{\muenn}{\Pmuon $\rightarrow$ \Pelectron \Pnu \APnu}
+
+
+\newcommand{\muec}{$\mu^{-} N \rightarrow e^{-} N$\xspace}
+%\newcommand{\muec}{\Pmuon $\rightarrow$ \Pelectron N}
+
+\newcommand{\muecaz}{$\mu^{-} + N(A,Z) \rightarrow e^{-} + N(A,Z)$\xspace}
+
+% some limits
 \newcommand{\sindrumlimit}
-{$\mathcal{B} (\mu^- + Au \rightarrow e^- +Au) < 7\times 10^{-13}$}
+{$\mathcal{B} (\mu^- + Au \rightarrow e^- +Au) < 7\times 10^{-13}$\xspace}
+
+\newcommand{\meglimit}
+{$\mathcal{B}(\mu^+ \rightarrow e^+ \gamma) < 5.7 \times 10^{-13}$\xspace}
+
+\newcommand{\brmeg}
+{$\mathcal{B}(\mu^+ \rightarrow e^+ \gamma)$\xspace}
+
+\newcommand{\micheldecay}{
+  $\mu^- \rightarrow e^- \nu_\mu \overline{\nu}_e$\xspace
+}
+\newcommand{\muenng}{
+$\mu^- \rightarrow e^- \nu_\mu \overline{\nu}_e \gamma$\xspace
+}
+\newcommand{\muennee}{
+$\mu^- \rightarrow e^- \nu_\mu \overline{\nu}_e e^+ e^-$\xspace
+}
+
+\newcommand{\mueconv}{$\mu-e$ conversion\xspace}
+
+%scientific notation, 
+\usepackage[]{xifthen}
+\newcommand{\sn}[2]
+{
+  \ifthenelse{\isempty{#1}}
+  {$10^{#2}$\xspace} %if the 1st argument is blank
+  {$#1 \times 10^{#2}$\xspace} %if both exist
+}
+
+\newcommand{\cc}{$c$\xspace}
+
+\newcommand{\rootana}{{\ttfamily rootana}}
+\newcommand{\alcapana}{{\ttfamily alcapana}}
+\newcommand{\tpulseisland}{{\ttfamily TPulseIsland}}
+\newcommand{\tanalysedpulse}{{\ttfamily TAnalysedPulse}}  

thesis/h-physrev.bst

@@ -219,9 +219,9 @@ if$
 }
 FUNCTION {format.title}
 { title empty$
-{ "" }
-{ title "t" change.case$ }
-if$
+  { "" }
+  { title "t" change.case$ }
+  if$
 }
 FUNCTION {n.dashify}
 { 't :=
@@ -435,19 +435,84 @@ if$
 }
 FUNCTION {format.inst.tr.num.date}
 { institution empty$
-{ "" "empty institution in " cite$ * warning$ }
-{ institution }
-if$
-" Report No." *
-number empty$
-{ "" }
-{ number tie.or.space.connect }
-if$
-year empty$
-{ "empty year in " cite$ * warning$ }
-{ ", " * year * " (unpublished)" * }
-if$
+  { "" "empty institution in " cite$ * warning$ }
+  { institution }
+  if$
+  " Report No." *
+  number empty$
+  { "" }
+  { number tie.or.space.connect }
+  if$
+  year empty$
+  { "empty year in " cite$ * warning$ }
+  { ", " * year * " (unpublished)" * }
+  if$
 }
+
+FUNCTION {format.inst.tr.num.prop}
+{ institution empty$
+  { "" "empty institution in " cite$ * warning$ }
+  { institution }
+  if$
+
+  type empty$
+  {" Report"}
+  {" " * type *}
+  if$
+
+  number empty$
+  { "" }
+  { number tie.or.space.connect embolden}
+  if$
+}
+
+FUNCTION {format.inst.tr.num}
+{ institution empty$
+  { "" "empty institution in " cite$ * warning$ }
+  { institution }
+  if$
+
+  type empty$
+  {" Report"}
+  {" " * type *}
+  if$
+
+  number empty$
+  { "" }
+  { number tie.or.space.connect embolden}
+  if$
+}
+
+FUNCTION {format.inst.tr.num.year}
+{ institution empty$
+  { "" "empty institution in " cite$ * warning$ }
+  { institution }
+  if$
+
+  type empty$
+  {" Report" *}
+  {" " * type *}
+  if$
+
+  number empty$
+  { "" tie.or.space.connect embolden}
+  { number tie.or.space.connect embolden}
+  if$
+
+  year empty$
+  {"" "empty year in " cite$ * warning$ }
+  { " (" * year * ")" * }
+  if$
+}
+
+FUNCTION {format.inst.tr.title}
+{ title empty$
+  { "" }
+  { title emphasize "t" change.case$ }
+  if$
+
+}
+
 FUNCTION {format.article.crossref}
 { key empty$
 { journal empty$
@@ -798,14 +863,16 @@ fin.entry
 }
 FUNCTION {techreport}
 { output.bibitem
-collaboration output
-format.authors "author" output.check
-new.block
-format.inst.tr.num.date output.nonnull
-eprint output
-new.block
-note output
-fin.entry
+  collaboration output
+  format.authors "author" output.check
+  new.block
+  format.inst.tr.title "title" output.check
+  new.block
+  format.inst.tr.num.year output.nonnull
+  eprint output
+  new.block
+  note output
+  fin.entry
 }
 FUNCTION {unpublished}
 { output.bibitem

thesis/mythesis.sty

@@ -1,66 +1,272 @@
-\ProvidesPackage{mythesis}[2005/07/28]
-%\RequirePackage{timing}
-\RequirePackage{hepnicenames,abhep}
-% \RequirePackage{siunitx}
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{mythesis}
 
-%% Citation spacing hack to bring the citation
-%% number a little closer to the referring text
-\let\@OldCite\cite
-\renewcommand{\cite}[1]{\mbox{\!\!\!\@OldCite{#1}}}
+%% -------------------------------------
+%% Packages
+%% -------------------------------------
+%$ Page layout
+\RequirePackage[top=1in, bottom=1in, 
+%inner=1.25in, outer=1in]{geometry}
+inner=1.25in, outer=1in, twoside]{geometry}
+\RequirePackage{amsmath}
 
-%% Maths
-\DeclareRobustCommand{\thesismath}[1]{\ensuremath{\maybebmsf{#1}}}
-\DeclareRobustCommand{\parenths}[1]{\mymath{\left({#1}\right)}}
-\DeclareRobustCommand{\braces}[1]{\mymath{\left\{{#1}\right\}}}
-\DeclareRobustCommand{\angles}[1]{\mymath{\left\langle{#1}\right\rangle}}
-\DeclareRobustCommand{\sqbracs}[1]{\mymath{\left[{#1}\right]}}
-\DeclareRobustCommand{\mods}[1]{\mymath{\left\lvert{#1}\right\rvert}}
-\DeclareRobustCommand{\modsq}[1]{\mymath{\mods{#1}^2}}
-\DeclareRobustCommand{\dblmods}[1]{\mymath{\left\lVert{#1}\right\rVert}}
-\DeclareRobustCommand{\expOf}[1]{\mymath{\exp{\!\parenths{#1}}}}
-\DeclareRobustCommand{\eexp}[1]{\mymath{e^{#1}}}
-\DeclareRobustCommand{\plusquad}{\mymath{\oplus}}
-\DeclareRobustCommand{\logOf}[1]{\log\!\parenths{#1}}
-\DeclareRobustCommand{\lnOf}[1]{\ln\!\parenths{#1}}
-\DeclareRobustCommand{\ofOrder}[1]{\mymath{ \mathcal{O}\parenths{#1} }}
+%$ Hyper-link ..
+\RequirePackage[%
+colorlinks=true,% color links instead of using boxes
+linkcolor=red,% color for internal (intra-document) links
+citecolor=green,% color for bibliographic links
+urlcolor=blue,% color for URL links
+hyperfootnotes=false,% disable links to footnotes (because feature broken)
+hyperindex,% make page numbers in index into hyperlinks
+pdfstartview={FitH},% startup page view: fit width of page to window
+bookmarks
+]{hyperref}
+\RequirePackage[all]{hypcap}
 
-%% General utility defns
-\DeclareRobustCommand{\arXivCode}[1]{arXiv:#1}
-\DeclareRobustCommand{\CPviolation}{\CP-violation\xspace}
-\DeclareRobustCommand{\CPv}{\CPviolation}
-\DeclareRobustCommand{\LHCb}{LHCb\xspace}
-\DeclareRobustCommand{\LHC}{LHC\xspace}
-\DeclareRobustCommand{\LEP}{LEP\xspace}
-\DeclareRobustCommand{\CERN}{CERN\xspace}
+\AtBeginDocument{\thispagestyle{plain}}
 
-%% Basic rate formalisms
-\DeclareRobustCommand{\Rate}{\thesismath{\Gamma}\xspace}
-\DeclareRobustCommand{\RateOf}[1]{\thesismath{\Gamma}\parenths{#1}\xspace}
+%% Custom header, no upper case, two sided 
+\RequirePackage{fancyhdr}
+\pagestyle{fancy}
+\fancyhf{}
+\fancyhead[LE,RO]{\thepage}
+\fancyhead[RE]{\nouppercase{\leftmark}}
+\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
+\setlength{\headheight}{15pt}
+\RequirePackage{emptypage}
+%% Others
+\RequirePackage{booktabs}
+\RequirePackage{cite}
+%\RequirePackage{morefloats}
+\RequirePackage{mathrsfs} % script font
+\RequirePackage{afterpage}
+%% Using Babel allows other languages to be used and mixed-in easily
+\RequirePackage[ngerman,english]{babel}
+\selectlanguage{english}
+\RequirePackage[babel]{csquotes}
 
-%% Phrases to be consistent about (with b/B)
-\DeclareRobustCommand{\bphysics}{\Pbottom-physics\xspace}
-\DeclareRobustCommand{\bhadron}{\Pbottom-hadron\xspace}
-\DeclareRobustCommand{\Bmeson}{\PB-meson\xspace}
-\DeclareRobustCommand{\bbaryon}{\Pbottom-baryon\xspace}
-\DeclareRobustCommand{\Bdecay}{\PB-decay\xspace}
-\DeclareRobustCommand{\bdecay}{\Pbottom-decay\xspace}
+\RequirePackage{subfig}
+\RequirePackage{tikz}
+\RequirePackage{fixltx2e}
+\RequirePackage{setspace}
+\RequirePackage{verbatim}
+\RequirePackage{lipsum}
+\RequirePackage{datatool}
+\RequirePackage[capitalise]{cleveref}
+\RequirePackage[final]{listings}
+\RequirePackage{xfrac}
+%% Units
+\RequirePackage[]{siunitx}
+%% Various fonts ...
+%\RequirePackage[T1]{fontenc}
+%\RequirePackage{charter}
+%\RequirePackage[expert]{mathdesign}
 
-%% Processes
-\DeclareRobustCommand{\BToKPi}{\HepProcess{ \PB \to \PK \, \Ppi }\xspace}
-\DeclareRobustCommand{\BToPiPi}{\HepProcess{ \PB \to \Ppi \, \Ppi }\xspace}
-\DeclareRobustCommand{\BToKK}{\HepProcess{\PB \to \PK \, \PK}\xspace}
-\DeclareRobustCommand{\BToRhoPi}{\HepProcess{ \PB \to \Prho \, \Ppi }\xspace}
-\DeclareRobustCommand{\BToRhoRho}{\HepProcess{ \PB \to \Prho \Prho }\xspace}
-\DeclareRobustCommand{\X}{\thesismath{X}\xspace}
-\DeclareRobustCommand{\Xbar}{\thesismath{\overline{X}}\xspace}
-\DeclareRobustCommand{\Xzero}{\HepGenParticle{X}{}{0}\xspace}
-\DeclareRobustCommand{\Xzerobar}{\HepGenAntiParticle{X}{}{0}\xspace}
-\DeclareRobustCommand{\epluseminus}{\Pelectron\Ppositron\xspace}
 
-% Fix hyperref labels in PDFTeX
-\@ifpackageloaded{hyperref}{%
-  \pdfstringdefDisableCommands{%
-      \def\pi{pi}%
-      \def\gamma{gamma}%
-  }%
-}{}
+%\usepackage[T1]{fontenc}
+%\usepackage[bitstream-charter]{mathdesign}
+
+
+%\RequirePackage{lmodern}
+%\RequirePackage{libertine} 
+%\RequirePackage[libertine]{newtxmath}
+
+% this works
+%\usepackage[]{mathpazo}   % With old-style figures and real smallcaps.
+%\linespread{1.025}              % Palatino leads a little more leading
+%\usepackage[small]{eulervm}
+
+\RequirePackage{tabularx}
+\RequirePackage{color}
+\RequirePackage{pifont}
+\RequirePackage{soul}
+\RequirePackage[]{dcolumn}
+\RequirePackage[]{sidecap}
+\RequirePackage[]{wrapfig}
+\RequirePackage{feynmp}
+\RequirePackage[]{afterpage}
+\RequirePackage[]{multirow}
+
+%% provide adjustwidth
+\RequirePackage{changepage}
+\RequirePackage{comment}
+
+%% -------------------------------------
+%%  More settings ...
+%% -------------------------------------
+%% Treat forced blank pages in the same way as chapter title pages
+\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else%
+  \hbox{}%
+  \thispagestyle{empty}%
+  %\thispagestyle{plain}%
+  \newpage%
+  \if@twocolumn\hbox{}\newpage\fi\fi\fi}%
+
+
+%% Provide mixed-case versions of the Table of contents,
+%% List of tables, List of figures, Bibliography etc. header names
+\DeclareRobustCommand{\contentsname}{Contents}
+\DeclareRobustCommand{\bibname}{Bibliography}
+\DeclareRobustCommand{\listfigurename}{List of figures}
+\DeclareRobustCommand{\listtablename}{List of tables}
+
+%% -------------------------------------
+%%  Extra environments, stole from hepthesis.cls
+%% -------------------------------------
+%% Extra margins for various sections
+\newlength{\@mainmatterextramargin}%
+\setlength{\@mainmatterextramargin}{0cm}%
+\newlength{\@backmatterextramargin}%
+\setlength{\@backmatterextramargin}{0cm}%
+\newlength{\@frontmatterextramargin}%
+\setlength{\@frontmatterextramargin}{0cm}%
+\newlength{\@appendixextramargin}%
+\setlength{\@appendixextramargin}{0cm}%
+\newlength{\@abstractextramargin}%
+\setlength{\@abstractextramargin}{1.5cm}%
+\newlength{\@declarationextramargin}%
+\setlength{\@declarationextramargin}{1cm}%
+\newlength{\@acknowledgementsextramargin}%
+\setlength{\@acknowledgementsextramargin}{0cm}%
+\newlength{\@prefaceextramargin}%
+\setlength{\@prefaceextramargin}{0cm}%
+\newlength{\@pagequoteextramargin}%
+\setlength{\@pagequoteextramargin}{2cm}%
+%% Top vertical spacing in the front matter
+\newlength{\@frontmattertopskip}%
+\newlength{\@frontmattertitletopskip}%
+\newlength{\frontmattertitleskip}%
+\addtolength{\frontmattertitleskip}{2cm}%
+\addtolength{\@frontmattertitletopskip}{0cm}%
+\setlength{\@frontmattertopskip}{\frontmattertitleskip}%
+\addtolength{\@frontmattertopskip}{\@frontmattertitletopskip}%
+
+%% Figure widths
+\newlength{\smallfigwidth}
+\newlength{\mediumfigwidth}
+\newlength{\largefigwidth}
+\newlength{\hugefigwidth}
+\setlength{\smallfigwidth}{0.45\textwidth}
+\setlength{\mediumfigwidth}{0.6\textwidth}
+\setlength{\largefigwidth}{0.75\textwidth}
+\setlength{\hugefigwidth}{0.9\textwidth}
+%% Environment for thesis abstract in frontmatter
+%% (argument is the thesis title)
+
+\newenvironment{abstract}[1][Abstract]{%
+  \adjustwidth{\@abstractextramargin}{\@abstractextramargin}%
+  \cleardoublepage%
+  \vspace*{\@frontmattertopskip}%
+  \begin{center}%
+    \begingroup
+      \ifx\@sftitles\@empty\else\sf\fi
+      {\LARGE\textbf{#1}}%
+    \endgroup
+  \end{center}%
+  \vspace*{1cm}%
+}{ \endadjustwidth \ignorespacesafterend }
+
+%% Environment for declaration rubrik page in frontmatter
+\newenvironment{declaration}{%
+  \cleardoublepage%
+  \adjustwidth{\@declarationextramargin}{\@declarationextramargin}%
+  \vspace*{\@frontmattertopskip}%
+  \begin{center}%
+    \begingroup
+    \ifx\@sftitles\@empty\else\sf\fi
+    {\LARGE\textbf{Declaration}}%
+    \endgroup
+  \end{center}%
+  \vspace*{1cm}%
+}{%
+  %\newline \newline \newline%
+  %\begin{flushright}
+  %  \thesisauthor\newline
+  %  \today\newline
+  %\end{flushright}
+  \endadjustwidth%
+  \ignorespacesafterend%
+}
+
+%% Change the spacing of lines
+\DeclareRobustCommand{\setspacing}[1]{%
+  \setfrontmatterspacing{#1}%
+  \setmainmatterspacing{#1}%
+  \setappendixspacing{#1}%
+  \setbackmatterspacing{#1}%
+}
+\DeclareRobustCommand{\setfrontmatterspacing}[1]{\def\@frontmatterspacing{#1spacing}}
+\DeclareRobustCommand{\setmainmatterspacing}[1]{\def\@mainmatterspacing{#1spacing}}
+\DeclareRobustCommand{\setappendixspacing}[1]{\def\@appendixspacing{#1spacing}}
+\DeclareRobustCommand{\setbackmatterspacing}[1]{\def\@backmatterspacing{#1spacing}}
+
+
+%% Change the extra margin size
+\DeclareRobustCommand{\setextramargins}[1]{%
+  \setfrontmatterextramargins{#1}%
+  \setmainmatterextramargins{#1}%
+  \setappendixextramargins{#1}%
+  \setbackmatterextramargins{#1}%
+}
+\DeclareRobustCommand{\setfrontmatterextramarginsg}[1]{\setlength{\@frontmatterextramargin}{#1}}
+\DeclareRobustCommand{\setmainmatterextramargins}[1]{\setlength{\@mainmatterextramargin}{#1}}
+\DeclareRobustCommand{\setappendixextramargins}[1]{\setlength{\@appendixextramargin}{#1}}
+\DeclareRobustCommand{\setbackmatterextramargins}[1]{\setlength{\@backmatterextramargin}{#1}}
+\DeclareRobustCommand{\setabstractextramargins}[1]{\setlength{\@abstractextramargin}{#1}}
+\DeclareRobustCommand{\setdeclarationextramargins}[1]{\setlength{\@declarationextramargin}{#1}}
+\DeclareRobustCommand{\setacknowledgementsextramargins}[1]{\setlength{\@acknowledgementsextramargin}{#1}}
+\DeclareRobustCommand{\setprefaceextramargins}[1]{\setlength{\@prefaceextramargin}{#1}}
+
+%% Part-wise spacing commands and definitions
+\def\@frontmatterspacing{onehalfspacing}
+\def\@mainmatterspacing{onehalfspacing}
+\def\@appendixspacing{onehalfspacing}
+\def\@backmatterspacing{onehalfspacing}
+%% An environment for the rubbish at the front of a typical thesis
+\let\@oldfrontmatter\frontmatter
+\specialcomment{frontmatter}{%
+  \setcounter{tocdepth}{2}% show down to subsections in contents
+  \setcounter{secnumdepth}{2}% number down to subsections
+  %\newcounter{iterlist}%
+  \@oldfrontmatter%
+  \adjustwidth{\@frontmatterextramargin}{\@frontmatterextramargin}%
+  \begin{\@frontmatterspacing}%
+}{%
+  \end{\@frontmatterspacing}%
+  \endadjustwidth%
+  \ignorespacesafterend%
+}
+
+
+%% Title page
+
+%% Use the \title and \author arguments to build the front page etc.
+\ifx\@requiretitling\@empty%
+%% Re-define \title and \author to store their args in \thetitle, \theauthor
+%variables
+\renewcommand*\title[1]{\gdef\@title{#1}\global\let\thetitle\@title}%
+\renewcommand*\author[1]{\gdef\@author{#1}\global\let\theauthor\@author}%
+\else%
+\RequirePackage{titling}%
+\fi
+%% Makes a thesis title page
+\let\@oldtitlepage\titlepage
+\let\@oldendtitlepage\endtitlepage
+\DeclareRobustCommand{\titlepage}[2][]{%
+  \thispagestyle{empty}%
+  \begingroup%
+  \ifx\@sftitles\@empty\else\sf\fi%
+  \begin{center}%
+    \vspace*{\frontmattertitleskip}%
+    \begin{doublespace}%
+      {\Huge\textbf{\thetitle}}\\%
+    \end{doublespace}%
+    \vspace*{3cm}%
+    %{\Large{{\theauthor} \\ {#1}}}\\%
+    {\Large{{\theauthor}\\}} 
+    \vspace*{8cm}%
+    {#2}%
+  \end{center}%
+  \endgroup%
+}
+\renewcommand{\maketitle}[1]{\titlepage{}}

thesis/thesis.tex

@@ -1,65 +1,43 @@
-\documentclass{mythesis}
-\usepackage{mythesis}
-\usepackage{hyperref}
-\usepackage{booktabs}
-\usepackage{tabularx}
-\usepackage{color}
+%\documentclass[11pt,a4paper, singlespace,oneside]{book}
+\documentclass[11pt,a4paper, openany]{book}
+\usepackage[]{mythesis}
+\input{custom_macro}
 
-\input{custom_macro.tex}
-%% You can set the line spacing this way
-%\setallspacing{double}
-%% or a section at a time like this
-%\setfrontmatterspacing{double}
-
-%% PDF metadata
 \makeatletter
-\@ifpackageloaded{hyperref}{%
-\hypersetup{%
+\@ifpackageloaded{hyperref}{
+\hypersetup{
 	pdftitle = {A Study of Muon Capture for Muon to Electron Conversion
 	Experiments},
-	pdfsubject = {Nam H Tran's PhD thesis},
+	pdfsubject = {NT's thesis},
 	pdfkeywords = {muon capture, muon to electron conversion, COMET},
-	pdfauthor = {\textcopyright\ Nam Hoai Tran}
+	pdfauthor = {\textcopyright\ Nam H. Tran}
 }
 }{}
 \makeatother
 
-%% Define the thesis title and author
-\title{A Study of Muon Capture for \\Muon to Electron Conversion Experiments}
+\title{A study of proton emission\\
+  \vspace{-7mm} %%ad-hoc hack to get the spacing roughly right
+following nuclear muon capture\\
+\vspace{2mm}
+for the COMET experiment}
 \author{Nam Hoai Tran}
+\date{September, 2014}
 
-%% Start the document
 \begin{document}
+%\begin{frontmatter}
+  %\input{chapters/frontmatter}
+%\end{frontmatter}
 
-%% Define the un-numbered front matter (cover pages, rubrik and table of contents)
-\begin{frontmatter}
-  \input{chapters/frontmatter}
-\end{frontmatter}
+\mainmatter
+%\input{chapters/chap1_intro}
+%\input{chapters/chap2_mu_e_conv}
+%\input{chapters/chap3_comet}
+%\input{chapters/chap4_alcap_phys}
+%\input{chapters/chap5_alcap_setup}
+\input{chapters/chap6_analysis}
+%\input{chapters/chap7_results}
 
-%% Start the content body of the thesis
-\begin{mainmatter}
-  %% Actually, more semantic chapter filenames are better, like "chap-bgtheory.tex"
-  \input{chapters/chap1}
-  %\input{chapters/chap2}
-  %\input{chapters/chap3}
-  %\input{chapters/chap4}
-  %\input{chapters/chap5}
-  %\input{chapters/chap6}
-  %% To ignore a specific chapter while working on another,
-  %% making the build faster, comment it out like this:
-  %\input{chapters/chap4}
-\end{mainmatter}
-
-%% Produce the appendices
-\begin{appendices}
-  %\input{chapters/appendices}
-\end{appendices}
-
-%% Produce the un-numbered back matter (e.g. colophon,
-%% bibliography, tables of figures etc., index...)
 \begin{backmatter}
   \input{chapters/backmatter}
 \end{backmatter}
-
-%% Close
 \end{document}

thesis2/Makefile

@@ -1,15 +0,0 @@
-DOCNAME = thesis
-
-INPUT = $(DOCNAME).tex
-TARGET= $(DOCNAME).pdf
-
-default: $(TARGET)
-
-$(TARGET): $(INPUT) Makefile chapters/*.tex custom_macro.tex mythesis.sty
-	@rm -f $(DOCNAME).{aux,toc,lof,lot}
-	pdflatex $< && bibtex $(DOCNAME) && pdflatex $< && pdflatex $<
-
-clean:
-	@rm -f *.{aux,toc,lof,lot}
-	@rm -f *.{aux,bbl,blg,log,nav,out,snm,toc,lot,lof} $(TARGET)
-	@rm -f comment.cut

thesis2/chapters/frontmatter.tex

@@ -1,74 +0,0 @@
-%% Title
-%\titlepage[\vspace{5mm}Department of Physics,\\
-%Graduate School of Science]%
-%{A dissertation submitted to the Osaka University\\
-%for the degree of Doctor of Philosophy}
-\titlepage[]{\vspace{5mm}Department of Physics, Graduate School of Science\\
-Osaka University}
-
-%% Abstract
-\begin{abstract}
-  %[\smaller \thetitle\\ \vspace*{1cm} \smaller {\theauthor}]
-  \thispagestyle{empty}
-COMET [1] is an experiment that aims to search for a charged lepton flavor
-violation (CLFV) process, the muon-to-electron conversion in the presence of
-a nucleus,
-\muec. The process is forbidden in the Standard Model (SM), however is
-predicted to occur in various extensions of SM, such as . Current experimental
-upper limit of the branching ratio is $BR(\mu^{-} + Au \rightarrow e^{-} + Au)
-< 7 \times 10^{-13}$, set by the SINDRUM II experiment [2].
-
-Using the J-PARC proton beam and the pion capture by
-a solenoidal field, COMET will have a single event sensitivity  10,000 times
-better than the current limit. The COMET collaboration has taken a phased
-approach in which the first phase, COMET Phase-I [3], starts in 2013 and
-initial data taking in around 2017. 
-
-In order to optimize detector design for the Phase-I, backgrounds from nuclear
-muon capture are crucial. We have proposed a dedicated experiment , namely
-AlCap, at PSI, Switzerland to study the backgrounds, including: heavy charged
-particles, neutrons and photons. The measurements of heavy charged particles
-have been carried out in the 2013 run and the preliminary analysis results are
-presented in this thesis.
-\end{abstract}
-
-
-%% Declaration
-\begin{declaration}
-  \thispagestyle{empty}
-  This dissertation is the result of my own work, except where explicit
-  reference is made to the work of others, and has not been submitted
-  for another qualification to this or any other university. 
-  \vspace*{1cm}
-  \begin{flushright}
-    Nam Hoai Tran
-  \end{flushright}
-\end{declaration}
-
-
-% Acknowledgements
-%\begin{acknowledgements}
-  %\thispagestyle{empty}
-  %Of the many people who deserve thanks, some are particularly prominent,
-  %such as my supervisor Professor Yoshitaka Kuno.
-%\end{acknowledgements}
-
-
-%% Preface
-%\begin{preface}
-  %\thispagestyle{empty}
-  %The thesis is about measurements of products of nuclear muon capture on an
-  %aluminum target, which is important for optimization of a tracking detector
-  %of a search for muon to electron conversion, the E21 experiment - so called
-  %COMET - at Japan Proton Accelerator Complex (J-PARC).
-%\end{preface}
-
-%% ToC
-\tableofcontents
-
-
-%% Strictly optional!
-%\frontquote{%
-	%Writing in English is the most ingenious torture\\
-%ever devised for sins committed in previous lives.}%
-%{James Joyce}

thesis2/custom_macro.tex

@@ -1,56 +0,0 @@
-\usepackage[]{xspace}
-\newcommand{\lagr}{\cal{L}}
-%%% muon decays
-\newcommand{\mueg}{$\mu^{+} \rightarrow e^{+}\gamma$\xspace}
-%\newcommand{\mueg}{\APmuon $\rightarrow$ \APelectron\Pphoton}
-
-%\newcommand{\mueee}{$\mu \rightarrow eee$}
-\newcommand{\mueee}{$\mu^+ \rightarrow e^+e^+e^+$\xspace}
-%\newcommand{\meee}{\Pmuon $\rightarrow$ \Pelectron\Pelectron\Pelectron}
-
-\newcommand{\muenn}{$\mu \rightarrow e \nu \overline{\nu}$\xspace}
-%\newcommand{\muenn}{\Pmuon $\rightarrow$ \Pelectron \Pnu \APnu}
-
-
-\newcommand{\muec}{$\mu^{-} N \rightarrow e^{-} N$\xspace}
-%\newcommand{\muec}{\Pmuon $\rightarrow$ \Pelectron N}
-
-\newcommand{\muecaz}{$\mu^{-} + N(A,Z) \rightarrow e^{-} + N(A,Z)$\xspace}
-
-% some limits
-\newcommand{\sindrumlimit}
-{$\mathcal{B} (\mu^- + Au \rightarrow e^- +Au) < 7\times 10^{-13}$\xspace}
-
-\newcommand{\meglimit}
-{$\mathcal{B}(\mu^+ \rightarrow e^+ \gamma) < 5.7 \times 10^{-13}$\xspace}
-
-\newcommand{\brmeg}
-{$\mathcal{B}(\mu^+ \rightarrow e^+ \gamma)$\xspace}
-
-\newcommand{\micheldecay}{
-  $\mu^- \rightarrow e^- \nu_\mu \overline{\nu}_e$\xspace
-}
-\newcommand{\muenng}{
-$\mu^- \rightarrow e^- \nu_\mu \overline{\nu}_e \gamma$\xspace
-}
-\newcommand{\muennee}{
-$\mu^- \rightarrow e^- \nu_\mu \overline{\nu}_e e^+ e^-$\xspace
-}
-
-\newcommand{\mueconv}{$\mu-e$ conversion\xspace}
-
-%scientific notation, 
-\usepackage[]{xifthen}
-\newcommand{\sn}[2]
-{
-  \ifthenelse{\isempty{#1}}
-  {$10^{#2}$\xspace} %if the 1st argument is blank
-  {$#1 \times 10^{#2}$\xspace} %if both exist
-}
-
-\newcommand{\cc}{$c$\xspace}
-
-\newcommand{\rootana}{{\ttfamily rootana}}
-\newcommand{\alcapana}{{\ttfamily alcapana}}
-\newcommand{\tpulseisland}{{\ttfamily TPulseIsland}}
-\newcommand{\tanalysedpulse}{{\ttfamily TAnalysedPulse}}  

thesis2/mythesis.sty

@@ -1,272 +0,0 @@
-\NeedsTeXFormat{LaTeX2e}
-\ProvidesPackage{mythesis}
-
-%% -------------------------------------
-%% Packages
-%% -------------------------------------
-%$ Page layout
-\RequirePackage[top=1in, bottom=1in, 
-%inner=1.25in, outer=1in]{geometry}
-inner=1.25in, outer=1in, twoside]{geometry}
-\RequirePackage{amsmath}
-
-%$ Hyper-link ..
-\RequirePackage[%
-colorlinks=true,% color links instead of using boxes
-linkcolor=red,% color for internal (intra-document) links
-citecolor=green,% color for bibliographic links
-urlcolor=blue,% color for URL links
-hyperfootnotes=false,% disable links to footnotes (because feature broken)
-hyperindex,% make page numbers in index into hyperlinks
-pdfstartview={FitH},% startup page view: fit width of page to window
-bookmarks
-]{hyperref}
-\RequirePackage[all]{hypcap}
-
-\AtBeginDocument{\thispagestyle{plain}}
-
-%% Custom header, no upper case, two sided 
-\RequirePackage{fancyhdr}
-\pagestyle{fancy}
-\fancyhf{}
-\fancyhead[LE,RO]{\thepage}
-\fancyhead[RE]{\nouppercase{\leftmark}}
-\renewcommand{\chaptermark}[1]{\markboth{#1}{}}
-\setlength{\headheight}{15pt}
-\RequirePackage{emptypage}
-%% Others
-\RequirePackage{booktabs}
-\RequirePackage{cite}
-%\RequirePackage{morefloats}
-\RequirePackage{mathrsfs} % script font
-\RequirePackage{afterpage}
-%% Using Babel allows other languages to be used and mixed-in easily
-\RequirePackage[ngerman,english]{babel}
-\selectlanguage{english}
-\RequirePackage[babel]{csquotes}
-
-\RequirePackage{subfig}
-\RequirePackage{tikz}
-\RequirePackage{fixltx2e}
-\RequirePackage{setspace}
-\RequirePackage{verbatim}
-\RequirePackage{lipsum}
-\RequirePackage{datatool}
-\RequirePackage[capitalise]{cleveref}
-\RequirePackage[final]{listings}
-\RequirePackage{xfrac}
-%% Units
-\RequirePackage[]{siunitx}
-%% Various fonts ...
-%\RequirePackage[T1]{fontenc}
-%\RequirePackage{charter}
-%\RequirePackage[expert]{mathdesign}
-
-
-%\usepackage[T1]{fontenc}
-%\usepackage[bitstream-charter]{mathdesign}
-
-
-%\RequirePackage{lmodern}
-%\RequirePackage{libertine} 
-%\RequirePackage[libertine]{newtxmath}
-
-% this works
-%\usepackage[]{mathpazo}   % With old-style figures and real smallcaps.
-%\linespread{1.025}              % Palatino leads a little more leading
-%\usepackage[small]{eulervm}
-
-\RequirePackage{tabularx}
-\RequirePackage{color}
-\RequirePackage{pifont}
-\RequirePackage{soul}
-\RequirePackage[]{dcolumn}
-\RequirePackage[]{sidecap}
-\RequirePackage[]{wrapfig}
-\RequirePackage{feynmp}
-\RequirePackage[]{afterpage}
-\RequirePackage[]{multirow}
-
-%% provide adjustwidth
-\RequirePackage{changepage}
-\RequirePackage{comment}
-
-%% -------------------------------------
-%%  More settings ...
-%% -------------------------------------
-%% Treat forced blank pages in the same way as chapter title pages
-\def\cleardoublepage{\clearpage\if@twoside \ifodd\c@page\else%
-  \hbox{}%
-  \thispagestyle{empty}%
-  %\thispagestyle{plain}%
-  \newpage%
-  \if@twocolumn\hbox{}\newpage\fi\fi\fi}%
-
-
-%% Provide mixed-case versions of the Table of contents,
-%% List of tables, List of figures, Bibliography etc. header names
-\DeclareRobustCommand{\contentsname}{Contents}
-\DeclareRobustCommand{\bibname}{Bibliography}
-\DeclareRobustCommand{\listfigurename}{List of figures}
-\DeclareRobustCommand{\listtablename}{List of tables}
-
-%% -------------------------------------
-%%  Extra environments, stole from hepthesis.cls
-%% -------------------------------------
-%% Extra margins for various sections
-\newlength{\@mainmatterextramargin}%
-\setlength{\@mainmatterextramargin}{0cm}%
-\newlength{\@backmatterextramargin}%
-\setlength{\@backmatterextramargin}{0cm}%
-\newlength{\@frontmatterextramargin}%
-\setlength{\@frontmatterextramargin}{0cm}%
-\newlength{\@appendixextramargin}%
-\setlength{\@appendixextramargin}{0cm}%
-\newlength{\@abstractextramargin}%
-\setlength{\@abstractextramargin}{1.5cm}%
-\newlength{\@declarationextramargin}%
-\setlength{\@declarationextramargin}{1cm}%
-\newlength{\@acknowledgementsextramargin}%
-\setlength{\@acknowledgementsextramargin}{0cm}%
-\newlength{\@prefaceextramargin}%
-\setlength{\@prefaceextramargin}{0cm}%
-\newlength{\@pagequoteextramargin}%
-\setlength{\@pagequoteextramargin}{2cm}%
-%% Top vertical spacing in the front matter
-\newlength{\@frontmattertopskip}%
-\newlength{\@frontmattertitletopskip}%
-\newlength{\frontmattertitleskip}%
-\addtolength{\frontmattertitleskip}{2cm}%
-\addtolength{\@frontmattertitletopskip}{0cm}%
-\setlength{\@frontmattertopskip}{\frontmattertitleskip}%
-\addtolength{\@frontmattertopskip}{\@frontmattertitletopskip}%
-
-%% Figure widths
-\newlength{\smallfigwidth}
-\newlength{\mediumfigwidth}
-\newlength{\largefigwidth}
-\newlength{\hugefigwidth}
-\setlength{\smallfigwidth}{0.45\textwidth}
-\setlength{\mediumfigwidth}{0.6\textwidth}
-\setlength{\largefigwidth}{0.75\textwidth}
-\setlength{\hugefigwidth}{0.9\textwidth}
-%% Environment for thesis abstract in frontmatter
-%% (argument is the thesis title)
-
-\newenvironment{abstract}[1][Abstract]{%
-  \adjustwidth{\@abstractextramargin}{\@abstractextramargin}%
-  \cleardoublepage%
-  \vspace*{\@frontmattertopskip}%
-  \begin{center}%
-    \begingroup
-      \ifx\@sftitles\@empty\else\sf\fi
-      {\LARGE\textbf{#1}}%
-    \endgroup
-  \end{center}%
-  \vspace*{1cm}%
-}{ \endadjustwidth \ignorespacesafterend }
-
-%% Environment for declaration rubrik page in frontmatter
-\newenvironment{declaration}{%
-  \cleardoublepage%
-  \adjustwidth{\@declarationextramargin}{\@declarationextramargin}%
-  \vspace*{\@frontmattertopskip}%
-  \begin{center}%
-    \begingroup
-    \ifx\@sftitles\@empty\else\sf\fi
-    {\LARGE\textbf{Declaration}}%
-    \endgroup
-  \end{center}%
-  \vspace*{1cm}%
-}{%
-  %\newline \newline \newline%
-  %\begin{flushright}
-  %  \thesisauthor\newline
-  %  \today\newline
-  %\end{flushright}
-  \endadjustwidth%
-  \ignorespacesafterend%
-}
-
-%% Change the spacing of lines
-\DeclareRobustCommand{\setspacing}[1]{%
-  \setfrontmatterspacing{#1}%
-  \setmainmatterspacing{#1}%
-  \setappendixspacing{#1}%
-  \setbackmatterspacing{#1}%
-}
-\DeclareRobustCommand{\setfrontmatterspacing}[1]{\def\@frontmatterspacing{#1spacing}}
-\DeclareRobustCommand{\setmainmatterspacing}[1]{\def\@mainmatterspacing{#1spacing}}
-\DeclareRobustCommand{\setappendixspacing}[1]{\def\@appendixspacing{#1spacing}}
-\DeclareRobustCommand{\setbackmatterspacing}[1]{\def\@backmatterspacing{#1spacing}}
-
-
-%% Change the extra margin size
-\DeclareRobustCommand{\setextramargins}[1]{%
-  \setfrontmatterextramargins{#1}%
-  \setmainmatterextramargins{#1}%
-  \setappendixextramargins{#1}%
-  \setbackmatterextramargins{#1}%
-}
-\DeclareRobustCommand{\setfrontmatterextramarginsg}[1]{\setlength{\@frontmatterextramargin}{#1}}
-\DeclareRobustCommand{\setmainmatterextramargins}[1]{\setlength{\@mainmatterextramargin}{#1}}
-\DeclareRobustCommand{\setappendixextramargins}[1]{\setlength{\@appendixextramargin}{#1}}
-\DeclareRobustCommand{\setbackmatterextramargins}[1]{\setlength{\@backmatterextramargin}{#1}}
-\DeclareRobustCommand{\setabstractextramargins}[1]{\setlength{\@abstractextramargin}{#1}}
-\DeclareRobustCommand{\setdeclarationextramargins}[1]{\setlength{\@declarationextramargin}{#1}}
-\DeclareRobustCommand{\setacknowledgementsextramargins}[1]{\setlength{\@acknowledgementsextramargin}{#1}}
-\DeclareRobustCommand{\setprefaceextramargins}[1]{\setlength{\@prefaceextramargin}{#1}}
-
-%% Part-wise spacing commands and definitions
-\def\@frontmatterspacing{onehalfspacing}
-\def\@mainmatterspacing{onehalfspacing}
-\def\@appendixspacing{onehalfspacing}
-\def\@backmatterspacing{onehalfspacing}
-%% An environment for the rubbish at the front of a typical thesis
-\let\@oldfrontmatter\frontmatter
-\specialcomment{frontmatter}{%
-  \setcounter{tocdepth}{2}% show down to subsections in contents
-  \setcounter{secnumdepth}{2}% number down to subsections
-  %\newcounter{iterlist}%
-  \@oldfrontmatter%
-  \adjustwidth{\@frontmatterextramargin}{\@frontmatterextramargin}%
-  \begin{\@frontmatterspacing}%
-}{%
-  \end{\@frontmatterspacing}%
-  \endadjustwidth%
-  \ignorespacesafterend%
-}
-
-
-%% Title page
-
-%% Use the \title and \author arguments to build the front page etc.
-\ifx\@requiretitling\@empty%
-%% Re-define \title and \author to store their args in \thetitle, \theauthor
-%variables
-\renewcommand*\title[1]{\gdef\@title{#1}\global\let\thetitle\@title}%
-\renewcommand*\author[1]{\gdef\@author{#1}\global\let\theauthor\@author}%
-\else%
-\RequirePackage{titling}%
-\fi
-%% Makes a thesis title page
-\let\@oldtitlepage\titlepage
-\let\@oldendtitlepage\endtitlepage
-\DeclareRobustCommand{\titlepage}[2][]{%
-  \thispagestyle{empty}%
-  \begingroup%
-  \ifx\@sftitles\@empty\else\sf\fi%
-  \begin{center}%
-    \vspace*{\frontmattertitleskip}%
-    \begin{doublespace}%
-      {\Huge\textbf{\thetitle}}\\%
-    \end{doublespace}%
-    \vspace*{3cm}%
-    %{\Large{{\theauthor} \\ {#1}}}\\%
-    {\Large{{\theauthor}\\}} 
-    \vspace*{8cm}%
-    {#2}%
-  \end{center}%
-  \endgroup%
-}
-\renewcommand{\maketitle}[1]{\titlepage{}}