%%% DOCUMENTCLASS 
%%%-------------------------------------------------------------------------------
\documentclass[
a4paper, % Stock and paper size.
11pt, % Type size.
% article,
% oneside, 
onecolumn, % Only one column of text on a page.
% openright, % Each chapter will start on a recto page.
% openleft, % Each chapter will start on a verso page.
openany, % A chapter may start on either a recto or verso page.
]{memoir}

%%% PACKAGES 
%%%------------------------------------------------------------------------------

\usepackage[utf8]{inputenc} % If utf8 encoding
% \usepackage[lantin1]{inputenc} % If not utf8 encoding, then this is probably the way to go
\usepackage[T1]{fontenc}    %
\usepackage{lmodern}
\usepackage[english]{babel} % English please
\usepackage[final]{microtype} % Less badboxes

% \usepackage{kpfonts} %Font

\usepackage{amsmath,amssymb,mathtools} % Math
\usepackage{pifont}% http://ctan.org/pkg/pifont
\newcommand{\cmark}{\ding{51}}%
\newcommand{\xmark}{\ding{55}}%

\usepackage{graphicx} % Include figures
\usepackage{makeidx}
\usepackage{import}

%%% PAGE LAYOUT 
%%%-----------------------------------------------------------------------------
\setlrmarginsandblock{0.15\paperwidth}{*}{1} % Left and right margin
\setulmarginsandblock{0.2\paperwidth}{*}{1}  % Upper and lower margin
\checkandfixthelayout

\newlength\forceindent
\setlength{\forceindent}{\parindent}
\setlength{\parindent}{0cm}
\renewcommand{\indent}{\hspace*{\forceindent}}
\setlength{\parskip}{1em}


%%% SECTIONAL DIVISIONS
%%%------------------------------------------------------------------------------
\maxsecnumdepth{paragraph} % Subsections (and higher) are numbered
\setsecnumdepth{paragraph}


\makeatletter %
\makechapterstyle{standard}{
  \setlength{\beforechapskip}{0\baselineskip}
  \setlength{\midchapskip}{1\baselineskip}
  \setlength{\afterchapskip}{8\baselineskip}
  \renewcommand{\chapterheadstart}{\vspace*{\beforechapskip}}
  \renewcommand{\chapnamefont}{\centering\normalfont\Large}
  \renewcommand{\printchaptername}{\chapnamefont \@chapapp}
  \renewcommand{\chapternamenum}{\space}
  \renewcommand{\chapnumfont}{\normalfont\Large}
  \renewcommand{\printchapternum}{\chapnumfont \thechapter}
  \renewcommand{\afterchapternum}{\par\nobreak\vskip \midchapskip}
  \renewcommand{\printchapternonum}{\vspace*{\midchapskip}\vspace*{5mm}}
  \renewcommand{\chaptitlefont}{\centering\bfseries\LARGE}
%  \renewcommand{\printchaptertitle}[1]{\chaptitlefont ##1}
  \renewcommand{\afterchaptertitle}{\par\nobreak\vskip \afterchapskip}
}
\makeatother

%\chapterstyle{standard}
\chapterstyle{madsen}


\setsecheadstyle{\normalfont\large\bfseries}
\setsubsecheadstyle{\normalfont\normalsize\bfseries}
\setparaheadstyle{\normalfont\normalsize\bfseries}
\setparaindent{0pt}\setafterparaskip{0pt}

%%% FLOATS AND CAPTIONS
%%%------------------------------------------------------------------------------

\makeatletter                  % You do not need to write [htpb] all the time
\renewcommand\fps@figure{htbp} %
\renewcommand\fps@table{htbp}  %
\makeatother                   %

\captiondelim{\space } % A space between caption name and text
\captionnamefont{\small\bfseries} % Font of the caption name
\captiontitlefont{\small\normalfont} % Font of the caption text

\changecaptionwidth          % Change the width of the caption
\captionwidth{1\textwidth} %

\usepackage{tabularx}

%%% ABSTRACT
%%%------------------------------------------------------------------------------

\renewcommand{\abstractnamefont}{\normalfont\small\bfseries} % Font of abstract title
\setlength{\absleftindent}{0.1\textwidth} % Width of abstract
\setlength{\absrightindent}{\absleftindent}

%%% HEADER AND FOOTER 
%%%------------------------------------------------------------------------------

\makepagestyle{standard} % Make standard pagestyle

\makeatletter                 % Define standard pagestyle
\makeevenfoot{standard}{}{}{} %
\makeoddfoot{standard}{}{}{}  %
\makeevenhead{standard}{\bfseries\thepage\normalfont\qquad\small\leftmark}{}{}
\makeoddhead{standard}{}{}{\small\rightmark\qquad\bfseries\thepage}
% \makeheadrule{standard}{\textwidth}{\normalrulethickness}
\makeatother                  %

\makeatletter
\makepsmarks{standard}{
\createmark{chapter}{both}{shownumber}{\@chapapp\ }{ \quad }
\createmark{section}{right}{shownumber}{}{ \quad }
\createplainmark{toc}{both}{\contentsname}
\createplainmark{lof}{both}{\listfigurename}
\createplainmark{lot}{both}{\listtablename}
\createplainmark{bib}{both}{\bibname}
\createplainmark{index}{both}{\indexname}
\createplainmark{glossary}{both}{\glossaryname}
}
\makeatother                               %

\makepagestyle{chap} % Make new chapter pagestyle

\makeatletter
\makeevenfoot{chap}{}{\small\bfseries\thepage}{} % Define new chapter pagestyle
\makeoddfoot{chap}{}{\small\bfseries\thepage}{}  %
\makeevenhead{chap}{}{}{}   %
\makeoddhead{chap}{}{}{}    %
% \makeheadrule{chap}{\textwidth}{\normalrulethickness}
\makeatother

\nouppercaseheads
\pagestyle{standard}               % Choosing pagestyle and chapter pagestyle
\aliaspagestyle{chapter}{chap} %


%%% NEW COMMANDS
%%%----------------------------------------------------------------------------% Definition of subsubsubsection
\newcommand{\subsubsubsection}[1]{\vspace{9pt}\noindent{\textbf{\em #1:}}\vspace*{3pt}}

% Nektar++ version
\usepackage{xspace}
\newcommand{\nekver} {\input{VERSION}\unskip}

\newcommand{\p}{\partial} %Partial
% Or what ever you want


%%% CODE SNIPPETS, COMMANDS, ETC
%%%-----------------------------------------------------------------------------
\usepackage{xcolor}
\usepackage{listings} % Display code / shell commands
\usepackage{lstautogobble}
%\newcommand{\shellcommand}[1]{\begin{lstlisting} \#1 \end{lstlisting}
\lstdefinestyle{BashInputStyle}{
  language=bash,
  basicstyle=\small\ttfamily,
%  numbers=left,
%  numberstyle=\tiny,
%  numbersep=3pt,
  frame=single,
  columns=fullflexible,
  backgroundcolor=\color{yellow!10},
  linewidth=\linewidth,
  xleftmargin=0.05\linewidth,
  keepspaces=true,
  framesep=5pt,
  rulecolor=\color{black!30},
  aboveskip=10pt,
  autogobble=true
}
\definecolor{gray}{rgb}{0.4,0.4,0.4}
\definecolor{darkblue}{rgb}{0.0,0.0,0.6}
\definecolor{cyan}{rgb}{0.0,0.6,0.6}
\definecolor{maroon}{rgb}{0.5,0.0,0.0}
\definecolor{darkgreen}{rgb}{0.0,0.5,0.0}
\lstdefinelanguage{XML}
{
  basicstyle=\ttfamily\footnotesize,
  morestring=[b]",
  moredelim=[s][\bfseries\color{maroon}]{<}{\ },
  moredelim=[s][\bfseries\color{maroon}]{</}{>},
  moredelim=[l][\bfseries\color{maroon}]{/>},
  moredelim=[l][\bfseries\color{maroon}]{>},
  morecomment=[s]{<?}{?>},
  morecomment=[s]{<!--}{-->},
  commentstyle=\color{gray},
  stringstyle=\color{orange},
  identifierstyle=\color{darkblue},
  showstringspaces=false
}
\lstdefinestyle{XMLStyle}{
  language=XML,
  basicstyle=\ttfamily\footnotesize,
  numbers=left,
  numberstyle=\tiny,
  numbersep=3pt,
  frame=,
  columns=fullflexible,
  backgroundcolor=\color{black!05},
  linewidth=\linewidth,
  xleftmargin=0.05\linewidth,
  keepspaces=true
}
\lstset{%
    escapeinside={(*}{*)},%
	breaklines=true,
}

\usepackage{tikz}
\ifdefined\HCode
\newcommand{\inltt}[1]{\texttt{#1}}
\newcommand{\inlsh}[1]{\texttt{#1}}
\else
\newcommand{\inltt}[1]{\tikz[anchor=base,baseline]\node[inner sep=3pt,
rounded corners,outer sep=0,draw=black!30,fill=black!05]{\small\texttt{#1}};}
\newcommand{\inlsh}[1]{\tikz[anchor=base,baseline]\node[inner sep=2pt,
outer sep=0,fill=black!05]{\texttt{#1}};}
\fi
\newcommand{\nekpp}{{\em Nektar++}\xspace}

% Highlight box
\usepackage{environ}
\usepackage[tikz]{bclogo}
\usetikzlibrary{calc}

% Only use fancy boxes for PDF
\ifdefined\HCode
\NewEnviron{notebox}{\textbf{Note:} \BODY}
\NewEnviron{warningbox}{\textbf{Warning:} \BODY}
\NewEnviron{tipbox}{\textbf{Tip:} \BODY}
\NewEnviron{custombox}[3]{\textbf{#1} \BODY}
\else
\NewEnviron{notebox}
  {\par\medskip\noindent
  \begin{tikzpicture}
    \node[inner sep=5pt,fill=black!10,draw=black!30] (box)
    {\parbox[t]{.99\linewidth}{%
      \begin{minipage}{.1\linewidth}
      \centering\tikz[scale=1]\node[scale=1.5]{\bcinfo};
      \end{minipage}%
      \begin{minipage}{.9\linewidth}
      \textbf{Note}\par\smallskip
      \BODY
      \end{minipage}\hfill}%
    };
   \end{tikzpicture}\par\medskip%
}
\NewEnviron{warningbox}
  {\par\medskip\noindent
  \begin{tikzpicture}
    \node[inner sep=5pt,fill=red!10,draw=black!30] (box)
    {\parbox[t]{.99\linewidth}{%
      \begin{minipage}{.1\linewidth}
      \centering\tikz[scale=1]\node[scale=1.5]{\bcdanger};
      \end{minipage}%
      \begin{minipage}{.9\linewidth}
      \textbf{Warning}\par\smallskip
      \BODY
      \end{minipage}\hfill}%
    };
   \end{tikzpicture}\par\medskip%
}
\NewEnviron{tipbox}
  {\par\medskip\noindent
  \begin{tikzpicture}
    \node[inner sep=5pt,fill=green!10,draw=black!30] (box)
    {\parbox[t]{.99\linewidth}{%
      \begin{minipage}{.1\linewidth}
      \centering\tikz[scale=1]\node[scale=1.5]{\bclampe};
      \end{minipage}%
      \begin{minipage}{.9\linewidth}
      \textbf{Tip}\par\smallskip
      \BODY
      \end{minipage}\hfill}%
    };
   \end{tikzpicture}\par\medskip%
}
\NewEnviron{custombox}[3]
  {\par\medskip\noindent
  \begin{tikzpicture}
    \node[inner sep=5pt,fill=#3!10,draw=black!30] (box)
    {\parbox[t]{.99\linewidth}{%
      \begin{minipage}{.1\linewidth}
      \centering\tikz[scale=1]\node[scale=1.5]{#2};
      \end{minipage}%
      \begin{minipage}{.9\linewidth}
      \textbf{#1}\par\smallskip
      \BODY
      \end{minipage}\hfill}%
    };
   \end{tikzpicture}\par\medskip%
}
\fi

%%% TABLE OF CONTENTS AND INDEX
%%%-----------------------------------------------------------------------------

\maxtocdepth{subsection} % Only parts, chapters and sections in the table of contents
\settocdepth{subsection}

\makeindex

%\AtEndDocument{\addtocontents{toc}{\par}} % Add a \par to the end of the TOC

%%% INTERNAL HYPERLINKS
%%%-----------------------------------------------------------------------------
\usepackage[linktoc=all,hyperfootnotes=false]{hyperref}   % Internal hyperlinks
\hypersetup{
colorlinks,
citecolor=darkblue,
filecolor=darkblue,
linkcolor=darkblue,
urlcolor=darkblue,
pdfborder={0 0 0},      % No borders around internal hyperlinks
pdfauthor={I am the Author} % author
}
\usepackage{memhfixc}   %

% \makeatletter
% \def\@setref#1#2#3{%
%   \ifx#1\relax
%    \protect\G@refundefinedtrue
%    \nfss@text{\reset@font\bfseries\huge\textcolor{red}{#3 undefined}}%
%    \@latex@warning{Reference `#3' on page \thepage \space
%              undefined}%
%   \else
%    \expandafter#2#1\null
%   \fi}
% \makeatother

%%% PRETTY TITLE PAGE FOR PDF DOC
%%%-----------------------------------------------------------------------------
\ifdefined\HCode
\else
\makeatletter
\newlength\drop
\newcommand{\br}{\hfill\break}
\newcommand*{\titlepage}{%
    \thispagestyle{empty}
    \begingroup% Gentle Madness
    \drop = 0.1\textheight
    \vspace*{\baselineskip}
    \vfill
    \hbox{%
      \hspace*{0.1\textwidth}%
      \rule{1pt}{\dimexpr\textheight-28pt\relax}%
      \hspace*{0.05\textwidth}% 
      \parbox[b]{0.85\textwidth}{%
        \vbox{%
          {\includegraphics[width=0.2\textwidth]{img/icon-blue.png}\par}
          \vskip1.00\baselineskip
          {\Huge\bfseries\raggedright\@title\par}
          \vskip2.37\baselineskip
          {\huge\bfseries Version \nekver\par}
          \vskip4\baselineskip
          {\huge\bfseries \textcolor{darkgreen}{User Guide}\par}
          \vskip1.0\baselineskip
          {\large\bfseries\@date\par}
          \vspace{0.3\textheight}
          {\small\noindent\@author}\\[\baselineskip]
        }% end of vbox
      }% end of parbox
    }% end of hbox
    \vfill
    \null
\endgroup}
\makeatother
\fi

%%% THE DOCUMENT
%%% Where all the important stuff is included!
%%%-------------------------------------------------------------------------------

\author{Department of Aeronautics, Imperial College London, UK\newline
Scientific Computing and Imaging Institute, University of Utah, USA}
\title{Nektar++: Spectral/hp Element Framework}
\date{\today}

\begin{document}


\frontmatter

% Render pretty title page if not building HTML
\ifdefined\HCode
\begin{center}
    \includegraphics[width=0.1\textwidth]{img/icon-blue.png}
\end{center}
\maketitle
\begin{center}
    \huge{Users Guide - Version \nekver}
\end{center}
\else
\titlepage
\fi

\clearpage

\ifx\HCode\undefined
\tableofcontents*
\fi

\clearpage

\import{introduction/}{introduction}

\mainmatter

\part{Getting Started}

\import{installation/}{installation}

\import{formulation/}{formulation}

\import{xml/}{xml}

\part{Preprocessing \& Postprocessing}
\label{p:prepost}

\import{utilities/}{preprocessing}

\import{utilities/}{postprocessing}

\part{Solver Applications}
\label{p:applications}

\import{solvers/}{solvers}

\part{Reference}
\import{optimisation/}{optimisation}

\import{command-line/}{command-line}

\import{faq/}{faq}


%\appendix


\backmatter

%%% BIBLIOGRAPHY
%%% -------------------------------------------------------------

\bibliographystyle{plain}
\bibliography{refs}

\printindex

\end{document}
