% Haero design document
\documentclass{book}

\usepackage{amsmath,amssymb,mathrsfs}
\usepackage{graphicx}
\usepackage{fullpage,times}
\usepackage{enumitem}
\usepackage{color}
\usepackage{booktabs,supertabular}
\usepackage{amsthm,thmtools}
\usepackage{xspace}
\usepackage{listings}
\usepackage{float}
\usepackage[ruled,lined,linesnumbered]{algorithm2e}

\theoremstyle{definition}
\newtheorem{defn}{Definition}
\newtheorem{appx}{Approximation}
\newtheorem{assume}{Assumption}


\theoremstyle{remark}
\newtheorem*{rem}{Remark}

% Line spacing
\setlength{\parindent}{0em}
\setlength{\parskip}{1em}

\usepackage[dvipsnames]{xcolor}

%---------
% configure-time stuff
\input{../haero_design_inc.tex}

%---------
% Draft writing tools
\newcommand{\todo}[1]{\ifinccomments\textcolor{Red}{\textbf{TODO:\xspace} #1}\fi}
\newcommand{\pbc}[1]{\ifinccomments\textcolor{MidnightBlue}{\textbf{PB comment:\xspace} #1 }\fi} % Pete
\newcommand{\jjc}[1]{\ifinccomments\textcolor{Cerulean}{\textbf{JJ comment:\xspace} #1}\fi} % Jeff
\newcommand{\hwc}[1]{\ifinccomments\textcolor{ForestGreen}{\textbf{HW comment:\xspace} #1}\fi} % Hui
\newcommand{\bsc}[1]{\ifinccomments\textcolor{BlueViolet}{\textbf{BS comment:\xspace} #1}\fi} % Balwinder
\newcommand{\msc}[1]{\ifinccomments\textcolor{Plum}{\textbf{MS comment:\xspace} #1}\fi} % Mike
\newcommand{\jsc}[1]{\ifinccomments\textcolor{Violet}{\textbf{JS comment:\xspace} #1}\fi} % Jian

% Bibliography stuff
\usepackage[sort, numbers]{natbib}
\bibliographystyle{acm}
\setcitestyle{square}

\usepackage{hyperref}

% Hold the serifs, please!
\renewcommand{\familydefault}{\sfdefault}
\usepackage{helvet}

%\usepackage[inline]{../trackchanges}
%\addeditor{Kai}
%\addeditor{Hui}

% We number subsections and paragraphs.
\setcounter{secnumdepth}{5}

% Labeling and referencing
\newcommand{\labeleq}[1]{\label{eq:#1}}
\newcommand{\labelfig}[1]{\label{fig:#1}}
\newcommand{\labelchapter}[1]{\label{ch:#1}}
\newcommand{\labelsection}[1]{\label{sec:#1}}
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% Annotating assumptions(!)
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\newcommand{\mw}[1]{M\dsub{w,#1}}
\newcommand{\rsag}{\rm H_{_2}SO_{_4}}
\newcommand{\rasf}{\rm SO_{_4}}
\newcommand{\rwater}{\rm H_{_2}O}
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\newcommand{\asf}{SO_{_4}}
\newcommand{\water}{H_{_2}O}
\newcommand{\numc}{N_{_{t,i}}}
\mathchardef\mhyphen="2D % Define a "math hyphen", make the dash shorter
\newcommand{\pluseq}{\mathrel{+}=}
\newcommand{\minuseq}{\mathrel{-}=}
\DeclareMathOperator{\sgn}{sgn}

% Norm and Absolute value
	\newcommand{\abs}[1]{\left\lvert#1\right\rvert}
	\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
% derivatives
	\newcommand{\partd}[2]{\frac{\partial #1 }{\partial #2}}
	\newcommand{\partdn}[3]{\frac{\partial^#3 #1}{\partial #2 ^#3}}
	\newcommand{\deriv}[2]{\frac{ d #1}{d #2}}
	\newcommand{\derivn}[3]{\frac{d^#3 #1}{d #2^#3}}
	\providecommand{\totd}[1]{\frac{D #1}{Dt}}

\begin{document}
\title{Haero Aerosol Model Design}
\author{EAGLES Computation Team}
%\date
\maketitle

\tableofcontents

% \include puts page breaks after each section, while \input does not.
\include{intro}
\include{physics}
\include{library}
\include{testing}
\include{processes}
\include{driver}

\appendix
\include{glossary}
\include{api}
\include{process_appendix}
\include{diagnostics}
\include{driver_input}
\chapter{List of assumptions and approximations}
\renewcommand{\listtheoremname}{}
\listoftheorems[ignoreall, show={assume,appx}, onlynamed]
\nocite{*}
\bibliography{haero_design}

\end{document}
