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refman.tex
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% Handle batch mode
% to overcome problems with too many open files
\let\mypdfximage\pdfximage\def\pdfximage{\immediate\mypdfximage}
% Set document class depending on configuration
\documentclass[twoside]{book}
%% moved from doxygen.sty due to workaround for LaTex 2019 version and unmaintained tabu package
\usepackage{ifthen}
\ifx\requestedLaTeXdate\undefined
\usepackage{array}
\else
\usepackage{array}[=2016-10-06]
\fi
%%
% Packages required by doxygen
\usepackage{fixltx2e} % for \textsubscript
\usepackage{doxygen}
\usepackage{graphicx}
\usepackage[utf8]{inputenc}
\usepackage{makeidx}
\PassOptionsToPackage{warn}{textcomp}
\usepackage{textcomp}
\usepackage[nointegrals]{wasysym}
\usepackage{ifxetex}
% NLS support packages
% Define default fonts
% Font selection
\usepackage[T1]{fontenc}
% set main and monospaced font
\usepackage[scaled=.90]{helvet}
\usepackage{courier}
\renewcommand{\familydefault}{\sfdefault}
\usepackage{sectsty}
\allsectionsfont{%
\fontseries{bc}\selectfont%
\color{darkgray}%
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\newcommand{\+}{\discretionary{\mbox{\scriptsize$\hookleftarrow$}}{}{}}
% Arguments of doxygenemoji:
% 1) ':<text>:' form of the emoji, already LaTeX-escaped
% 2) file with the name of the emoji without the .png extension
% in case image exist use this otherwise use the ':<text>:' form
\newcommand{\doxygenemoji}[2]{%
\IfFileExists{./#2.png}{\raisebox{-0.1em}{\includegraphics[height=0.9em]{./#2.png}}}{#1}%
}
% Page & text layout
\usepackage{geometry}
\geometry{%
a4paper,%
top=2.5cm,%
bottom=2.5cm,%
left=2.5cm,%
right=2.5cm%
}
% Allow a bit of overflow to go unnoticed by other means
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\setlength{\emergencystretch}{15pt}
\setlength{\parindent}{0cm}
\newcommand{\doxynormalparskip}{\setlength{\parskip}{3ex plus 2ex minus 2ex}}
\newcommand{\doxytocparskip}{\setlength{\parskip}{1ex plus 0ex minus 0ex}}
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% Redefine paragraph/subparagraph environments, using sectsty fonts
\makeatletter
\renewcommand{\paragraph}{%
\@startsection{paragraph}{4}{0ex}{-1.0ex}{1.0ex}{%
\normalfont\normalsize\bfseries\SS@parafont%
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}%
}
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% Headers & footers
\usepackage{fancyhdr}
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\renewcommand{\footrulewidth}{0.4pt}
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\fancyhead[LE, RO]{\bfseries\thepage}
\fancyhead[LO]{\bfseries\rightmark}
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\fancyfoot[LO, RE]{\bfseries\scriptsize Generated by Doxygen }
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}
\pagestyle{fancyplain}
\renewcommand{\chaptermark}[1]{%
\markboth{#1}{}%
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\renewcommand{\sectionmark}[1]{%
\markright{\thesection\ #1}%
}
% ToC, LoF, LoT, bibliography, and index
% Indices & bibliography
\usepackage{natbib}
\usepackage[titles]{tocloft}
\setcounter{tocdepth}{3}
\setcounter{secnumdepth}{5}
% creating indexes
\makeindex
\usepackage{newunicodechar}
\newunicodechar{⁻}{${}^{-}$}% Superscript minus
\newunicodechar{²}{${}^{2}$}% Superscript two
\newunicodechar{³}{${}^{3}$}% Superscript three
% Hyperlinks
% Hyperlinks (required, but should be loaded last)
\ifpdf
\usepackage[pdftex,pagebackref=true]{hyperref}
\else
\ifxetex
\usepackage[pagebackref=true]{hyperref}
\else
\usepackage[ps2pdf,pagebackref=true]{hyperref}
\fi
\fi
\hypersetup{%
colorlinks=true,%
linkcolor=blue,%
citecolor=blue,%
unicode,%
pdftitle={Simulation},%
pdfsubject={}%
}
% Custom commands used by the header
% Custom commands
\newcommand{\clearemptydoublepage}{%
\newpage{\pagestyle{empty}\cleardoublepage}%
}
% caption style definition
\usepackage{caption}
\captionsetup{labelsep=space,justification=centering,font={bf},singlelinecheck=off,skip=4pt,position=top}
% in page table of contents
\usepackage{etoc}
\etocsettocstyle{\doxytocparskip}{\doxynormalparskip}
% prevent numbers overlap the titles in toc
\renewcommand{\numberline}[1]{#1~}
% End of preamble, now comes the document contents
%===== C O N T E N T S =====
\begin{document}
\raggedbottom
% Titlepage & ToC
% To avoid duplicate page anchors due to reuse of same numbers for
% the index (be it as roman numbers)
\hypersetup{pageanchor=false,
bookmarksnumbered=true,
pdfencoding=unicode
}
\pagenumbering{alph}
\begin{titlepage}
\vspace*{7cm}
\begin{center}%
{\Large Simulation}\\
\vspace*{1cm}
{\large Generated by Doxygen 1.9.4}\\
\end{center}
\end{titlepage}
\clearemptydoublepage
\pagenumbering{roman}
\tableofcontents
\clearemptydoublepage
\pagenumbering{arabic}
% re-enable anchors again
\hypersetup{pageanchor=true}
%--- Begin generated contents ---
\chapter{Hierarchical Index}
\input{hierarchy}
\chapter{Class Index}
\input{annotated}
\chapter{File Index}
\input{files}
\chapter{Class Documentation}
\input{classsimulation_1_1aggregation__condition}
\input{classsimulation_1_1boundary__conditions}
\input{classsimulation_1_1brownian__movement}
\input{classsimulation_1_1brownian__movement__offlattice}
\input{classsimulation_1_1check__aggregation}
\input{classsimulation_1_1check__aggregation__offlattice}
\input{classsimulation_1_1check__aggregation__onlattice}
\input{classsimulation_1_1cluster}
\input{classsimulation_1_1constituent}
\input{classsimulation_1_1dlma__iterator}
\input{classsimulation_1_1dlma__save__config}
\input{classsimulation_1_1dlma__system}
\input{classsimulation_1_1dlma__system__offlattice}
\input{classsimulation_1_1dlma__system__onlattice}
\input{classsimulation_1_1iterator__factory}
\input{classsimulation_1_1mass__aggregation__condition}
\input{classsimulation_1_1normal__bind}
\input{classsimulation_1_1off__lattice}
\input{classsimulation_1_1on__lattice}
\input{classsimulation_1_1particle}
\input{classsimulation_1_1particle__lj}
\input{classsimulation_1_1particle__movement}
\input{classsimulation_1_1periodic__bc}
\input{classsimulation_1_1save__config}
\input{classsimulation_1_1simulation__box}
\input{classsimulation_1_1system}
\input{classsimulation_1_1system__factory}
\input{classsimulation_1_1system__iterator}
\chapter{File Documentation}
\input{aggregation__condition_8hh_source}
\input{boundary__conditions_8hh_source}
\input{brownian__movement_8hh_source}
\input{brownian__movement__offlattice_8hh_source}
\input{check__aggregation_8hh_source}
\input{check__aggregation__offlattice_8hh_source}
\input{check__aggregation__onlattice_8hh_source}
\input{cluster_8hh_source}
\input{constituent_8hh_source}
\input{dlma__iterator_8hh_source}
\input{dlma__save__config_8hh_source}
\input{dlma__system_8hh_source}
\input{dlma__system__offlattice_8hh_source}
\input{dlma__system__onlattice_8hh_source}
\input{iterator__factory_8hh_source}
\input{mass__aggregation__condition_8hh_source}
\input{normal__bind_8hh_source}
\input{off__lattice_8hh_source}
\input{on__lattice_8hh_source}
\input{particle_8hh_source}
\input{particle__lj_8hh_source}
\input{particle__movement_8hh_source}
\input{periodic__bc_8hh_source}
\input{save__config_8hh_source}
\input{simulation__box_8hh_source}
\input{split__string_8hh_source}
\input{system_8hh_source}
\input{system__factory_8hh_source}
\input{system__iterator_8hh_source}
%--- End generated contents ---
% Index
\backmatter
\newpage
\phantomsection
\clearemptydoublepage
\addcontentsline{toc}{chapter}{\indexname}
\printindex
% Required for some languages (in combination with latexdocumentpre from the header)
\end{document}

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