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freeenergy.tex
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% !TeX encoding = UTF-8
% !TeX spellcheck = en_US
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% LaTeX book template %%
%% Author: Amber Jain (http://amberj.devio.us/) %%
%% License: ISC license %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\documentclass[a4paper,11pt]{book}
\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
\usepackage{lmodern}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{mathrsfs}
\usepackage{mathtools}
\usepackage{textcomp}
%\usepackage[page,toc,titletoc,title]{appendix}
%\usepackage[titletoc]{appendix}
\usepackage[toc,header]{appendix}
%\usepackage{tocloft}
\usepackage[nottoc,notlot,notlof]{tocbibind}
\usepackage{graphicx}
\usepackage{chngcntr}
\usepackage{tikz}
\usepackage{pgfplots}
\usepackage[version=4]{mhchem}
\usepackage{chemfig}
\usepackage{xcolor}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Source: http://en.wikibooks.org/wiki/LaTeX/Hyperlinks %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{graphicx}
\usepackage[english]{babel}
\usepackage[pdfencoding=auto]{hyperref}
\usepackage{accsupp}
\counterwithin{equation}{subsection}
\newcommand*\diff{\mathop{}\!\mathrm{d}}
\newcommand*\Diff[1]{\mathop{}\!\mathrm{d^#1}}
\DeclareMathOperator{\Tr}{Tr}
\DeclareMathOperator{\erfc}{erfc}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 'dedication' environment: To add a dedication paragraph at the start of book %
% Source: http://www.tug.org/pipermail/texhax/2010-June/015184.html %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\newenvironment{dedication}
{
\cleardoublepage
\thispagestyle{empty}
\vspace*{\stretch{1}}
\hfill\begin{minipage}[t]{0.66\textwidth}
\raggedright
}
{
\end{minipage}
\vspace*{\stretch{3}}
\clearpage
}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Chapter quote at the start of chapter %
% Source: http://tex.stackexchange.com/a/53380 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\makeatletter
\renewcommand{\@chapapp}{}% Not necessary...
\newenvironment{chapquote}[2][2em]
{\setlength{\@tempdima}{#1}%
\def\chapquote@author{#2}%
\parshape 1 \@tempdima \dimexpr\textwidth-2\@tempdima\relax%
\itshape}
{\par\normalfont\hfill--\ \chapquote@author\hspace*{\@tempdima}\par\bigskip}
\makeatother
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% First page of book which contains 'stuff' like: %
% - Book title, subtitle %
% - Book author name %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Book's title and subtitle
\title{\Huge \textbf{Enhanced Sampling\\ \& \\Free Energy Calculations} \\ \huge Methods Based on Equilibrium and Non-equilibrium Simulations}
% Author
\author{\textsc{Ye Mei}\thanks{samuel.y.mei{\fontfamily{ptm}\selectfont @}gmail.com} \\
\textsc{Pengfei Li}\thanks{lipengfei\underline{\hspace{0.5em}}mail{\fontfamily{ptm}\selectfont @}126.com}\\
\textsc{Haohao Fu}\thanks{fhh2626{\fontfamily{ptm}\selectfont @}mail.nankai.edu.cn}}
\begin{document}
\frontmatter
\maketitle
\begin{dedication}
For internal$\cap$noncommercial use only.
\end{dedication}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Add a dedication paragraph to dedicate your book to someone %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{dedication}
Dedicated to \\
Dr. Bernard Brooks and Dr. Gerhard K\"onig.\\
\end{dedication}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Auto-generated table of contents, list of figures and list of tables %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\tableofcontents
\listoffigures
\listoftables
\mainmatter
\input {chapters/preface.tex}
\input {chapters/introduction.tex}
\input {chapters/enhancesampling.tex}
\input {chapters/postprocessing.tex}
\input {chapters/evaluation.tex}
\input {chapters/appendix.tex}
%\bibliographystyle{apalike} % Bibliography: Author-Date system
\bibliographystyle{unsrt} % Bibliography: Author-Date system
\bibliography{bib/freeenergy} % pls. call your database here
\end{document}
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