qmcpack/manual/qmcpack_manual.tex

\documentclass[11pt,usletter]{report}
\usepackage{bibtopic}
\bibliographystyle{ieeetr}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{delarray}
\usepackage{algorithmic}
\usepackage{algorithm}
\usepackage{makeidx}
\usepackage{ifpdf}
\usepackage{fancyhdr}
\usepackage{hyperref} %for urls
%\usepackage{url}
\usepackage{tabularx}
\usepackage{placeins}
% environment for shaded verbatim
\usepackage{verbatim}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{graphicx}
\usepackage{epsfig}

% making listing behave properly
%   with setting below, listings now render correctly
%   copy/paste from pdf is still messed up (is this even possible to fix?)
%     -indentation whitespace is not preserved (needed for Python)
%     -copy/paste can result in mangled text
%     -mangling depends on pdf viewer (it is different for acroread and evince)
%     -verbatim suffers from this also
\usepackage{upquote}  % render ' properly
\usepackage{listings}

\lstloadlanguages{C++,XML,Python}


\lstset{language=xml, 
  basicstyle=\footnotesize\ttfamily,  % copy/paste from pdf w/o mangled quotes
  keywordstyle=\color{black}\bfseries, 
  frame=single,
  breaklines=true,
  escapeinside={<:}{:>},
  columns=fullflexible,   % copy/paste from pdf w/o added spaces
  keepspaces=true,        % but do keep the spaces that are already there
  showstringspaces=false, % avoid showing underbrackets in quoted text
}

\lstset{language=C++,
  basicstyle=\ttfamily \scriptsize,
  keywordstyle=\color{blue}\ttfamily,
  stringstyle=\color{red}\ttfamily,
  commentstyle=\color{gray}\ttfamily,
  morecomment=[l][\color{magenta}]{\#},
  frame=single
}



\ifpdf
\usepackage{framed}
\usepackage{xcolor}
\pagecolor{white}
\definecolor{shadecolor}{rgb}{.9, .9, .9}

\newenvironment{shade}%
   {\snugshade\verbatim}%
   {\endverbatim\endsnugshade}


\else

\usepackage{xcolor}
\definecolor{verbgray}{gray}{0.9}

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%\newenvironment{shade}
%    {\HCode{<div class='code'>}\verbatim}
%    {\endverbatim\HCode{</div>}}

\fi


% set margins for whole document, lots of wasted space at top and bottom originally
\usepackage[left=1.0in,right=1.0in,top=1.0in,bottom=1.0in]{geometry}




\newcommand{\HRule}{\rule{\linewidth}{0.5mm}}
\newcommand{\courier}[1]{{\fontfamily{pcr}\selectfont #1}}

% for markup, as needed
\newcommand{\red}[1]{{\color{red} #1}}
\newcommand{\blue}[1]{{\color{blue} #1}}

% hide or show text relevant to developers
\newcommand{\dev}[1]{#1}
%\newcommand{\dev}[1]{}

% efficiently comment out/hide blocks of text for any purpose
\newcommand{\hide}[1]{}


% control display of instructions in the labs
%   normally one only wants to show the 'workstation' way of running the labs
\newif\ifws
%\wstrue
%   for the pdf used during the labs, one wants to show the host supercomputer way
\wsfalse
%  command for switching inline text (do not wrap verbatim environments with this!)
\ifws
\newcommand{\labsw}[2]{#1}
\else
\newcommand{\labsw}[2]{#2}
\fi


\oddsidemargin 0cm
\evensidemargin 0cm
\textwidth 6.5in


% proper rendering of qmcpack
\newcommand{\qmcpack}{{QMCPACK} } % apparently the trailing whitespace is significant

% mathematics convenience commands
\newcommand{\abs}[1]{\lvert #1 \rvert}
\newcommand{\norm}[1]{\lVert #1 \rVert}
\newcommand{\pnorm}[2]{\lVert #1 \rVert_{#2}}
\newcommand{\mean}[1]{\langle #1 \rangle}
\newcommand{\ket}[1]{\lvert #1 \rangle}
\newcommand{\bra}[1]{\langle #1 \rvert}
\newcommand{\expval}[3]{\bra{#1}#2\ket{#3}}
\newcommand{\expvalh}[3]{\bra{#1}\hat{#2}\ket{#3}}
\newcommand{\overlap}[2]{\langle #1 \lvert #2 \rangle}
\newcommand{\operator}[3]{\ket{#1} #2 \bra{#3}}
\newcommand{\idop}{\hat{\mathbb{1}}}


\begin{document}

\input{title.tex}
\newpage
\tableofcontents
\newpage

\begin{btUnit}
\begin{btSect}{bibliography}

\input{introduction}
\input{features}
\input{installation}
\input{running}

\input{units}

\input{input_overview}

\chapter{Specifying the system to be simulated}
\input{simulationcell}
\input{particleset}

\chapter{Trial wavefunction specification}
\input{intro_wavefunction}
\input{spo}
\input{jastrow}
\input{multideterminants}
\input{backflow}
\input{fdlr}
\input{ionwf}

\input{hamiltonianobservable}

\input{methods}
\input{vmc}
\input{opt}
\input{dmc}
\input{reptation}

\input{output_overview}
\input{analysis}

\input{afqmc}
\input{integrals_for_afqmc}

\input{examples}

% labs: import each as a separate chapter for now
\input{lab_qmc_statistics}
\input{lab_qmc_basics}
\input{lab_advanced_molecules}
\input{lab_condensed_matter}


\input{additional_tools}
\input{contributing}
\input{unit_testing}

\input{design_features}
\input{developing}

\chapter{References}
%\begingroup  % Avoid "References" section title
%\renewcommand{\section}[2]{}%
%\bibliographystyle{ieeetr}
%\bibliography{bibliography}
%\endgroup

\btPrintCited
\end{btSect}
\end{btUnit}

\appendix
\input{appendices}
\begin{btUnit}
\input{qmcpack_papers}
\end{btUnit}
\end{document}