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\documentclass[a4paper, 11pt]{report}
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\geometry{a4paper}
\usepackage[utf8]{inputenc}
\usepackage{textcomp}
\usepackage{graphicx}
\usepackage{amsmath,amssymb}
\usepackage{algorithm}
\usepackage{algpseudocode}
\usepackage{bm}
\usepackage[pdftex,bookmarks,colorlinks,breaklinks]{hyperref}
\usepackage{memhfixc}
\usepackage{pdfsync}
\usepackage{fancyhdr}
\pagestyle{fancy}
\usepackage{listings}
\usepackage{hyperref}
\usepackage{xcolor}
\usepackage{booktabs}
\usepackage{float}
\usepackage{caption}
\usepackage{subcaption}
\usepackage{svg}
\usepackage{parskip} % spacing between paragraphs (Connor)
%hypersetup{linkcolor=black,citecolor=black,filecolor=black,urlcolor=black} % black links, for printed output
% For pdf_tex figures (connor)
\graphicspath{{./Figures/}}
% Fancy captions (also Connor)
\usepackage{caption}
\captionsetup{margin=0.5cm} % Sets a 1cm margin on both sides
\captionsetup{labelfont=bf}
% -- Custom 'note' command for adding editing comments in text
\newcommand{\note}[1]{\textcolor{red}{\textbf{[NOTE: #1]}}}
% -- Custom 'code' text for referring to program elements
\def\code#1{\texttt{#1}}
% -- Custom 'O' command for big-O notation
\def\O#1{\mathcal{O}(#1)}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\title{HPC Project 2: Langevin Dynamics Simulation}
\author{Reyhaneh Bahranifard, Connor Moore, Addison Olstad, Joe Ruse}
% \date{}
\begin{document}
\maketitle
\tableofcontents
\include{Chapters/introduction}
\include{Chapters/simulation}
% can you simulate enough particles for a long enough time to see all qualitative behaviour of the RMS displacement?
\include{Chapters/optimization}
% what is the order of complexity?
% How efficient is the multi-threading? How does the efficiency depend on the numbers of particles and sectors?
% We keep all threads alive for the whole loop over time steps. How efficient is the parallel processing of writing to disk, fetching PRNs and updating the velocities and positions? You can use VTune to find out.
\include{Chapters/results}
% How does the science look? (LD related results like MSD, energy, etc)
%What do you expect from the RMS displacement given Langevin’s results and our domain and BC?
% if time allows: implement a form of “thermostatting” to smooth over the initial configuration and prevent the rapid loss of particles.
\bibliographystyle{plain}
\bibliography{references}
\appendix
\include{Chapters/algorithms}
\end{document}
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