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\documentclass[11pt]{article} |
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\renewcommand\citemid{\ } % no comma in optional reference note |
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\chapter{\label{chapt:oopse}OOPSE: AN OPEN SOURCE OBJECT-ORIENTED PARALLEL SIMULATION ENGINE FOR MOLECULAR DYNAMICS} |
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\begin{document} |
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\lstset{language=C,float,frame=tblr,frameround=tttt} |
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\renewcommand{\lstlistingname}{Scheme} |
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\title{{\sc oopse}: An Open Source Object-Oriented Parallel Simulation |
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Engine for Molecular Dynamics} |
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\author{Matthew A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher J. Fennell and J. Daniel Gezelter\\ |
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Department of Chemistry and Biochemistry\\ |
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University of Notre Dame\\ |
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Notre Dame, Indiana 46556} |
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\date{\today} |
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\maketitle |
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%% \begin{abstract} |
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%% We detail the capabilities of a new open-source parallel simulation |
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%% package ({\sc oopse}) that can perform molecular dynamics simulations |
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%% on atom types that are missing from other popular packages. In |
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%% particular, {\sc oopse} is capable of performing orientational |
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%% dynamics on dipolar systems, and it can handle simulations of metallic |
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%% systems using the embedded atom method ({\sc eam}). |
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%% \end{abstract} |
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\begin{abstract} |
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We detail the capabilities of a new open-source parallel simulation |
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package ({\sc oopse}) that can perform molecular dynamics simulations |
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on atom types that are missing from other popular packages. In |
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particular, {\sc oopse} is capable of performing orientational |
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dynamics on dipolar systems, and it can handle simulations of metallic |
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systems using the embedded atom method ({\sc eam}). |
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\end{abstract} |
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\lstset{language=C,frame=TB,basicstyle=\small,basicstyle=\ttfamily, % |
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xleftmargin=0.5in, xrightmargin=0.5in,captionpos=b, % |
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abovecaptionskip=0.5cm, belowcaptionskip=0.5cm} |
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\newpage |
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\section{\label{oopseSec:foreword}Foreword} |
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\section{\label{sec:intro}Introduction} |
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In this chapter, I present and detail the capabilities of the open |
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source simulation package {\sc oopse}. It is important to note, that a |
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simulation package of this size and scope would not have been possible |
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without the collaborative efforts of my colleagues: Charles |
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F.~Vardeman II, Teng Lin, Christopher J.~Fennell and J.~Daniel |
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Gezelter. Although my contributions to [\sc oopse} are signifigant, |
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consideration of my work apart from the others, would not give a |
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complete description to the package's capabilities. As such, all |
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contributions to {\sc oopse} to date are presented in this chapter. |
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\begin{itemize} |
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{\sc give final breakdown of who wrote which section here.} |
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\item Need for package / Niche to fill |
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\section{\label{sec:intro}Introduction} |
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\item Design Goal |
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When choosing to simulate a chemical system with molecular dynamics, |
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there are a variety of options available. For simple systems, one |
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might consider writing one's own programming code. However, as systems |
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grow larger and more complex, building and maintaining code for the |
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simulations becomes a time consuming task. In such cases it is usually |
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more convienent for a researcher to turn to pre-existing simulation |
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packages. These packages, such as {\sc amber}\cite{pearlman:1995} and |
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{\sc charmm}\cite{Brooks83}, provide powerful tools for researchers to |
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conduct simulations of their systems without spending their time |
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developing a code base to conduct their research. This then frees them |
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to perhaps explore experimental analouges to their models. |
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\item Open Source |
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Despite their utility, problems with these packages arise when |
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researchers try to develop techniques or energetic models that the |
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code was not originally designed to do. Examples of uncommonly |
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implemented techniques and energetics include; dipole-dipole |
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interactions, rigid body dynamics, and metallic emmbedded |
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potentials. When faced with these obstacles, a researcher must either |
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develop their own code or license and extend one of the commercial |
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packages. What we have elected to do, is develop a package of |
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simulation code capable of implementing the types of models upon which |
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our research is based. |
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\item Discussion of Paper Layout |
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\end{itemize} |
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\section{\label{sec:empiricalEnergy}The Empirical Energy Functions} |
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Having written {\sc oopse} we are implementing the concept of Open |
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Source dcevelopment, and releaseing our source code into the public |
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domain. It is our intent that by doing so, other researchers might |
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benefit from our work, and add their own contributions to the |
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package. The license under which {\sc oopse} is distributed allows any |
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researcher to download and modify the source code for their own |
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use. In this way further development of {\sc oopse} is not limited to |
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only the models of interest to ourselves, but also those of the |
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community of scientists who contribute back to the project. |
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\subsection{\label{sec:atomsMolecules}Atoms, Molecules and Rigid Bodies} |
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We have structured this chapter to first discuss the emperical energy |
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functions that {\sc oopse } implements in |
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Sec.~\ref{oopseSec:empericalEnergy}. Following that is a discusion of |
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the various input and output files associated with the package |
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(Sec.~\ref{oopseSec:IOfiles}). In Sec.~\ref{oopseSec:Mechanics} |
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elucidates the various Molecular Dynamics algorithms {\sc oopse} |
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mplements in the integration of the Newtonian equations of |
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motion. Basic analysis of the trajectories obtained from the |
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simulation is discussed in Sec.~\ref{oopseSec:props}. Program design |
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considerations as well as the software distribution license is |
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presented in Sec.~\ref{oopseSec:design}. And lastly, |
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Sec.~\ref{oopseSec:conclusion} concludes the chapter. |
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\section{\label{oopseSec:empiricalEnergy}The Empirical Energy Functions} |
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\subsection{\label{oopseSec:atomsMolecules}Atoms, Molecules and Rigid Bodies} |
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The basic unit of an {\sc oopse} simulation is the atom. The |
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parameters describing the atom are generalized to make the atom as |
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flexible a representation as possible. They may represent specific |
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directional components associated with them (\emph{e.g.}~permanent |
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dipoles). Charges on atoms are not currently supported by {\sc oopse}. |
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\begin{lstlisting}[caption={[Specifier for molecules and atoms] A sample specification of the simple Ar molecule},label=sch:AtmMole] |
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\begin{lstlisting}[float,caption={[Specifier for molecules and atoms] A sample specification of the simple Ar molecule},label=sch:AtmMole] |
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molecule{ |
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name = "Ar"; |
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nAtoms = 1; |
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} |
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\end{lstlisting} |
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Atoms can be collected into secondary srtructures such as rigid bodies |
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or molecules. The molecule is a way for {\sc oopse} to keep track of |
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the atoms in a simulation in logical manner. Molecular units store the |
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placements of the atoms relative to the origin of the rigid body, |
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which itself has a position relative to the origin of the molecule. |
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\begin{lstlisting}[caption={[Defining rigid bodies]A sample definition of a rigid body},label={sch:rigidBody}] |
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\begin{lstlisting}[float,caption={[Defining rigid bodies]A sample definition of a rigid body},label={sch:rigidBody}] |
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molecule{ |
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name = "TIP3P_water"; |
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nRigidBodies = 1; |
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shows a system of 108 Ar particles simulated with the Lennard-Jones |
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force field. |
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\begin{lstlisting}[caption={[Invocation of the Lennard-Jones force field] A sample system using the Lennard-Jones force field.},label={sch:LJFF}] |
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\begin{lstlisting}[float,caption={[Invocation of the Lennard-Jones force field] A sample system using the Lennard-Jones force field.},label={sch:LJFF}] |
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/* |
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* The Ar molecule is specified |
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\subsection{\label{sec:DUFF}Dipolar Unified-Atom Force Field} |
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\subsection{\label{oopseSec:DUFF}Dipolar Unified-Atom Force Field} |
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The dipolar unified-atom force field ({\sc duff}) was developed to |
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simulate lipid bilayers. The simulations require a model capable of |
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\emph{et al.}\cite{liu96:new_model} |
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\begin{figure} |
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\epsfxsize=\linewidth |
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\epsfbox{lipidModel.eps} |
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\centering |
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\includegraphics[width=\linewidth]{lipidModel.eps} |
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\caption{A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ % |
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is the bend angle, $\mu$ is the dipole moment of the head group, and n |
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is the chain length.} |
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\label{fig:lipidModel} |
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\label{oopseFig:lipidModel} |
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\end{figure} |
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We have used a set of scalable parameters to model the alkyl groups |
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used when integrating the equations of motion. A simulation using {\sc |
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duff} is illustrated in Scheme \ref{sch:DUFF}. |
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\begin{lstlisting}[caption={[Invocation of {\sc duff}]Sample \texttt{.bass} file showing a simulation utilizing {\sc duff}},label={sch:DUFF}] |
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\begin{lstlisting}[float,caption={[Invocation of {\sc duff}]Sample \texttt{.bass} file showing a simulation utilizing {\sc duff}},label={sch:DUFF}] |
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#include "water.mdl" |
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#include "lipid.mdl" |
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\end{lstlisting} |
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\subsubsection{\label{subSec:energyFunctions}{\sc duff} Energy Functions} |
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\subsection{\label{oopseSec:energyFunctions}{\sc duff} Energy Functions} |
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The total potential energy function in {\sc duff} is |
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\begin{equation} |
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density corrected SSD models can be found in reference |
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\ref{Gezelter04}. |
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\begin{lstlisting}[caption={[A simulation of {\sc ssd} water]An example file showing a simulation including {\sc ssd} water.},label={sch:ssd}] |
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\begin{lstlisting}[float,caption={[A simulation of {\sc ssd} water]An example file showing a simulation including {\sc ssd} water.},label={sch:ssd}] |
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#include "water.mdl" |
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\end{lstlisting} |
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\subsection{\label{sec:eam}Embedded Atom Method} |
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\subsection{\label{oopseSec:eam}Embedded Atom Method} |
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Several other molecular dynamics packages\cite{dynamo86} exist which have the |
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capacity to simulate metallic systems, including some that have |
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interactions. Foiles et al. fit EAM potentials for fcc metals Cu, Ag, Au, Ni, Pd, Pt and alloys of these metals\cite{FDB86}. These potential fits are in the DYNAMO 86 format and are included with {\sc oopse}. |
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\subsection{\label{Sec:pbc}Periodic Boundary Conditions} |
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\subsection{\label{oopseSec:pbc}Periodic Boundary Conditions} |
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\newcommand{\roundme}{\operatorname{round}} |
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\begin{equation} |
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\roundme(x)=\left\{ |
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\begin{array}{cc}% |
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\lfloor{x+0.5}\rfloor & \text{if \ }x\geqslant0\\ |
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\lfloor{x+0.5}\rfloor & \text{if \ }x\geqslant 0 \\ |
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\lceil{x-0.5}\rceil & \text{otherwise}% |
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\end{array} |
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\right. |
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\end{equation} |
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\section{Input and Output Files} |
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\section{\label{oopseSec:IOfiles}Input and Output Files} |
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\subsection{{\sc bass} and Model Files} |
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Fig.~\ref{fig:bassExample}. |
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\begin{figure} |
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\centering |
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\framebox[\linewidth]{\rule{0cm}{0.75\linewidth}I'm a {\sc bass} file!} |
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\caption{Here is an example \texttt{.bass} file} |
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molecular prototype once, then simply include it into each simulation |
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containing that molecule. |
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\subsection{\label{subSec:coordFiles}Coordinate Files} |
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\subsection{\label{oopseSec:coordFiles}Coordinate Files} |
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The standard format for storage of a systems coordinates is a modified |
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xyz-file syntax, the exact details of which can be seen in |
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the integrator. The statistics file is denoted with the \texttt{.stat} |
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file extension. |
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\section{\label{sec:mechanics}Mechanics} |
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\section{\label{oopseSec:mechanics}Mechanics} |
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\subsection{\label{integrate}Integrating the Equations of Motion: the Symplectic Step Integrator} |
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\ref{timestep}. |
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\begin{figure} |
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\epsfxsize=6in |
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\epsfbox{timeStep.epsi} |
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\centering |
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\includegraphics[width=\linewidth]{timeStep.eps} |
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\caption{Energy conservation using quaternion based integration versus |
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the symplectic step method proposed by Dullweber \emph{et al.} with |
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increasing time step. For each time step, the dotted line is total |
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\begin{equation} |
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\xi(z,t)=\langle\delta F(z,t)\delta F(z,0)\rangle/k_{B}T |
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\end{equation} |
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where% |
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\begin{equation} |
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\delta F(z,t)=F(z,t)-\langle F(z,t)\rangle |
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Worthy of mention, other kinds of potential functions can also be used to |
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drive the z-constraint molecule. |
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\section{\label{sec:analysis}Trajectory Analysis} |
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\section{\label{oopseSec:props}Trajectory Analysis} |
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\subsection{\label{subSec:staticProps}Static Property Analysis} |
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\subsection{\label{oopseSec:staticProps}Static Property Analysis} |
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The static properties of the trajectories are analyzed with the |
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program \texttt{staticProps}. The code is capable of calculating the following |
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multiple reads on the same file. |
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|
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\begin{figure} |
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\epsfxsize=6in |
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\epsfbox{dynamicPropsMem.eps} |
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\centering |
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\includegraphics[width=\linewidth]{dynamicPropsMem.eps} |
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\caption{This diagram illustrates the dynamic memory allocation used by \texttt{dynamicProps}, which follows the scheme: $\sum^{N_{\text{memory blocks}}}_{i=1}[ \operatorname{self}(i) + \sum^{N_{\text{memory blocks}}}_{j>i} \operatorname{cross}(i,j)]$. The shaded region represents the self correlation of the memory block, and the open blocks are read one at a time and the cross correlations between blocks are calculated.} |
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\label{fig:dynamicPropsMemory} |
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\end{figure} |
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\section{\label{sec:ProgramDesign}Program Design} |
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\section{\label{oopseSec:design}Program Design} |
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|
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\subsection{\label{sec:architecture} OOPSE Architecture} |
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|
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developed around the parseing engine and {\texttt libmdtools} is the |
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software library developed around the simulation engine. |
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\subsection{\label{sec:programLang} Programming Languages } |
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\subsection{\label{sec:parallelization} Parallelization of OOPSE} |
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Although processor power is doubling roughly every 18 months according |
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favorably then spatial decomposition up to 10,000 atoms and favorably |
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competes with spatial methods for up to 100,000 atoms. |
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|
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\subsection{\label{sec:memory}Memory Allocation in Analysis} |
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|
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\subsection{\label{sec:documentation}Documentation} |
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|
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\subsection{\label{openSource}Open Source and Distribution License} |
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\section{\label{sec:conclusion}Conclusion} |
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\section{\label{oopseSec:conclusion}Conclusion} |
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|
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\begin{itemize} |
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|
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\item How well does it meet the primary goal |
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|
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\end{itemize} |
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\section{Acknowledgments} |
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The authors would like to thank espresso for fueling this work, and |
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would also like to send a special acknowledgement to single malt |
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scotch for its wonderful calming effects and its ability to make the |
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troubles of the world float away. |
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\bibliographystyle{achemso} |
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|
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\bibliography{oopse} |
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|
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\end{document} |
