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Revision 1044 by mmeineke, Mon Feb 9 21:44:01 2004 UTC vs.
Revision 1045 by mmeineke, Tue Feb 10 20:52:03 2004 UTC

# Line 1 | Line 1
1 < \documentclass[11pt]{article}
2 < \usepackage{amsmath}
3 < \usepackage{amssymb}
4 < \usepackage{endfloat}
5 < \usepackage{berkeley}
6 < \usepackage{listings}
7 < \usepackage{epsf}
8 < \usepackage[ref]{overcite}
9 < \usepackage{setspace}
10 < \usepackage{tabularx}
11 < \pagestyle{plain}
12 < \pagenumbering{arabic}
13 < \oddsidemargin 0.0cm \evensidemargin 0.0cm
14 < \topmargin -21pt \headsep 10pt
15 < \textheight 9.0in \textwidth 6.5in
16 < \brokenpenalty=10000
17 < \renewcommand{\baselinestretch}{1.2}
18 < \renewcommand\citemid{\ } % no comma in optional reference note
1 > \chapter{\label{chapt:oopse}OOPSE: AN OPEN SOURCE OBJECT-ORIENTED PARALLEL SIMULATION ENGINE FOR MOLECULAR DYNAMICS}
2  
20 – \begin{document}
21 – \lstset{language=C,float,frame=tblr,frameround=tttt}
22 – \renewcommand{\lstlistingname}{Scheme}
23 – \title{{\sc oopse}: An Open Source Object-Oriented Parallel Simulation
24 – Engine for Molecular Dynamics}
3  
26 – \author{Matthew A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher J. Fennell and J. Daniel Gezelter\\
27 – Department of Chemistry and Biochemistry\\
28 – University of Notre Dame\\
29 – Notre Dame, Indiana 46556}
4  
5 < \date{\today}
6 < \maketitle
7 <
8 < \begin{abstract}
9 < We detail the capabilities of a new open-source parallel simulation
10 < package ({\sc oopse}) that can perform molecular dynamics simulations
11 < on atom types that are missing from other popular packages.  In
12 < particular, {\sc oopse} is capable of performing orientational
39 < dynamics on dipolar systems, and it can handle simulations of metallic
40 < systems using the embedded atom method ({\sc eam}).
41 < \end{abstract}
42 <
43 < \newpage
5 > %% \begin{abstract}
6 > %% We detail the capabilities of a new open-source parallel simulation
7 > %% package ({\sc oopse}) that can perform molecular dynamics simulations
8 > %% on atom types that are missing from other popular packages.  In
9 > %% particular, {\sc oopse} is capable of performing orientational
10 > %% dynamics on dipolar systems, and it can handle simulations of metallic
11 > %% systems using the embedded atom method ({\sc eam}).
12 > %% \end{abstract}
13  
14 + \lstset{language=C,frame=TB,basicstyle=\small,basicstyle=\ttfamily, %
15 +        xleftmargin=0.5in, xrightmargin=0.5in,captionpos=b, %
16 +        abovecaptionskip=0.5cm, belowcaptionskip=0.5cm}
17   \section{\label{sec:intro}Introduction}
18  
19   \begin{itemize}
# Line 68 | Line 40 | dipoles). Charges on atoms are not currently supported
40   directional components associated with them (\emph{e.g.}~permanent
41   dipoles). Charges on atoms are not currently supported by {\sc oopse}.
42  
43 < \begin{lstlisting}[caption={[Specifier for molecules and atoms] A sample specification of the simple Ar molecule},label=sch:AtmMole]
43 > \begin{lstlisting}[float,caption={[Specifier for molecules and atoms] A sample specification of the simple Ar molecule},label=sch:AtmMole]
44   molecule{
45    name = "Ar";
46    nAtoms = 1;
# Line 79 | Line 51 | Atoms can be collected into secondary srtructures such
51   }
52   \end{lstlisting}
53  
54 +
55   Atoms can be collected into secondary srtructures such as rigid bodies
56   or molecules. The molecule is a way for {\sc oopse} to keep track of
57   the atoms in a simulation in logical manner. Molecular units store the
# Line 142 | Line 115 | which itself has a position relative to the origin of
115   placements of the atoms relative to the origin of the rigid body,
116   which itself has a position relative to the origin of the molecule.
117  
118 < \begin{lstlisting}[caption={[Defining rigid bodies]A sample definition of a rigid body},label={sch:rigidBody}]
118 > \begin{lstlisting}[float,caption={[Defining rigid bodies]A sample definition of a rigid body},label={sch:rigidBody}]
119   molecule{
120    name = "TIP3P_water";
121    nRigidBodies = 1;
# Line 187 | Line 160 | force field.
160   shows a system of 108 Ar particles simulated with the Lennard-Jones
161   force field.
162  
163 < \begin{lstlisting}[caption={[Invocation of the Lennard-Jones force field] A sample system using the Lennard-Jones force field.},label={sch:LJFF}]
163 > \begin{lstlisting}[float,caption={[Invocation of the Lennard-Jones force field] A sample system using the Lennard-Jones force field.},label={sch:LJFF}]
164  
165   /*
166   * The Ar molecule is specified
# Line 268 | Line 241 | reparameterization of the soft sticky dipole (SSD) mod
241   \emph{et al.}\cite{liu96:new_model}
242  
243   \begin{figure}
244 < \epsfxsize=\linewidth
245 < \epsfbox{lipidModel.eps}
244 > \centering
245 > \includegraphics[width=\linewidth]{lipidModel.eps}
246   \caption{A representation of the lipid model. $\phi$ is the torsion angle, $\theta$ %
247   is the bend angle, $\mu$ is the dipole moment of the head group, and n
248   is the chain length.}
249 < \label{fig:lipidModel}
249 > \label{oopseFig:lipidModel}
250   \end{figure}
251  
252   We have used a set of scalable parameters to model the alkyl groups
# Line 296 | Line 269 | duff} is illustrated in Scheme \ref{sch:DUFF}.
269   used when integrating the equations of motion. A simulation using {\sc
270   duff} is illustrated in Scheme \ref{sch:DUFF}.
271  
272 < \begin{lstlisting}[caption={[Invocation of {\sc duff}]Sample \texttt{.bass} file showing a simulation utilizing {\sc duff}},label={sch:DUFF}]
272 > \begin{lstlisting}[float,caption={[Invocation of {\sc duff}]Sample \texttt{.bass} file showing a simulation utilizing {\sc duff}},label={sch:DUFF}]
273  
274   #include "water.mdl"
275   #include "lipid.mdl"
# Line 511 | Line 484 | density corrected SSD models can be found in reference
484   density corrected SSD models can be found in reference
485   \ref{Gezelter04}.
486  
487 < \begin{lstlisting}[caption={[A simulation of {\sc ssd} water]An example file showing a simulation including {\sc ssd} water.},label={sch:ssd}]
487 > \begin{lstlisting}[float,caption={[A simulation of {\sc ssd} water]An example file showing a simulation including {\sc ssd} water.},label={sch:ssd}]
488  
489   #include "water.mdl"
490  
# Line 628 | Line 601 | where
601   \begin{equation}
602   \roundme(x)=\left\{
603   \begin{array}{cc}%
604 < \lfloor{x+0.5}\rfloor & \text{if \ }x\geqslant0\\
604 > \lfloor{x+0.5}\rfloor & \text{if \ }x\geqslant 0 \\
605   \lceil{x-0.5}\rceil & \text{otherwise}%
606   \end{array}
607   \right.
# Line 659 | Line 632 | Fig.~\ref{fig:bassExample}.
632   Fig.~\ref{fig:bassExample}.
633  
634   \begin{figure}
662 –
635   \centering
636   \framebox[\linewidth]{\rule{0cm}{0.75\linewidth}I'm a {\sc bass} file!}
637   \caption{Here is an example \texttt{.bass} file}
# Line 773 | Line 745 | energy conservation of the two methods as illustrated
745   \ref{timestep}.
746  
747   \begin{figure}
748 < \epsfxsize=6in
749 < \epsfbox{timeStep.epsi}
748 > \centering
749 > \includegraphics[width=\linewidth]{timeStep.eps}
750   \caption{Energy conservation using quaternion based integration versus
751   the symplectic step method proposed by Dullweber \emph{et al.} with
752   increasing time step. For each time step, the dotted line is total
# Line 1043 | Line 1015 | multiple reads on the same file.  
1015   multiple reads on the same file.  
1016  
1017   \begin{figure}
1018 < \epsfxsize=6in
1019 < \epsfbox{dynamicPropsMem.eps}
1018 > \centering
1019 > \includegraphics[width=\linewidth]{dynamicPropsMem.eps}
1020   \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.}
1021   \label{fig:dynamicPropsMemory}
1022   \end{figure}
# Line 1134 | Line 1106 | competes with spatial methods for up to 100,000 atoms.
1106   \item How well does it meet the primary goal
1107  
1108   \end{itemize}
1137 – \section{Acknowledgments}
1138 – The authors would like to thank espresso for fueling this work, and
1139 – would also like to send a special acknowledgement to single malt
1140 – scotch for its wonderful calming effects and its ability to make the
1141 – troubles of the world float away.
1142 – \bibliographystyle{achemso}
1143 –
1144 – \bibliography{oopse}
1145 –
1146 – \end{document}

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