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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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\section{\label{sec:intro}Introduction} |
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|
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\begin{itemize} |
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\section{\label{oopseSec:foreword}Foreword} |
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|
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\item Need for package / Niche to fill |
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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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|
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\item Design Goal |
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{\sc give final breakdown of who wrote which section here.} |
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|
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\item Open Source |
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> |
\section{\label{sec:intro}Introduction} |
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|
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< |
\item Discussion of Paper Layout |
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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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|
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< |
\end{itemize} |
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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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|
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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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|
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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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|
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\section{\label{oopseSec:empiricalEnergy}The Empirical Energy Functions} |
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+ |
|
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\subsection{\label{oopseSec:atomsMolecules}Atoms, Molecules and Rigid Bodies} |
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|
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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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|
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|
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|
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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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|
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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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|
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\end{lstlisting} |
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|
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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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|
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The total potential energy function in {\sc duff} is |
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\begin{equation} |
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\end{lstlisting} |
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|
| 570 |
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|
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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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|
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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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|
| 609 |
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|
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< |
\subsection{\label{Sec:pbc}Periodic Boundary Conditions} |
| 610 |
> |
\subsection{\label{oopseSec:pbc}Periodic Boundary Conditions} |
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|
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\newcommand{\roundme}{\operatorname{round}} |
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|
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\end{equation} |
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|
| 669 |
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|
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< |
\section{Input and Output Files} |
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> |
\section{\label{oopseSec:IOfiles}Input and Output Files} |
| 671 |
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|
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|
\subsection{{\sc bass} and Model Files} |
| 673 |
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|
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molecular prototype once, then simply include it into each simulation |
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containing that molecule. |
| 702 |
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|
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< |
\subsection{\label{subSec:coordFiles}Coordinate Files} |
| 703 |
> |
\subsection{\label{oopseSec:coordFiles}Coordinate Files} |
| 704 |
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|
| 705 |
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The standard format for storage of a systems coordinates is a modified |
| 706 |
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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. |
| 754 |
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|
| 755 |
< |
\section{\label{sec:mechanics}Mechanics} |
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> |
\section{\label{oopseSec:mechanics}Mechanics} |
| 756 |
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|
| 757 |
|
\subsection{\label{integrate}Integrating the Equations of Motion: the Symplectic Step Integrator} |
| 758 |
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|
| 873 |
|
\begin{equation} |
| 874 |
|
\xi(z,t)=\langle\delta F(z,t)\delta F(z,0)\rangle/k_{B}T |
| 875 |
|
\end{equation} |
| 827 |
– |
|
| 828 |
– |
|
| 876 |
|
where% |
| 877 |
|
\begin{equation} |
| 878 |
|
\delta F(z,t)=F(z,t)-\langle F(z,t)\rangle |
| 927 |
|
Worthy of mention, other kinds of potential functions can also be used to |
| 928 |
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drive the z-constraint molecule. |
| 929 |
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|
| 930 |
< |
\section{\label{sec:analysis}Trajectory Analysis} |
| 930 |
> |
\section{\label{oopseSec:props}Trajectory Analysis} |
| 931 |
|
|
| 932 |
< |
\subsection{\label{subSec:staticProps}Static Property Analysis} |
| 932 |
> |
\subsection{\label{oopseSec:staticProps}Static Property Analysis} |
| 933 |
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|
| 934 |
|
The static properties of the trajectories are analyzed with the |
| 935 |
|
program \texttt{staticProps}. The code is capable of calculating the following |
| 1068 |
|
\label{fig:dynamicPropsMemory} |
| 1069 |
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\end{figure} |
| 1070 |
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|
| 1071 |
< |
\section{\label{sec:ProgramDesign}Program Design} |
| 1071 |
> |
\section{\label{oopseSec:design}Program Design} |
| 1072 |
|
|
| 1073 |
|
\subsection{\label{sec:architecture} OOPSE Architecture} |
| 1074 |
|
|
| 1077 |
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developed around the parseing engine and {\texttt libmdtools} is the |
| 1078 |
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software library developed around the simulation engine. |
| 1079 |
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|
| 1033 |
– |
|
| 1034 |
– |
|
| 1035 |
– |
\subsection{\label{sec:programLang} Programming Languages } |
| 1036 |
– |
|
| 1080 |
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\subsection{\label{sec:parallelization} Parallelization of OOPSE} |
| 1081 |
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|
| 1082 |
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Although processor power is doubling roughly every 18 months according |
| 1123 |
|
favorably then spatial decomposition up to 10,000 atoms and favorably |
| 1124 |
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competes with spatial methods for up to 100,000 atoms. |
| 1125 |
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|
| 1083 |
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\subsection{\label{sec:memory}Memory Allocation in Analysis} |
| 1084 |
– |
|
| 1085 |
– |
\subsection{\label{sec:documentation}Documentation} |
| 1086 |
– |
|
| 1126 |
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\subsection{\label{openSource}Open Source and Distribution License} |
| 1127 |
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|
| 1128 |
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|
| 1129 |
< |
\section{\label{sec:conclusion}Conclusion} |
| 1129 |
> |
\section{\label{oopseSec:conclusion}Conclusion} |
| 1130 |
|
|
| 1131 |
|
\begin{itemize} |
| 1132 |
|
|
