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\usepackage{amssymb} |
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\usepackage{endfloat} |
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\usepackage{listings} |
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\usepackage{palatino} |
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\usepackage{berkeley} |
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\usepackage{graphicx} |
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\usepackage[ref]{overcite} |
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\usepackage{setspace} |
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\maketitle |
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\begin{abstract} |
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Need an abstract. |
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{\sc oopse} is a new molecular dynamics simulation program which is |
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capable of efficiently integrating equations of motion for atom types |
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with orientational degrees of freedom (e.g. ``sticky'' atoms and point |
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dipoles). Transition metals can also be simulated using the embedded |
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atom method ({\sc eam}) potential included in the code. Parallel |
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simulations are carried out using the force-based decomposition |
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method. Simulations are specified using a very simple C-based |
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meta-data language. A number of advanced integrators are included, |
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and the base integrator for orientational dynamics provides |
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substantial improvements over older quaternion-base schemes. All |
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source code is available under a very permissive (BSD-style) Open |
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Source license. |
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\end{abstract} |
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\section{\label{sec:intro}Introduction} |
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|
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UNDERWAY |
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There are a number of excellent molecular dynamics packages available |
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to the chemical physics |
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community.\cite{Brooks83,MacKerell98,pearlman:1995,Gromacs,Gromacs3,DL_POLY,Tinker,Paradyn} |
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All of these packages are stable, polished programs which solve many |
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problems of interest. Most are now capable of performing molecular |
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dynamics simulations on parallel computers. Some have source code |
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which is freely available to the entire scientific community. Few, |
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however, are capable of efficiently integrating the equations of |
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motion for atom types with orientational degrees of freedom |
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(e.g. point dipoles, and ``sticky'' atoms). And only one of the |
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programs referenced can handle transition metal force fields like the |
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Embedded Atom Method ({\sc eam}). The direction our research program |
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has taken us now involves the use of atoms with orientational degrees |
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of freedom and transition metals. Since these simulation methods may |
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be of some use to other researchers, we have decided to release our |
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program to the scientific community with a permissive open source |
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license. |
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|
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We have structured this paper to first discuss the underlying concepts |
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in this simulation package (Sec. \ref{oopseSec:IOfiles}). The |
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empirical energy functions implemented are discussed in |
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Sec.~\ref{oopseSec:empiricalEnergy}. Sec.~\ref{oopseSec:mechanics} |
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describes the various Molecular Dynamics algorithms {\sc oopse} |
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implements in the integration of the Newtonian equations of motion. |
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Program design considerations for parallel computing are presented in |
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This paper communicates the algorithmic details of our program, which |
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we have been calling the Open source Object-oriented Parallel |
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Simulation Engine (i.e. {\sc oopse}). We have structured this paper |
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to first discuss the underlying concepts in this simulation package |
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(Sec. \ref{oopseSec:IOfiles}). The empirical energy functions |
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implemented are discussed in Sec.~\ref{oopseSec:empiricalEnergy}. |
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Sec.~\ref{oopseSec:mechanics} describes the various Molecular Dynamics |
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algorithms {\sc oopse} implements in the integration of Hamilton's |
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equations of motion. Program design considerations for parallel |
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computing are presented in |
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Sec.~\ref{oopseSec:parallelization}. Concluding remarks are presented |
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in Sec.~\ref{oopseSec:conclusion}. |
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Sec.~\ref{oopseSec:minimizer}. The {\tt forceField} statement is |
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important for the selection of which forces will be used in the course |
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of the simulation. {\sc oopse} supports several force fields, as |
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outlined in Sec.~\ref{oopseSec:empericalEnergy}. The force fields are |
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outlined in Sec.~\ref{oopseSec:empiricalEnergy}. The force fields are |
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interchangeable between simulations, with the only requirement being |
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that all atoms needed by the simulation are defined within the |
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selected force field. |
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\end{table} |
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\section{\label{sec:minimize}Energy Minimization} |
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\section{\label{oopseSec:minimizer}Energy Minimization} |
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As one of the basic procedures of molecular modeling, energy |
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minimization is used to identify local configurations that are stable |
