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}; |
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\end{lstlisting} |
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\section{\label{appendixSection:concepts}Concepts} |
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OOPSE manipulates both traditional atoms as well as some objects |
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that {\it behave like atoms}. These objects can be rigid |
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collections of atoms or atoms which have orientational degrees of |
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freedom. Here is a diagram of the class heirarchy: |
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|
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freedom. A diagram of the class heirarchy is illustrated in |
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Fig.~\ref{oopseFig:heirarchy}. Every Molecule, Atom and |
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DirectionalAtom in {\sc OOPSE} have their own names which are |
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specified in the {\tt .md} file. In contrast, RigidBodies are |
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denoted by their membership and index inside a particular molecule: |
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[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
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on the specifics of the simulation). The names of rigid bodies are |
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generated automatically. For example, the name of the first rigid |
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body in a DMPC molecule is DMPC\_RB\_0. |
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\begin{figure} |
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\centering |
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\includegraphics[width=3in]{heirarchy.eps} |
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\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
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The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
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selection syntax allows the user to select any of the objects that |
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are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
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\end{figure} |
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|
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\includegraphics[width=\linewidth]{heirarchy.eps} |
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\caption[Class heirarchy for StuntDoubles in {\sc OOPSE}]{ The class |
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heirarchy of StuntDoubles in {\sc OOPSE}. |
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\begin{itemize} |
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\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
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integrators and minimizers. |
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\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
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DirectionalAtom}s which behaves as a single unit. |
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\end{itemize} |
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|
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Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
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own names which are specified in the {\tt .md} file. In contrast, |
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RigidBodies are denoted by their membership and index inside a |
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particular molecule: [MoleculeName]\_RB\_[index] (the contents |
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inside the brackets depend on the specifics of the simulation). The |
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names of rigid bodies are generated automatically. For example, the |
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name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
| 321 |
> |
} \label{oopseFig:heirarchy} |
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\end{figure} |
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|
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\section{\label{appendixSection:syntax}Syntax of the Select Command} |
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|
