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Meta-data Files

OOPSE uses a C-based script syntax to parse the meta-data files at run time. These files allow the user to completely describe the system they wish to simulate, as well as tailor OOPSE's behavior during the simulation. Meta-data files are typically denoted with the extension .md (which can stand for Meta-Data or Molecular Dynamics or Molecule Definition depending on the user's mood). An example meta-data file is shown in Scheme 2.1.

$\begin{lstlisting}[float,caption={[An example of a complete meta-data file]An ex... ...le frequency statusTime = 50; // statistics file frequency \par \end{lstlisting}$

Within the meta-data file it is necessary to provide a complete description of the molecule before it is actually placed in the simulation. OOPSE's meta-data syntax was originally developed with this goal in mind, and allows for the use of include files to specify all atoms in a molecular prototype, as well as any bonds, bends, or torsions. Include files allow the user to describe a molecular prototype once, then simply include it into each simulation containing that molecule. Returning to the example in Scheme 2.1, the include file's contents would be Scheme 2.2, and the new meta-data file would become Scheme 2.3.

$\begin{lstlisting}[float,caption={An example molecule definition in an include f... ...; atom[0]{ type=''Ar''; position( 0.0, 0.0, 0.0 ); } } \par \end{lstlisting}$

$\begin{lstlisting}[float,caption={Revised meta-data example.},label={sch:mdExPri... ... = 1.0; runTime = 1e3; sampleTime = 100; statusTime = 50; \par \end{lstlisting}$

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Updated on January 16, 2006