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\section{Input and Output Files} |
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\subsection{{\sc bass} and Model Files} |
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Every {\sc oopse} simuation begins with a {\sc bass} file. {\sc bass} |
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(\underline{B}izarre \underline{A}tom \underline{S}imulation |
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\underline{S}yntax) is a script syntax that is parsed by {\sc oopse} at |
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runtime. The {\sc bass} file allows for the user to completely describe the |
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system they are to simulate, as well as tailor {\sc oopse}'s behavior during |
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the simulation. {\sc bass} files are denoted with the extension |
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\texttt{.bass}, an example file is shown in |
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Fig.~\ref{fig:bassExample}. |
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\begin{figure} |
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\centering |
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\framebox[\linewidth]{\rule{0cm}{0.75\linewidth}I'm a {\sc bass} file!} |
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\caption{Here is an example \texttt{.bass} file} |
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\label{fig:bassExample} |
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\end{figure} |
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Within the \texttt{.bass} file it is neccassary to provide a complete |
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description of the molecule before it is actually placed in the |
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simulation. The {\sc bass} syntax was originally developed with this goal in |
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mind, and allows for the specification of all the atoms in a molecular |
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prototype, as well as any bonds, bends, or torsions. These |
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descriptions can become lengthy for complex molecules, and it would be |
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inconvient to duplicate the simulation at the begining of each {\sc bass} |
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script. Addressing this issue {\sc bass} allows for the inclusion of model |
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files at the top of a \texttt{.bass} file. These model files, denoted |
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with the \texttt{.mdl} extension, allow the user to describe a |
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molecular prototype once, then simply include it into each simulation |
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containing that molecule. |
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\subsection{\label{subSec:coordFiles}Coordinate Files} |
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The standard format for storage of a systems coordinates is a modified |
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xyz-file syntax, the exact details of which can be seen in |
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App.~\ref{appCoordFormat}. As all bonding and molecular information is |
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stored in the \texttt{.bass} and \texttt{.mdl} files, the coordinate |
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files are simply the complete set of coordinates for each atom at a |
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given simulation time. |
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There are three major files used by {\sc oopse} written in the coordinate |
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format, they are as follows: the initialization file, the simulation |
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trajectory file, and the final coordinates of the simulation. The |
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initialization file is neccassary for {\sc oopse} to start the simulation |
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with the proper coordinates. It is typically denoted with the |
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extension \texttt{.init}. The trajectory file is created at the |
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beginning of the simulation, and is used to store snapshots of the |
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simulation at regular intervals. The first frame is a duplication of |
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the \texttt{.init} file, and each subsequent frame is appended to the |
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file at an interval specified in the \texttt{.bass} file. The |
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trajectory file is given the extension \texttt{.dump}. The final |
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coordinate file is the end of run or \texttt{.eor} file. The |
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\texttt{.eor} file stores the final configuration of teh system for a |
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given simulation. The file is updated at the same time as the |
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\texttt{.dump} file. However, it only contains the most recent |
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frame. In this way, an \texttt{.eor} file may be used as the |
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initialization file to a second simulation in order to continue or |
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recover the previous simulation. |
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\subsection{Generation of Initial Coordinates} |
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As was stated in Sec.~\ref{subSec:coordFiles}, an initialization file |
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is needed to provide the starting coordinates for a simulation. The |
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{\sc oopse} package provides a program called \texttt{sysBuilder} to aid in |
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the creation of the \texttt{.init} file. \texttt{sysBuilder} is {\sc bass} |
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aware, and will recognize arguments and parameters in the |
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\texttt{.bass} file that would otherwise be ignored by the |
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simulation. The program itself is under contiunual development, and is |
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offered here as a helper tool only. |
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\subsection{The Statistics File} |
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The last output file generated by {\sc oopse} is the statistics file. This |
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file records such statistical quantities as the instantaneous |
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temperature, volume, pressure, etc. It is written out with the |
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frequency specified in the \texttt{.bass} file. The file allows the |
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user to observe the system variables as a function od simulation time |
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while the simulation is in progress. One useful function the |
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statistics file serves is to monitor the conserved quantity of a given |
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simulation ensemble, this allows the user to observe the stability of |
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the integrator. The statistics file is denoted with the \texttt{.stat} |
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file extension. |
