| 1 |
|
| 2 |
\section{Input and Output Files} |
| 3 |
|
| 4 |
\subsection{BASS and Model Files} |
| 5 |
|
| 6 |
Every OOPSE simuation begins with a BASS file. BASS |
| 7 |
(\underline{B}izarre \underline{A}tom \underline{S}imulation |
| 8 |
\underline{S}yntax) is a script syntax that is parsed by OOPSE at |
| 9 |
runtime. The BASS file allows for the user to completely describe the |
| 10 |
system they are to simulate, as well as tailor OOPSE's behavior during |
| 11 |
the simulation. BASS files are denoted with the extension |
| 12 |
\texttt{.bass}, an example file is shown in |
| 13 |
Fig.~\ref{fig:bassExample}. |
| 14 |
|
| 15 |
\begin{figure} |
| 16 |
|
| 17 |
\centering |
| 18 |
\framebox[\linewidth]{\rule{0cm}{0.75\linewidth}I'm a BASS file!} |
| 19 |
\caption{Here is an example \texttt{.bass} file} |
| 20 |
\label{fig:bassExample} |
| 21 |
\end{figure} |
| 22 |
|
| 23 |
Within the \texttt{.bass} file it is neccassary to provide a complete |
| 24 |
description of the molecule before it is actually placed in the |
| 25 |
simulation. The BASS syntax was originally developed with this goal in |
| 26 |
mind, and allows for the specification of all the atoms in a molecular |
| 27 |
prototype, as well as any bonds, bends, or torsions. These |
| 28 |
descriptions can become lengthy for complex molecules, and it would be |
| 29 |
inconvient to duplicate the simulation at the begining of each BASS |
| 30 |
script. Addressing this issue BASS allows for the inclusion of model |
| 31 |
files at the top of a \texttt{.bass} file. These model files, denoted |
| 32 |
with the \texttt{.mdl} extension, allow the user to describe a |
| 33 |
molecular prototype once, then simply include it into each simulation |
| 34 |
containing that molecule. |
| 35 |
|
| 36 |
\subsection{\label{subSec:coordFiles}Coordinate Files} |
| 37 |
|
| 38 |
The standard format for storage of a systems coordinates is a modified |
| 39 |
xyz-file syntax, the exact details of which can be seen in |
| 40 |
App.~\ref{appCoordFormat}. As all bonding and molecular information is |
| 41 |
stored in the \texttt{.bass} and \texttt{.mdl} files, the coordinate |
| 42 |
files are simply the complete set of coordinates for each atom at a |
| 43 |
given simulation time. |
| 44 |
|
| 45 |
There are three major files used by OOPSE written in the coordinate |
| 46 |
format, they are as follows: the initialization file, the simulation |
| 47 |
trajectory file, and the final coordinates of the simulation. The |
| 48 |
initialization file is neccassary for OOPSE to start the simulation |
| 49 |
with the proper coordinates. It is typically denoted with the |
| 50 |
extension \texttt{.init}. The trajectory file is created at the |
| 51 |
beginning of the simulation, and is used to store snapshots of the |
| 52 |
simulation at regular intervals. The first frame is a duplication of |
| 53 |
the \texttt{.init} file, and each subsequent frame is appended to the |
| 54 |
file at an interval specified in the \texttt{.bass} file. The |
| 55 |
trajectory file is given the extension \texttt{.dump}. The final |
| 56 |
coordinate file is the end of run or \texttt{.eor} file. The |
| 57 |
\texttt{.eor} file stores the final configuration of teh system for a |
| 58 |
given simulation. The file is updated at the same time as the |
| 59 |
\texttt{.dump} file. However, it only contains the most recent |
| 60 |
frame. In this way, an \texttt{.eor} file may be used as the |
| 61 |
initialization file to a second simulation in order to continue or |
| 62 |
recover the previous simulation. |
| 63 |
|
| 64 |
\subsection{Generation of Initial Coordinates} |
| 65 |
|
| 66 |
As was stated in Sec.~\ref{subSec:coordFiles}, an initialization file |
| 67 |
is needed to provide the starting coordinates for a simulation. The |
| 68 |
OOPSE package provides a program called \texttt{sysBuilder} to aid in |
| 69 |
the creation of the \texttt{.init} file. \texttt{sysBuilder} is BASS |
| 70 |
aware, and will recognize arguments and parameters in the |
| 71 |
\texttt{.bass} file that would otherwise be ignored by the |
| 72 |
simulation. The program itself is under contiunual development, and is |
| 73 |
offered here as a helper tool only. |
| 74 |
|
| 75 |
\subsection{The Statistics File} |
| 76 |
|
| 77 |
The last output file generated by OOPSE is the statistics file. This |
| 78 |
file records such statistical quantities as the instantaneous |
| 79 |
temperature, volume, pressure, etc. It is written out with the |
| 80 |
frequency specified in the \texttt{.bass} file. The file allows the |
| 81 |
user to observe the system variables as a function od simulation time |
| 82 |
while the simulation is in progress. One useful function the |
| 83 |
statistics file serves is to monitor the conserved quantity of a given |
| 84 |
simulation ensemble, this allows the user to observe the stability of |
| 85 |
the integrator. The statistics file is denoted with the \texttt{.stat} |
| 86 |
file extension. |
