| 4 |
|
The absence of modern software development practices has been a |
| 5 |
|
bottleneck limiting progress in the Scientific Computing |
| 6 |
|
community. In the last 20 years, a large number of |
| 7 |
< |
few MD packages\cite{Brooks1983, Vincent1995, Kale1999} were |
| 7 |
> |
MD packages\cite{Brooks1983, Vincent1995, Kale1999} were |
| 8 |
|
developed to solve common MD problems and perform robust simulations |
| 9 |
|
. Most of these are commercial programs that are either poorly |
| 10 |
|
written or extremely complicated to use correctly. This situation |
| 133 |
|
structure of a Visitor pattern which is used extensively in {\tt |
| 134 |
|
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
| 135 |
|
distinct operations are performed on different StuntDoubles (See the |
| 136 |
< |
class hierarchy in Scheme.~\ref{oopseFig:hierarchy} and the |
| 136 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the |
| 137 |
|
declaration in Scheme.~\ref{appendixScheme:element}). Since the |
| 138 |
|
hierarchies remain stable, it is easy to define a visit operation |
| 139 |
|
(see Scheme.~\ref{appendixScheme:visitor}) for each class of |
| 380 |
|
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
| 381 |
|
O\_TIP3P |
| 382 |
|
atoms belonging to TIP3P molecules \\ |
| 383 |
< |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
| 383 |
> |
& select DMPC\_RB\_0.PO4 & select the PO4 atoms belonging to |
| 384 |
|
the first |
| 385 |
|
RigidBody in each DMPC molecule \\ |
| 386 |
|
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
