| 4 |
|
Designing object-oriented software is hard, and designing reusable |
| 5 |
|
object-oriented scientific software is even harder. Absence of |
| 6 |
|
applying modern software development practices is the bottleneck of |
| 7 |
< |
Scientific Computing community\cite{wilson}. For instance, in the |
| 7 |
> |
Scientific Computing community\cite{Wilson}. For instance, in the |
| 8 |
|
last 20 years , there are quite a few MD packages that were |
| 9 |
|
developed to solve common MD problems and perform robust simulations |
| 10 |
|
. However, many of the codes are legacy programs that are either |
| 19 |
|
|
| 20 |
|
Design patterns are optimal solutions to commonly-occurring problems |
| 21 |
|
in software design. Although originated as an architectural concept |
| 22 |
< |
for buildings and towns by Christopher Alexander \cite{alexander}, |
| 23 |
< |
software patterns first became popular with the wide acceptance of |
| 24 |
< |
the book, Design Patterns: Elements of Reusable Object-Oriented |
| 25 |
< |
Software \cite{gamma94}. Patterns reflect the experience, knowledge |
| 26 |
< |
and insights of developers who have successfully used these patterns |
| 27 |
< |
in their own work. Patterns are reusable. They provide a ready-made |
| 28 |
< |
solution that can be adapted to different problems as necessary. |
| 29 |
< |
Pattern are expressive. they provide a common vocabulary of |
| 30 |
< |
solutions that can express large solutions succinctly. |
| 22 |
> |
for buildings and towns by Christopher Alexander |
| 23 |
> |
\cite{Alexander1987}, software patterns first became popular with |
| 24 |
> |
the wide acceptance of the book, Design Patterns: Elements of |
| 25 |
> |
Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
| 26 |
> |
the experience, knowledge and insights of developers who have |
| 27 |
> |
successfully used these patterns in their own work. Patterns are |
| 28 |
> |
reusable. They provide a ready-made solution that can be adapted to |
| 29 |
> |
different problems as necessary. Pattern are expressive. they |
| 30 |
> |
provide a common vocabulary of solutions that can express large |
| 31 |
> |
solutions succinctly. |
| 32 |
|
|
| 33 |
|
Patterns are usually described using a format that includes the |
| 34 |
|
following information: |
| 76 |
|
|
| 77 |
|
\subsection{\label{appendixSection:templateMethod}Template Method} |
| 78 |
|
|
| 78 |
– |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 79 |
– |
|
| 79 |
|
\section{\label{appendixSection:concepts}Concepts} |
| 80 |
|
|
| 81 |
|
OOPSE manipulates both traditional atoms as well as some objects |
| 83 |
|
collections of atoms or atoms which have orientational degrees of |
| 84 |
|
freedom. Here is a diagram of the class heirarchy: |
| 85 |
|
|
| 86 |
< |
\begin{figure} |
| 87 |
< |
\centering |
| 88 |
< |
\includegraphics[width=3in]{heirarchy.eps} |
| 89 |
< |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
| 90 |
< |
The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
| 91 |
< |
selection syntax allows the user to select any of the objects that |
| 92 |
< |
are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
| 93 |
< |
\end{figure} |
| 86 |
> |
%\begin{figure} |
| 87 |
> |
%\centering |
| 88 |
> |
%\includegraphics[width=3in]{heirarchy.eps} |
| 89 |
> |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
| 90 |
> |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
| 91 |
> |
%selection syntax allows the user to select any of the objects that |
| 92 |
> |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
| 93 |
> |
%\end{figure} |
| 94 |
|
|
| 95 |
|
\begin{itemize} |
| 96 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
| 240 |
|
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
| 241 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
| 242 |
|
atoms. |
| 244 |
– |
|
| 245 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
| 243 |
|
|
| 247 |
– |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
| 244 |
|
|
| 245 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
| 250 |
< |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
| 251 |
< |
The options available for Dump2XYZ are as follows: |
| 245 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 246 |
|
|
| 253 |
– |
|
| 254 |
– |
\begin{longtable}[c]{|EFG|} |
| 255 |
– |
\caption{Dump2XYZ Command-line Options} |
| 256 |
– |
\\ \hline |
| 257 |
– |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 258 |
– |
\endhead |
| 259 |
– |
\hline |
| 260 |
– |
\endfoot |
| 261 |
– |
-h & {\tt -{}-help} & Print help and exit \\ |
| 262 |
– |
-V & {\tt -{}-version} & Print version and exit \\ |
| 263 |
– |
-i & {\tt -{}-input=filename} & input dump file \\ |
| 264 |
– |
-o & {\tt -{}-output=filename} & output file name \\ |
| 265 |
– |
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
| 266 |
– |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
| 267 |
– |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
| 268 |
– |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
| 269 |
– |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
| 270 |
– |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
| 271 |
– |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
| 272 |
– |
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
| 273 |
– |
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
| 274 |
– |
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
| 275 |
– |
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 276 |
– |
converted. \\ |
| 277 |
– |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
| 278 |
– |
& {\tt -{}-refsele} & In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}. |
| 279 |
– |
\end{longtable} |
| 280 |
– |
|
| 281 |
– |
|
| 247 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
| 248 |
|
|
| 249 |
|
{\tt StaticProps} can compute properties which are averaged over |
| 319 |
|
\endfoot |
| 320 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 321 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 322 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 323 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 324 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
| 325 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
| 326 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
| 327 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 328 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
| 329 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
| 330 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
| 331 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 332 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
| 333 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
| 334 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
| 322 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 323 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 324 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
| 325 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
| 326 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
| 327 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 328 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
| 329 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
| 330 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
| 331 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 332 |
> |
& {\tt -{}-molname} & molecule name \\ |
| 333 |
> |
& {\tt -{}-begin} & begin internal index \\ |
| 334 |
> |
& {\tt -{}-end} & end internal index \\ |
| 335 |
|
\hline |
| 336 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 337 |
|
\hline |
| 380 |
|
\endfoot |
| 381 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 382 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 383 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 384 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 385 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
| 386 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 383 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 384 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 385 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
| 386 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 387 |
|
\hline |
| 388 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 389 |
|
\hline |
| 392 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
| 393 |
|
\end{longtable} |
| 394 |
|
|
| 395 |
+ |
\section{\label{appendixSection:tools}Other Useful Utilities} |
| 396 |
+ |
|
| 397 |
+ |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
| 398 |
+ |
|
| 399 |
+ |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
| 400 |
+ |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
| 401 |
+ |
The options available for Dump2XYZ are as follows: |
| 402 |
+ |
|
| 403 |
+ |
|
| 404 |
+ |
\begin{longtable}[c]{|EFG|} |
| 405 |
+ |
\caption{Dump2XYZ Command-line Options} |
| 406 |
+ |
\\ \hline |
| 407 |
+ |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 408 |
+ |
\endhead |
| 409 |
+ |
\hline |
| 410 |
+ |
\endfoot |
| 411 |
+ |
-h & {\tt -{}-help} & Print help and exit \\ |
| 412 |
+ |
-V & {\tt -{}-version} & Print version and exit \\ |
| 413 |
+ |
-i & {\tt -{}-input} & input dump file \\ |
| 414 |
+ |
-o & {\tt -{}-output} & output file name \\ |
| 415 |
+ |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
| 416 |
+ |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
| 417 |
+ |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
| 418 |
+ |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
| 419 |
+ |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
| 420 |
+ |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
| 421 |
+ |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
| 422 |
+ |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
| 423 |
+ |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
| 424 |
+ |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
| 425 |
+ |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 426 |
+ |
converted. \\ |
| 427 |
+ |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
| 428 |
+ |
& {\tt -{}-refsele} & In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}. |
| 429 |
+ |
\end{longtable} |
| 430 |
+ |
|
| 431 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
| 432 |
+ |
|
| 433 |
+ |
\begin{longtable}[c]{|EFG|} |
| 434 |
+ |
\caption{Hydrodynamics Command-line Options} |
| 435 |
+ |
\\ \hline |
| 436 |
+ |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 437 |
+ |
\endhead |
| 438 |
+ |
\hline |
| 439 |
+ |
\endfoot |
| 440 |
+ |
-h & {\tt -{}-help} & Print help and exit \\ |
| 441 |
+ |
-V & {\tt -{}-version} & Print version and exit \\ |
| 442 |
+ |
-i & {\tt -{}-input} & input dump file \\ |
| 443 |
+ |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
| 444 |
+ |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
| 445 |
+ |
& {\tt -{}-model} & hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
| 446 |
+ |
\end{longtable} |
