| 1 |
|
\appendix |
| 2 |
< |
\chapter{\label{chapt:appendix}APPENDIX} |
| 2 |
> |
\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine (OOPSE)} |
| 3 |
|
|
| 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 |
| 8 |
< |
last 20 years , there are quite a few MD packages that were |
| 7 |
> |
Scientific Computing community\cite{Wilson2006}. For instance, in |
| 8 |
> |
the 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 |
| 11 |
|
poorly organized or extremely complex. Usually, these packages were |
| 15 |
|
most MD programs also suffer from missing design and implement |
| 16 |
|
documents which is crucial to the maintenance and extensibility. |
| 17 |
|
|
| 18 |
+ |
\section{\label{appendixSection:architecture }Architecture} |
| 19 |
+ |
|
| 20 |
+ |
\begin{figure} |
| 21 |
+ |
\centering |
| 22 |
+ |
\includegraphics[width=3in]{architecture.eps} |
| 23 |
+ |
\caption[The architecture of {\sc oopse}-3.0] {The architecture |
| 24 |
+ |
of{\sc oopse}-3.0.} \label{appendixFig:architecture} |
| 25 |
+ |
\end{figure} |
| 26 |
+ |
|
| 27 |
|
\section{\label{appendixSection:desginPattern}Design Pattern} |
| 28 |
|
|
| 29 |
|
Design patterns are optimal solutions to commonly-occurring problems |
| 84 |
|
|
| 85 |
|
|
| 86 |
|
\subsection{\label{appendixSection:templateMethod}Template Method} |
| 78 |
– |
|
| 79 |
– |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 87 |
|
|
| 88 |
|
\section{\label{appendixSection:concepts}Concepts} |
| 89 |
|
|
| 250 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
| 251 |
|
atoms. |
| 252 |
|
|
| 246 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
| 253 |
|
|
| 254 |
< |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
| 249 |
< |
|
| 250 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
| 251 |
< |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
| 252 |
< |
The options available for Dump2XYZ are as follows: |
| 253 |
< |
|
| 254 |
< |
|
| 255 |
< |
\begin{longtable}[c]{|EFG|} |
| 256 |
< |
\caption{Dump2XYZ Command-line Options} |
| 257 |
< |
\\ \hline |
| 258 |
< |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 259 |
< |
\endhead |
| 260 |
< |
\hline |
| 261 |
< |
\endfoot |
| 262 |
< |
-h & {\tt -{}-help} & Print help and exit \\ |
| 263 |
< |
-V & {\tt -{}-version} & Print version and exit \\ |
| 264 |
< |
-i & {\tt -{}-input=filename} & input dump file \\ |
| 265 |
< |
-o & {\tt -{}-output=filename} & output file name \\ |
| 266 |
< |
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
| 267 |
< |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
| 268 |
< |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
| 269 |
< |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
| 270 |
< |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
| 271 |
< |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
| 272 |
< |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
| 273 |
< |
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
| 274 |
< |
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
| 275 |
< |
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
| 276 |
< |
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 277 |
< |
converted. \\ |
| 278 |
< |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
| 279 |
< |
& {\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}. |
| 280 |
< |
\end{longtable} |
| 254 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 255 |
|
|
| 282 |
– |
|
| 256 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
| 257 |
|
|
| 258 |
|
{\tt StaticProps} can compute properties which are averaged over |
| 328 |
|
\endfoot |
| 329 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 330 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 331 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 332 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 333 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
| 334 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
| 335 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
| 336 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 337 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
| 338 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
| 339 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
| 340 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 341 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
| 342 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
| 343 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
| 331 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 332 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 333 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
| 334 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
| 335 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
| 336 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 337 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
| 338 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
| 339 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
| 340 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 341 |
> |
& {\tt -{}-molname} & molecule name \\ |
| 342 |
> |
& {\tt -{}-begin} & begin internal index \\ |
| 343 |
> |
& {\tt -{}-end} & end internal index \\ |
| 344 |
|
\hline |
| 345 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 346 |
|
\hline |
| 389 |
|
\endfoot |
| 390 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 391 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 392 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 393 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 394 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
| 395 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 392 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 393 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 394 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
| 395 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 396 |
|
\hline |
| 397 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 398 |
|
\hline |
| 401 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
| 402 |
|
\end{longtable} |
| 403 |
|
|
| 404 |
+ |
\section{\label{appendixSection:tools}Other Useful Utilities} |
| 405 |
+ |
|
| 406 |
+ |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
| 407 |
+ |
|
| 408 |
+ |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
| 409 |
+ |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
| 410 |
+ |
The options available for Dump2XYZ are as follows: |
| 411 |
+ |
|
| 412 |
+ |
|
| 413 |
+ |
\begin{longtable}[c]{|EFG|} |
| 414 |
+ |
\caption{Dump2XYZ Command-line Options} |
| 415 |
+ |
\\ \hline |
| 416 |
+ |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 417 |
+ |
\endhead |
| 418 |
+ |
\hline |
| 419 |
+ |
\endfoot |
| 420 |
+ |
-h & {\tt -{}-help} & Print help and exit \\ |
| 421 |
+ |
-V & {\tt -{}-version} & Print version and exit \\ |
| 422 |
+ |
-i & {\tt -{}-input} & input dump file \\ |
| 423 |
+ |
-o & {\tt -{}-output} & output file name \\ |
| 424 |
+ |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
| 425 |
+ |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
| 426 |
+ |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
| 427 |
+ |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
| 428 |
+ |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
| 429 |
+ |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
| 430 |
+ |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
| 431 |
+ |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
| 432 |
+ |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
| 433 |
+ |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
| 434 |
+ |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
| 435 |
+ |
converted. \\ |
| 436 |
+ |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
| 437 |
+ |
& {\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}. |
| 438 |
+ |
\end{longtable} |
| 439 |
+ |
|
| 440 |
|
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
| 441 |
+ |
|
| 442 |
+ |
\begin{longtable}[c]{|EFG|} |
| 443 |
+ |
\caption{Hydrodynamics Command-line Options} |
| 444 |
+ |
\\ \hline |
| 445 |
+ |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
| 446 |
+ |
\endhead |
| 447 |
+ |
\hline |
| 448 |
+ |
\endfoot |
| 449 |
+ |
-h & {\tt -{}-help} & Print help and exit \\ |
| 450 |
+ |
-V & {\tt -{}-version} & Print version and exit \\ |
| 451 |
+ |
-i & {\tt -{}-input} & input dump file \\ |
| 452 |
+ |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
| 453 |
+ |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
| 454 |
+ |
& {\tt -{}-model} & hydrodynamics model (support ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
| 455 |
+ |
\end{longtable} |
