| 76 |
|
|
| 77 |
|
\subsection{\label{appendixSection:templateMethod}Template Method} |
| 78 |
|
|
| 79 |
– |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 80 |
– |
|
| 79 |
|
\section{\label{appendixSection:concepts}Concepts} |
| 80 |
|
|
| 81 |
|
OOPSE manipulates both traditional atoms as well as some objects |
| 241 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
| 242 |
|
atoms. |
| 243 |
|
|
| 246 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
| 244 |
|
|
| 245 |
< |
\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} & input dump file \\ |
| 265 |
< |
-o & {\tt -{}-output} & output file name \\ |
| 266 |
< |
-n & {\tt -{}-frame} & 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} & The number of images to repeat in the x direction (default=`0') \\ |
| 274 |
< |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
| 275 |
< |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
| 276 |
< |
-s & {\tt -{}-selection} & 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} |
| 245 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
| 246 |
|
|
| 282 |
– |
|
| 247 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
| 248 |
|
|
| 249 |
|
{\tt StaticProps} can compute properties which are averaged over |
| 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} |
