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} |