| 1 |
+ |
\appendix |
| 2 |
|
\chapter{\label{chapt:appendix}APPENDIX} |
| 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 |
| 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: |
| 85 |
|
collections of atoms or atoms which have orientational degrees of |
| 86 |
|
freedom. Here is a diagram of the class heirarchy: |
| 87 |
|
|
| 88 |
< |
\begin{figure} |
| 89 |
< |
\centering |
| 90 |
< |
\includegraphics[width=3in]{heirarchy.eps} |
| 91 |
< |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
| 92 |
< |
The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
| 93 |
< |
selection syntax allows the user to select any of the objects that |
| 94 |
< |
are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
| 95 |
< |
\end{figure} |
| 88 |
> |
%\begin{figure} |
| 89 |
> |
%\centering |
| 90 |
> |
%\includegraphics[width=3in]{heirarchy.eps} |
| 91 |
> |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
| 92 |
> |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
| 93 |
> |
%selection syntax allows the user to select any of the objects that |
| 94 |
> |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
| 95 |
> |
%\end{figure} |
| 96 |
|
|
| 97 |
|
\begin{itemize} |
| 98 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
| 145 |
|
\subsection{\label{appendixSection:name}Name expressions} |
| 146 |
|
|
| 147 |
|
\begin{center} |
| 148 |
< |
\begin{tabular}{|llp{3in}|} |
| 148 |
> |
\begin{tabular}{|llp{2in}|} |
| 149 |
|
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
| 150 |
|
of |
| 151 |
|
examples} \\ |
| 229 |
|
\end{center} |
| 230 |
|
|
| 231 |
|
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
| 232 |
< |
wouldselect StuntDoubles which have mass greater than 16.0 and |
| 232 |
> |
would select StuntDoubles which have mass greater than 16.0 and |
| 233 |
|
charges less than -2. |
| 234 |
|
|
| 235 |
|
\subsection{\label{appendixSection:within}Within expressions} |
| 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') \\ |
| 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=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 |
| 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}. |
| 338 |
|
|
| 339 |
|
\begin{figure} |
| 340 |
|
\centering |
| 341 |
< |
\includegraphics[width=3in]{definition.pdf} |
| 341 |
> |
\includegraphics[width=3in]{definition.eps} |
| 342 |
|
\caption[Definitions of the angles between directional objects]{ \\ |
| 343 |
|
Any two directional objects (DirectionalAtoms and RigidBodies) have |
| 344 |
|
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
| 355 |
|
\endfoot |
| 356 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 357 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 358 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 359 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 360 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
| 361 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
| 362 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
| 363 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 364 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
| 365 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
| 366 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
| 367 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 368 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
| 369 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
| 370 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
| 358 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 359 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 360 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
| 361 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
| 362 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
| 363 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
| 364 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
| 365 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
| 366 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
| 367 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
| 368 |
> |
& {\tt -{}-molname} & molecule name \\ |
| 369 |
> |
& {\tt -{}-begin} & begin internal index \\ |
| 370 |
> |
& {\tt -{}-end} & end internal index \\ |
| 371 |
|
\hline |
| 372 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 373 |
|
\hline |
| 416 |
|
\endfoot |
| 417 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
| 418 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
| 419 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
| 420 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
| 421 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
| 422 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 419 |
> |
-i& {\tt -{}-input} & input dump file \\ |
| 420 |
> |
-o& {\tt -{}-output} & output file name \\ |
| 421 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
| 422 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
| 423 |
|
\hline |
| 424 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
| 425 |
|
\hline |
