1 |
< |
\chapter{\label{chapt:appendix}APPENDIX} |
1 |
> |
\appendix |
2 |
> |
\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
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 |
14 |
|
coordination to enforce design and programming guidelines. Moreover, |
15 |
|
most MD programs also suffer from missing design and implement |
16 |
|
documents which is crucial to the maintenance and extensibility. |
17 |
+ |
Along the way of studying structural and dynamic processes in |
18 |
+ |
condensed phase systems like biological membranes and nanoparticles, |
19 |
+ |
we developed and maintained an Object-Oriented Parallel Simulation |
20 |
+ |
Engine ({\sc OOPSE}). This new molecular dynamics package has some |
21 |
+ |
unique features |
22 |
+ |
\begin{enumerate} |
23 |
+ |
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
24 |
+ |
atom types (transition metals, point dipoles, sticky potentials, |
25 |
+ |
Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
26 |
+ |
degrees of freedom), as well as rigid bodies. |
27 |
+ |
\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
28 |
+ |
Beowulf clusters to obtain very efficient parallelism. |
29 |
+ |
\item {\sc OOPSE} integrates the equations of motion using advanced methods for |
30 |
+ |
orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T |
31 |
+ |
ensembles. |
32 |
+ |
\item {\sc OOPSE} can carry out simulations on metallic systems using the |
33 |
+ |
Embedded Atom Method (EAM) as well as the Sutton-Chen potential. |
34 |
+ |
\item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals. |
35 |
+ |
\item {\sc OOPSE} can simulate systems containing the extremely efficient |
36 |
+ |
extended-Soft Sticky Dipole (SSD/E) model for water. |
37 |
+ |
\end{enumerate} |
38 |
|
|
39 |
+ |
\section{\label{appendixSection:architecture }Architecture} |
40 |
+ |
|
41 |
+ |
Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE} |
42 |
+ |
uses C++ Standard Template Library (STL) and fortran modules as the |
43 |
+ |
foundation. As an extensive set of the STL and Fortran90 modules, |
44 |
+ |
{\sc Base Classes} provide generic implementations of mathematical |
45 |
+ |
objects (e.g., matrices, vectors, polynomials, random number |
46 |
+ |
generators) and advanced data structures and algorithms(e.g., tuple, |
47 |
+ |
bitset, generic data, string manipulation). The molecular data |
48 |
+ |
structures for the representation of atoms, bonds, bends, torsions, |
49 |
+ |
rigid bodies and molecules \textit{etc} are contained in the {\sc |
50 |
+ |
Kernel} which is implemented with {\sc Base Classes} and are |
51 |
+ |
carefully designed to provide maximum extensibility and flexibility. |
52 |
+ |
The functionality required for applications is provide by the third |
53 |
+ |
layer which contains Input/Output, Molecular Mechanics and Structure |
54 |
+ |
modules. Input/Output module not only implements general methods for |
55 |
+ |
file handling, but also defines a generic force field interface. |
56 |
+ |
Another important component of Input/Output module is the meta-data |
57 |
+ |
file parser, which is rewritten using ANother Tool for Language |
58 |
+ |
Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular |
59 |
+ |
Mechanics module consists of energy minimization and a wide |
60 |
+ |
varieties of integration methods(see Chap.~\ref{chapt:methodology}). |
61 |
+ |
The structure module contains a flexible and powerful selection |
62 |
+ |
library which syntax is elaborated in |
63 |
+ |
Sec.~\ref{appendixSection:syntax}. The top layer is made of the main |
64 |
+ |
program of the package, \texttt{oopse} and it corresponding parallel |
65 |
+ |
version \texttt{oopse\_MPI}, as well as other useful utilities, such |
66 |
+ |
as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
67 |
+ |
\texttt{DynamicProps} (see |
68 |
+ |
Sec.~\ref{appendixSection:appendixSection:DynamicProps}), |
69 |
+ |
\texttt{Dump2XYZ} (see |
70 |
+ |
Sec.~\ref{appendixSection:appendixSection:Dump2XYZ}), \texttt{Hydro} |
71 |
+ |
(see Sec.~\ref{appendixSection:appendixSection:hydrodynamics}) |
72 |
+ |
\textit{etc}. |
73 |
+ |
|
74 |
+ |
\begin{figure} |
75 |
+ |
\centering |
76 |
+ |
\includegraphics[width=\linewidth]{architecture.eps} |
77 |
+ |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
78 |
+ |
of {\sc OOPSE}} \label{appendixFig:architecture} |
79 |
+ |
\end{figure} |
80 |
+ |
|
81 |
|
\section{\label{appendixSection:desginPattern}Design Pattern} |
82 |
|
|
83 |
|
Design patterns are optimal solutions to commonly-occurring problems |
84 |
|
in software design. Although originated as an architectural concept |
85 |
< |
for buildings and towns by Christopher Alexander \cite{alexander}, |
86 |
< |
software patterns first became popular with the wide acceptance of |
87 |
< |
the book, Design Patterns: Elements of Reusable Object-Oriented |
88 |
< |
Software \cite{gamma94}. Patterns reflect the experience, knowledge |
89 |
< |
and insights of developers who have successfully used these patterns |
90 |
< |
in their own work. Patterns are reusable. They provide a ready-made |
91 |
< |
solution that can be adapted to different problems as necessary. |
92 |
< |
Pattern are expressive. they provide a common vocabulary of |
93 |
< |
solutions that can express large solutions succinctly. |
85 |
> |
for buildings and towns by Christopher Alexander |
86 |
> |
\cite{Alexander1987}, software patterns first became popular with |
87 |
> |
the wide acceptance of the book, Design Patterns: Elements of |
88 |
> |
Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
89 |
> |
the experience, knowledge and insights of developers who have |
90 |
> |
successfully used these patterns in their own work. Patterns are |
91 |
> |
reusable. They provide a ready-made solution that can be adapted to |
92 |
> |
different problems as necessary. Pattern are expressive. they |
93 |
> |
provide a common vocabulary of solutions that can express large |
94 |
> |
solutions succinctly. |
95 |
|
|
96 |
|
Patterns are usually described using a format that includes the |
97 |
|
following information: |
112 |
|
|
113 |
|
As one of the latest advanced techniques emerged from |
114 |
|
object-oriented community, design patterns were applied in some of |
115 |
< |
the modern scientific software applications, such as JMol, OOPSE |
116 |
< |
\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
115 |
> |
the modern scientific software applications, such as JMol, {\sc |
116 |
> |
OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
117 |
> |
The following sections enumerates some of the patterns used in {\sc |
118 |
> |
OOPSE}. |
119 |
|
|
120 |
|
\subsection{\label{appendixSection:singleton}Singleton} |
121 |
|
The Singleton pattern ensures that only one instance of a class is |
130 |
|
subclasses can then override to specify the derived type of product |
131 |
|
that will be created. |
132 |
|
|
66 |
– |
|
133 |
|
\subsection{\label{appendixSection:visitorPattern}Visitor} |
134 |
|
The purpose of the Visitor Pattern is to encapsulate an operation |
135 |
|
that you want to perform on the elements of a data structure. In |
137 |
|
structure without the need of changing the classes of the elements |
138 |
|
that you are operating on. |
139 |
|
|
74 |
– |
|
75 |
– |
\subsection{\label{appendixSection:templateMethod}Template Method} |
76 |
– |
|
77 |
– |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
78 |
– |
|
140 |
|
\section{\label{appendixSection:concepts}Concepts} |
141 |
|
|
142 |
|
OOPSE manipulates both traditional atoms as well as some objects |
144 |
|
collections of atoms or atoms which have orientational degrees of |
145 |
|
freedom. Here is a diagram of the class heirarchy: |
146 |
|
|
147 |
< |
\begin{figure} |
148 |
< |
\centering |
149 |
< |
\includegraphics[width=3in]{heirarchy.eps} |
150 |
< |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
151 |
< |
The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
152 |
< |
selection syntax allows the user to select any of the objects that |
153 |
< |
are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
154 |
< |
\end{figure} |
147 |
> |
%\begin{figure} |
148 |
> |
%\centering |
149 |
> |
%\includegraphics[width=3in]{heirarchy.eps} |
150 |
> |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
151 |
> |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
152 |
> |
%selection syntax allows the user to select any of the objects that |
153 |
> |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
154 |
> |
%\end{figure} |
155 |
|
|
156 |
|
\begin{itemize} |
157 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
162 |
|
DirectionalAtom}s which behaves as a single unit. |
163 |
|
\end{itemize} |
164 |
|
|
165 |
< |
Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
165 |
> |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
166 |
|
own names which are specified in the {\tt .md} file. In contrast, |
167 |
|
RigidBodies are denoted by their membership and index inside a |
168 |
|
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
173 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
174 |
|
|
175 |
|
The most general form of the select command is: {\tt select {\it |
176 |
< |
expression}} |
176 |
> |
expression}}. This expression represents an arbitrary set of |
177 |
> |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
178 |
> |
composed of either name expressions, index expressions, predefined |
179 |
> |
sets, user-defined expressions, comparison operators, within |
180 |
> |
expressions, or logical combinations of the above expression types. |
181 |
> |
Expressions can be combined using parentheses and the Boolean |
182 |
> |
operators. |
183 |
|
|
117 |
– |
This expression represents an arbitrary set of StuntDoubles (Atoms |
118 |
– |
or RigidBodies) in {\sc oopse}. Expressions are composed of either |
119 |
– |
name expressions, index expressions, predefined sets, user-defined |
120 |
– |
expressions, comparison operators, within expressions, or logical |
121 |
– |
combinations of the above expression types. Expressions can be |
122 |
– |
combined using parentheses and the Boolean operators. |
123 |
– |
|
184 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
185 |
|
|
186 |
|
The logical operators allow complex queries to be constructed out of |
203 |
|
\subsection{\label{appendixSection:name}Name expressions} |
204 |
|
|
205 |
|
\begin{center} |
206 |
< |
\begin{tabular}{|llp{3in}|} |
206 |
> |
\begin{tabular}{|llp{2in}|} |
207 |
|
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
208 |
|
of |
209 |
|
examples} \\ |
262 |
|
Users can define arbitrary terms to represent groups of |
263 |
|
StuntDoubles, and then use the define terms in select commands. The |
264 |
|
general form for the define command is: {\bf define {\it term |
265 |
< |
expression}} |
265 |
> |
expression}}. Once defined, the user can specify such terms in |
266 |
> |
boolean expressions |
267 |
|
|
207 |
– |
Once defined, the user can specify such terms in boolean expressions |
208 |
– |
|
268 |
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
269 |
|
|
270 |
|
{\tt select SSDWATER} |
286 |
|
\end{center} |
287 |
|
|
288 |
|
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
289 |
< |
wouldselect StuntDoubles which have mass greater than 16.0 and |
289 |
> |
would select StuntDoubles which have mass greater than 16.0 and |
290 |
|
charges less than -2. |
291 |
|
|
292 |
|
\subsection{\label{appendixSection:within}Within expressions} |
300 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
301 |
|
atoms. |
302 |
|
|
244 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
303 |
|
|
304 |
< |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
247 |
< |
|
248 |
< |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
249 |
< |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
250 |
< |
The options available for Dump2XYZ are as follows: |
251 |
< |
|
252 |
< |
|
253 |
< |
\begin{longtable}[c]{|EFG|} |
254 |
< |
\caption{Dump2XYZ Command-line Options} |
255 |
< |
\\ \hline |
256 |
< |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
257 |
< |
\endhead |
258 |
< |
\hline |
259 |
< |
\endfoot |
260 |
< |
-h & {\tt -{}-help} & Print help and exit \\ |
261 |
< |
-V & {\tt -{}-version} & Print version and exit \\ |
262 |
< |
-i & {\tt -{}-input=filename} & input dump file \\ |
263 |
< |
-o & {\tt -{}-output=filename} & output file name \\ |
264 |
< |
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
265 |
< |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
266 |
< |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
267 |
< |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
268 |
< |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
269 |
< |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
270 |
< |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
271 |
< |
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
272 |
< |
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
273 |
< |
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
274 |
< |
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
275 |
< |
converted. \\ |
276 |
< |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
277 |
< |
& {\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}. |
278 |
< |
\end{longtable} |
304 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
305 |
|
|
280 |
– |
|
306 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
307 |
|
|
308 |
|
{\tt StaticProps} can compute properties which are averaged over |
309 |
|
some or all of the configurations that are contained within a dump |
310 |
|
file. The most common example of a static property that can be |
311 |
|
computed is the pair distribution function between atoms of type $A$ |
312 |
< |
and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
313 |
< |
used to compute the density distributions of other molecules in a |
314 |
< |
reference frame {\it fixed to the body-fixed reference frame} of a |
315 |
< |
selected atom or rigid body. |
312 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
313 |
> |
also be used to compute the density distributions of other molecules |
314 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
315 |
> |
of a selected atom or rigid body. |
316 |
|
|
317 |
|
There are five seperate radial distribution functions availiable in |
318 |
|
OOPSE. Since every radial distrbution function invlove the |
361 |
|
|
362 |
|
\begin{figure} |
363 |
|
\centering |
364 |
< |
\includegraphics[width=3in]{definition.pdf} |
364 |
> |
\includegraphics[width=3in]{definition.eps} |
365 |
|
\caption[Definitions of the angles between directional objects]{ \\ |
366 |
|
Any two directional objects (DirectionalAtoms and RigidBodies) have |
367 |
|
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
368 |
|
their body-fixed frames.} \label{oopseFig:gofr} |
369 |
|
\end{figure} |
370 |
|
|
371 |
+ |
Due to the fact that the selected StuntDoubles from two selections |
372 |
+ |
may be overlapped, {\tt StaticProps} performs the calculation in |
373 |
+ |
three stages which are illustrated in |
374 |
+ |
Fig.~\ref{oopseFig:staticPropsProcess}. |
375 |
+ |
|
376 |
+ |
\begin{figure} |
377 |
+ |
\centering |
378 |
+ |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
379 |
+ |
\caption[A representation of the three-stage correlations in |
380 |
+ |
\texttt{StaticProps}]{Three-stage processing in |
381 |
+ |
\texttt{StaticProps}. $S_1$ and $S_2$ are the numbers of selected |
382 |
+ |
stuntdobules from {\tt -{}-sele1} and {\tt -{}-sele2} respectively, |
383 |
+ |
while $C$ is the number of stuntdobules appearing at both sets. The |
384 |
+ |
first stage($S_1-C$ and $S_2$) and second stages ($S_1$ and $S_2-C$) |
385 |
+ |
are completely non-overlapping. On the contrary, the third stage($C$ |
386 |
+ |
and $C$) are completely overlapping} |
387 |
+ |
\label{oopseFig:staticPropsProcess} |
388 |
+ |
\end{figure} |
389 |
+ |
|
390 |
|
The options available for {\tt StaticProps} are as follows: |
391 |
|
\begin{longtable}[c]{|EFG|} |
392 |
|
\caption{StaticProps Command-line Options} |
397 |
|
\endfoot |
398 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
399 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
400 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
401 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
402 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
403 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
404 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
405 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
406 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
407 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
408 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
409 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
410 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
411 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
412 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
400 |
> |
-i& {\tt -{}-input} & input dump file \\ |
401 |
> |
-o& {\tt -{}-output} & output file name \\ |
402 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
403 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
404 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
405 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
406 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
407 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
408 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
409 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
410 |
> |
& {\tt -{}-molname} & molecule name \\ |
411 |
> |
& {\tt -{}-begin} & begin internal index \\ |
412 |
> |
& {\tt -{}-end} & end internal index \\ |
413 |
|
\hline |
414 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
415 |
|
\hline |
448 |
|
different vectors). The ability to use two selection scripts to |
449 |
|
select different types of atoms is already present in the code. |
450 |
|
|
451 |
+ |
For large simulations, the trajectory files can sometimes reach |
452 |
+ |
sizes in excess of several gigabytes. In order to effectively |
453 |
+ |
analyze that amount of data. In order to prevent a situation where |
454 |
+ |
the program runs out of memory due to large trajectories, |
455 |
+ |
\texttt{dynamicProps} will estimate the size of free memory at |
456 |
+ |
first, and determine the number of frames in each block, which |
457 |
+ |
allows the operating system to load two blocks of data |
458 |
+ |
simultaneously without swapping. Upon reading two blocks of the |
459 |
+ |
trajectory, \texttt{dynamicProps} will calculate the time |
460 |
+ |
correlation within the first block and the cross correlations |
461 |
+ |
between the two blocks. This second block is then freed and then |
462 |
+ |
incremented and the process repeated until the end of the |
463 |
+ |
trajectory. Once the end is reached, the first block is freed then |
464 |
+ |
incremented, until all frame pairs have been correlated in time. |
465 |
+ |
|
466 |
|
The options available for DynamicProps are as follows: |
467 |
|
\begin{longtable}[c]{|EFG|} |
468 |
|
\caption{DynamicProps Command-line Options} |
473 |
|
\endfoot |
474 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
475 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
476 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
477 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
478 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
479 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
476 |
> |
-i& {\tt -{}-input} & input dump file \\ |
477 |
> |
-o& {\tt -{}-output} & output file name \\ |
478 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
479 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
480 |
|
\hline |
481 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
482 |
|
\hline |
485 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
486 |
|
\end{longtable} |
487 |
|
|
488 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
488 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
489 |
> |
|
490 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
491 |
> |
|
492 |
> |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
493 |
> |
be opened by other molecular dynamics viewers such as Jmol and |
494 |
> |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
495 |
> |
follows: |
496 |
> |
|
497 |
> |
|
498 |
> |
\begin{longtable}[c]{|EFG|} |
499 |
> |
\caption{Dump2XYZ Command-line Options} |
500 |
> |
\\ \hline |
501 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
502 |
> |
\endhead |
503 |
> |
\hline |
504 |
> |
\endfoot |
505 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
506 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
507 |
> |
-i & {\tt -{}-input} & input dump file \\ |
508 |
> |
-o & {\tt -{}-output} & output file name \\ |
509 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
510 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
511 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
512 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
513 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
514 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
515 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
516 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
517 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
518 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
519 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
520 |
> |
converted. \\ |
521 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
522 |
> |
& {\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}. |
523 |
> |
\end{longtable} |
524 |
> |
|
525 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
526 |
> |
The options available for Hydro are as follows: |
527 |
> |
\begin{longtable}[c]{|EFG|} |
528 |
> |
\caption{Hydrodynamics Command-line Options} |
529 |
> |
\\ \hline |
530 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
531 |
> |
\endhead |
532 |
> |
\hline |
533 |
> |
\endfoot |
534 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
535 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
536 |
> |
-i & {\tt -{}-input} & input dump file \\ |
537 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
538 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
539 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
540 |
> |
\end{longtable} |