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{} \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 |
122 |
+ |
created. All objects that use an instance of that class use the same |
123 |
+ |
instance. |
124 |
+ |
|
125 |
|
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
126 |
|
The Factory Method pattern is a creational pattern which deals with |
127 |
|
the problem of creating objects without specifying the exact class |
130 |
|
subclasses can then override to specify the derived type of product |
131 |
|
that will be created. |
132 |
|
|
61 |
– |
|
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 |
|
|
140 |
+ |
\section{\label{appendixSection:concepts}Concepts} |
141 |
|
|
142 |
< |
\subsection{\label{appendixSection:templateMethod}Template Method} |
142 |
> |
OOPSE manipulates both traditional atoms as well as some objects |
143 |
> |
that {\it behave like atoms}. These objects can be rigid |
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} |
155 |
|
|
156 |
< |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
156 |
> |
\begin{itemize} |
157 |
> |
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
158 |
> |
integrators and minimizers. |
159 |
> |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
160 |
> |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
161 |
> |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
162 |
> |
DirectionalAtom}s which behaves as a single unit. |
163 |
> |
\end{itemize} |
164 |
|
|
165 |
< |
\section{\label{appendixSection:hierarchy}Hierarchy} |
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 |
169 |
> |
inside the brackets depend on the specifics of the simulation). The |
170 |
> |
names of rigid bodies are generated automatically. For example, the |
171 |
> |
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
172 |
|
|
173 |
< |
\subsection{\label{appendixSection:selectionSyntax}Selection Syntax} |
173 |
> |
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
174 |
|
|
175 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
175 |
> |
The most general form of the select command is: {\tt select {\it |
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 |
|
|
184 |
< |
\subsection{\label{appendixSection:staticProps}Static Properties} |
184 |
> |
\subsection{\label{appendixSection:logical}Logical expressions} |
185 |
|
|
186 |
< |
\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
186 |
> |
The logical operators allow complex queries to be constructed out of |
187 |
> |
simpler ones using the standard boolean connectives {\bf and}, {\bf |
188 |
> |
or}, {\bf not}. Parentheses can be used to alter the precedence of |
189 |
> |
the operators. |
190 |
> |
|
191 |
> |
\begin{center} |
192 |
> |
\begin{tabular}{|ll|} |
193 |
> |
\hline |
194 |
> |
{\bf logical operator} & {\bf equivalent operator} \\ |
195 |
> |
\hline |
196 |
> |
and & ``\&'', ``\&\&'' \\ |
197 |
> |
or & ``$|$'', ``$||$'', ``,'' \\ |
198 |
> |
not & ``!'' \\ |
199 |
> |
\hline |
200 |
> |
\end{tabular} |
201 |
> |
\end{center} |
202 |
> |
|
203 |
> |
\subsection{\label{appendixSection:name}Name expressions} |
204 |
> |
|
205 |
> |
\begin{center} |
206 |
> |
\begin{tabular}{|llp{2in}|} |
207 |
> |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
208 |
> |
of |
209 |
> |
examples} \\ |
210 |
> |
\hline expression without ``.'' & select DMPC & select all |
211 |
> |
StuntDoubles |
212 |
> |
belonging to all DMPC molecules \\ |
213 |
> |
& select C* & select all atoms which have atom types beginning with C |
214 |
> |
\\ |
215 |
> |
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
216 |
> |
only select the rigid bodies, and not the atoms belonging to them). \\ |
217 |
> |
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
218 |
> |
O\_TIP3P |
219 |
> |
atoms belonging to TIP3P molecules \\ |
220 |
> |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
221 |
> |
the first |
222 |
> |
RigidBody in each DMPC molecule \\ |
223 |
> |
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
224 |
> |
molecule \\ |
225 |
> |
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
226 |
> |
select all atoms |
227 |
> |
belonging to all rigid bodies within all DMPC molecules \\ |
228 |
> |
\hline |
229 |
> |
\end{tabular} |
230 |
> |
\end{center} |
231 |
> |
|
232 |
> |
\subsection{\label{appendixSection:index}Index expressions} |
233 |
> |
|
234 |
> |
\begin{center} |
235 |
> |
\begin{tabular}{|lp{4in}|} |
236 |
> |
\hline |
237 |
> |
{\bf examples} & {\bf translation of examples} \\ |
238 |
> |
\hline |
239 |
> |
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
240 |
> |
select 20 to 30 & select all of the StuntDoubles belonging to |
241 |
> |
molecules which have global indices between 20 (inclusive) and 30 |
242 |
> |
(exclusive) \\ |
243 |
> |
\hline |
244 |
> |
\end{tabular} |
245 |
> |
\end{center} |
246 |
> |
|
247 |
> |
\subsection{\label{appendixSection:predefined}Predefined sets} |
248 |
> |
|
249 |
> |
\begin{center} |
250 |
> |
\begin{tabular}{|ll|} |
251 |
> |
\hline |
252 |
> |
{\bf keyword} & {\bf description} \\ |
253 |
> |
\hline |
254 |
> |
all & select all StuntDoubles \\ |
255 |
> |
none & select none of the StuntDoubles \\ |
256 |
> |
\hline |
257 |
> |
\end{tabular} |
258 |
> |
\end{center} |
259 |
> |
|
260 |
> |
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
261 |
> |
|
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}}. Once defined, the user can specify such terms in |
266 |
> |
boolean expressions |
267 |
> |
|
268 |
> |
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
269 |
> |
|
270 |
> |
{\tt select SSDWATER} |
271 |
> |
|
272 |
> |
\subsection{\label{appendixSection:comparison}Comparison expressions} |
273 |
> |
|
274 |
> |
StuntDoubles can be selected by using comparision operators on their |
275 |
> |
properties. The general form for the comparison command is: a |
276 |
> |
property name, followed by a comparision operator and then a number. |
277 |
> |
|
278 |
> |
\begin{center} |
279 |
> |
\begin{tabular}{|l|l|} |
280 |
> |
\hline |
281 |
> |
{\bf property} & mass, charge \\ |
282 |
> |
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
283 |
> |
``$<=$'', ``$!=$'' \\ |
284 |
> |
\hline |
285 |
> |
\end{tabular} |
286 |
> |
\end{center} |
287 |
> |
|
288 |
> |
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
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} |
293 |
> |
|
294 |
> |
The ``within'' keyword allows the user to select all StuntDoubles |
295 |
> |
within the specified distance (in Angstroms) from a selection, |
296 |
> |
including the selected atom itself. The general form for within |
297 |
> |
selection is: {\tt select within(distance, expression)} |
298 |
> |
|
299 |
> |
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
300 |
> |
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
301 |
> |
atoms. |
302 |
> |
|
303 |
> |
|
304 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
305 |
> |
|
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 $B$, $g_{AB}(r)$. {\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 |
319 |
> |
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
320 |
> |
-{}-sele2} must be specified to tell StaticProps which bodies to |
321 |
> |
include in the calculation. |
322 |
> |
|
323 |
> |
\begin{description} |
324 |
> |
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
325 |
> |
\begin{equation*} |
326 |
> |
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
327 |
> |
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
328 |
> |
\end{equation*} |
329 |
> |
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
330 |
> |
function. The angle is defined by the intermolecular vector |
331 |
> |
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
332 |
> |
\begin{equation*} |
333 |
> |
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
334 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
335 |
> |
\theta_{ij} - \cos \theta)\rangle |
336 |
> |
\end{equation*} |
337 |
> |
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
338 |
> |
function. The angle is defined by the $z$-axes of the two |
339 |
> |
DirectionalAtoms A and B. |
340 |
> |
\begin{equation*} |
341 |
> |
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
342 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
343 |
> |
\omega_{ij} - \cos \omega)\rangle |
344 |
> |
\end{equation*} |
345 |
> |
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
346 |
> |
space $\theta, \omega$ defined by the two angles mentioned above. |
347 |
> |
\begin{equation*} |
348 |
> |
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
349 |
> |
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
350 |
> |
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
351 |
> |
\omega)\rangle |
352 |
> |
\end{equation*} |
353 |
> |
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
354 |
> |
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
355 |
> |
and {\tt -{}-refsele} must be given to define A's internal |
356 |
> |
coordinate set as the reference frame for the calculation. |
357 |
> |
\end{description} |
358 |
> |
|
359 |
> |
The vectors (and angles) associated with these angular pair |
360 |
> |
distribution functions are most easily seen in the figure below: |
361 |
> |
|
362 |
> |
\begin{figure} |
363 |
> |
\centering |
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}]{This diagram illustrates three-stage |
381 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
382 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
383 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
384 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
385 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
386 |
> |
the contrary, the third stage($C$ and $C$) are completely |
387 |
> |
overlapping} \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} |
393 |
> |
\\ \hline |
394 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
395 |
> |
\endhead |
396 |
> |
\hline |
397 |
> |
\endfoot |
398 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
399 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
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 |
416 |
> |
& {\tt -{}-gofr} & $g(r)$ \\ |
417 |
> |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
418 |
> |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
419 |
> |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
420 |
> |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
421 |
> |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
422 |
> |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
423 |
> |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
424 |
> |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
425 |
> |
\end{longtable} |
426 |
> |
|
427 |
> |
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
428 |
> |
|
429 |
> |
{\tt DynamicProps} computes time correlation functions from the |
430 |
> |
configurations stored in a dump file. Typical examples of time |
431 |
> |
correlation functions are the mean square displacement and the |
432 |
> |
velocity autocorrelation functions. Once again, the selection |
433 |
> |
syntax can be used to specify the StuntDoubles that will be used for |
434 |
> |
the calculation. A general time correlation function can be thought |
435 |
> |
of as: |
436 |
> |
\begin{equation} |
437 |
> |
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
438 |
> |
\end{equation} |
439 |
> |
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
440 |
> |
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
441 |
> |
vector property associated with an atom of type $B$ at a different |
442 |
> |
time $t^{\prime}$. In most autocorrelation functions, the vector |
443 |
> |
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
444 |
> |
$B$) are identical, and the three calculations built in to {\tt |
445 |
> |
DynamicProps} make these assumptions. It is possible, however, to |
446 |
> |
make simple modifications to the {\tt DynamicProps} code to allow |
447 |
> |
the use of {\it cross} time correlation functions (i.e. with |
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 |
> |
This process is illustrated in |
466 |
> |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
467 |
> |
|
468 |
> |
\begin{figure} |
469 |
> |
\centering |
470 |
> |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
471 |
> |
\caption[A representation of the block correlations in |
472 |
> |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
473 |
> |
processing in \texttt{dynamicProps}. The shaded region represents |
474 |
> |
the self correlation of the block, and the open blocks are read one |
475 |
> |
at a time and the cross correlations between blocks are calculated.} |
476 |
> |
\label{oopseFig:dynamicPropsProcess} |
477 |
> |
\end{figure} |
478 |
> |
|
479 |
> |
The options available for DynamicProps are as follows: |
480 |
> |
\begin{longtable}[c]{|EFG|} |
481 |
> |
\caption{DynamicProps Command-line Options} |
482 |
> |
\\ \hline |
483 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
484 |
> |
\endhead |
485 |
> |
\hline |
486 |
> |
\endfoot |
487 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
488 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
489 |
> |
-i& {\tt -{}-input} & input dump file \\ |
490 |
> |
-o& {\tt -{}-output} & output file name \\ |
491 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
492 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
493 |
> |
\hline |
494 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
495 |
> |
\hline |
496 |
> |
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
497 |
> |
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
498 |
> |
-d& {\tt -{}-dcorr} & compute dipole correlation function |
499 |
> |
\end{longtable} |
500 |
> |
|
501 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
502 |
> |
|
503 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
504 |
> |
|
505 |
> |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
506 |
> |
be opened by other molecular dynamics viewers such as Jmol and |
507 |
> |
VMD\cite{Humphrey1996}. The options available for Dump2XYZ are as |
508 |
> |
follows: |
509 |
> |
|
510 |
> |
|
511 |
> |
\begin{longtable}[c]{|EFG|} |
512 |
> |
\caption{Dump2XYZ Command-line Options} |
513 |
> |
\\ \hline |
514 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
515 |
> |
\endhead |
516 |
> |
\hline |
517 |
> |
\endfoot |
518 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
519 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
520 |
> |
-i & {\tt -{}-input} & input dump file \\ |
521 |
> |
-o & {\tt -{}-output} & output file name \\ |
522 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
523 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
524 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
525 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
526 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
527 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
528 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
529 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
530 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
531 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
532 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
533 |
> |
converted. \\ |
534 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
535 |
> |
& {\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}. |
536 |
> |
\end{longtable} |
537 |
> |
|
538 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
539 |
> |
The options available for Hydro are as follows: |
540 |
> |
\begin{longtable}[c]{|EFG|} |
541 |
> |
\caption{Hydrodynamics Command-line Options} |
542 |
> |
\\ \hline |
543 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
544 |
> |
\endhead |
545 |
> |
\hline |
546 |
> |
\endfoot |
547 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
548 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
549 |
> |
-i & {\tt -{}-input} & input dump file \\ |
550 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
551 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
552 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
553 |
> |
\end{longtable} |