1 |
< |
\chapter{\label{chapt:appendix}APPENDIX} |
1 |
> |
\appendix |
2 |
> |
\chapter{\label{chapt:oopse}Object-Oriented Parallel Simulation Engine} |
3 |
|
|
4 |
+ |
Absence of applying modern software development practices is the |
5 |
+ |
bottleneck of Scientific Computing community\cite{Wilson2006}. In |
6 |
+ |
the last 20 years , there are quite a few MD packages that were |
7 |
+ |
developed to solve common MD problems and perform robust simulations |
8 |
+ |
. However, many of the codes are legacy programs that are either |
9 |
+ |
poorly organized or extremely complex. Usually, these packages were |
10 |
+ |
contributed by scientists without official computer science |
11 |
+ |
training. The development of most MD applications are lack of strong |
12 |
+ |
coordination to enforce design and programming guidelines. Moreover, |
13 |
+ |
most MD programs also suffer from missing design and implement |
14 |
+ |
documents which is crucial to the maintenance and extensibility. |
15 |
+ |
Along the way of studying structural and dynamic processes in |
16 |
+ |
condensed phase systems like biological membranes and nanoparticles, |
17 |
+ |
we developed and maintained an Object-Oriented Parallel Simulation |
18 |
+ |
Engine ({\sc OOPSE}). This new molecular dynamics package has some |
19 |
+ |
unique features |
20 |
+ |
\begin{enumerate} |
21 |
+ |
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
22 |
+ |
atom types (transition metals, point dipoles, sticky potentials, |
23 |
+ |
Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
24 |
+ |
degrees of freedom), as well as rigid bodies. |
25 |
+ |
\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
26 |
+ |
Beowulf clusters to obtain very efficient parallelism. |
27 |
+ |
\item {\sc OOPSE} integrates the equations of motion using advanced methods for |
28 |
+ |
orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T |
29 |
+ |
ensembles. |
30 |
+ |
\item {\sc OOPSE} can carry out simulations on metallic systems using the |
31 |
+ |
Embedded Atom Method (EAM) as well as the Sutton-Chen potential. |
32 |
+ |
\item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals. |
33 |
+ |
\item {\sc OOPSE} can simulate systems containing the extremely efficient |
34 |
+ |
extended-Soft Sticky Dipole (SSD/E) model for water. |
35 |
+ |
\end{enumerate} |
36 |
+ |
|
37 |
+ |
\section{\label{appendixSection:architecture }Architecture} |
38 |
+ |
|
39 |
+ |
Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE} |
40 |
+ |
uses C++ Standard Template Library (STL) and fortran modules as the |
41 |
+ |
foundation. As an extensive set of the STL and Fortran90 modules, |
42 |
+ |
{\sc Base Classes} provide generic implementations of mathematical |
43 |
+ |
objects (e.g., matrices, vectors, polynomials, random number |
44 |
+ |
generators) and advanced data structures and algorithms(e.g., tuple, |
45 |
+ |
bitset, generic data, string manipulation). The molecular data |
46 |
+ |
structures for the representation of atoms, bonds, bends, torsions, |
47 |
+ |
rigid bodies and molecules \textit{etc} are contained in the {\sc |
48 |
+ |
Kernel} which is implemented with {\sc Base Classes} and are |
49 |
+ |
carefully designed to provide maximum extensibility and flexibility. |
50 |
+ |
The functionality required for applications is provide by the third |
51 |
+ |
layer which contains Input/Output, Molecular Mechanics and Structure |
52 |
+ |
modules. Input/Output module not only implements general methods for |
53 |
+ |
file handling, but also defines a generic force field interface. |
54 |
+ |
Another important component of Input/Output module is the meta-data |
55 |
+ |
file parser, which is rewritten using ANother Tool for Language |
56 |
+ |
Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular |
57 |
+ |
Mechanics module consists of energy minimization and a wide |
58 |
+ |
varieties of integration methods(see Chap.~\ref{chapt:methodology}). |
59 |
+ |
The structure module contains a flexible and powerful selection |
60 |
+ |
library which syntax is elaborated in |
61 |
+ |
Sec.~\ref{appendixSection:syntax}. The top layer is made of the main |
62 |
+ |
program of the package, \texttt{oopse} and it corresponding parallel |
63 |
+ |
version \texttt{oopse\_MPI}, as well as other useful utilities, such |
64 |
+ |
as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
65 |
+ |
\texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}), |
66 |
+ |
\texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}), |
67 |
+ |
\texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics}) |
68 |
+ |
\textit{etc}. |
69 |
+ |
|
70 |
+ |
\begin{figure} |
71 |
+ |
\centering |
72 |
+ |
\includegraphics[width=\linewidth]{architecture.eps} |
73 |
+ |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
74 |
+ |
of {\sc OOPSE}} \label{appendixFig:architecture} |
75 |
+ |
\end{figure} |
76 |
+ |
|
77 |
|
\section{\label{appendixSection:desginPattern}Design Pattern} |
78 |
|
|
79 |
+ |
Design patterns are optimal solutions to commonly-occurring problems |
80 |
+ |
in software design. Although originated as an architectural concept |
81 |
+ |
for buildings and towns by Christopher Alexander |
82 |
+ |
\cite{Alexander1987}, software patterns first became popular with |
83 |
+ |
the wide acceptance of the book, Design Patterns: Elements of |
84 |
+ |
Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
85 |
+ |
the experience, knowledge and insights of developers who have |
86 |
+ |
successfully used these patterns in their own work. Patterns are |
87 |
+ |
reusable. They provide a ready-made solution that can be adapted to |
88 |
+ |
different problems as necessary. Pattern are expressive. they |
89 |
+ |
provide a common vocabulary of solutions that can express large |
90 |
+ |
solutions succinctly. |
91 |
|
|
92 |
< |
\subsection{\label{appendixSection:visitorPattern}Visitor Pattern} |
92 |
> |
Patterns are usually described using a format that includes the |
93 |
> |
following information: |
94 |
> |
\begin{enumerate} |
95 |
> |
\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
96 |
> |
discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
97 |
> |
in the literature. In this case it is common practice to document these nicknames or synonyms under |
98 |
> |
the heading of \emph{Aliases} or \emph{Also Known As}. |
99 |
> |
\item The \emph{motivation} or \emph{context} that this pattern applies |
100 |
> |
to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
101 |
> |
\item The \emph{solution} to the problem that the pattern |
102 |
> |
addresses. It describes how to construct the necessary work products. The description may include |
103 |
> |
pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
104 |
> |
collaborations, to show how the problem is solved. |
105 |
> |
\item The \emph{consequences} of using the given solution to solve a |
106 |
> |
problem, both positive and negative. |
107 |
> |
\end{enumerate} |
108 |
|
|
109 |
< |
\subsection{\label{appendixSection:templatePattern}Template Pattern} |
109 |
> |
As one of the latest advanced techniques emerged from |
110 |
> |
object-oriented community, design patterns were applied in some of |
111 |
> |
the modern scientific software applications, such as JMol, {\sc |
112 |
> |
OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2005} |
113 |
> |
\textit{etc}. The following sections enumerates some of the patterns |
114 |
> |
used in {\sc OOPSE}. |
115 |
|
|
116 |
< |
\subsection{\label{appendixSection:factoryPattern}Factory Pattern} |
116 |
> |
\subsection{\label{appendixSection:singleton}Singleton} |
117 |
|
|
118 |
< |
\section{\label{appendixSection:hierarchy}Hierarchy} |
118 |
> |
The Singleton pattern not only provides a mechanism to restrict |
119 |
> |
instantiation of a class to one object, but also provides a global |
120 |
> |
point of access to the object. Currently implemented as a global |
121 |
> |
variable, the logging utility which reports error and warning |
122 |
> |
messages to the console in {\sc OOPSE} is a good candidate for |
123 |
> |
applying the Singleton pattern to avoid the global namespace |
124 |
> |
pollution.Although the singleton pattern can be implemented in |
125 |
> |
various ways to account for different aspects of the software |
126 |
> |
designs, such as lifespan control \textit{etc}, we only use the |
127 |
> |
static data approach in {\sc OOPSE}. IntegratorFactory class is |
128 |
> |
declared as |
129 |
|
|
130 |
< |
\section{\label{appendixSection:selectionSyntax}Selection Syntax} |
130 |
> |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
131 |
|
|
132 |
< |
\section{\label{appendixSection:hydrodynamics}Hydrodynamics} |
132 |
> |
class IntegratorFactory { |
133 |
> |
public: |
134 |
> |
static IntegratorFactory* |
135 |
> |
getInstance(); |
136 |
> |
protected: |
137 |
> |
IntegratorFactory(); |
138 |
> |
private: |
139 |
> |
static IntegratorFactory* instance_; |
140 |
> |
}; |
141 |
|
|
142 |
< |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
142 |
> |
\end{lstlisting} |
143 |
|
|
144 |
< |
\subsection{\label{appendixSection:staticProps}Factory Properties} |
144 |
> |
The corresponding implementation is |
145 |
|
|
146 |
< |
\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
146 |
> |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
147 |
> |
|
148 |
> |
IntegratorFactory::instance_ = NULL; |
149 |
> |
|
150 |
> |
IntegratorFactory* getInstance() { |
151 |
> |
if (instance_ == NULL){ |
152 |
> |
instance_ = new IntegratorFactory; |
153 |
> |
} |
154 |
> |
return instance_; |
155 |
> |
} |
156 |
> |
|
157 |
> |
\end{lstlisting} |
158 |
> |
|
159 |
> |
Since constructor is declared as protected, a client can not |
160 |
> |
instantiate IntegratorFactory directly. Moreover, since the member |
161 |
> |
function getInstance serves as the only entry of access to |
162 |
> |
IntegratorFactory, this approach fulfills the basic requirement, a |
163 |
> |
single instance. Another consequence of this approach is the |
164 |
> |
automatic destruction since static data are destroyed upon program |
165 |
> |
termination. |
166 |
> |
|
167 |
> |
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
168 |
> |
|
169 |
> |
Categoried as a creational pattern, the Factory Method pattern deals |
170 |
> |
with the problem of creating objects without specifying the exact |
171 |
> |
class of object that will be created. Factory Method is typically |
172 |
> |
implemented by delegating the creation operation to the subclasses. |
173 |
> |
Parameterized Factory pattern where factory method ( |
174 |
> |
createIntegrator member function) creates products based on the |
175 |
> |
identifier (see List.~\ref{appendixScheme:factoryDeclaration}). If |
176 |
> |
the identifier has been already registered, the factory method will |
177 |
> |
invoke the corresponding creator (see List.~\ref{integratorCreator}) |
178 |
> |
which utilizes the modern C++ template technique to avoid excess |
179 |
> |
subclassing. |
180 |
> |
|
181 |
> |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
182 |
> |
|
183 |
> |
class IntegratorFactory { |
184 |
> |
public: |
185 |
> |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
186 |
> |
|
187 |
> |
bool registerIntegrator(IntegratorCreator* creator) { |
188 |
> |
return creatorMap_.insert(creator->getIdent(), creator).second; |
189 |
> |
} |
190 |
> |
|
191 |
> |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
192 |
> |
Integrator* result = NULL; |
193 |
> |
CreatorMapType::iterator i = creatorMap_.find(id); |
194 |
> |
if (i != creatorMap_.end()) { |
195 |
> |
result = (i->second)->create(info); |
196 |
> |
} |
197 |
> |
return result; |
198 |
> |
} |
199 |
> |
|
200 |
> |
private: |
201 |
> |
CreatorMapType creatorMap_; |
202 |
> |
}; |
203 |
> |
\end{lstlisting} |
204 |
> |
|
205 |
> |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
206 |
> |
|
207 |
> |
class IntegratorCreator { |
208 |
> |
public: |
209 |
> |
IntegratorCreator(const string& ident) : ident_(ident) {} |
210 |
> |
|
211 |
> |
const string& getIdent() const { return ident_; } |
212 |
> |
|
213 |
> |
virtual Integrator* create(SimInfo* info) const = 0; |
214 |
> |
|
215 |
> |
private: |
216 |
> |
string ident_; |
217 |
> |
}; |
218 |
> |
|
219 |
> |
template<class ConcreteIntegrator> |
220 |
> |
class IntegratorBuilder : public IntegratorCreator { |
221 |
> |
public: |
222 |
> |
IntegratorBuilder(const string& ident) |
223 |
> |
: IntegratorCreator(ident) {} |
224 |
> |
virtual Integrator* create(SimInfo* info) const { |
225 |
> |
return new ConcreteIntegrator(info); |
226 |
> |
} |
227 |
> |
}; |
228 |
> |
\end{lstlisting} |
229 |
> |
|
230 |
> |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
231 |
> |
|
232 |
> |
The visitor pattern is designed to decouple the data structure and |
233 |
> |
algorithms used upon them by collecting related operation from |
234 |
> |
element classes into other visitor classes, which is equivalent to |
235 |
> |
adding virtual functions into a set of classes without modifying |
236 |
> |
their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
237 |
> |
structure of Visitor pattern which is used extensively in {\tt |
238 |
> |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
239 |
> |
distinct operations are performed on different StuntDoubles (See the |
240 |
> |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
241 |
> |
in List.~\ref{appendixScheme:element}). Since the hierarchies |
242 |
> |
remains stable, it is easy to define a visit operation (see |
243 |
> |
List.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
244 |
> |
Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
245 |
> |
manages a priority visitor list and handles the execution of every |
246 |
> |
visitor in the priority list on different StuntDoubles. |
247 |
> |
|
248 |
> |
\begin{figure} |
249 |
> |
\centering |
250 |
> |
\includegraphics[width=\linewidth]{visitor.eps} |
251 |
> |
\caption[The UML class diagram of Visitor patten] {The UML class |
252 |
> |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
253 |
> |
\end{figure} |
254 |
> |
|
255 |
> |
\begin{figure} |
256 |
> |
\centering |
257 |
> |
\includegraphics[width=\linewidth]{hierarchy.eps} |
258 |
> |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
259 |
> |
the class hierarchy. } \label{oopseFig:hierarchy} |
260 |
> |
\end{figure} |
261 |
> |
|
262 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
263 |
> |
|
264 |
> |
class StuntDouble { public: |
265 |
> |
virtual void accept(BaseVisitor* v) = 0; |
266 |
> |
}; |
267 |
> |
|
268 |
> |
class Atom: public StuntDouble { public: |
269 |
> |
virtual void accept{BaseVisitor* v*} { |
270 |
> |
v->visit(this); |
271 |
> |
} |
272 |
> |
}; |
273 |
> |
|
274 |
> |
class DirectionalAtom: public Atom { public: |
275 |
> |
virtual void accept{BaseVisitor* v*} { |
276 |
> |
v->visit(this); |
277 |
> |
} |
278 |
> |
}; |
279 |
> |
|
280 |
> |
class RigidBody: public StuntDouble { public: |
281 |
> |
virtual void accept{BaseVisitor* v*} { |
282 |
> |
v->visit(this); |
283 |
> |
} |
284 |
> |
}; |
285 |
> |
|
286 |
> |
\end{lstlisting} |
287 |
> |
|
288 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
289 |
> |
|
290 |
> |
class BaseVisitor{ |
291 |
> |
public: |
292 |
> |
virtual void visit(Atom* atom); |
293 |
> |
virtual void visit(DirectionalAtom* datom); |
294 |
> |
virtual void visit(RigidBody* rb); |
295 |
> |
}; |
296 |
> |
|
297 |
> |
class BaseAtomVisitor:public BaseVisitor{ public: |
298 |
> |
virtual void visit(Atom* atom); |
299 |
> |
virtual void visit(DirectionalAtom* datom); |
300 |
> |
virtual void visit(RigidBody* rb); |
301 |
> |
}; |
302 |
> |
|
303 |
> |
class SSDAtomVisitor:public BaseAtomVisitor{ public: |
304 |
> |
virtual void visit(Atom* atom); |
305 |
> |
virtual void visit(DirectionalAtom* datom); |
306 |
> |
virtual void visit(RigidBody* rb); |
307 |
> |
}; |
308 |
> |
|
309 |
> |
class CompositeVisitor: public BaseVisitor { |
310 |
> |
public: |
311 |
> |
|
312 |
> |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
313 |
> |
typedef VistorListType::iterator VisitorListIterator; |
314 |
> |
virtual void visit(Atom* atom) { |
315 |
> |
VisitorListIterator i; |
316 |
> |
BaseVisitor* curVisitor; |
317 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
318 |
> |
atom->accept(*i); |
319 |
> |
} |
320 |
> |
} |
321 |
> |
|
322 |
> |
virtual void visit(DirectionalAtom* datom) { |
323 |
> |
VisitorListIterator i; |
324 |
> |
BaseVisitor* curVisitor; |
325 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) { |
326 |
> |
atom->accept(*i); |
327 |
> |
} |
328 |
> |
} |
329 |
> |
|
330 |
> |
virtual void visit(RigidBody* rb) { |
331 |
> |
VisitorListIterator i; |
332 |
> |
std::vector<Atom*> myAtoms; |
333 |
> |
std::vector<Atom*>::iterator ai; |
334 |
> |
myAtoms = rb->getAtoms(); |
335 |
> |
for(i = visitorList.begin();i != visitorList.end();++i) {{ |
336 |
> |
rb->accept(*i); |
337 |
> |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
338 |
> |
(*ai)->accept(*i); |
339 |
> |
} |
340 |
> |
} |
341 |
> |
|
342 |
> |
void addVisitor(BaseVisitor* v, int priority); |
343 |
> |
|
344 |
> |
protected: |
345 |
> |
VistorListType visitorList; |
346 |
> |
}; |
347 |
> |
|
348 |
> |
\end{lstlisting} |
349 |
> |
|
350 |
> |
\section{\label{appendixSection:concepts}Concepts} |
351 |
> |
|
352 |
> |
OOPSE manipulates both traditional atoms as well as some objects |
353 |
> |
that {\it behave like atoms}. These objects can be rigid |
354 |
> |
collections of atoms or atoms which have orientational degrees of |
355 |
> |
freedom. A diagram of the class hierarchy is illustrated in |
356 |
> |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
357 |
> |
DirectionalAtom in {\sc OOPSE} have their own names which are |
358 |
> |
specified in the {\tt .md} file. In contrast, RigidBodies are |
359 |
> |
denoted by their membership and index inside a particular molecule: |
360 |
> |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
361 |
> |
on the specifics of the simulation). The names of rigid bodies are |
362 |
> |
generated automatically. For example, the name of the first rigid |
363 |
> |
body in a DMPC molecule is DMPC\_RB\_0. |
364 |
> |
\begin{itemize} |
365 |
> |
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
366 |
> |
integrators and minimizers. |
367 |
> |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
368 |
> |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
369 |
> |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
370 |
> |
DirectionalAtom}s which behaves as a single unit. |
371 |
> |
\end{itemize} |
372 |
> |
|
373 |
> |
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
374 |
> |
|
375 |
> |
{\sc OOPSE} provides a powerful selection utility to select |
376 |
> |
StuntDoubles. The most general form of the select command is: |
377 |
> |
|
378 |
> |
{\tt select {\it expression}}. |
379 |
> |
|
380 |
> |
This expression represents an arbitrary set of StuntDoubles (Atoms |
381 |
> |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
382 |
> |
name expressions, index expressions, predefined sets, user-defined |
383 |
> |
expressions, comparison operators, within expressions, or logical |
384 |
> |
combinations of the above expression types. Expressions can be |
385 |
> |
combined using parentheses and the Boolean operators. |
386 |
> |
|
387 |
> |
\subsection{\label{appendixSection:logical}Logical expressions} |
388 |
> |
|
389 |
> |
The logical operators allow complex queries to be constructed out of |
390 |
> |
simpler ones using the standard boolean connectives {\bf and}, {\bf |
391 |
> |
or}, {\bf not}. Parentheses can be used to alter the precedence of |
392 |
> |
the operators. |
393 |
> |
|
394 |
> |
\begin{center} |
395 |
> |
\begin{tabular}{|ll|} |
396 |
> |
\hline |
397 |
> |
{\bf logical operator} & {\bf equivalent operator} \\ |
398 |
> |
\hline |
399 |
> |
and & ``\&'', ``\&\&'' \\ |
400 |
> |
or & ``$|$'', ``$||$'', ``,'' \\ |
401 |
> |
not & ``!'' \\ |
402 |
> |
\hline |
403 |
> |
\end{tabular} |
404 |
> |
\end{center} |
405 |
> |
|
406 |
> |
\subsection{\label{appendixSection:name}Name expressions} |
407 |
> |
|
408 |
> |
\begin{center} |
409 |
> |
\begin{tabular}{|llp{2in}|} |
410 |
> |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
411 |
> |
of |
412 |
> |
examples} \\ |
413 |
> |
\hline expression without ``.'' & select DMPC & select all |
414 |
> |
StuntDoubles |
415 |
> |
belonging to all DMPC molecules \\ |
416 |
> |
& select C* & select all atoms which have atom types beginning with C |
417 |
> |
\\ |
418 |
> |
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
419 |
> |
only select the rigid bodies, and not the atoms belonging to them). \\ |
420 |
> |
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
421 |
> |
O\_TIP3P |
422 |
> |
atoms belonging to TIP3P molecules \\ |
423 |
> |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
424 |
> |
the first |
425 |
> |
RigidBody in each DMPC molecule \\ |
426 |
> |
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
427 |
> |
molecule \\ |
428 |
> |
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
429 |
> |
select all atoms |
430 |
> |
belonging to all rigid bodies within all DMPC molecules \\ |
431 |
> |
\hline |
432 |
> |
\end{tabular} |
433 |
> |
\end{center} |
434 |
> |
|
435 |
> |
\subsection{\label{appendixSection:index}Index expressions} |
436 |
> |
|
437 |
> |
\begin{center} |
438 |
> |
\begin{tabular}{|lp{4in}|} |
439 |
> |
\hline |
440 |
> |
{\bf examples} & {\bf translation of examples} \\ |
441 |
> |
\hline |
442 |
> |
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
443 |
> |
select 20 to 30 & select all of the StuntDoubles belonging to |
444 |
> |
molecules which have global indices between 20 (inclusive) and 30 |
445 |
> |
(exclusive) \\ |
446 |
> |
\hline |
447 |
> |
\end{tabular} |
448 |
> |
\end{center} |
449 |
> |
|
450 |
> |
\subsection{\label{appendixSection:predefined}Predefined sets} |
451 |
> |
|
452 |
> |
\begin{center} |
453 |
> |
\begin{tabular}{|ll|} |
454 |
> |
\hline |
455 |
> |
{\bf keyword} & {\bf description} \\ |
456 |
> |
\hline |
457 |
> |
all & select all StuntDoubles \\ |
458 |
> |
none & select none of the StuntDoubles \\ |
459 |
> |
\hline |
460 |
> |
\end{tabular} |
461 |
> |
\end{center} |
462 |
> |
|
463 |
> |
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
464 |
> |
|
465 |
> |
Users can define arbitrary terms to represent groups of |
466 |
> |
StuntDoubles, and then use the define terms in select commands. The |
467 |
> |
general form for the define command is: {\bf define {\it term |
468 |
> |
expression}}. Once defined, the user can specify such terms in |
469 |
> |
boolean expressions |
470 |
> |
|
471 |
> |
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
472 |
> |
|
473 |
> |
{\tt select SSDWATER} |
474 |
> |
|
475 |
> |
\subsection{\label{appendixSection:comparison}Comparison expressions} |
476 |
> |
|
477 |
> |
StuntDoubles can be selected by using comparision operators on their |
478 |
> |
properties. The general form for the comparison command is: a |
479 |
> |
property name, followed by a comparision operator and then a number. |
480 |
> |
|
481 |
> |
\begin{center} |
482 |
> |
\begin{tabular}{|l|l|} |
483 |
> |
\hline |
484 |
> |
{\bf property} & mass, charge \\ |
485 |
> |
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
486 |
> |
``$<=$'', ``$!=$'' \\ |
487 |
> |
\hline |
488 |
> |
\end{tabular} |
489 |
> |
\end{center} |
490 |
> |
|
491 |
> |
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
492 |
> |
would select StuntDoubles which have mass greater than 16.0 and |
493 |
> |
charges less than -2. |
494 |
> |
|
495 |
> |
\subsection{\label{appendixSection:within}Within expressions} |
496 |
> |
|
497 |
> |
The ``within'' keyword allows the user to select all StuntDoubles |
498 |
> |
within the specified distance (in Angstroms) from a selection, |
499 |
> |
including the selected atom itself. The general form for within |
500 |
> |
selection is: {\tt select within(distance, expression)} |
501 |
> |
|
502 |
> |
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
503 |
> |
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
504 |
> |
atoms. |
505 |
> |
|
506 |
> |
|
507 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
508 |
> |
|
509 |
> |
\subsection{\label{appendixSection:StaticProps}StaticProps} |
510 |
> |
|
511 |
> |
{\tt StaticProps} can compute properties which are averaged over |
512 |
> |
some or all of the configurations that are contained within a dump |
513 |
> |
file. The most common example of a static property that can be |
514 |
> |
computed is the pair distribution function between atoms of type $A$ |
515 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
516 |
> |
also be used to compute the density distributions of other molecules |
517 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
518 |
> |
of a selected atom or rigid body. |
519 |
> |
|
520 |
> |
There are five seperate radial distribution functions availiable in |
521 |
> |
OOPSE. Since every radial distrbution function invlove the |
522 |
> |
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
523 |
> |
-{}-sele2} must be specified to tell StaticProps which bodies to |
524 |
> |
include in the calculation. |
525 |
> |
|
526 |
> |
\begin{description} |
527 |
> |
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
528 |
> |
\begin{equation*} |
529 |
> |
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
530 |
> |
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
531 |
> |
\end{equation*} |
532 |
> |
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
533 |
> |
function. The angle is defined by the intermolecular vector |
534 |
> |
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
535 |
> |
\begin{equation*} |
536 |
> |
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
537 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
538 |
> |
\theta_{ij} - \cos \theta)\rangle |
539 |
> |
\end{equation*} |
540 |
> |
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
541 |
> |
function. The angle is defined by the $z$-axes of the two |
542 |
> |
DirectionalAtoms A and B. |
543 |
> |
\begin{equation*} |
544 |
> |
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
545 |
> |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
546 |
> |
\omega_{ij} - \cos \omega)\rangle |
547 |
> |
\end{equation*} |
548 |
> |
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
549 |
> |
space $\theta, \omega$ defined by the two angles mentioned above. |
550 |
> |
\begin{equation*} |
551 |
> |
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
552 |
> |
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
553 |
> |
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
554 |
> |
\omega)\rangle |
555 |
> |
\end{equation*} |
556 |
> |
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
557 |
> |
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
558 |
> |
and {\tt -{}-refsele} must be given to define A's internal |
559 |
> |
coordinate set as the reference frame for the calculation. |
560 |
> |
\end{description} |
561 |
> |
|
562 |
> |
The vectors (and angles) associated with these angular pair |
563 |
> |
distribution functions are most easily seen in the figure below: |
564 |
> |
|
565 |
> |
\begin{figure} |
566 |
> |
\centering |
567 |
> |
\includegraphics[width=3in]{definition.eps} |
568 |
> |
\caption[Definitions of the angles between directional objects]{ \\ |
569 |
> |
Any two directional objects (DirectionalAtoms and RigidBodies) have |
570 |
> |
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
571 |
> |
their body-fixed frames.} \label{oopseFig:gofr} |
572 |
> |
\end{figure} |
573 |
> |
|
574 |
> |
Due to the fact that the selected StuntDoubles from two selections |
575 |
> |
may be overlapped, {\tt StaticProps} performs the calculation in |
576 |
> |
three stages which are illustrated in |
577 |
> |
Fig.~\ref{oopseFig:staticPropsProcess}. |
578 |
> |
|
579 |
> |
\begin{figure} |
580 |
> |
\centering |
581 |
> |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
582 |
> |
\caption[A representation of the three-stage correlations in |
583 |
> |
\texttt{StaticProps}]{This diagram illustrates three-stage |
584 |
> |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
585 |
> |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
586 |
> |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
587 |
> |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
588 |
> |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
589 |
> |
the contrary, the third stage($C$ and $C$) are completely |
590 |
> |
overlapping} \label{oopseFig:staticPropsProcess} |
591 |
> |
\end{figure} |
592 |
> |
|
593 |
> |
The options available for {\tt StaticProps} are as follows: |
594 |
> |
\begin{longtable}[c]{|EFG|} |
595 |
> |
\caption{StaticProps Command-line Options} |
596 |
> |
\\ \hline |
597 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
598 |
> |
\endhead |
599 |
> |
\hline |
600 |
> |
\endfoot |
601 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
602 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
603 |
> |
-i& {\tt -{}-input} & input dump file \\ |
604 |
> |
-o& {\tt -{}-output} & output file name \\ |
605 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
606 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
607 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
608 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
609 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
610 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
611 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
612 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
613 |
> |
& {\tt -{}-molname} & molecule name \\ |
614 |
> |
& {\tt -{}-begin} & begin internal index \\ |
615 |
> |
& {\tt -{}-end} & end internal index \\ |
616 |
> |
\hline |
617 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
618 |
> |
\hline |
619 |
> |
& {\tt -{}-gofr} & $g(r)$ \\ |
620 |
> |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
621 |
> |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
622 |
> |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
623 |
> |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
624 |
> |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
625 |
> |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
626 |
> |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
627 |
> |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
628 |
> |
\end{longtable} |
629 |
> |
|
630 |
> |
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
631 |
> |
|
632 |
> |
{\tt DynamicProps} computes time correlation functions from the |
633 |
> |
configurations stored in a dump file. Typical examples of time |
634 |
> |
correlation functions are the mean square displacement and the |
635 |
> |
velocity autocorrelation functions. Once again, the selection |
636 |
> |
syntax can be used to specify the StuntDoubles that will be used for |
637 |
> |
the calculation. A general time correlation function can be thought |
638 |
> |
of as: |
639 |
> |
\begin{equation} |
640 |
> |
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
641 |
> |
\end{equation} |
642 |
> |
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
643 |
> |
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
644 |
> |
vector property associated with an atom of type $B$ at a different |
645 |
> |
time $t^{\prime}$. In most autocorrelation functions, the vector |
646 |
> |
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
647 |
> |
$B$) are identical, and the three calculations built in to {\tt |
648 |
> |
DynamicProps} make these assumptions. It is possible, however, to |
649 |
> |
make simple modifications to the {\tt DynamicProps} code to allow |
650 |
> |
the use of {\it cross} time correlation functions (i.e. with |
651 |
> |
different vectors). The ability to use two selection scripts to |
652 |
> |
select different types of atoms is already present in the code. |
653 |
> |
|
654 |
> |
For large simulations, the trajectory files can sometimes reach |
655 |
> |
sizes in excess of several gigabytes. In order to effectively |
656 |
> |
analyze that amount of data. In order to prevent a situation where |
657 |
> |
the program runs out of memory due to large trajectories, |
658 |
> |
\texttt{dynamicProps} will estimate the size of free memory at |
659 |
> |
first, and determine the number of frames in each block, which |
660 |
> |
allows the operating system to load two blocks of data |
661 |
> |
simultaneously without swapping. Upon reading two blocks of the |
662 |
> |
trajectory, \texttt{dynamicProps} will calculate the time |
663 |
> |
correlation within the first block and the cross correlations |
664 |
> |
between the two blocks. This second block is then freed and then |
665 |
> |
incremented and the process repeated until the end of the |
666 |
> |
trajectory. Once the end is reached, the first block is freed then |
667 |
> |
incremented, until all frame pairs have been correlated in time. |
668 |
> |
This process is illustrated in |
669 |
> |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
670 |
> |
|
671 |
> |
\begin{figure} |
672 |
> |
\centering |
673 |
> |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
674 |
> |
\caption[A representation of the block correlations in |
675 |
> |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
676 |
> |
processing in \texttt{dynamicProps}. The shaded region represents |
677 |
> |
the self correlation of the block, and the open blocks are read one |
678 |
> |
at a time and the cross correlations between blocks are calculated.} |
679 |
> |
\label{oopseFig:dynamicPropsProcess} |
680 |
> |
\end{figure} |
681 |
> |
|
682 |
> |
The options available for DynamicProps are as follows: |
683 |
> |
\begin{longtable}[c]{|EFG|} |
684 |
> |
\caption{DynamicProps Command-line Options} |
685 |
> |
\\ \hline |
686 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
687 |
> |
\endhead |
688 |
> |
\hline |
689 |
> |
\endfoot |
690 |
> |
-h& {\tt -{}-help} & Print help and exit \\ |
691 |
> |
-V& {\tt -{}-version} & Print version and exit \\ |
692 |
> |
-i& {\tt -{}-input} & input dump file \\ |
693 |
> |
-o& {\tt -{}-output} & output file name \\ |
694 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
695 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
696 |
> |
\hline |
697 |
> |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
698 |
> |
\hline |
699 |
> |
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
700 |
> |
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
701 |
> |
-d& {\tt -{}-dcorr} & compute dipole correlation function |
702 |
> |
\end{longtable} |
703 |
> |
|
704 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
705 |
> |
|
706 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
707 |
> |
|
708 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
709 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
710 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
711 |
> |
as follows: |
712 |
> |
|
713 |
> |
|
714 |
> |
\begin{longtable}[c]{|EFG|} |
715 |
> |
\caption{Dump2XYZ Command-line Options} |
716 |
> |
\\ \hline |
717 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
718 |
> |
\endhead |
719 |
> |
\hline |
720 |
> |
\endfoot |
721 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
722 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
723 |
> |
-i & {\tt -{}-input} & input dump file \\ |
724 |
> |
-o & {\tt -{}-output} & output file name \\ |
725 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
726 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
727 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
728 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
729 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
730 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
731 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
732 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
733 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
734 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
735 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
736 |
> |
converted. \\ |
737 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
738 |
> |
& {\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}. |
739 |
> |
\end{longtable} |
740 |
> |
|
741 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
742 |
> |
|
743 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
744 |
> |
center of resistance. Both tensors at the center of diffusion can |
745 |
> |
also be reported from the program, as well as the coordinates for |
746 |
> |
the beads which are used to approximate the arbitrary shapes. The |
747 |
> |
options available for Hydro are as follows: |
748 |
> |
\begin{longtable}[c]{|EFG|} |
749 |
> |
\caption{Hydrodynamics Command-line Options} |
750 |
> |
\\ \hline |
751 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
752 |
> |
\endhead |
753 |
> |
\hline |
754 |
> |
\endfoot |
755 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
756 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
757 |
> |
-i & {\tt -{}-input} & input dump file \\ |
758 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
759 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
760 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
761 |
> |
\end{longtable} |