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 |
7 |
packages\cite{Brooks1983, Vincent1995, Kale1999} that were developed |
8 |
to solve common MD problems and perform robust simulations . |
9 |
Unfortunately, most of them are commercial programs that are either |
10 |
poorly written or extremely complicate. Consequently, it prevents |
11 |
the researchers to reuse or extend those packages to do cutting-edge |
12 |
research effectively. Along the way of studying structural and |
13 |
dynamic processes in condensed phase systems like biological |
14 |
membranes and nanoparticles, we developed an open source |
15 |
Object-Oriented Parallel Simulation Engine ({\sc OOPSE}). This new |
16 |
molecular dynamics package has some unique features |
17 |
\begin{enumerate} |
18 |
\item {\sc OOPSE} performs Molecular Dynamics (MD) simulations on non-standard |
19 |
atom types (transition metals, point dipoles, sticky potentials, |
20 |
Gay-Berne ellipsoids, or other "lumpy"atoms with orientational |
21 |
degrees of freedom), as well as rigid bodies. |
22 |
\item {\sc OOPSE} uses a force-based decomposition algorithm using MPI on cheap |
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Beowulf clusters to obtain very efficient parallelism. |
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\item {\sc OOPSE} integrates the equations of motion using advanced methods for |
25 |
orientational dynamics in NVE, NVT, NPT, NPAT, and NP$\gamma$T |
26 |
ensembles. |
27 |
\item {\sc OOPSE} can carry out simulations on metallic systems using the |
28 |
Embedded Atom Method (EAM) as well as the Sutton-Chen potential. |
29 |
\item {\sc OOPSE} can perform simulations on Gay-Berne liquid crystals. |
30 |
\item {\sc OOPSE} can simulate systems containing the extremely efficient |
31 |
extended-Soft Sticky Dipole (SSD/E) model for water. |
32 |
\end{enumerate} |
33 |
|
34 |
\section{\label{appendixSection:architecture }Architecture} |
35 |
|
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Mainly written by \texttt{C/C++} and \texttt{Fortran90}, {\sc OOPSE} |
37 |
uses C++ Standard Template Library (STL) and fortran modules as the |
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foundation. As an extensive set of the STL and Fortran90 modules, |
39 |
{\sc Base Classes} provide generic implementations of mathematical |
40 |
objects (e.g., matrices, vectors, polynomials, random number |
41 |
generators) and advanced data structures and algorithms(e.g., tuple, |
42 |
bitset, generic data, string manipulation). The molecular data |
43 |
structures for the representation of atoms, bonds, bends, torsions, |
44 |
rigid bodies and molecules \textit{etc} are contained in the {\sc |
45 |
Kernel} which is implemented with {\sc Base Classes} and are |
46 |
carefully designed to provide maximum extensibility and flexibility. |
47 |
The functionality required for applications is provide by the third |
48 |
layer which contains Input/Output, Molecular Mechanics and Structure |
49 |
modules. Input/Output module not only implements general methods for |
50 |
file handling, but also defines a generic force field interface. |
51 |
Another important component of Input/Output module is the meta-data |
52 |
file parser, which is rewritten using ANother Tool for Language |
53 |
Recognition(ANTLR)\cite{Parr1995, Schaps1999} syntax. The Molecular |
54 |
Mechanics module consists of energy minimization and a wide |
55 |
varieties of integration methods(see Chap.~\ref{chapt:methodology}). |
56 |
The structure module contains a flexible and powerful selection |
57 |
library which syntax is elaborated in |
58 |
Sec.~\ref{appendixSection:syntax}. The top layer is made of the main |
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program of the package, \texttt{oopse} and it corresponding parallel |
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version \texttt{oopse\_MPI}, as well as other useful utilities, such |
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as \texttt{StatProps} (see Sec.~\ref{appendixSection:StaticProps}), |
62 |
\texttt{DynamicProps} (see Sec.~\ref{appendixSection:DynamicProps}), |
63 |
\texttt{Dump2XYZ} (see Sec.~\ref{appendixSection:Dump2XYZ}), |
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\texttt{Hydro} (see Sec.~\ref{appendixSection:hydrodynamics}) |
65 |
\textit{etc}. |
66 |
|
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\begin{figure} |
68 |
\centering |
69 |
\includegraphics[width=\linewidth]{architecture.eps} |
70 |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
71 |
of {\sc OOPSE}} \label{appendixFig:architecture} |
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\end{figure} |
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|
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\section{\label{appendixSection:desginPattern}Design Pattern} |
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|
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Design patterns are optimal solutions to commonly-occurring problems |
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in software design. Although originated as an architectural concept |
78 |
for buildings and towns by Christopher Alexander |
79 |
\cite{Alexander1987}, software patterns first became popular with |
80 |
the wide acceptance of the book, Design Patterns: Elements of |
81 |
Reusable Object-Oriented Software \cite{Gamma1994}. Patterns reflect |
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the experience, knowledge and insights of developers who have |
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successfully used these patterns in their own work. Patterns are |
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reusable. They provide a ready-made solution that can be adapted to |
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different problems as necessary. Pattern are expressive. they |
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provide a common vocabulary of solutions that can express large |
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solutions succinctly. As one of the latest advanced techniques |
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emerged from object-oriented community, design patterns were applied |
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in some of the modern scientific software applications, such as |
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JMol, {\sc OOPSE}\cite{Meineke2005} and PROTOMOL\cite{Matthey2004} |
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\textit{etc}. The following sections enumerates some of the patterns |
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used in {\sc OOPSE}. |
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|
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\subsection{\label{appendixSection:singleton}Singleton} |
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|
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The Singleton pattern not only provides a mechanism to restrict |
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instantiation of a class to one object, but also provides a global |
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point of access to the object. Currently implemented as a global |
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variable, the logging utility which reports error and warning |
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messages to the console in {\sc OOPSE} is a good candidate for |
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applying the Singleton pattern to avoid the global namespace |
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pollution. Although the singleton pattern can be implemented in |
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various ways to account for different aspects of the software |
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designs, such as lifespan control \textit{etc}, we only use the |
105 |
static data approach in {\sc OOPSE}. The declaration and |
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implementation of IntegratorFactory class are given by declared in |
107 |
List.~\ref{appendixScheme:singletonDeclaration} and |
108 |
Scheme.~\ref{appendixScheme:singletonImplementation} respectively. |
109 |
Since constructor is declared as protected, a client can not |
110 |
instantiate IntegratorFactory directly. Moreover, since the member |
111 |
function getInstance serves as the only entry of access to |
112 |
IntegratorFactory, this approach fulfills the basic requirement, a |
113 |
single instance. Another consequence of this approach is the |
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automatic destruction since static data are destroyed upon program |
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termination. |
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\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] The declaration of of simple Singleton pattern.},label={appendixScheme:singletonDeclaration}] |
117 |
|
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class IntegratorFactory { |
119 |
public: |
120 |
static IntegratorFactory* |
121 |
getInstance(); |
122 |
protected: |
123 |
IntegratorFactory(); |
124 |
private: |
125 |
static IntegratorFactory* instance_; |
126 |
}; |
127 |
|
128 |
\end{lstlisting} |
129 |
|
130 |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] The implementation of simple Singleton pattern.},label={appendixScheme:singletonImplementation}] |
131 |
|
132 |
IntegratorFactory::instance_ = NULL; |
133 |
|
134 |
IntegratorFactory* getInstance() { |
135 |
if (instance_ == NULL){ |
136 |
instance_ = new IntegratorFactory; |
137 |
} |
138 |
return instance_; |
139 |
} |
140 |
|
141 |
\end{lstlisting} |
142 |
|
143 |
|
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\subsection{\label{appendixSection:factoryMethod}Factory Method} |
145 |
|
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Categoried as a creational pattern, the Factory Method pattern deals |
147 |
with the problem of creating objects without specifying the exact |
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class of object that will be created. Factory Method is typically |
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implemented by delegating the creation operation to the subclasses. |
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Parameterized Factory pattern where factory method ( |
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createIntegrator member function) creates products based on the |
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identifier (see Scheme.~\ref{appendixScheme:factoryDeclaration}). If |
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the identifier has been already registered, the factory method will |
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invoke the corresponding creator (see |
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Scheme.~\ref{appendixScheme:integratorCreator}) which utilizes the |
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modern C++ template technique to avoid excess subclassing. |
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|
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\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (I)]Source code of IntegratorFactory class.},label={appendixScheme:factoryDeclaration}] |
159 |
|
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class IntegratorFactory { |
161 |
public: |
162 |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
163 |
|
164 |
bool registerIntegrator(IntegratorCreator* creator) { |
165 |
return creatorMap_.insert(creator->getIdent(), creator).second; |
166 |
} |
167 |
|
168 |
Integrator* createIntegrator(const string& id, SimInfo* info) { |
169 |
Integrator* result = NULL; |
170 |
CreatorMapType::iterator i = creatorMap_.find(id); |
171 |
if (i != creatorMap_.end()) { |
172 |
result = (i->second)->create(info); |
173 |
} |
174 |
return result; |
175 |
} |
176 |
|
177 |
private: |
178 |
CreatorMapType creatorMap_; |
179 |
}; |
180 |
\end{lstlisting} |
181 |
|
182 |
\begin{lstlisting}[float,caption={[The implementation of Parameterized Factory pattern (III)]Source code of creator classes.},label={appendixScheme:integratorCreator}] |
183 |
|
184 |
class IntegratorCreator { |
185 |
public: |
186 |
IntegratorCreator(const string& ident) : ident_(ident) {} |
187 |
|
188 |
const string& getIdent() const { return ident_; } |
189 |
|
190 |
virtual Integrator* create(SimInfo* info) const = 0; |
191 |
|
192 |
private: |
193 |
string ident_; |
194 |
}; |
195 |
|
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template<class ConcreteIntegrator> |
197 |
class IntegratorBuilder : public IntegratorCreator { |
198 |
public: |
199 |
IntegratorBuilder(const string& ident) |
200 |
: IntegratorCreator(ident) {} |
201 |
virtual Integrator* create(SimInfo* info) const { |
202 |
return new ConcreteIntegrator(info); |
203 |
} |
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}; |
205 |
\end{lstlisting} |
206 |
|
207 |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
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|
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The visitor pattern is designed to decouple the data structure and |
210 |
algorithms used upon them by collecting related operation from |
211 |
element classes into other visitor classes, which is equivalent to |
212 |
adding virtual functions into a set of classes without modifying |
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their interfaces. Fig.~\ref{appendixFig:visitorUML} demonstrates the |
214 |
structure of Visitor pattern which is used extensively in {\tt |
215 |
Dump2XYZ}. In order to convert an OOPSE dump file, a series of |
216 |
distinct operations are performed on different StuntDoubles (See the |
217 |
class hierarchy in Fig.~\ref{oopseFig:hierarchy} and the declaration |
218 |
in Scheme.~\ref{appendixScheme:element}). Since the hierarchies |
219 |
remains stable, it is easy to define a visit operation (see |
220 |
Scheme.~\ref{appendixScheme:visitor}) for each class of StuntDouble. |
221 |
Note that using Composite pattern\cite{Gamma1994}, CompositVisitor |
222 |
manages a priority visitor list and handles the execution of every |
223 |
visitor in the priority list on different StuntDoubles. |
224 |
|
225 |
\begin{figure} |
226 |
\centering |
227 |
\includegraphics[width=\linewidth]{visitor.eps} |
228 |
\caption[The UML class diagram of Visitor patten] {The UML class |
229 |
diagram of Visitor patten.} \label{appendixFig:visitorUML} |
230 |
\end{figure} |
231 |
|
232 |
\begin{figure} |
233 |
\centering |
234 |
\includegraphics[width=\linewidth]{hierarchy.eps} |
235 |
\caption[Class hierarchy for ojects in {\sc OOPSE}]{ A diagram of |
236 |
the class hierarchy. } \label{oopseFig:hierarchy} |
237 |
\end{figure} |
238 |
|
239 |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
240 |
|
241 |
class StuntDouble { public: |
242 |
virtual void accept(BaseVisitor* v) = 0; |
243 |
}; |
244 |
|
245 |
class Atom: public StuntDouble { public: |
246 |
virtual void accept{BaseVisitor* v*} { |
247 |
v->visit(this); |
248 |
} |
249 |
}; |
250 |
|
251 |
class DirectionalAtom: public Atom { public: |
252 |
virtual void accept{BaseVisitor* v*} { |
253 |
v->visit(this); |
254 |
} |
255 |
}; |
256 |
|
257 |
class RigidBody: public StuntDouble { public: |
258 |
virtual void accept{BaseVisitor* v*} { |
259 |
v->visit(this); |
260 |
} |
261 |
}; |
262 |
|
263 |
\end{lstlisting} |
264 |
|
265 |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
266 |
|
267 |
class BaseVisitor{ |
268 |
public: |
269 |
virtual void visit(Atom* atom); |
270 |
virtual void visit(DirectionalAtom* datom); |
271 |
virtual void visit(RigidBody* rb); |
272 |
}; |
273 |
|
274 |
class BaseAtomVisitor:public BaseVisitor{ public: |
275 |
virtual void visit(Atom* atom); |
276 |
virtual void visit(DirectionalAtom* datom); |
277 |
virtual void visit(RigidBody* rb); |
278 |
}; |
279 |
|
280 |
class CompositeVisitor: public BaseVisitor { |
281 |
public: |
282 |
|
283 |
typedef list<pair<BaseVisitor*, int> > VistorListType; |
284 |
typedef VistorListType::iterator VisitorListIterator; |
285 |
virtual void visit(Atom* atom) { |
286 |
VisitorListIterator i; |
287 |
BaseVisitor* curVisitor; |
288 |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
289 |
atom->accept(*i); |
290 |
} |
291 |
} |
292 |
|
293 |
virtual void visit(DirectionalAtom* datom) { |
294 |
VisitorListIterator i; |
295 |
BaseVisitor* curVisitor; |
296 |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) { |
297 |
atom->accept(*i); |
298 |
} |
299 |
} |
300 |
|
301 |
virtual void visit(RigidBody* rb) { |
302 |
VisitorListIterator i; |
303 |
std::vector<Atom*> myAtoms; |
304 |
std::vector<Atom*>::iterator ai; |
305 |
myAtoms = rb->getAtoms(); |
306 |
for(i = visitorScheme.begin();i != visitorScheme.end();++i) {{ |
307 |
rb->accept(*i); |
308 |
for(ai = myAtoms.begin(); ai != myAtoms.end(); ++ai){ |
309 |
(*ai)->accept(*i); |
310 |
} |
311 |
} |
312 |
|
313 |
void addVisitor(BaseVisitor* v, int priority); |
314 |
|
315 |
protected: |
316 |
VistorListType visitorList; |
317 |
}; |
318 |
\end{lstlisting} |
319 |
|
320 |
\section{\label{appendixSection:concepts}Concepts} |
321 |
|
322 |
OOPSE manipulates both traditional atoms as well as some objects |
323 |
that {\it behave like atoms}. These objects can be rigid |
324 |
collections of atoms or atoms which have orientational degrees of |
325 |
freedom. A diagram of the class hierarchy is illustrated in |
326 |
Fig.~\ref{oopseFig:hierarchy}. Every Molecule, Atom and |
327 |
DirectionalAtom in {\sc OOPSE} have their own names which are |
328 |
specified in the {\tt .md} file. In contrast, RigidBodies are |
329 |
denoted by their membership and index inside a particular molecule: |
330 |
[MoleculeName]\_RB\_[index] (the contents inside the brackets depend |
331 |
on the specifics of the simulation). The names of rigid bodies are |
332 |
generated automatically. For example, the name of the first rigid |
333 |
body in a DMPC molecule is DMPC\_RB\_0. |
334 |
\begin{itemize} |
335 |
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
336 |
integrators and minimizers. |
337 |
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
338 |
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
339 |
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
340 |
DirectionalAtom}s which behaves as a single unit. |
341 |
\end{itemize} |
342 |
|
343 |
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
344 |
|
345 |
{\sc OOPSE} provides a powerful selection utility to select |
346 |
StuntDoubles. The most general form of the select command is: |
347 |
|
348 |
{\tt select {\it expression}}. |
349 |
|
350 |
This expression represents an arbitrary set of StuntDoubles (Atoms |
351 |
or RigidBodies) in {\sc OOPSE}. Expressions are composed of either |
352 |
name expressions, index expressions, predefined sets, user-defined |
353 |
expressions, comparison operators, within expressions, or logical |
354 |
combinations of the above expression types. Expressions can be |
355 |
combined using parentheses and the Boolean operators. |
356 |
|
357 |
\subsection{\label{appendixSection:logical}Logical expressions} |
358 |
|
359 |
The logical operators allow complex queries to be constructed out of |
360 |
simpler ones using the standard boolean connectives {\bf and}, {\bf |
361 |
or}, {\bf not}. Parentheses can be used to alter the precedence of |
362 |
the operators. |
363 |
|
364 |
\begin{center} |
365 |
\begin{tabular}{|ll|} |
366 |
\hline |
367 |
{\bf logical operator} & {\bf equivalent operator} \\ |
368 |
\hline |
369 |
and & ``\&'', ``\&\&'' \\ |
370 |
or & ``$|$'', ``$||$'', ``,'' \\ |
371 |
not & ``!'' \\ |
372 |
\hline |
373 |
\end{tabular} |
374 |
\end{center} |
375 |
|
376 |
\subsection{\label{appendixSection:name}Name expressions} |
377 |
|
378 |
\begin{center} |
379 |
\begin{tabular}{|llp{2in}|} |
380 |
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
381 |
of |
382 |
examples} \\ |
383 |
\hline expression without ``.'' & select DMPC & select all |
384 |
StuntDoubles |
385 |
belonging to all DMPC molecules \\ |
386 |
& select C* & select all atoms which have atom types beginning with C |
387 |
\\ |
388 |
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
389 |
only select the rigid bodies, and not the atoms belonging to them). \\ |
390 |
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
391 |
O\_TIP3P |
392 |
atoms belonging to TIP3P molecules \\ |
393 |
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
394 |
the first |
395 |
RigidBody in each DMPC molecule \\ |
396 |
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
397 |
molecule \\ |
398 |
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
399 |
select all atoms |
400 |
belonging to all rigid bodies within all DMPC molecules \\ |
401 |
\hline |
402 |
\end{tabular} |
403 |
\end{center} |
404 |
|
405 |
\subsection{\label{appendixSection:index}Index expressions} |
406 |
|
407 |
\begin{center} |
408 |
\begin{tabular}{|lp{4in}|} |
409 |
\hline |
410 |
{\bf examples} & {\bf translation of examples} \\ |
411 |
\hline |
412 |
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
413 |
select 20 to 30 & select all of the StuntDoubles belonging to |
414 |
molecules which have global indices between 20 (inclusive) and 30 |
415 |
(exclusive) \\ |
416 |
\hline |
417 |
\end{tabular} |
418 |
\end{center} |
419 |
|
420 |
\subsection{\label{appendixSection:predefined}Predefined sets} |
421 |
|
422 |
\begin{center} |
423 |
\begin{tabular}{|ll|} |
424 |
\hline |
425 |
{\bf keyword} & {\bf description} \\ |
426 |
\hline |
427 |
all & select all StuntDoubles \\ |
428 |
none & select none of the StuntDoubles \\ |
429 |
\hline |
430 |
\end{tabular} |
431 |
\end{center} |
432 |
|
433 |
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
434 |
|
435 |
Users can define arbitrary terms to represent groups of |
436 |
StuntDoubles, and then use the define terms in select commands. The |
437 |
general form for the define command is: {\bf define {\it term |
438 |
expression}}. Once defined, the user can specify such terms in |
439 |
boolean expressions |
440 |
|
441 |
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
442 |
|
443 |
{\tt select SSDWATER} |
444 |
|
445 |
\subsection{\label{appendixSection:comparison}Comparison expressions} |
446 |
|
447 |
StuntDoubles can be selected by using comparision operators on their |
448 |
properties. The general form for the comparison command is: a |
449 |
property name, followed by a comparision operator and then a number. |
450 |
|
451 |
\begin{center} |
452 |
\begin{tabular}{|l|l|} |
453 |
\hline |
454 |
{\bf property} & mass, charge \\ |
455 |
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
456 |
``$<=$'', ``$!=$'' \\ |
457 |
\hline |
458 |
\end{tabular} |
459 |
\end{center} |
460 |
|
461 |
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
462 |
would select StuntDoubles which have mass greater than 16.0 and |
463 |
charges less than -2. |
464 |
|
465 |
\subsection{\label{appendixSection:within}Within expressions} |
466 |
|
467 |
The ``within'' keyword allows the user to select all StuntDoubles |
468 |
within the specified distance (in Angstroms) from a selection, |
469 |
including the selected atom itself. The general form for within |
470 |
selection is: {\tt select within(distance, expression)} |
471 |
|
472 |
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
473 |
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
474 |
atoms. |
475 |
|
476 |
|
477 |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
478 |
|
479 |
\subsection{\label{appendixSection:StaticProps}StaticProps} |
480 |
|
481 |
{\tt StaticProps} can compute properties which are averaged over |
482 |
some or all of the configurations that are contained within a dump |
483 |
file. The most common example of a static property that can be |
484 |
computed is the pair distribution function between atoms of type $A$ |
485 |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
486 |
also be used to compute the density distributions of other molecules |
487 |
in a reference frame {\it fixed to the body-fixed reference frame} |
488 |
of a selected atom or rigid body. Due to the fact that the selected |
489 |
StuntDoubles from two selections may be overlapped, {\tt |
490 |
StaticProps} performs the calculation in three stages which are |
491 |
illustrated in Fig.~\ref{oopseFig:staticPropsProcess}. |
492 |
|
493 |
\begin{figure} |
494 |
\centering |
495 |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
496 |
\caption[A representation of the three-stage correlations in |
497 |
\texttt{StaticProps}]{This diagram illustrates three-stage |
498 |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
499 |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
500 |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
501 |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
502 |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
503 |
the contrary, the third stage($C$ and $C$) are completely |
504 |
overlapping} \label{oopseFig:staticPropsProcess} |
505 |
\end{figure} |
506 |
|
507 |
There are five seperate radial distribution functions availiable in |
508 |
OOPSE. Since every radial distrbution function invlove the |
509 |
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
510 |
-{}-sele2} must be specified to tell StaticProps which bodies to |
511 |
include in the calculation. |
512 |
|
513 |
\begin{description} |
514 |
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
515 |
\begin{equation*} |
516 |
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
517 |
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
518 |
\end{equation*} |
519 |
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
520 |
function. The angle is defined by the intermolecular vector |
521 |
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
522 |
\begin{equation*} |
523 |
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
524 |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
525 |
\theta_{ij} - \cos \theta)\rangle |
526 |
\end{equation*} |
527 |
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
528 |
function. The angle is defined by the $z$-axes of the two |
529 |
DirectionalAtoms A and B. |
530 |
\begin{equation*} |
531 |
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
532 |
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
533 |
\omega_{ij} - \cos \omega)\rangle |
534 |
\end{equation*} |
535 |
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
536 |
space $\theta, \omega$ defined by the two angles mentioned above. |
537 |
\begin{equation*} |
538 |
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
539 |
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
540 |
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
541 |
\omega)\rangle |
542 |
\end{equation*} |
543 |
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
544 |
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
545 |
and {\tt -{}-refsele} must be given to define A's internal |
546 |
coordinate set as the reference frame for the calculation. |
547 |
\end{description} |
548 |
|
549 |
The vectors (and angles) associated with these angular pair |
550 |
distribution functions are most easily seen in |
551 |
Fig.~\ref{oopseFig:gofr} |
552 |
|
553 |
\begin{figure} |
554 |
\centering |
555 |
\includegraphics[width=3in]{definition.eps} |
556 |
\caption[Definitions of the angles between directional objects]{ \\ |
557 |
Any two directional objects (DirectionalAtoms and RigidBodies) have |
558 |
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
559 |
their body-fixed frames.} \label{oopseFig:gofr} |
560 |
\end{figure} |
561 |
|
562 |
The options available for {\tt StaticProps} are as follows: |
563 |
\begin{longtable}[c]{|EFG|} |
564 |
\caption{StaticProps Command-line Options} |
565 |
\\ \hline |
566 |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
567 |
\endhead |
568 |
\hline |
569 |
\endfoot |
570 |
-h& {\tt -{}-help} & Print help and exit \\ |
571 |
-V& {\tt -{}-version} & Print version and exit \\ |
572 |
-i& {\tt -{}-input} & input dump file \\ |
573 |
-o& {\tt -{}-output} & output file name \\ |
574 |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
575 |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
576 |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
577 |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
578 |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
579 |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
580 |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
581 |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
582 |
& {\tt -{}-molname} & molecule name \\ |
583 |
& {\tt -{}-begin} & begin internal index \\ |
584 |
& {\tt -{}-end} & end internal index \\ |
585 |
\hline |
586 |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
587 |
\hline |
588 |
& {\tt -{}-gofr} & $g(r)$ \\ |
589 |
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
590 |
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
591 |
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
592 |
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
593 |
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
594 |
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
595 |
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
596 |
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
597 |
\end{longtable} |
598 |
|
599 |
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
600 |
|
601 |
{\tt DynamicProps} computes time correlation functions from the |
602 |
configurations stored in a dump file. Typical examples of time |
603 |
correlation functions are the mean square displacement and the |
604 |
velocity autocorrelation functions. Once again, the selection |
605 |
syntax can be used to specify the StuntDoubles that will be used for |
606 |
the calculation. A general time correlation function can be thought |
607 |
of as: |
608 |
\begin{equation} |
609 |
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
610 |
\end{equation} |
611 |
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
612 |
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
613 |
vector property associated with an atom of type $B$ at a different |
614 |
time $t^{\prime}$. In most autocorrelation functions, the vector |
615 |
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
616 |
$B$) are identical, and the three calculations built in to {\tt |
617 |
DynamicProps} make these assumptions. It is possible, however, to |
618 |
make simple modifications to the {\tt DynamicProps} code to allow |
619 |
the use of {\it cross} time correlation functions (i.e. with |
620 |
different vectors). The ability to use two selection scripts to |
621 |
select different types of atoms is already present in the code. |
622 |
|
623 |
For large simulations, the trajectory files can sometimes reach |
624 |
sizes in excess of several gigabytes. In order to prevent a |
625 |
situation where the program runs out of memory due to large |
626 |
trajectories, \texttt{dynamicProps} will estimate the size of free |
627 |
memory at first, and determine the number of frames in each block, |
628 |
which allows the operating system to load two blocks of data |
629 |
simultaneously without swapping. Upon reading two blocks of the |
630 |
trajectory, \texttt{dynamicProps} will calculate the time |
631 |
correlation within the first block and the cross correlations |
632 |
between the two blocks. This second block is then freed and then |
633 |
incremented and the process repeated until the end of the |
634 |
trajectory. Once the end is reached, the first block is freed then |
635 |
incremented, until all frame pairs have been correlated in time. |
636 |
This process is illustrated in |
637 |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
638 |
|
639 |
\begin{figure} |
640 |
\centering |
641 |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
642 |
\caption[A representation of the block correlations in |
643 |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
644 |
processing in \texttt{dynamicProps}. The shaded region represents |
645 |
the self correlation of the block, and the open blocks are read one |
646 |
at a time and the cross correlations between blocks are calculated.} |
647 |
\label{oopseFig:dynamicPropsProcess} |
648 |
\end{figure} |
649 |
|
650 |
The options available for DynamicProps are as follows: |
651 |
\begin{longtable}[c]{|EFG|} |
652 |
\caption{DynamicProps Command-line Options} |
653 |
\\ \hline |
654 |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
655 |
\endhead |
656 |
\hline |
657 |
\endfoot |
658 |
-h& {\tt -{}-help} & Print help and exit \\ |
659 |
-V& {\tt -{}-version} & Print version and exit \\ |
660 |
-i& {\tt -{}-input} & input dump file \\ |
661 |
-o& {\tt -{}-output} & output file name \\ |
662 |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
663 |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
664 |
\hline |
665 |
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
666 |
\hline |
667 |
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
668 |
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
669 |
-d& {\tt -{}-dcorr} & compute dipole correlation function |
670 |
\end{longtable} |
671 |
|
672 |
\section{\label{appendixSection:tools}Other Useful Utilities} |
673 |
|
674 |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
675 |
|
676 |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
677 |
which can be opened by other molecular dynamics viewers such as Jmol |
678 |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
679 |
as follows: |
680 |
|
681 |
|
682 |
\begin{longtable}[c]{|EFG|} |
683 |
\caption{Dump2XYZ Command-line Options} |
684 |
\\ \hline |
685 |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
686 |
\endhead |
687 |
\hline |
688 |
\endfoot |
689 |
-h & {\tt -{}-help} & Print help and exit \\ |
690 |
-V & {\tt -{}-version} & Print version and exit \\ |
691 |
-i & {\tt -{}-input} & input dump file \\ |
692 |
-o & {\tt -{}-output} & output file name \\ |
693 |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
694 |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
695 |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
696 |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
697 |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
698 |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
699 |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
700 |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
701 |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
702 |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
703 |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
704 |
converted. \\ |
705 |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
706 |
& {\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}. |
707 |
\end{longtable} |
708 |
|
709 |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
710 |
|
711 |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
712 |
center of resistance. Both tensors at the center of diffusion can |
713 |
also be reported from the program, as well as the coordinates for |
714 |
the beads which are used to approximate the arbitrary shapes. The |
715 |
options available for Hydro are as follows: |
716 |
\begin{longtable}[c]{|EFG|} |
717 |
\caption{Hydrodynamics Command-line Options} |
718 |
\\ \hline |
719 |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
720 |
\endhead |
721 |
\hline |
722 |
\endfoot |
723 |
-h & {\tt -{}-help} & Print help and exit \\ |
724 |
-V & {\tt -{}-version} & Print version and exit \\ |
725 |
-i & {\tt -{}-input} & input dump file \\ |
726 |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
727 |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
728 |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
729 |
\end{longtable} |