1 |
|
\appendix |
2 |
< |
\chapter{\label{chapt:appendix}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 |
112 |
|
|
113 |
|
As one of the latest advanced techniques emerged from |
114 |
|
object-oriented community, design patterns were applied in some of |
115 |
< |
the modern scientific software applications, such as JMol, OOPSE |
116 |
< |
\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
115 |
> |
the modern scientific software applications, such as JMol, {\sc |
116 |
> |
OOPSE}\cite{Meineke05} and PROTOMOL\cite{Matthey05} \textit{etc}. |
117 |
> |
The following sections enumerates some of the patterns used in {\sc |
118 |
> |
OOPSE}. |
119 |
|
|
120 |
|
\subsection{\label{appendixSection:singleton}Singleton} |
121 |
< |
The Singleton pattern ensures that only one instance of a class is |
122 |
< |
created. All objects that use an instance of that class use the same |
123 |
< |
instance. |
121 |
> |
The Singleton pattern not only provides a mechanism to restrict |
122 |
> |
instantiation of a class to one object, but also provides a global |
123 |
> |
point of access to the object. Currently implemented as a global |
124 |
> |
variable, the logging utility which reports error and warning |
125 |
> |
messages to the console in {\sc OOPSE} is a good candidate for |
126 |
> |
applying the Singleton pattern to avoid the global namespace |
127 |
> |
pollution.Although the singleton pattern can be implemented in |
128 |
> |
various ways to account for different aspects of the software |
129 |
> |
designs, such as lifespan control \textit{etc}, we only use the |
130 |
> |
static data approach in {\sc OOPSE}. {\tt IntegratorFactory} class |
131 |
> |
is declared as |
132 |
> |
\begin{lstlisting}[float,caption={[A classic Singleton design pattern implementation(I)] Declaration of {\tt IntegratorFactory} class.},label={appendixScheme:singletonDeclaration}] |
133 |
|
|
134 |
+ |
class IntegratorFactory { |
135 |
+ |
public: |
136 |
+ |
static IntegratorFactory* getInstance(); |
137 |
+ |
protected: |
138 |
+ |
IntegratorFactory(); |
139 |
+ |
private: |
140 |
+ |
static IntegratorFactory* instance_; |
141 |
+ |
}; |
142 |
+ |
|
143 |
+ |
\end{lstlisting} |
144 |
+ |
The corresponding implementation is |
145 |
+ |
\begin{lstlisting}[float,caption={[A classic implementation of Singleton design pattern (II)] Implementation of {\tt IntegratorFactory} class.},label={appendixScheme:singletonImplementation}] |
146 |
+ |
|
147 |
+ |
IntegratorFactory::instance_ = NULL; |
148 |
+ |
|
149 |
+ |
IntegratorFactory* getInstance() { |
150 |
+ |
if (instance_ == NULL){ |
151 |
+ |
instance_ = new IntegratorFactory; |
152 |
+ |
} |
153 |
+ |
return instance_; |
154 |
+ |
} |
155 |
+ |
|
156 |
+ |
\end{lstlisting} |
157 |
+ |
Since constructor is declared as {\tt protected}, a client can not |
158 |
+ |
instantiate {\tt IntegratorFactory} directly. Moreover, since the |
159 |
+ |
member function {\tt getInstance} serves as the only entry of access |
160 |
+ |
to {\tt IntegratorFactory}, this approach fulfills the basic |
161 |
+ |
requirement, a single instance. Another consequence of this approach |
162 |
+ |
is the automatic destruction since static data are destroyed upon |
163 |
+ |
program termination. |
164 |
+ |
|
165 |
|
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
61 |
– |
The Factory Method pattern is a creational pattern which deals with |
62 |
– |
the problem of creating objects without specifying the exact class |
63 |
– |
of object that will be created. Factory Method solves this problem |
64 |
– |
by defining a separate method for creating the objects, which |
65 |
– |
subclasses can then override to specify the derived type of product |
66 |
– |
that will be created. |
166 |
|
|
167 |
+ |
Categoried as a creational pattern, the Factory Method pattern deals |
168 |
+ |
with the problem of creating objects without specifying the exact |
169 |
+ |
class of object that will be created. Factory Method is typically |
170 |
+ |
implemented by delegating the creation operation to the subclasses. |
171 |
|
|
172 |
+ |
Registers a creator with a type identifier. Looks up the type |
173 |
+ |
identifier in the internal map. If it is found, it invokes the |
174 |
+ |
corresponding creator for the type identifier and returns its |
175 |
+ |
result. |
176 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (I)].},label={appendixScheme:factoryDeclaration}] |
177 |
+ |
|
178 |
+ |
class IntegratorFactory { |
179 |
+ |
public: |
180 |
+ |
typedef std::map<string, IntegratorCreator*> CreatorMapType; |
181 |
+ |
|
182 |
+ |
bool registerIntegrator(IntegratorCreator* creator); |
183 |
+ |
|
184 |
+ |
Integrator* createIntegrator(const string& id, SimInfo* info); |
185 |
+ |
|
186 |
+ |
private: |
187 |
+ |
CreatorMapType creatorMap_; |
188 |
+ |
}; |
189 |
+ |
|
190 |
+ |
\end{lstlisting} |
191 |
+ |
|
192 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (II)].},label={appendixScheme:factoryDeclarationImplementation}] |
193 |
+ |
|
194 |
+ |
bool IntegratorFactory::unregisterIntegrator(const string& id) { |
195 |
+ |
return creatorMap_.erase(id) == 1; |
196 |
+ |
} |
197 |
+ |
|
198 |
+ |
Integrator* IntegratorFactory::createIntegrator(const string& id, |
199 |
+ |
SimInfo* info) { |
200 |
+ |
CreatorMapType::iterator i = creatorMap_.find(id); |
201 |
+ |
if (i != creatorMap_.end()) { |
202 |
+ |
return (i->second)->create(info); |
203 |
+ |
} else { |
204 |
+ |
return NULL; |
205 |
+ |
} |
206 |
+ |
} |
207 |
+ |
|
208 |
+ |
\end{lstlisting} |
209 |
+ |
|
210 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Factory pattern (III)].},label={appendixScheme:integratorCreator}] |
211 |
+ |
|
212 |
+ |
class IntegratorCreator { |
213 |
+ |
public: |
214 |
+ |
IntegratorCreator(const string& ident) : ident_(ident) {} |
215 |
+ |
|
216 |
+ |
const string& getIdent() const { return ident_; } |
217 |
+ |
|
218 |
+ |
virtual Integrator* create(SimInfo* info) const = 0; |
219 |
+ |
|
220 |
+ |
private: |
221 |
+ |
string ident_; |
222 |
+ |
}; |
223 |
+ |
|
224 |
+ |
template<class ConcreteIntegrator> |
225 |
+ |
class IntegratorBuilder : public IntegratorCreator { |
226 |
+ |
public: |
227 |
+ |
IntegratorBuilder(const string& ident) : IntegratorCreator(ident) {} |
228 |
+ |
virtual Integrator* create(SimInfo* info) const { |
229 |
+ |
return new ConcreteIntegrator(info); |
230 |
+ |
} |
231 |
+ |
}; |
232 |
+ |
\end{lstlisting} |
233 |
+ |
|
234 |
|
\subsection{\label{appendixSection:visitorPattern}Visitor} |
235 |
+ |
|
236 |
|
The purpose of the Visitor Pattern is to encapsulate an operation |
237 |
< |
that you want to perform on the elements of a data structure. In |
238 |
< |
this way, you can change the operation being performed on a |
239 |
< |
structure without the need of changing the classes of the elements |
240 |
< |
that you are operating on. |
237 |
> |
that you want to perform on the elements. The operation being |
238 |
> |
performed on a structure can be switched without changing the |
239 |
> |
interfaces of the elements. In other words, one can add virtual |
240 |
> |
functions into a set of classes without modifying their interfaces. |
241 |
> |
The UML class diagram of Visitor patten is shown in |
242 |
> |
Fig.~\ref{appendixFig:visitorUML}. {\tt Dump2XYZ} program in |
243 |
> |
Sec.~\ref{appendixSection:Dump2XYZ} uses Visitor pattern |
244 |
> |
extensively. |
245 |
|
|
246 |
+ |
\begin{figure} |
247 |
+ |
\centering |
248 |
+ |
\includegraphics[width=\linewidth]{visitor.eps} |
249 |
+ |
\caption[The architecture of {\sc OOPSE}] {Overview of the structure |
250 |
+ |
of {\sc OOPSE}} \label{appendixFig:visitorUML} |
251 |
+ |
\end{figure} |
252 |
|
|
253 |
< |
\subsection{\label{appendixSection:templateMethod}Template Method} |
253 |
> |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (I)]Source code of the visitor classes.},label={appendixScheme:visitor}] |
254 |
|
|
255 |
< |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
255 |
> |
class BaseVisitor{ |
256 |
> |
public: |
257 |
> |
virtual void visit(Atom* atom); |
258 |
> |
virtual void visit(DirectionalAtom* datom); |
259 |
> |
virtual void visit(RigidBody* rb); |
260 |
> |
}; |
261 |
|
|
262 |
+ |
\end{lstlisting} |
263 |
+ |
|
264 |
+ |
\begin{lstlisting}[float,caption={[The implementation of Visitor pattern (II)]Source code of the element classes.},label={appendixScheme:element}] |
265 |
+ |
|
266 |
+ |
class StuntDouble { |
267 |
+ |
public: |
268 |
+ |
virtual void accept(BaseVisitor* v) = 0; |
269 |
+ |
}; |
270 |
+ |
|
271 |
+ |
class Atom: public StuntDouble { |
272 |
+ |
public: |
273 |
+ |
virtual void accept{BaseVisitor* v*} { |
274 |
+ |
v->visit(this); |
275 |
+ |
} |
276 |
+ |
}; |
277 |
+ |
|
278 |
+ |
class DirectionalAtom: public Atom { |
279 |
+ |
public: |
280 |
+ |
virtual void accept{BaseVisitor* v*} { |
281 |
+ |
v->visit(this); |
282 |
+ |
} |
283 |
+ |
}; |
284 |
+ |
|
285 |
+ |
class RigidBody: public StuntDouble { |
286 |
+ |
public: |
287 |
+ |
virtual void accept{BaseVisitor* v*} { |
288 |
+ |
v->visit(this); |
289 |
+ |
} |
290 |
+ |
}; |
291 |
+ |
|
292 |
+ |
\end{lstlisting} |
293 |
|
\section{\label{appendixSection:concepts}Concepts} |
294 |
|
|
295 |
|
OOPSE manipulates both traditional atoms as well as some objects |
297 |
|
collections of atoms or atoms which have orientational degrees of |
298 |
|
freedom. Here is a diagram of the class heirarchy: |
299 |
|
|
300 |
< |
%\begin{figure} |
301 |
< |
%\centering |
302 |
< |
%\includegraphics[width=3in]{heirarchy.eps} |
303 |
< |
%\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
304 |
< |
%The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
93 |
< |
%selection syntax allows the user to select any of the objects that |
94 |
< |
%are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
95 |
< |
%\end{figure} |
96 |
< |
|
300 |
> |
\begin{figure} |
301 |
> |
\centering |
302 |
> |
\includegraphics[width=3in]{heirarchy.eps} |
303 |
> |
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ The |
304 |
> |
class heirarchy of StuntDoubles in {\sc oopse}-3.0. |
305 |
|
\begin{itemize} |
306 |
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
307 |
|
integrators and minimizers. |
309 |
|
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
310 |
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
311 |
|
DirectionalAtom}s which behaves as a single unit. |
312 |
< |
\end{itemize} |
312 |
> |
\end{itemize}} \label{oopseFig:heirarchy} |
313 |
> |
\end{figure} |
314 |
|
|
315 |
< |
Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
315 |
> |
Every Molecule, Atom and DirectionalAtom in {\sc OOPSE} have their |
316 |
|
own names which are specified in the {\tt .md} file. In contrast, |
317 |
|
RigidBodies are denoted by their membership and index inside a |
318 |
|
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
323 |
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
324 |
|
|
325 |
|
The most general form of the select command is: {\tt select {\it |
326 |
< |
expression}} |
326 |
> |
expression}}. This expression represents an arbitrary set of |
327 |
> |
StuntDoubles (Atoms or RigidBodies) in {\sc OOPSE}. Expressions are |
328 |
> |
composed of either name expressions, index expressions, predefined |
329 |
> |
sets, user-defined expressions, comparison operators, within |
330 |
> |
expressions, or logical combinations of the above expression types. |
331 |
> |
Expressions can be combined using parentheses and the Boolean |
332 |
> |
operators. |
333 |
|
|
119 |
– |
This expression represents an arbitrary set of StuntDoubles (Atoms |
120 |
– |
or RigidBodies) in {\sc oopse}. Expressions are composed of either |
121 |
– |
name expressions, index expressions, predefined sets, user-defined |
122 |
– |
expressions, comparison operators, within expressions, or logical |
123 |
– |
combinations of the above expression types. Expressions can be |
124 |
– |
combined using parentheses and the Boolean operators. |
125 |
– |
|
334 |
|
\subsection{\label{appendixSection:logical}Logical expressions} |
335 |
|
|
336 |
|
The logical operators allow complex queries to be constructed out of |
412 |
|
Users can define arbitrary terms to represent groups of |
413 |
|
StuntDoubles, and then use the define terms in select commands. The |
414 |
|
general form for the define command is: {\bf define {\it term |
415 |
< |
expression}} |
415 |
> |
expression}}. Once defined, the user can specify such terms in |
416 |
> |
boolean expressions |
417 |
|
|
209 |
– |
Once defined, the user can specify such terms in boolean expressions |
210 |
– |
|
418 |
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
419 |
|
|
420 |
|
{\tt select SSDWATER} |
449 |
|
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
450 |
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
451 |
|
atoms. |
245 |
– |
|
246 |
– |
\section{\label{appendixSection:tools}Tools which use the selection command} |
247 |
– |
|
248 |
– |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
249 |
– |
|
250 |
– |
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
251 |
– |
be opened by other molecular dynamics viewers such as Jmol and VMD. |
252 |
– |
The options available for Dump2XYZ are as follows: |
452 |
|
|
453 |
|
|
454 |
< |
\begin{longtable}[c]{|EFG|} |
256 |
< |
\caption{Dump2XYZ Command-line Options} |
257 |
< |
\\ \hline |
258 |
< |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
259 |
< |
\endhead |
260 |
< |
\hline |
261 |
< |
\endfoot |
262 |
< |
-h & {\tt -{}-help} & Print help and exit \\ |
263 |
< |
-V & {\tt -{}-version} & Print version and exit \\ |
264 |
< |
-i & {\tt -{}-input=filename} & input dump file \\ |
265 |
< |
-o & {\tt -{}-output=filename} & output file name \\ |
266 |
< |
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
267 |
< |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
268 |
< |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
269 |
< |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
270 |
< |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
271 |
< |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
272 |
< |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
273 |
< |
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
274 |
< |
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
275 |
< |
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
276 |
< |
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
277 |
< |
converted. \\ |
278 |
< |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
279 |
< |
& {\tt -{}-refsele} & In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}. |
280 |
< |
\end{longtable} |
454 |
> |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
455 |
|
|
282 |
– |
|
456 |
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
457 |
|
|
458 |
|
{\tt StaticProps} can compute properties which are averaged over |
459 |
|
some or all of the configurations that are contained within a dump |
460 |
|
file. The most common example of a static property that can be |
461 |
|
computed is the pair distribution function between atoms of type $A$ |
462 |
< |
and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
463 |
< |
used to compute the density distributions of other molecules in a |
464 |
< |
reference frame {\it fixed to the body-fixed reference frame} of a |
465 |
< |
selected atom or rigid body. |
462 |
> |
and other atoms of type $B$, $g_{AB}(r)$. {\tt StaticProps} can |
463 |
> |
also be used to compute the density distributions of other molecules |
464 |
> |
in a reference frame {\it fixed to the body-fixed reference frame} |
465 |
> |
of a selected atom or rigid body. |
466 |
|
|
467 |
|
There are five seperate radial distribution functions availiable in |
468 |
|
OOPSE. Since every radial distrbution function invlove the |
518 |
|
their body-fixed frames.} \label{oopseFig:gofr} |
519 |
|
\end{figure} |
520 |
|
|
521 |
+ |
Due to the fact that the selected StuntDoubles from two selections |
522 |
+ |
may be overlapped, {\tt StaticProps} performs the calculation in |
523 |
+ |
three stages which are illustrated in |
524 |
+ |
Fig.~\ref{oopseFig:staticPropsProcess}. |
525 |
+ |
|
526 |
+ |
\begin{figure} |
527 |
+ |
\centering |
528 |
+ |
\includegraphics[width=\linewidth]{staticPropsProcess.eps} |
529 |
+ |
\caption[A representation of the three-stage correlations in |
530 |
+ |
\texttt{StaticProps}]{This diagram illustrates three-stage |
531 |
+ |
processing used by \texttt{StaticProps}. $S_1$ and $S_2$ are the |
532 |
+ |
numbers of selected stuntdobules from {\tt -{}-sele1} and {\tt |
533 |
+ |
-{}-sele2} respectively, while $C$ is the number of stuntdobules |
534 |
+ |
appearing at both sets. The first stage($S_1-C$ and $S_2$) and |
535 |
+ |
second stages ($S_1$ and $S_2-C$) are completely non-overlapping. On |
536 |
+ |
the contrary, the third stage($C$ and $C$) are completely |
537 |
+ |
overlapping} \label{oopseFig:staticPropsProcess} |
538 |
+ |
\end{figure} |
539 |
+ |
|
540 |
|
The options available for {\tt StaticProps} are as follows: |
541 |
|
\begin{longtable}[c]{|EFG|} |
542 |
|
\caption{StaticProps Command-line Options} |
547 |
|
\endfoot |
548 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
549 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
550 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
551 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
552 |
< |
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
553 |
< |
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
554 |
< |
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
555 |
< |
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
556 |
< |
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
557 |
< |
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
558 |
< |
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
559 |
< |
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
560 |
< |
& {\tt -{}-molname=STRING} & molecule name \\ |
561 |
< |
& {\tt -{}-begin=INT} & begin internal index \\ |
562 |
< |
& {\tt -{}-end=INT} & end internal index \\ |
550 |
> |
-i& {\tt -{}-input} & input dump file \\ |
551 |
> |
-o& {\tt -{}-output} & output file name \\ |
552 |
> |
-n& {\tt -{}-step} & process every n frame (default=`1') \\ |
553 |
> |
-r& {\tt -{}-nrbins} & number of bins for distance (default=`100') \\ |
554 |
> |
-a& {\tt -{}-nanglebins} & number of bins for cos(angle) (default= `50') \\ |
555 |
> |
-l& {\tt -{}-length} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
556 |
> |
& {\tt -{}-sele1} & select the first StuntDouble set \\ |
557 |
> |
& {\tt -{}-sele2} & select the second StuntDouble set \\ |
558 |
> |
& {\tt -{}-sele3} & select the third StuntDouble set \\ |
559 |
> |
& {\tt -{}-refsele} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
560 |
> |
& {\tt -{}-molname} & molecule name \\ |
561 |
> |
& {\tt -{}-begin} & begin internal index \\ |
562 |
> |
& {\tt -{}-end} & end internal index \\ |
563 |
|
\hline |
564 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
565 |
|
\hline |
598 |
|
different vectors). The ability to use two selection scripts to |
599 |
|
select different types of atoms is already present in the code. |
600 |
|
|
601 |
+ |
For large simulations, the trajectory files can sometimes reach |
602 |
+ |
sizes in excess of several gigabytes. In order to effectively |
603 |
+ |
analyze that amount of data. In order to prevent a situation where |
604 |
+ |
the program runs out of memory due to large trajectories, |
605 |
+ |
\texttt{dynamicProps} will estimate the size of free memory at |
606 |
+ |
first, and determine the number of frames in each block, which |
607 |
+ |
allows the operating system to load two blocks of data |
608 |
+ |
simultaneously without swapping. Upon reading two blocks of the |
609 |
+ |
trajectory, \texttt{dynamicProps} will calculate the time |
610 |
+ |
correlation within the first block and the cross correlations |
611 |
+ |
between the two blocks. This second block is then freed and then |
612 |
+ |
incremented and the process repeated until the end of the |
613 |
+ |
trajectory. Once the end is reached, the first block is freed then |
614 |
+ |
incremented, until all frame pairs have been correlated in time. |
615 |
+ |
This process is illustrated in |
616 |
+ |
Fig.~\ref{oopseFig:dynamicPropsProcess}. |
617 |
+ |
|
618 |
+ |
\begin{figure} |
619 |
+ |
\centering |
620 |
+ |
\includegraphics[width=\linewidth]{dynamicPropsProcess.eps} |
621 |
+ |
\caption[A representation of the block correlations in |
622 |
+ |
\texttt{dynamicProps}]{This diagram illustrates block correlations |
623 |
+ |
processing in \texttt{dynamicProps}. The shaded region represents |
624 |
+ |
the self correlation of the block, and the open blocks are read one |
625 |
+ |
at a time and the cross correlations between blocks are calculated.} |
626 |
+ |
\label{oopseFig:dynamicPropsProcess} |
627 |
+ |
\end{figure} |
628 |
+ |
|
629 |
|
The options available for DynamicProps are as follows: |
630 |
|
\begin{longtable}[c]{|EFG|} |
631 |
|
\caption{DynamicProps Command-line Options} |
636 |
|
\endfoot |
637 |
|
-h& {\tt -{}-help} & Print help and exit \\ |
638 |
|
-V& {\tt -{}-version} & Print version and exit \\ |
639 |
< |
-i& {\tt -{}-input=filename} & input dump file \\ |
640 |
< |
-o& {\tt -{}-output=filename} & output file name \\ |
641 |
< |
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
642 |
< |
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
639 |
> |
-i& {\tt -{}-input} & input dump file \\ |
640 |
> |
-o& {\tt -{}-output} & output file name \\ |
641 |
> |
& {\tt -{}-sele1} & select first StuntDouble set \\ |
642 |
> |
& {\tt -{}-sele2} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
643 |
|
\hline |
644 |
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
645 |
|
\hline |
648 |
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
649 |
|
\end{longtable} |
650 |
|
|
651 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
651 |
> |
\section{\label{appendixSection:tools}Other Useful Utilities} |
652 |
> |
|
653 |
> |
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
654 |
> |
|
655 |
> |
{\tt Dump2XYZ} can transform an OOPSE dump file into a xyz file |
656 |
> |
which can be opened by other molecular dynamics viewers such as Jmol |
657 |
> |
and VMD\cite{Humphrey1996}. The options available for Dump2XYZ are |
658 |
> |
as follows: |
659 |
> |
|
660 |
> |
|
661 |
> |
\begin{longtable}[c]{|EFG|} |
662 |
> |
\caption{Dump2XYZ Command-line Options} |
663 |
> |
\\ \hline |
664 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
665 |
> |
\endhead |
666 |
> |
\hline |
667 |
> |
\endfoot |
668 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
669 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
670 |
> |
-i & {\tt -{}-input} & input dump file \\ |
671 |
> |
-o & {\tt -{}-output} & output file name \\ |
672 |
> |
-n & {\tt -{}-frame} & print every n frame (default=`1') \\ |
673 |
> |
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
674 |
> |
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
675 |
> |
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
676 |
> |
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
677 |
> |
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
678 |
> |
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
679 |
> |
& {\tt -{}-repeatX} & The number of images to repeat in the x direction (default=`0') \\ |
680 |
> |
& {\tt -{}-repeatY} & The number of images to repeat in the y direction (default=`0') \\ |
681 |
> |
& {\tt -{}-repeatZ} & The number of images to repeat in the z direction (default=`0') \\ |
682 |
> |
-s & {\tt -{}-selection} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
683 |
> |
converted. \\ |
684 |
> |
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
685 |
> |
& {\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}. |
686 |
> |
\end{longtable} |
687 |
> |
|
688 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydro} |
689 |
> |
|
690 |
> |
{\tt Hydro} can calculate resistance and diffusion tensors at the |
691 |
> |
center of resistance. Both tensors at the center of diffusion can |
692 |
> |
also be reported from the program, as well as the coordinates for |
693 |
> |
the beads which are used to approximate the arbitrary shapes. The |
694 |
> |
options available for Hydro are as follows: |
695 |
> |
\begin{longtable}[c]{|EFG|} |
696 |
> |
\caption{Hydrodynamics Command-line Options} |
697 |
> |
\\ \hline |
698 |
> |
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
699 |
> |
\endhead |
700 |
> |
\hline |
701 |
> |
\endfoot |
702 |
> |
-h & {\tt -{}-help} & Print help and exit \\ |
703 |
> |
-V & {\tt -{}-version} & Print version and exit \\ |
704 |
> |
-i & {\tt -{}-input} & input dump file \\ |
705 |
> |
-o & {\tt -{}-output} & output file prefix (default=`hydro') \\ |
706 |
> |
-b & {\tt -{}-beads} & generate the beads only, hydrodynamics calculation will not be performed (default=off)\\ |
707 |
> |
& {\tt -{}-model} & hydrodynamics model (supports ``AnalyticalModel'', ``RoughShell'' and ``BeadModel'') \\ |
708 |
> |
\end{longtable} |