1 |
tim |
2685 |
\chapter{\label{chapt:appendix}APPENDIX} |
2 |
|
|
|
3 |
tim |
2688 |
Designing object-oriented software is hard, and designing reusable |
4 |
|
|
object-oriented scientific software is even harder. Absence of |
5 |
|
|
applying modern software development practices is the bottleneck of |
6 |
|
|
Scientific Computing community\cite{wilson}. For instance, in the |
7 |
|
|
last 20 years , there are quite a few MD packages that were |
8 |
|
|
developed to solve common MD problems and perform robust simulations |
9 |
|
|
. However, many of the codes are legacy programs that are either |
10 |
|
|
poorly organized or extremely complex. Usually, these packages were |
11 |
|
|
contributed by scientists without official computer science |
12 |
|
|
training. The development of most MD applications are lack of strong |
13 |
|
|
coordination to enforce design and programming guidelines. Moreover, |
14 |
|
|
most MD programs also suffer from missing design and implement |
15 |
|
|
documents which is crucial to the maintenance and extensibility. |
16 |
|
|
|
17 |
tim |
2685 |
\section{\label{appendixSection:desginPattern}Design Pattern} |
18 |
|
|
|
19 |
tim |
2688 |
Design patterns are optimal solutions to commonly-occurring problems |
20 |
|
|
in software design. Although originated as an architectural concept |
21 |
|
|
for buildings and towns by Christopher Alexander \cite{alexander}, |
22 |
|
|
software patterns first became popular with the wide acceptance of |
23 |
|
|
the book, Design Patterns: Elements of Reusable Object-Oriented |
24 |
|
|
Software \cite{gamma94}. Patterns reflect the experience, knowledge |
25 |
|
|
and insights of developers who have successfully used these patterns |
26 |
|
|
in their own work. Patterns are reusable. They provide a ready-made |
27 |
|
|
solution that can be adapted to different problems as necessary. |
28 |
|
|
Pattern are expressive. they provide a common vocabulary of |
29 |
|
|
solutions that can express large solutions succinctly. |
30 |
tim |
2685 |
|
31 |
tim |
2688 |
Patterns are usually described using a format that includes the |
32 |
|
|
following information: |
33 |
|
|
\begin{enumerate} |
34 |
|
|
\item The \emph{name} that is commonly used for the pattern. Good pattern names form a vocabulary for |
35 |
|
|
discussing conceptual abstractions. a pattern may have more than one commonly used or recognizable name |
36 |
|
|
in the literature. In this case it is common practice to document these nicknames or synonyms under |
37 |
|
|
the heading of \emph{Aliases} or \emph{Also Known As}. |
38 |
|
|
\item The \emph{motivation} or \emph{context} that this pattern applies |
39 |
|
|
to. Sometimes, it will include some prerequisites that should be satisfied before deciding to use a pattern |
40 |
|
|
\item The \emph{solution} to the problem that the pattern |
41 |
|
|
addresses. It describes how to construct the necessary work products. The description may include |
42 |
|
|
pictures, diagrams and prose which identify the pattern's structure, its participants, and their |
43 |
|
|
collaborations, to show how the problem is solved. |
44 |
|
|
\item The \emph{consequences} of using the given solution to solve a |
45 |
|
|
problem, both positive and negative. |
46 |
|
|
\end{enumerate} |
47 |
tim |
2685 |
|
48 |
tim |
2688 |
As one of the latest advanced techniques emerged from |
49 |
|
|
object-oriented community, design patterns were applied in some of |
50 |
|
|
the modern scientific software applications, such as JMol, OOPSE |
51 |
tim |
2693 |
\cite{Meineke05} and PROTOMOL \cite{Matthey05} \textit{etc}. |
52 |
tim |
2685 |
|
53 |
tim |
2693 |
\subsection{\label{appendixSection:singleton}Singleton} |
54 |
|
|
The Singleton pattern ensures that only one instance of a class is |
55 |
|
|
created. All objects that use an instance of that class use the same |
56 |
|
|
instance. |
57 |
|
|
|
58 |
tim |
2688 |
\subsection{\label{appendixSection:factoryMethod}Factory Method} |
59 |
|
|
The Factory Method pattern is a creational pattern which deals with |
60 |
|
|
the problem of creating objects without specifying the exact class |
61 |
|
|
of object that will be created. Factory Method solves this problem |
62 |
|
|
by defining a separate method for creating the objects, which |
63 |
|
|
subclasses can then override to specify the derived type of product |
64 |
|
|
that will be created. |
65 |
tim |
2685 |
|
66 |
|
|
|
67 |
tim |
2688 |
\subsection{\label{appendixSection:visitorPattern}Visitor} |
68 |
|
|
The purpose of the Visitor Pattern is to encapsulate an operation |
69 |
|
|
that you want to perform on the elements of a data structure. In |
70 |
|
|
this way, you can change the operation being performed on a |
71 |
|
|
structure without the need of changing the classes of the elements |
72 |
|
|
that you are operating on. |
73 |
tim |
2685 |
|
74 |
|
|
|
75 |
tim |
2688 |
\subsection{\label{appendixSection:templateMethod}Template Method} |
76 |
|
|
|
77 |
tim |
2685 |
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
78 |
|
|
|
79 |
tim |
2730 |
\section{\label{appendixSection:concepts}Concepts} |
80 |
tim |
2685 |
|
81 |
tim |
2730 |
OOPSE manipulates both traditional atoms as well as some objects |
82 |
|
|
that {\it behave like atoms}. These objects can be rigid |
83 |
|
|
collections of atoms or atoms which have orientational degrees of |
84 |
|
|
freedom. Here is a diagram of the class heirarchy: |
85 |
tim |
2688 |
|
86 |
tim |
2730 |
\begin{figure} |
87 |
|
|
\centering |
88 |
|
|
\includegraphics[width=3in]{heirarchy.pdf} |
89 |
|
|
\caption[Class heirarchy for StuntDoubles in {\sc oopse}-3.0]{ \\ |
90 |
|
|
The class heirarchy of StuntDoubles in {\sc oopse}-3.0. The |
91 |
|
|
selection syntax allows the user to select any of the objects that |
92 |
|
|
are descended from a StuntDouble.} \label{oopseFig:heirarchy} |
93 |
|
|
\end{figure} |
94 |
tim |
2688 |
|
95 |
tim |
2730 |
\begin{itemize} |
96 |
|
|
\item A {\bf StuntDouble} is {\it any} object that can be manipulated by the |
97 |
|
|
integrators and minimizers. |
98 |
|
|
\item An {\bf Atom} is a fundamental point-particle that can be moved around during a simulation. |
99 |
|
|
\item A {\bf DirectionalAtom} is an atom which has {\it orientational} as well as translational degrees of freedom. |
100 |
|
|
\item A {\bf RigidBody} is a collection of {\bf Atom}s or {\bf |
101 |
|
|
DirectionalAtom}s which behaves as a single unit. |
102 |
|
|
\end{itemize} |
103 |
tim |
2688 |
|
104 |
tim |
2730 |
Every Molecule, Atom and DirectionalAtom in {\sc oopse} have their |
105 |
|
|
own names which are specified in the {\tt .md} file. In contrast, |
106 |
|
|
RigidBodies are denoted by their membership and index inside a |
107 |
|
|
particular molecule: [MoleculeName]\_RB\_[index] (the contents |
108 |
|
|
inside the brackets depend on the specifics of the simulation). The |
109 |
|
|
names of rigid bodies are generated automatically. For example, the |
110 |
|
|
name of the first rigid body in a DMPC molecule is DMPC\_RB\_0. |
111 |
|
|
|
112 |
|
|
\section{\label{appendixSection:syntax}Syntax of the Select Command} |
113 |
|
|
|
114 |
|
|
The most general form of the select command is: {\tt select {\it |
115 |
|
|
expression}} |
116 |
|
|
|
117 |
|
|
This expression represents an arbitrary set of StuntDoubles (Atoms |
118 |
|
|
or RigidBodies) in {\sc oopse}. Expressions are composed of either |
119 |
|
|
name expressions, index expressions, predefined sets, user-defined |
120 |
|
|
expressions, comparison operators, within expressions, or logical |
121 |
|
|
combinations of the above expression types. Expressions can be |
122 |
|
|
combined using parentheses and the Boolean operators. |
123 |
|
|
|
124 |
|
|
\subsection{\label{appendixSection:logical}Logical expressions} |
125 |
|
|
|
126 |
|
|
The logical operators allow complex queries to be constructed out of |
127 |
|
|
simpler ones using the standard boolean connectives {\bf and}, {\bf |
128 |
|
|
or}, {\bf not}. Parentheses can be used to alter the precedence of |
129 |
|
|
the operators. |
130 |
|
|
|
131 |
|
|
\begin{center} |
132 |
|
|
\begin{tabular}{|ll|} |
133 |
|
|
\hline |
134 |
|
|
{\bf logical operator} & {\bf equivalent operator} \\ |
135 |
|
|
\hline |
136 |
|
|
and & ``\&'', ``\&\&'' \\ |
137 |
|
|
or & ``$|$'', ``$||$'', ``,'' \\ |
138 |
|
|
not & ``!'' \\ |
139 |
|
|
\hline |
140 |
|
|
\end{tabular} |
141 |
|
|
\end{center} |
142 |
|
|
|
143 |
|
|
\subsection{\label{appendixSection:name}Name expressions} |
144 |
|
|
|
145 |
|
|
\begin{center} |
146 |
|
|
\begin{tabular}{|llp{3in}|} |
147 |
|
|
\hline {\bf type of expression} & {\bf examples} & {\bf translation |
148 |
|
|
of |
149 |
|
|
examples} \\ |
150 |
|
|
\hline expression without ``.'' & select DMPC & select all |
151 |
|
|
StuntDoubles |
152 |
|
|
belonging to all DMPC molecules \\ |
153 |
|
|
& select C* & select all atoms which have atom types beginning with C |
154 |
|
|
\\ |
155 |
|
|
& select DMPC\_RB\_* & select all RigidBodies in DMPC molecules (but |
156 |
|
|
only select the rigid bodies, and not the atoms belonging to them). \\ |
157 |
|
|
\hline expression has one ``.'' & select TIP3P.O\_TIP3P & select the |
158 |
|
|
O\_TIP3P |
159 |
|
|
atoms belonging to TIP3P molecules \\ |
160 |
|
|
& select DMPC\_RB\_O.PO4 & select the PO4 atoms belonging to |
161 |
|
|
the first |
162 |
|
|
RigidBody in each DMPC molecule \\ |
163 |
|
|
& select DMPC.20 & select the twentieth StuntDouble in each DMPC |
164 |
|
|
molecule \\ |
165 |
|
|
\hline expression has two ``.''s & select DMPC.DMPC\_RB\_?.* & |
166 |
|
|
select all atoms |
167 |
|
|
belonging to all rigid bodies within all DMPC molecules \\ |
168 |
|
|
\hline |
169 |
|
|
\end{tabular} |
170 |
|
|
\end{center} |
171 |
|
|
|
172 |
|
|
\subsection{\label{appendixSection:index}Index expressions} |
173 |
|
|
|
174 |
|
|
\begin{center} |
175 |
|
|
\begin{tabular}{|lp{4in}|} |
176 |
|
|
\hline |
177 |
|
|
{\bf examples} & {\bf translation of examples} \\ |
178 |
|
|
\hline |
179 |
|
|
select 20 & select all of the StuntDoubles belonging to Molecule 20 \\ |
180 |
|
|
select 20 to 30 & select all of the StuntDoubles belonging to |
181 |
|
|
molecules which have global indices between 20 (inclusive) and 30 |
182 |
|
|
(exclusive) \\ |
183 |
|
|
\hline |
184 |
|
|
\end{tabular} |
185 |
|
|
\end{center} |
186 |
|
|
|
187 |
|
|
\subsection{\label{appendixSection:predefined}Predefined sets} |
188 |
|
|
|
189 |
|
|
\begin{center} |
190 |
|
|
\begin{tabular}{|ll|} |
191 |
|
|
\hline |
192 |
|
|
{\bf keyword} & {\bf description} \\ |
193 |
|
|
\hline |
194 |
|
|
all & select all StuntDoubles \\ |
195 |
|
|
none & select none of the StuntDoubles \\ |
196 |
|
|
\hline |
197 |
|
|
\end{tabular} |
198 |
|
|
\end{center} |
199 |
|
|
|
200 |
|
|
\subsection{\label{appendixSection:userdefined}User-defined expressions} |
201 |
|
|
|
202 |
|
|
Users can define arbitrary terms to represent groups of |
203 |
|
|
StuntDoubles, and then use the define terms in select commands. The |
204 |
|
|
general form for the define command is: {\bf define {\it term |
205 |
|
|
expression}} |
206 |
|
|
|
207 |
|
|
Once defined, the user can specify such terms in boolean expressions |
208 |
|
|
|
209 |
|
|
{\tt define SSDWATER SSD or SSD1 or SSDRF} |
210 |
|
|
|
211 |
|
|
{\tt select SSDWATER} |
212 |
|
|
|
213 |
|
|
\subsection{\label{appendixSection:comparison}Comparison expressions} |
214 |
|
|
|
215 |
|
|
StuntDoubles can be selected by using comparision operators on their |
216 |
|
|
properties. The general form for the comparison command is: a |
217 |
|
|
property name, followed by a comparision operator and then a number. |
218 |
|
|
|
219 |
|
|
\begin{center} |
220 |
|
|
\begin{tabular}{|l|l|} |
221 |
|
|
\hline |
222 |
|
|
{\bf property} & mass, charge \\ |
223 |
|
|
{\bf comparison operator} & ``$>$'', ``$<$'', ``$=$'', ``$>=$'', |
224 |
|
|
``$<=$'', ``$!=$'' \\ |
225 |
|
|
\hline |
226 |
|
|
\end{tabular} |
227 |
|
|
\end{center} |
228 |
|
|
|
229 |
|
|
For example, the phrase {\tt select mass > 16.0 and charge < -2} |
230 |
|
|
wouldselect StuntDoubles which have mass greater than 16.0 and |
231 |
|
|
charges less than -2. |
232 |
|
|
|
233 |
|
|
\subsection{\label{appendixSection:within}Within expressions} |
234 |
|
|
|
235 |
|
|
The ``within'' keyword allows the user to select all StuntDoubles |
236 |
|
|
within the specified distance (in Angstroms) from a selection, |
237 |
|
|
including the selected atom itself. The general form for within |
238 |
|
|
selection is: {\tt select within(distance, expression)} |
239 |
|
|
|
240 |
|
|
For example, the phrase {\tt select within(2.5, PO4 or NC4)} would |
241 |
|
|
select all StuntDoubles which are within 2.5 angstroms of PO4 or NC4 |
242 |
|
|
atoms. |
243 |
|
|
|
244 |
|
|
\section{\label{appendixSection:tools}Tools which use the selection command} |
245 |
|
|
|
246 |
|
|
\subsection{\label{appendixSection:Dump2XYZ}Dump2XYZ} |
247 |
|
|
|
248 |
|
|
Dump2XYZ can transform an OOPSE dump file into a xyz file which can |
249 |
|
|
be opened by other molecular dynamics viewers such as Jmol and VMD. |
250 |
|
|
The options available for Dump2XYZ are as follows: |
251 |
|
|
|
252 |
|
|
|
253 |
|
|
\begin{longtable}[c]{|EFG|} |
254 |
|
|
\caption{Dump2XYZ Command-line Options} |
255 |
|
|
\\ \hline |
256 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
257 |
|
|
\endhead |
258 |
|
|
\hline |
259 |
|
|
\endfoot |
260 |
|
|
-h & {\tt -{}-help} & Print help and exit \\ |
261 |
|
|
-V & {\tt -{}-version} & Print version and exit \\ |
262 |
|
|
-i & {\tt -{}-input=filename} & input dump file \\ |
263 |
|
|
-o & {\tt -{}-output=filename} & output file name \\ |
264 |
|
|
-n & {\tt -{}-frame=INT} & print every n frame (default=`1') \\ |
265 |
|
|
-w & {\tt -{}-water} & skip the the waters (default=off) \\ |
266 |
|
|
-m & {\tt -{}-periodicBox} & map to the periodic box (default=off)\\ |
267 |
|
|
-z & {\tt -{}-zconstraint} & replace the atom types of zconstraint molecules (default=off) \\ |
268 |
|
|
-r & {\tt -{}-rigidbody} & add a pseudo COM atom to rigidbody (default=off) \\ |
269 |
|
|
-t & {\tt -{}-watertype} & replace the atom type of water model (default=on) \\ |
270 |
|
|
-b & {\tt -{}-basetype} & using base atom type (default=off) \\ |
271 |
|
|
& {\tt -{}-repeatX=INT} & The number of images to repeat in the x direction (default=`0') \\ |
272 |
|
|
& {\tt -{}-repeatY=INT} & The number of images to repeat in the y direction (default=`0') \\ |
273 |
|
|
& {\tt -{}-repeatZ=INT} & The number of images to repeat in the z direction (default=`0') \\ |
274 |
|
|
-s & {\tt -{}-selection=selection script} & By specifying {\tt -{}-selection}=``selection command'' with Dump2XYZ, the user can select an arbitrary set of StuntDoubles to be |
275 |
|
|
converted. \\ |
276 |
|
|
& {\tt -{}-originsele} & By specifying {\tt -{}-originsele}=``selection command'' with Dump2XYZ, the user can re-center the origin of the system around a specific StuntDouble \\ |
277 |
|
|
& {\tt -{}-refsele} & In order to rotate the system, {\tt -{}-originsele} and {\tt -{}-refsele} must be given to define the new coordinate set. A StuntDouble which contains a dipole (the direction of the dipole is always (0, 0, 1) in body frame) is specified by {\tt -{}-originsele}. The new x-z plane is defined by the direction of the dipole and the StuntDouble is specified by {\tt -{}-refsele}. |
278 |
|
|
\end{longtable} |
279 |
|
|
|
280 |
|
|
|
281 |
|
|
\subsection{\label{appendixSection:StaticProps}StaticProps} |
282 |
|
|
|
283 |
|
|
{\tt StaticProps} can compute properties which are averaged over |
284 |
|
|
some or all of the configurations that are contained within a dump |
285 |
|
|
file. The most common example of a static property that can be |
286 |
|
|
computed is the pair distribution function between atoms of type $A$ |
287 |
|
|
and other atoms of type $B$, $g_{AB}(r)$. StaticProps can also be |
288 |
|
|
used to compute the density distributions of other molecules in a |
289 |
|
|
reference frame {\it fixed to the body-fixed reference frame} of a |
290 |
|
|
selected atom or rigid body. |
291 |
|
|
|
292 |
|
|
There are five seperate radial distribution functions availiable in |
293 |
|
|
OOPSE. Since every radial distrbution function invlove the |
294 |
|
|
calculation between pairs of bodies, {\tt -{}-sele1} and {\tt |
295 |
|
|
-{}-sele2} must be specified to tell StaticProps which bodies to |
296 |
|
|
include in the calculation. |
297 |
|
|
|
298 |
|
|
\begin{description} |
299 |
|
|
\item[{\tt -{}-gofr}] Computes the pair distribution function, |
300 |
|
|
\begin{equation*} |
301 |
|
|
g_{AB}(r) = \frac{1}{\rho_B}\frac{1}{N_A} \langle \sum_{i \in A} |
302 |
|
|
\sum_{j \in B} \delta(r - r_{ij}) \rangle |
303 |
|
|
\end{equation*} |
304 |
|
|
\item[{\tt -{}-r\_theta}] Computes the angle-dependent pair distribution |
305 |
|
|
function. The angle is defined by the intermolecular vector |
306 |
|
|
$\vec{r}$ and $z$-axis of DirectionalAtom A, |
307 |
|
|
\begin{equation*} |
308 |
|
|
g_{AB}(r, \cos \theta) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
309 |
|
|
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
310 |
|
|
\theta_{ij} - \cos \theta)\rangle |
311 |
|
|
\end{equation*} |
312 |
|
|
\item[{\tt -{}-r\_omega}] Computes the angle-dependent pair distribution |
313 |
|
|
function. The angle is defined by the $z$-axes of the two |
314 |
|
|
DirectionalAtoms A and B. |
315 |
|
|
\begin{equation*} |
316 |
|
|
g_{AB}(r, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} \langle |
317 |
|
|
\sum_{i \in A} \sum_{j \in B} \delta(r - r_{ij}) \delta(\cos |
318 |
|
|
\omega_{ij} - \cos \omega)\rangle |
319 |
|
|
\end{equation*} |
320 |
|
|
\item[{\tt -{}-theta\_omega}] Computes the pair distribution in the angular |
321 |
|
|
space $\theta, \omega$ defined by the two angles mentioned above. |
322 |
|
|
\begin{equation*} |
323 |
|
|
g_{AB}(\cos\theta, \cos \omega) = \frac{1}{\rho_B}\frac{1}{N_A} |
324 |
|
|
\langle \sum_{i \in A} \sum_{j \in B} \langle \delta(\cos |
325 |
|
|
\theta_{ij} - \cos \theta) \delta(\cos \omega_{ij} - \cos |
326 |
|
|
\omega)\rangle |
327 |
|
|
\end{equation*} |
328 |
|
|
\item[{\tt -{}-gxyz}] Calculates the density distribution of particles of type |
329 |
|
|
B in the body frame of particle A. Therefore, {\tt -{}-originsele} |
330 |
|
|
and {\tt -{}-refsele} must be given to define A's internal |
331 |
|
|
coordinate set as the reference frame for the calculation. |
332 |
|
|
\end{description} |
333 |
|
|
|
334 |
|
|
The vectors (and angles) associated with these angular pair |
335 |
|
|
distribution functions are most easily seen in the figure below: |
336 |
|
|
|
337 |
|
|
\begin{figure} |
338 |
|
|
\centering |
339 |
|
|
\includegraphics[width=3in]{definition.pdf} |
340 |
|
|
\caption[Definitions of the angles between directional objects]{ \\ |
341 |
|
|
Any two directional objects (DirectionalAtoms and RigidBodies) have |
342 |
|
|
a set of two angles ($\theta$, and $\omega$) between the z-axes of |
343 |
|
|
their body-fixed frames.} \label{oopseFig:gofr} |
344 |
|
|
\end{figure} |
345 |
|
|
|
346 |
|
|
The options available for {\tt StaticProps} are as follows: |
347 |
|
|
\begin{longtable}[c]{|EFG|} |
348 |
|
|
\caption{StaticProps Command-line Options} |
349 |
|
|
\\ \hline |
350 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
351 |
|
|
\endhead |
352 |
|
|
\hline |
353 |
|
|
\endfoot |
354 |
|
|
-h& {\tt -{}-help} & Print help and exit \\ |
355 |
|
|
-V& {\tt -{}-version} & Print version and exit \\ |
356 |
|
|
-i& {\tt -{}-input=filename} & input dump file \\ |
357 |
|
|
-o& {\tt -{}-output=filename} & output file name \\ |
358 |
|
|
-n& {\tt -{}-step=INT} & process every n frame (default=`1') \\ |
359 |
|
|
-r& {\tt -{}-nrbins=INT} & number of bins for distance (default=`100') \\ |
360 |
|
|
-a& {\tt -{}-nanglebins=INT} & number of bins for cos(angle) (default= `50') \\ |
361 |
|
|
-l& {\tt -{}-length=DOUBLE} & maximum length (Defaults to 1/2 smallest length of first frame) \\ |
362 |
|
|
& {\tt -{}-sele1=selection script} & select the first StuntDouble set \\ |
363 |
|
|
& {\tt -{}-sele2=selection script} & select the second StuntDouble set \\ |
364 |
|
|
& {\tt -{}-sele3=selection script} & select the third StuntDouble set \\ |
365 |
|
|
& {\tt -{}-refsele=selection script} & select reference (can only be used with {\tt -{}-gxyz}) \\ |
366 |
|
|
& {\tt -{}-molname=STRING} & molecule name \\ |
367 |
|
|
& {\tt -{}-begin=INT} & begin internal index \\ |
368 |
|
|
& {\tt -{}-end=INT} & end internal index \\ |
369 |
|
|
\hline |
370 |
|
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
371 |
|
|
\hline |
372 |
|
|
& {\tt -{}-gofr} & $g(r)$ \\ |
373 |
|
|
& {\tt -{}-r\_theta} & $g(r, \cos(\theta))$ \\ |
374 |
|
|
& {\tt -{}-r\_omega} & $g(r, \cos(\omega))$ \\ |
375 |
|
|
& {\tt -{}-theta\_omega} & $g(\cos(\theta), \cos(\omega))$ \\ |
376 |
|
|
& {\tt -{}-gxyz} & $g(x, y, z)$ \\ |
377 |
|
|
& {\tt -{}-p2} & $P_2$ order parameter ({\tt -{}-sele1} and {\tt -{}-sele2} must be specified) \\ |
378 |
|
|
& {\tt -{}-scd} & $S_{CD}$ order parameter(either {\tt -{}-sele1}, {\tt -{}-sele2}, {\tt -{}-sele3} are specified or {\tt -{}-molname}, {\tt -{}-begin}, {\tt -{}-end} are specified) \\ |
379 |
|
|
& {\tt -{}-density} & density plot ({\tt -{}-sele1} must be specified) \\ |
380 |
|
|
& {\tt -{}-slab\_density} & slab density ({\tt -{}-sele1} must be specified) |
381 |
|
|
\end{longtable} |
382 |
|
|
|
383 |
|
|
\subsection{\label{appendixSection:DynamicProps}DynamicProps} |
384 |
|
|
|
385 |
|
|
{\tt DynamicProps} computes time correlation functions from the |
386 |
|
|
configurations stored in a dump file. Typical examples of time |
387 |
|
|
correlation functions are the mean square displacement and the |
388 |
|
|
velocity autocorrelation functions. Once again, the selection |
389 |
|
|
syntax can be used to specify the StuntDoubles that will be used for |
390 |
|
|
the calculation. A general time correlation function can be thought |
391 |
|
|
of as: |
392 |
|
|
\begin{equation} |
393 |
|
|
C_{AB}(t) = \langle \vec{u}_A(t) \cdot \vec{v}_B(0) \rangle |
394 |
|
|
\end{equation} |
395 |
|
|
where $\vec{u}_A(t)$ is a vector property associated with an atom of |
396 |
|
|
type $A$ at time $t$, and $\vec{v}_B(t^{\prime})$ is a different |
397 |
|
|
vector property associated with an atom of type $B$ at a different |
398 |
|
|
time $t^{\prime}$. In most autocorrelation functions, the vector |
399 |
|
|
properties ($\vec{v}$ and $\vec{u}$) and the types of atoms ($A$ and |
400 |
|
|
$B$) are identical, and the three calculations built in to {\tt |
401 |
|
|
DynamicProps} make these assumptions. It is possible, however, to |
402 |
|
|
make simple modifications to the {\tt DynamicProps} code to allow |
403 |
|
|
the use of {\it cross} time correlation functions (i.e. with |
404 |
|
|
different vectors). The ability to use two selection scripts to |
405 |
|
|
select different types of atoms is already present in the code. |
406 |
|
|
|
407 |
|
|
The options available for DynamicProps are as follows: |
408 |
|
|
\begin{longtable}[c]{|EFG|} |
409 |
|
|
\caption{DynamicProps Command-line Options} |
410 |
|
|
\\ \hline |
411 |
|
|
{\bf option} & {\bf verbose option} & {\bf behavior} \\ \hline |
412 |
|
|
\endhead |
413 |
|
|
\hline |
414 |
|
|
\endfoot |
415 |
|
|
-h& {\tt -{}-help} & Print help and exit \\ |
416 |
|
|
-V& {\tt -{}-version} & Print version and exit \\ |
417 |
|
|
-i& {\tt -{}-input=filename} & input dump file \\ |
418 |
|
|
-o& {\tt -{}-output=filename} & output file name \\ |
419 |
|
|
& {\tt -{}-sele1=selection script} & select first StuntDouble set \\ |
420 |
|
|
& {\tt -{}-sele2=selection script} & select second StuntDouble set (if sele2 is not set, use script from sele1) \\ |
421 |
|
|
\hline |
422 |
|
|
\multicolumn{3}{|l|}{One option from the following group of options is required:} \\ |
423 |
|
|
\hline |
424 |
|
|
-r& {\tt -{}-rcorr} & compute mean square displacement \\ |
425 |
|
|
-v& {\tt -{}-vcorr} & compute velocity correlation function \\ |
426 |
|
|
-d& {\tt -{}-dcorr} & compute dipole correlation function |
427 |
|
|
\end{longtable} |
428 |
|
|
|
429 |
|
|
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |