76 |
|
|
77 |
|
\section{\label{appendixSection:analysisFramework}Analysis Framework} |
78 |
|
|
79 |
< |
\section{\label{appendixSection:hierarchy}Hierarchy} |
79 |
> |
\section{\label{appendixSection:concepts}Concepts} |
80 |
|
|
81 |
< |
\subsection{\label{appendixSection:selectionSyntax}Selection Syntax} |
81 |
> |
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 |
|
|
86 |
< |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
86 |
> |
\begin{figure} |
87 |
> |
\centering |
88 |
> |
\includegraphics[width=3in]{heirarchy.eps} |
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 |
|
|
95 |
< |
\subsection{\label{appendixSection:staticProps}Static Properties} |
95 |
> |
\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 |
|
|
104 |
< |
\subsection{\label{appendixSection:dynamicProps}Dynamics Properties} |
104 |
> |
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} |