| 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.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 |
|
|
| 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 |
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> |
{\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} |
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> |
|
| 429 |
> |
\subsection{\label{appendixSection:hydrodynamics}Hydrodynamics} |
