| 11 |
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associated with them, often in the form of a dipole. Charges on atoms |
| 12 |
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are not currently suported by {\sc oopse}. |
| 13 |
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|
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+ |
\begin{lstlisting}[caption={[Specifier for molecules and atoms] An example specifing the simple Ar molecule},label=sch:AtmMole] |
| 15 |
+ |
molecule{ |
| 16 |
+ |
name = "Ar"; |
| 17 |
+ |
nAtoms = 1; |
| 18 |
+ |
atom[0]{ |
| 19 |
+ |
type="Ar"; |
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+ |
position( 0.0, 0.0, 0.0 ); |
| 21 |
+ |
} |
| 22 |
+ |
} |
| 23 |
+ |
\end{lstlisting} |
| 24 |
+ |
|
| 25 |
|
The second most basic building block of a simulation is the |
| 26 |
|
molecule. The molecule is a way for {\sc oopse} to keep track of the |
| 27 |
|
atoms in a simulation in logical manner. This particular unit will |
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\subsection{\label{sec:SSD}The {\sc DUFF} Water Models: SSD/E and SSD/RF} |
| 283 |
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|
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In the interest of computational efficiency, the default solvent used |
| 285 |
< |
in {\sc oopse} is the Soft Sticky Dipole (SSD) water model. SSD was |
| 286 |
< |
developed by Ichiye \emph{et al.} as a modified form of the |
| 287 |
< |
hard-sphere water model proposed by Bratko, Blum, and |
| 285 |
> |
by {\sc oopse} is the extended Soft Sticky Dipole (SSD/E) water |
| 286 |
> |
model.\cite{Gezelter04} The original SSD was developed by Ichiye |
| 287 |
> |
\emph{et al.}\cite{Ichiye96} as a modified form of the hard-sphere |
| 288 |
> |
water model proposed by Bratko, Blum, and |
| 289 |
|
Luzar.\cite{Bratko85,Bratko95} It consists of a single point dipole |
| 290 |
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with a Lennard-Jones core and a sticky potential that directs the |
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|
particles to assume the proper hydrogen bond orientation in the first |
| 344 |
|
{\it charged} multi-point models. In the original Monte Carlo |
| 345 |
|
simulations using this model, Ichiye {\it et al.} reported that using |
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|
SSD decreased computer time by a factor of 6-7 compared to other |
| 347 |
< |
models.\cite{Ichiye96} What is most impressive is that this savings |
| 347 |
> |
models.\cite{Ichiye96} What is most impressive is that these savings |
| 348 |
|
did not come at the expense of accurate depiction of the liquid state |
| 349 |
|
properties. Indeed, SSD maintains reasonable agreement with the Soper |
| 350 |
< |
data for the structural features of liquid |
| 350 |
> |
diffraction data for the structural features of liquid |
| 351 |
|
water.\cite{Soper86,Ichiye96} Additionally, the dynamical properties |
| 352 |
|
exhibited by SSD agree with experiment better than those of more |
| 353 |
|
computationally expensive models (like TIP3P and |
| 358 |
|
Recent constant pressure simulations revealed issues in the original |
| 359 |
|
SSD model that led to lower than expected densities at all target |
| 360 |
|
pressures.\cite{Ichiye03,Gezelter04} The default model in {\sc oopse} |
| 361 |
< |
is SSD/E, a density corrected derivative of SSD that exhibits improved |
| 362 |
< |
liquid structure and transport behavior. If the use of a reaction |
| 363 |
< |
field long-range interaction correction is desired, it is recommended |
| 364 |
< |
that the parameters be modified to those of the SSD/RF model. Solvent |
| 365 |
< |
parameters can be easily modified in an accompanying {\sc BASS} file |
| 366 |
< |
as illustrated in the scheme below. A table of the parameter values |
| 367 |
< |
and the drawbacks and benefits of the different density corrected SSD |
| 368 |
< |
models can be found in reference \ref{Gezelter04}. |
| 361 |
> |
is therefore SSD/E, a density corrected derivative of SSD that |
| 362 |
> |
exhibits improved liquid structure and transport behavior. If the use |
| 363 |
> |
of a reaction field long-range interaction correction is desired, it |
| 364 |
> |
is recommended that the parameters be modified to those of the SSD/RF |
| 365 |
> |
model. Solvent parameters can be easily modified in an accompanying |
| 366 |
> |
{\sc BASS} file as illustrated in the scheme below. A table of the |
| 367 |
> |
parameter values and the drawbacks and benefits of the different |
| 368 |
> |
density corrected SSD models can be found in reference |
| 369 |
> |
\ref{Gezelter04}. |
| 370 |
|
|
| 371 |
|
!!!Place a {\sc BASS} scheme showing SSD parameters around here!!! |
| 372 |
|
|
| 410 |
|
|
| 411 |
|
|
| 412 |
|
\subsection{\label{Sec:pbc}Periodic Boundary Conditions} |
| 413 |
+ |
|
| 414 |
+ |
\newcommand{\roundme}{\operatorname{round}} |
| 415 |
|
|
| 416 |
|
\textit{Periodic boundary conditions} are widely used to simulate truly |
| 417 |
|
macroscopic systems with a relatively small number of particles. The |
| 444 |
|
\end{equation} |
| 445 |
|
And then, each element of $\mathbf{s}$ is wrapped to lie between -0.5 to 0.5, |
| 446 |
|
\begin{equation} |
| 447 |
< |
s_{i}^{\prime}=s_{i}-round(s_{i}) |
| 447 |
> |
s_{i}^{\prime}=s_{i}-\roundme(s_{i}) |
| 448 |
|
\end{equation} |
| 449 |
|
where |
| 450 |
|
|
| 451 |
|
% |
| 452 |
|
|
| 453 |
|
\begin{equation} |
| 454 |
< |
round(x)=\left\{ |
| 455 |
< |
\begin{array}[c]{c}% |
| 454 |
> |
\roundme(x)=\left\{ |
| 455 |
> |
\begin{array}{cc} |
| 456 |
|
\lfloor{x+0.5}\rfloor & \text{if \ }x\geqslant0\\ |
| 457 |
|
\lceil{x-0.5}\rceil & \text{otherwise}% |
| 458 |
|
\end{array} |
| 459 |
|
\right. |
| 460 |
|
\end{equation} |
| 461 |
+ |
For example, $\roundme(3.6)=4$, $\roundme(3.1)=3$, $\roundme(-3.6)=-4$, |
| 462 |
+ |
$\roundme(-3.1)=-3$. |
| 463 |
|
|
| 447 |
– |
|
| 448 |
– |
For example, $round(3.6)=4$,$round(3.1)=3$, $round(-3.6)=-4$, |
| 449 |
– |
$round(-3.1)=-3$. |
| 450 |
– |
|
| 464 |
|
Finally, we obtain the minimum image coordinates by transforming back |
| 465 |
|
to real space,% |
| 466 |
|
|
