| 1022 |
|
evaluation is to apply cutoff where particles farther than a |
| 1023 |
|
predetermined distance, are not included in the calculation |
| 1024 |
|
\cite{Frenkel1996}. The use of a cutoff radius will cause a |
| 1025 |
< |
discontinuity in the potential energy curve |
| 1026 |
< |
(Fig.~\ref{introFig:shiftPot}). Fortunately, one can shift the |
| 1027 |
< |
potential to ensure the potential curve go smoothly to zero at the |
| 1028 |
< |
cutoff radius. Cutoff strategy works pretty well for Lennard-Jones |
| 1029 |
< |
interaction because of its short range nature. However, simply |
| 1030 |
< |
truncating the electrostatic interaction with the use of cutoff has |
| 1031 |
< |
been shown to lead to severe artifacts in simulations. Ewald |
| 1032 |
< |
summation, in which the slowly conditionally convergent Coulomb |
| 1033 |
< |
potential is transformed into direct and reciprocal sums with rapid |
| 1034 |
< |
and absolute convergence, has proved to minimize the periodicity |
| 1035 |
< |
artifacts in liquid simulations. Taking the advantages of the fast |
| 1036 |
< |
Fourier transform (FFT) for calculating discrete Fourier transforms, |
| 1037 |
< |
the particle mesh-based methods are accelerated from $O(N^{3/2})$ to |
| 1038 |
< |
$O(N logN)$. An alternative approach is \emph{fast multipole |
| 1039 |
< |
method}, which treats Coulombic interaction exactly at short range, |
| 1040 |
< |
and approximate the potential at long range through multipolar |
| 1041 |
< |
expansion. In spite of their wide acceptances at the molecular |
| 1042 |
< |
simulation community, these two methods are hard to be implemented |
| 1043 |
< |
correctly and efficiently. Instead, we use a damped and |
| 1044 |
< |
charge-neutralized Coulomb potential method developed by Wolf and |
| 1045 |
< |
his coworkers. The shifted Coulomb potential for particle $i$ and |
| 1046 |
< |
particle $j$ at distance $r_{rj}$ is given by: |
| 1025 |
> |
discontinuity in the potential energy curve. Fortunately, one can |
| 1026 |
> |
shift the potential to ensure the potential curve go smoothly to |
| 1027 |
> |
zero at the cutoff radius. Cutoff strategy works pretty well for |
| 1028 |
> |
Lennard-Jones interaction because of its short range nature. |
| 1029 |
> |
However, simply truncating the electrostatic interaction with the |
| 1030 |
> |
use of cutoff has been shown to lead to severe artifacts in |
| 1031 |
> |
simulations. Ewald summation, in which the slowly conditionally |
| 1032 |
> |
convergent Coulomb potential is transformed into direct and |
| 1033 |
> |
reciprocal sums with rapid and absolute convergence, has proved to |
| 1034 |
> |
minimize the periodicity artifacts in liquid simulations. Taking the |
| 1035 |
> |
advantages of the fast Fourier transform (FFT) for calculating |
| 1036 |
> |
discrete Fourier transforms, the particle mesh-based methods are |
| 1037 |
> |
accelerated from $O(N^{3/2})$ to $O(N logN)$. An alternative |
| 1038 |
> |
approach is \emph{fast multipole method}, which treats Coulombic |
| 1039 |
> |
interaction exactly at short range, and approximate the potential at |
| 1040 |
> |
long range through multipolar expansion. In spite of their wide |
| 1041 |
> |
acceptances at the molecular simulation community, these two methods |
| 1042 |
> |
are hard to be implemented correctly and efficiently. Instead, we |
| 1043 |
> |
use a damped and charge-neutralized Coulomb potential method |
| 1044 |
> |
developed by Wolf and his coworkers. The shifted Coulomb potential |
| 1045 |
> |
for particle $i$ and particle $j$ at distance $r_{rj}$ is given by: |
| 1046 |
|
\begin{equation} |
| 1047 |
|
V(r_{ij})= \frac{q_i q_j \textrm{erfc}(\alpha |
| 1048 |
|
r_{ij})}{r_{ij}}-\lim_{r_{ij}\rightarrow |
| 1262 |
|
In general, there are two ways to satisfy the holonomic constraints. |
| 1263 |
|
We can use constraint force provided by lagrange multiplier on the |
| 1264 |
|
normal manifold to keep the motion on constraint space. Or we can |
| 1265 |
< |
simply evolve the system in constraint manifold. The two method are |
| 1266 |
< |
proved to be equivalent. The holonomic constraint and equations of |
| 1267 |
< |
motions define a constraint manifold for rigid body |
| 1265 |
> |
simply evolve the system in constraint manifold. These two methods |
| 1266 |
> |
are proved to be equivalent. The holonomic constraint and equations |
| 1267 |
> |
of motions define a constraint manifold for rigid body |
| 1268 |
|
\[ |
| 1269 |
|
M = \left\{ {(Q,P):Q^T Q = 1,Q^T PJ^{ - 1} + J^{ - 1} P^T Q = 0} |
| 1270 |
|
\right\}. |
| 1477 |
|
\] |
| 1478 |
|
The equations of motion corresponding to potential energy and |
| 1479 |
|
kinetic energy are listed in the below table, |
| 1480 |
+ |
\begin{table} |
| 1481 |
+ |
\caption{Equations of motion due to Potential and Kinetic Energies} |
| 1482 |
|
\begin{center} |
| 1483 |
|
\begin{tabular}{|l|l|} |
| 1484 |
|
\hline |
| 1491 |
|
\hline |
| 1492 |
|
\end{tabular} |
| 1493 |
|
\end{center} |
| 1494 |
< |
A second-order symplectic method is now obtained by the composition |
| 1495 |
< |
of the flow maps, |
| 1494 |
> |
\end{table} |
| 1495 |
> |
A second-order symplectic method is now obtained by the |
| 1496 |
> |
composition of the flow maps, |
| 1497 |
|
\[ |
| 1498 |
|
\varphi _{\Delta t} = \varphi _{\Delta t/2,V} \circ \varphi |
| 1499 |
|
_{\Delta t,T} \circ \varphi _{\Delta t/2,V}. |
| 1789 |
|
when the system become more and more complicate. Instead, various |
| 1790 |
|
approaches based on hydrodynamics have been developed to calculate |
| 1791 |
|
the friction coefficients. The friction effect is isotropic in |
| 1792 |
< |
Equation, \zeta can be taken as a scalar. In general, friction |
| 1793 |
< |
tensor \Xi is a $6\times 6$ matrix given by |
| 1792 |
> |
Equation, $\zeta$ can be taken as a scalar. In general, friction |
| 1793 |
> |
tensor $\Xi$ is a $6\times 6$ matrix given by |
| 1794 |
|
\[ |
| 1795 |
|
\Xi = \left( {\begin{array}{*{20}c} |
| 1796 |
|
{\Xi _{}^{tt} } & {\Xi _{}^{rt} } \\ |
