Parameters in DPD (Dissipative P

2020-01-15 本文已影响0人 Yawei551

by Yawei Liu @Sydney, Australia 2020/01/16

DPD model

In the DPD model, one DPD bead represents $N_m$ fluid (e.g. water) molecules. Here, $N_m$ is also called coarse-graining (CG) degree. The DPD beads interact with each other via a conservative force $\textbf{F}_{ij}^C$ , a dissipative force $\textbf{F}_{ij}^D$ and a random force $\textbf{F}_{ij}^R$ given by
$\begin{eqnarray} \textbf{F}_{ij}^C &=& A (1-r_{ij}/r_c) \textbf{e}_{ij} && r_{ij}<r_c \\ \textbf{F}_{ij}^D &=& -\gamma(1-r_{ij}/r_c)^2 (\textbf{e}_{ij} \cdot \textbf{v}_{ij}) \textbf{e}_{ij} &&r_{ij}<r_c \\ \textbf{F}_{ij}^R &=& \xi (1-r_{ij}/r_c) \theta_{ij} (\Delta t)^{-1/2} \textbf{e}_{ij} && r_{ij}<r_c \end{eqnarray}$
between bead $i$ and $j$ .

$r_{ij}=|\textbf{r}_{ij}|$ : the centre-to-centre distance between the two beads.
$\textbf{e}_{ij}=\textbf{r}_{ij}/r_{ij}$ : the direction vector pointing between the two beads.
$\textbf{v}_{ij}$ : the vector difference in velocities between the two beads.
$A$ : the repulsion coefficient.
$\gamma$ : the dissipative coefficient.
$\xi$ : the the noise strength, and $\xi=\sqrt{2k_BT\gamma}$ with $k_B$ the Boltzmann constant and $T$ the temperature.
$\theta_{ij}$ : a Gaussian white noise variable.
$\Delta t$ : the simulation time step.
$r_c$ : the cutoff distance, and also can be treated as the size (diameter) of the DPD bead.

Determine paramters

$r_c$ , $k_BT$ , $m$ (bead mass) and $\tau$ (time)
In simulations, the reduced units are often used. For DPD model, all units are often scaled by the length unit $r_c$ , the mass unit $m$ , the energy unit $k_BT$ , and the time unit $\tau$ . Hence, $r_c^* = m^* = (k_BT)^* =\tau^* =1$ in the simulations. The superscript asterisk ( $^*$ ) means the quality is in reduced units. Units of other quantities are from these four basic units. For example, the unit for the mass density is $m/r_c^3$ , the unit for the diffusion constant is $r_c^2/\tau$ .
$\rho$ (density)
The DPD simulations are normally carried out within a $NVT$ ensemble, and the number of particles are often determined by setting $\rho^*=3$ . When $\rho^*>2$ , a simple scaling relation between the density and excess pressure exits $^1$ . In principle the density chosen for the simulation is a free parameter, but for efficiency reasons one would thus choose the lowest possible density where the scaling relation still holds.
$A$ and $N_m$
In order to match the compressibility of DPD fluid with a liquid having the dimensionless compressibility of $\Psi$ , the interparticle repulsion coefficient $A$ is given by
$A\approx \frac{\Psi N_m -1}{0.2\rho^*}(k_BT)^*.$
For water, $\Psi\approx 16$ yields $A^*=25$ for $N_m=1$ and $A^*=104$ for $N_m=4$ .
$\gamma$ and $\Delta t$
As a reasonable compromise between fast temperature equilibration, a fast simulation and a stable, physically meaningful system, simulation with $\Delta t^*=0.04$ and $\gamma^*=4.5$ is often recommended.
However, above choice for $\Delta t$ and $\gamma$ yields very small Schmidt number (i.e. the ratio of viscosity to diffusion) ( $Sc\sim1$ ) compared to the real fluid such as water ( $Sc\sim10^3$ ). A possible solution to this problem is increasing $\gamma$ . At the same time though, $\Delta t$ would have to be reduced to maintain the temperature control.
There is no unique way to determine the parameters for DPD model. For a given physical problem, with a characteristic length scale, we may always put a given number of DPD particles and parametrize the model in order to recover some macroscopic information (e.g. compressibilities, viscosity and diffusion constant).

Units conversation

The conversation between DPD units ( $r_c$ , $k_BT$ , $m$ and $\tau$ ) and real units ([m], [J], [kg] and [s]) is obtained from the key macroscopic information recovered by the model. If quantities in DPD units are labeled with $_{sim}$ and in real units are labeled with $_{real}$ , one would have

$m=N_m M_{real}/N_A$ with $M_{real}$ the mole mass of the fluid (e.g. water) and $N_A$ the Avogadro constant.
$r_c=(m\rho_{sim}/\rho_{real})^{1/3}$ with $\rho_{real}$ the mass density of the fluid.
$k_BT = k_B \cdot T$ with $k_B=1.38064853e-23 J\cdot K$ and $T$ is the system temperature in $K$ .
The time unit can be chosen in different ways.
- By taking the long-term self-diffusion constant into account, $\tau=N_m r_c^2 D_{sim}/D_{real}$ with $D$ the diffusion constant. Sometimes, this relation is also used to determine $N_m$ .
- If the viscous processes are the main parts, then $\tau=r_c^2 \nu_{sim}/\nu_{real}$ with $\nu$ the kinematic viscosity.
- Or $\tau=r_c/U_{ref}$ in which the reference velocity $U_{ref}$ is chosen as either system thermal velocity $(k_BT/m)^{1/2}$ or the characteristic velocity of the real flow.

Example

A NVT simulation with 1000 DPD beads in a cubic box is carried out by LAMMPS. The parameters are: $\rho^*=3$ ; $A=104$ for $N_m=4$ ; $\gamma=100$ ; $\Delta t=0.005$ . Then, by comparing the DPD fluid with the water at $T=298 K$ , we have:

Mass $m=1.1969\times10^{-25}$ [kg] ( $m=N_m M_{real}/N_A$ )
Length $r_c=7.1125\times10^{-10}$ [m] ( $r_c=(m\rho_{sim}/\rho_{real})^{1/3}$ )
Energy $k_BT = 4.1143\times10^{-21}$ [J] ( $k_BT = k_B \cdot T$ )
Time $\tau = 3.8363\times10^{-12}$ [s] ( $\tau=r_c\sqrt{m/k_BT}$ )
As a results, the kinematic viscosity for the DPD fluid is $\nu=1.569 r_c^2/\tau = 2.069\times10^{-7}$ [m $^2$ /s] ( $\nu=8.935\times10^{-7}$ [m $^2$ /s] for water).

References

(1) Groot, R. D.; Warren, P. B. Dissipative Particle Dynamics: Bridging the Gap between Atomistic and Mesoscopic Simulation. J. Chem. Phys. 1997, 107 (11), 4423–4435.