Re: [ESPResSo-users] Setting up Lattice Boltzmann

[Vincent Ustach]

Stefan,

Thanks for your reply! I have the code running but of course I still have a lot of work to do. I did not want the discussion to get stale, however, so I am replying now with the info that I have.

I am abandoning the DPD thermostat and using LB for a thermostat and for the HIs. I was not using inter_dpd. Sorry that I was not clear.

I will look into the pore constraint, but I don't want to restrict myself to cylindrical and conical pores.

This is indeed a concentration gradient driven diffusion, however electrostatics will be involved later. Viscosity seems to be (0.8 Pa * s) *10^-3. What are the units for friction?

I am working on printing the fluid velocity field to an output file and then hopefully it will shed some light on if the wall of particles serves as an adequate LB boundary.

I'll update ASAP.

Best,

Vincent

--Vincent Ustach
  University of California, Davis

On Mon, May 6, 2013 at 12:05 AM, Stefan Kesselheim <address@hidden> wrote:

Dear Vincent,

I' like to ask a few questions back:

On May 6, 2013, at 3:12 AM, Vincent Ustach <address@hidden> wrote:

> Hello everyone,
>
> I have a working script of spheres diffusing from a source to a sink through a pore with pore walls simulated by particles that are fixed in space. The box size is (30*sigma)^3. Rather than partial periodic conditions (x and y periodic, z not periodic), the system has another wall of fixed particles at z = 29*sigma so there is no diffusion from source to sink except through the pore. The thermostat and solvent are simulated through dissipative particle dynamics. I would like to add the Lattice Boltzmann system to the simulation to model the hydrodynamic interactions and I have a few questions.

* Why would u use DPD+LB? Are you referring to the (conservative) soft particle interaction of DPD type or the thermostat? Is it clear to you that inter_dpd is not the conservative DPD interaction?
* Are you familiar with the pore constraint? It might be a replacement for your particles. The wall constraint can probably replace the other walls.

> 1) Are there reasonable parameters to use as a starting point for lbfluid? The fluid should be quiescent water with no external force. The wall particle size is (2.55*sigma) and the diffusing sphere size is (0.1*sigma) as dictated by the LJ interaction parameters which might influence the choice for the agrid parameter. The time step for MD is 0.001. I am confused by the term "LB units" in the user guide which is why I don't know where to start.

LB intrinsically uses a different unit system, in which the (LB time-step is 1), however the interface is always made so that you interact with it in (usual) MD units.
The right choice of LB parameters however is a tricky thing. It depends on the effects you expect in your system. Are you expecting collective transport (e.g. diffusophoretic effects), such as fluid transport due to a concentration gradient? Or are pairwise interactions important?

>From my experience a good starting point are the LB parameters:
density 1 viscosity 0.8 friction 10 agrid 1 tau 0.01

Then the hydrodynamic radius of the particles will be 0.45 sigma. I'd recommend to scale up the rest of the system.

> 2) Will the walls (fixed particles) serve as hydrodynamic boundaries for the fluid or do I need to add the LB boundaries as dictated by the pore dimensions?

This is not clear yet. lbboundaries use the link bounce back method, which is considered a "good" method for boundaries. If a set of particles is a "good" boundary depends e.g. on the friction, on the density etc. Usually the combination of a "constraint" and an identical "lbboundary" is the way to go, but implementing own shapes is tedious.

Cheers and good luck
Stefan