Hey Benyamin,
in my humble experience, it is extremely difficult to set-up the system
exactly how you described it. From what I understand, you are trying to
simulate a nanometer sized object in some sort of channel that is in the
centimetre range that has a flow inside. Therefore, the characteristic
lengths (size of your particle and size of the channel) are separated by
several orders of magnitude, which is also true for the time scales of
those systems. This poses a huge issue on its own and usually requires
special techniques to achieve, depending also on the effects you want to
capture in your system. The fact that you want to simulate several
seconds, paired with the fact that typical time-scales in simulation on
that particle scale are, as you already found out, picoseconds or even
smaller, means that you would need insanely long simulations.
Apart from the time-scale, if you want to stick to the correct ratio
between your particle and channel size, you will get technically
unmanageable system sizes. In my opinion it would be worth to reconsider
what the effects are that you want to measure and to rescale the system
to a more manageable size.
Regarding the simulation parameters, I remember a sentence about the
parameters in the tutorials saying something along the lines of “we use
those parameters for no other reason than them being stable”. I have not
looked at the tutorials in a while, so I don’t know if this is still
true, but keep that in mind. It is always advised to triple check and
calculate your parameters, which can be troublesome when using LB. The
guys from reference [1] did a great job with LB and it helped us a lot
when setting up our own systems. There is only a limited range of
parameters for with LB is stable, so you not being able to increase your
tilmestep beyond your given value does not surprise me. I can also
recommend book [2], especially sections about stability, to get an
overview over the possibilities within LB.
I hope that helps.
Best,
Martin
[1] Kreissl, Patrick, Christian Holm, and Rudolf Weeber.
"Frequency-dependent magnetic susceptibility of magnetic nanoparticles
in a polymer solution: a simulation study." /arXiv preprint
arXiv:2010.00299/ (2020). https://arxiv.org/abs/2010.00299
[2] Krüger, Timm, et al. "The lattice Boltzmann method." /Springer
International Publishing/ 10.978-3 (2017): 4-15.
===========================
Martin Kaiser, M.Sc.
Computational and Soft Matter Physics
Dipolar Soft Matter Group
Faculty of Physics, University of Vienna
Kolingasse 14-16, 1090, Vienna, Austria
On 28.06.2021, at 18:38, Benyamin Naranjani <bnaranjani@gmail.com
<mailto:bnaranjani@gmail.com>> wrote:
Hi,
I intend to simulate transport of one particle representing an insulin
molecule in a macro-scale fluid flow ~cm using lattice-Boltzmann
coupling. I notice that in tutorials values for friction coefficient
and particle mass are close to unity. In this case, the user is able
to vary time step value in a reasonable range. I assume this is
because the friction coefficient and particle mass which are on both
sides of the coupling equation would be roughly of the same order of
magnitude. This would allow the user to vary the value for time step
without causing any numerical issues for the integration procedure.
In my simulation, I set values for Boltzmann constant times
temperature parameter, gamma, and particle mass based on
Stokes-Einstein's relation in SI units. I calculate the gamma
according to the diffusivity value of the insulin molecule. For the
particle's mass, I set it to be equal to the mass of one insulin
molecule. In this manner, the value of gamma and particle's mass would
be significantly different as they are 2.85e-11 [kg/s] and 9.64e-24
[kg], respectively.
Under this condition, I cannot increase the time step value to be over
5e-13 [s], otherwise, the jupyter notebook kernel would die. Since I
am interested in studying transport of this molecule in larger
time/length scales for instance in tens of seconds, I need to be able
to increase the time step value significantly. I would really
appreciate your thoughts on the applicability/possibility of
increasing the time step.
All the best,
Benyamin
----------------------------------------------------------
Benyamin Naranjani; PhD candidate
Department of Pharmacy
Uppsala University
Sweden