Dear Ivan,
Thank you so much.
Kind regards,
Pouyan
From: Ivan Cimrak <icimrak@gmail.com>
Sent: Thursday, July 30, 2020 9:18:48 AM
To: Pouyan Keshavarz
Cc: espressomd-users@nongnu.org; Iva Jancigova
Subject: Re: Cell-wall interaction using object-in-fluid with espresso 4.1.3
Dear Pouyan,
You need to do the things in the right order.
1. First, you need to setup the particle system (in our case the cell)
2. Then all the interactions, including the soft_sphere interaction.
3. Then you need to setup the fluid.
4. Then you need to setup the boundaries for the fluid.
In your very first email, your steps were
1. Particle system
2. fluid
3. fluid boundaries
4. soft_sphere interaction
After I suggested to move the fluid at the end, you moved the fluid, but left the boundaries intact, so your order was
1. Particle system
2. fluid boundaries
3. soft_sphere interaction
4. fluid
Since the boundaries were defined before the fluid, they were not activated. Therefore your fluid flew through the boundary and caused much more deformation of the cell, because the cell indeed felt the boudary, so the cell was dragged by the
fluid flowing through the boundary.
When you use this order
1. particles
2. soft_sphere interactions
3. fluid
4. fluid boundaries
everything will be all right.
I hope this helps,
Ivan
Dear all,
Thanks Ivan. I changed the line and it works but something more strange came up.
I noticed that the results have drastic differences in new version of espresso (version 4.3.1) with the version 4.0.0. I added two screenshot related to my simulations here. The first one (#1) was performed
with 4.0.0 and the second one (#2) was performed with 4.1.3. The second simulation is the same as the first one, except for the second one I add system.thermostat.set_lb(Lb_fluid=lbf, gamma=friction). Did anybody face this before and have a solution for this?
Kind regards,
Pouyan
Hello,
I can not see the code right now but try to move the lines for lbfluid after you define cell-wall interactions....
Ivan
On July 22, 2020 03:37:42 Pouyan Keshavarz <pouyan.keshavarz@uwaterloo.ca> wrote:
Dear all,
I have problem in modelling cell-wall interaction with the use of OIF module in espresso 4.1.3 and will be grateful if anybody can help me. More specifically, I face the error below whenever I try to
run my code.
"ERROR: The CPU LB does not currently support handling changes of the MD cell geometry. Setup the cell system, skin and interactions before activating the CPU LB.
Traceback (most recent call last):
File "test11.py", line 108, in <module>
system.integrator.run(steps=100)
File "integrate.pyx", line 104, in espressomd.integrate.Integrator.run
File "utils.pyx", line 265, in espressomd.utils.handle_errors
Exception: Encountered errors during integrate: ERROR: The CPU LB does not currently support handling changes of the MD cell geometry. Setup the cell system, skin and interactions before activating the CPU LB."
It is worth mentioning that when I removed the line related to cell-wall interaction the simulation ran correctly. Also I have been attached the code I used, here.
Thanks in advanced.
Kind regards
Pouyan
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