Re: Cell-wall interaction using object-in-fluid with espresso 4.1.3

[Pouyan Keshavarz]

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From: Pouyan Keshavarz
Sent: Wednesday, July 22, 2020 8:49:52 AM
To: Ivan Cimrak; espressomd-users@nongnu.org
Subject: Re: Cell-wall interaction using object-in-fluid with espresso 4.1.3

 

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

 

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From: Ivan Cimrak <icimrak@gmail.com>
Sent: Wednesday, July 22, 2020 12:25:12 AM
To: Pouyan Keshavarz; espressomd-users@nongnu.org
Subject: Re: Cell-wall interaction using object-in-fluid with espresso 4.1.3

 

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