[lammps-users] output stops after failure to insert molecule with fix deposit

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1

Dear all,
I’m running a deposition on a gold substrate of two molecules. At some point in the runtime it gives me a warning that it fails to insert a molecule. The anomaly, however, is that it stops outputting anything after the warning. However it doesn’t terminate properly. And it leaves a ghost process.

I’m on the 2020-10-29 version.
the part of the code where there might be an issue
molecule thiol_fc rigid_fc
molecule thiol thiolmodel
fix dep1 new deposit 20 0 30000 321 region depreg mol thiol_fc near 3 attempt 1000 vz -100e-5 -180e-5 vx -10e-5 10e-5 vy -10e-5 10e-5
fix dep2 new deposit 60 0 9000 321 region depreg mol thiol near 3 attempt 1000 vz -180e-5 -220e-5 vx -10e-5 10e-5 vy -10e-5 10e-5

2

This sounds a lot like this issue: https://github.com/lammps/lammps/issues/2755

3

Thanks for the quick reply.

it seems to be the problem

Are there any workaround? or should I wait until I can request to get lammps updated on Monday?
Thank you,
Mattia

(PS. sorry, I got distracted and hit reply instead of reply all)

4

The only workaround that I can think of would to reduce the insertion frequency and / or make other changes so you don’t get the failed insertion warning state, where the deadlock happens.