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Error while collecting #63

Open LAPikachu opened 2 weeks ago

LAPikachu commented 2 weeks ago

I am running a Pyiron job with customized lammps input files. It creates the dump files as expected but fails when trying to collect. The following error.out is created in the projects directory:

pandas.errors.EmptyDataError: No columns to parse from file

What could be the problem here?

jan-janssen commented 2 weeks ago

Can you post your thermo and thermo_modify commands? Pyiron tries to parse the log.lammps file but seems to not find the right tags.

LAPikachu commented 2 weeks ago

Certainly - these are the different instances:
thermo 100
thermo_style custom step pe fnorm fmax vol lx ly lz pxx pyy pzz pxy pxz pyz c_eatoms
...

thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms fnorm
...
thermo 10
thermo_style custom step pe lx ly lz press pxx pyy pzz c_eatoms fnorm

jan-janssen commented 2 weeks ago

Based on your input script having multiple thermo and thermo_style commands, I conclude that you also have multiple minimize / run commands, correct? This is currently not supported in pyiron_atomistics. We recommend to have one minimize / run command per pyiron job and then connect those jobs with the job.restart() function. This allows us to track the dependence of multiple calculation already on the pyiron database level.