Restart leads to Missing steps in output.log error in diagnostics.py

[jakobcasa]

Dear all

I have run an MD situation (dt =0.5fs, 400 steps). After ~1/3 (e.g. 66 fs), the time limit of the cluster is reached. I had to restart the MD. After the 400 steps were completed, I ran the diagnostics.py file, and in every traj, it gave me the same output: that the missing steps were at the time when I restarted the MD. I want to send you the data produced, but the files are too big. Is there another way to send you the data?

Is there a way to avoid a rerun of the complete traj? And can the diagnostics.py be run while the traj is still running to avoid time lost?

Thank you

Best Jakob

The output from diagnostics.py of the traj, which I would like to send you, is:

    Output files:     .lis .. .log .. .dat .. .xyz .. OK
    Restart files:    ctrl .. traj .. restart/ ..     OK
    Progress:         [=========================]     200.0 of 200.0 fs
    Status:                                           FINISHED
    Data extractor...                                 OK
    Energy:                                           OK
    Population:                                       OK
    Intruder states:  Missing steps in output.log     at 67.50 fs