korintje / dftbplus_restarter Goto Github PK

There is a problem reading the dftb_in.hsd template in restart_filemaker.py when there are comments in certain hsd blocks. For example:

Geometry = GenFormat {
<<< my_file # this is a comment
}

As the script will then try to read the file "my_file # this is a comment" instead of "my_file". It's not clear to me whether this is best solved in the hsd library or the script.

Hello,

If this thermostat is not written at every iteration:

MDRestartFrequency = 2

there is a problem with:

66, in load_thermostat
iter_lines = iter_lines_list[self.iter_num]
IndexError: list index out of range

From the input file obtained with the new version of the script, the one with the "restart-from-iter" option, the initial charges seem not to be correctly read by the program, even in the option ReadInitialCharges = Yes is specified. The output does not show the typical step 0 where old charges are read, which should appear as follows due to the zero difference in the energies:

*** Geometry step: 0

iSCC Total electronic Diff electronic SCC error
1 0.00000000E+00 0.00000000E+00 0.21845085E-05

Differently, the program tries to optimize the charges for the step 0 and fails in the optimization. Since the output says that the charges are correctly read from the charges.bin file, this should mean that the coordinates do not correspond to the last step of the previous run. This probably derives from some error in the production of the Geometry with the current format (the "explicit geometry specification", as indicated in the DFTB+ manual) instead of the GenFormat, which was employed in the previous version of the python script.

Dear authors,

thank you very much for the useful tool. I was wondering if there is a way to restart from a given step number (not the last one). I tried the --max-iter option but with poor results.
This is usually needed because in NVT runs also the data about the thermostat must be restarted, which are contained in the md.out file. However, the program writes this file after the geo_end.xyz one, so that if the run crashes for some reason (e.g., exceeded wall time), one cannot restart from the last step written in the trajectory file, but must select the last step for which the thermostat parameters have been written.
Also, adding a restart function for the thermostat in the python script would be very useful.

Thank you in advance.
Regards,
mbusato