Lammps parser hangs within parse_method() for new example

[JFRudzinski]

I am having trouble with this new lammps example. I placed it under tests/data/lammps/polymer_melt/Equil/ in my md-workflow-observables branch. The corresponding nomad branch is 970-add-RDF-MSD-plots-to-overview-GUI-page-for-molecular-dynamics-trajectories.

When I try to parse nohup.out the parser hangs (at least for 10-20 min) at line 1181 masses = self.data_parser.get('Masses', None) in lammps/parser.py. If I set masses=None on this line instead, everything finishes correctly in ~10s. The data_parser.mainfile is correct, and I see the "Masses" section within this file. So, I don't understand what is happening and I'm unsure how to debug this. At some point during my testing the parsing worked correctly with this line in there but took a long time. But all my changes (to my knowledge) have to do with parse_workflow() so I can't see how I have caused this problem.

Another related issue/confusion is the following: Here I am parsing nohup.out which is the screen output when I run the lammps simulation. The native output file log.lammps has a similar header but does not contain any of the input info like read_data and such. So, I cannot parse this one successfully. @ladinesa : Have you experienced this? Is it meant that we parse the screen output and not the native lammps log file??

[ladinesa]

I put up a fix in md-workflow-observables. Can you try it? If the fix works, I will apply it to the master branch

[JFRudzinski]

I'm getting an error now: TypeError: _log() got an unexpected keyword argument 'data' when parsing nohup.out. Do you have an idea of what the issue is?

---

IndexError Traceback (most recent call last)
~/work/soft/nomad/nomad/parsing/file_parser/text_parser.py in _add_value(self, quantity, value, units)
386 try:
--> 387 value_processed = quantity.to_data(value)
388 for i in range(len(value_processed)):

~/work/soft/nomad/nomad/parsing/file_parser/text_parser.py in to_data(self, val_in)
217
--> 218 val_out = [process(val) for val in val_in]
219

~/work/soft/nomad/nomad/parsing/file_parser/text_parser.py in (.0)
217
--> 218 val_out = [process(val) for val in val_in]
219

~/work/soft/nomad/nomad/parsing/file_parser/text_parser.py in process(val)
159 if self.str_operation is not None:
--> 160 val = self.str_operation(val)
161

~/work/soft/nomad/dependencies/parsers/atomistic/atomisticparsers/lammps/parser.py in get_section_value(val)
147
--> 148 if val[0][0] == '#':
...
-> 1390 self._log(WARNING, msg, args, **kwargs)
1391
1392 def warn(self, msg, *args, **kwargs):

TypeError: _log() got an unexpected keyword argument 'data'

[ladinesa]

I missed one more fix, should be included now in latest commit.

[JFRudzinski]

indeed, it works now 👍