Error parsing stdout file

[gcapes]

In some simulations, the DAMASK stdout file isn't parsed properly and the vis files (.vti) aren't created.

Loading mpi/intel-18.0/openmpi/4.1.0
  Loading requirement: compilers/intel/18.0.3 libs/ucx/1.9.0
Traceback (most recent call last):
  File "/net/scratch/j06992lg/3D_EBSD_workflow/Lighter_Zr_microstructure_10gridZ_cooling_T300_2026-03-20_110541/artifacts/submissions/0/scripts/simulate_VE_loading_damask_act_5.py", line 48, in <module>
    output = read_log(**func_kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/net/scratch/j06992lg/3D_EBSD_workflow/Lighter_Zr_microstructure_10gridZ_cooling_T300_2026-03-20_110541/artifacts/submissions/0/scripts/simulate_VE_loading_damask_act_5.py", line 8, in read_log
    return read_spectral_stdout(path=damask_stdout_file, encoding="utf8")
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/iusers01/jf01/j06992lg/.venv_cooling/lib/python3.11/site-packages/damask_parse/readers.py", line 231, in read_spectral_stdout
    parsed_inc = parse_increment(i)
                 ^^^^^^^^^^^^^^^^^^
  File "/mnt/iusers01/jf01/j06992lg/.venv_cooling/lib/python3.11/site-packages/damask_parse/readers.py", line 109, in parse_increment
    inc_iter_i = parse_increment_iteration(i)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/mnt/iusers01/jf01/j06992lg/.venv_cooling/lib/python3.11/site-packages/damask_parse/readers.py", line 37, in parse_increment_iteration
    dg_str = dg_match.group(1)
             ^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'group'
[2026-03-22T11:26:43.029] error: *** JOB 12354150 ON node1232 CANCELLED AT 2026-03-22T11:26:43 DUE TO TIME LIMIT ***

The task is to figure out what is in the log file that isn't expected by damask parse.

[gcapes]

Well this is getting complicated :) Brain dump:

As things stand, for non-thermal simulations, the log file gets split into increment iterations containing deformation_gradient_aim and piola_kirchhoff_stress, which are then saved into dictionary for each iteration, and then put into a list for each increment.
The problem comes in that the thermal reporting is every 5 increments, so I can't just add in the regex and save the values. I'm looking at having a conditional that tries a regex match for the original variables, and if it fails, tries to match a regex for the section containing thermal conduction converged.
If that works I'll then need to figure out what to do with the returned thermal data, as currently damask parse is not set up to expect it.