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Fix bug with Lr leading to an #69

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merged 4 commits into from
Oct 30, 2024
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  • fix bug with Lr leading to an "out of bounds" error: atom list should have 103, and not 102 entries (when trying to include actinides completely

This was the error, I've received (from SG):

✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔✔multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
 File "/home/grimme/miniforge3/envs/mindlessgen/lib/python3.12/multiprocessing/pool.py", line 125, in worker
   result = (True, func(*args, **kwds))
                   ^^^^^^^^^^^^^^^^^^^
 File "/home/grimme/miniforge3/envs/mindlessgen/lib/python3.12/multiprocessing/pool.py", line 51, in starmapstar
   return list(itertools.starmap(args[0], args[1]))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/home/grimme/source/MindlessGen/src/mindlessgen/generator/main.py", line 164, in single_molecule_generator
   mol = generate_random_molecule(config.generate, config.general.verbosity)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 File "/home/grimme/source/MindlessGen/src/mindlessgen/molecules/generate_molecule.py", line 32, in generate_random_molecule
   mol.atlist = generate_atom_list(
                ^^^^^^^^^^^^^^^^^^^
 File "/home/grimme/source/MindlessGen/src/mindlessgen/molecules/generate_molecule.py", line 321, in generate_atom_list
   check_composition()
 File "/home/grimme/source/MindlessGen/src/mindlessgen/molecules/generate_molecule.py", line 302, in check_composition
   if min_count is not None and natoms[elem] < min_count:
                                ~~~~~~^^^^^^
IndexError: index 102 is out of bounds for axis 0 with size 102

@jonathan-schoeps Should be something for you, please verify and check if that's the appropriate fix.

Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
Signed-off-by: Marcel Müller <marcel.mueller@thch.uni-bonn.de>
@marcelmbn marcelmbn added the bug Something isn't working label Oct 29, 2024
@marcelmbn marcelmbn added this to the v1.0.0 milestone Oct 29, 2024
@marcelmbn marcelmbn self-assigned this Oct 29, 2024
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@jonathan-schoeps Apparently, the unit tests are also in conflict with this. Can you update them too, and push your changes to this PR?

Signed-off-by: Jonathan Schöps <s6jtscho@uni-bonn.de>
@marcelmbn marcelmbn merged commit d064d3d into grimme-lab:main Oct 30, 2024
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@marcelmbn marcelmbn deleted the fix/Lr branch October 30, 2024 12:18
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