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Bugfix: Interactive calculation array comparison #1542

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merged 2 commits into from
Jul 19, 2024
Merged

Bugfix: Interactive calculation array comparison #1542

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Bugfix: Interactive calculation array comparison
jan-janssen Jul 19, 2024
8436d53
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 19, 2024
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25 changes: 15 additions & 10 deletions pyiron_base/jobs/job/interactive.py
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Original file line number Diff line number Diff line change
Expand Up @@ -268,16 +268,21 @@ def interactive_flush(self, path="interactive", include_last_step=False):
step=self.interactive_write_frequency,
include_last=include_last_step,
)
if (
len(data) > 0
and isinstance(data[0], list)
and len(np.shape(data)) == 1
):
self._extend_hdf(h5=h5, path=path, key=key, data=data)
elif np.array(data).dtype == np.dtype("O"):
self._extend_hdf(h5=h5, path=path, key=key, data=data)
else:
self._extend_hdf(h5=h5, path=path, key=key, data=np.array(data))
try:
if (
len(data) > 0
and isinstance(data[0], list)
and len(np.shape(data)) == 1
):
self._extend_hdf(h5=h5, path=path, key=key, data=data)
elif np.array(data).dtype == np.dtype("O"):
self._extend_hdf(h5=h5, path=path, key=key, data=data)
else:
self._extend_hdf(h5=h5, path=path, key=key, data=np.array(data))
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All these calls to the same function are very similar. Actually, why can the stuff from the except clause not be done here? If not a dtype=O, then construct such an array instead of a regular one?

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With the recent numpy version np.array(data) fails, unless np.array(data, dtype="object") is set.

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This probably means that this clause elif np.array(data).dtype == np.dtype("O") is never trigger, because it raises an exception.

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I agree, but I am not sure. The clean way would require the user to specify if the number of atoms is going to change in their simulation or not and then choose the corresponding approach for storing the structures. So this is really just a quick fix to use interactive jobs to evaluate machine learned interatomic potentials to calculate the energies and forces for the test and training set.

except ValueError:
self._extend_hdf(
h5=h5, path=path, key=key, data=np.array(data, dtype="object")
)
self.interactive_cache[key] = []

def interactive_open(self):
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