Use FlattenedStorage in NeighborsTrajectory

[pmrv]

This also allows it to be used with grand-canonical trajectories. Has some small fixes for DataContainer compat too, see commit messages.

[sudarsan-surendralal]

This looks good to me. If possible, can you also add a test to check if the shapes are consistent?

[pmrv]

I realize now that this will change the shape of the attributes neighbor_indices, etc. because you can't put them in full numpy arrays anymore. (Actually right now the code stores the flat arrays, but that probably breaks you old code).

What if I make it so that the property methods check whether the trajectory canonical or grand-canonical and in the latter case return full arrays with filler values (basically like @samwaseda does it for the neighbor class). Then old code won't break and new code that wants to deal with grand-canonical trajectories is better off dealing with the underlying FlattenedStorage anyway.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[sudarsan-surendralal]

LGTM!

[sudarsan-surendralal]

Oops one of the tests fail

AttributeError: 'float' object has no attribute 'sqrt'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/runner/work/pyiron_atomistics/pyiron_atomistics/tests/lammps/test_base.py", line 412, in test_dump_parser_water
    self.assertTrue(np.allclose(np.linalg.norm(neigh_traj_obj.vecs, axis=-1),
  File "<__array_function__ internals>", line 5, in norm
  File "/usr/share/miniconda/envs/test/lib/python3.9/site-packages/numpy/linalg/linalg.py", line 2561, in norm
    return sqrt(add.reduce(s, axis=axis, keepdims=keepdims))
TypeError: loop of ufunc does not support argument 0 of type float which has no callable sqrt method

[pmrv]

Seems it's a bug in FlattenedStorage, will fix in base.

[coveralls]

Pull Request Test Coverage Report for Build 1507327506

• 17 of 20 (85.0%) changed or added relevant lines in 2 files are covered.
• 50 unchanged lines in 1 file lost coverage.
• Overall coverage decreased (-0.02%) to 69.782%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron_atomistics/atomistics/structure/neighbors.py	16	19	84.21%

Files with Coverage Reduction	New Missed Lines	%
pyiron_atomistics/atomistics/job/atomistic.py	50	72.87%

Totals
Change from base Build 1500854841:	-0.02%
Covered Lines:	11438
Relevant Lines:	16391

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💛 - Coveralls