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If nperiodic_dimensions=2 the structure adapter can only properly convert it to ase #1212

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unkcpz opened this issue May 31, 2022 · 1 comment · Fixed by #1233
Closed

If nperiodic_dimensions=2 the structure adapter can only properly convert it to ase #1212

unkcpz opened this issue May 31, 2022 · 1 comment · Fixed by #1233
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@unkcpz
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unkcpz commented May 31, 2022

The structure below, will not include cell information if converted to cif, pymatgen, pbd. Only ase structure works fine with cell included.

StructureResourceAttributes(immutable_id='015b55ae-5657-4441-bc5e-0eef090ecf97', last_modified=datetime.datetime(2021, 9, 13, 14, 26, 29, tzinfo=datetime.timezone.utc), elements=['C'], nelements=1, elements_ratios=[1.0], chemical_formula_descriptive='C2', chemical_formula_reduced='C', chemical_formula_hill='C2', chemical_formula_anonymous='A', dimension_types=[<Periodicity.PERIODIC: 1>, <Periodicity.PERIODIC: 1>, <Periodicity.APERIODIC: 0>], nperiodic_dimensions=2, lattice_vectors=[[2.46484131245562, 0.0, 0.0], [-1.23242065622219, -2.13461519293843, 0.0], [0.0, 0.0, 20.0000002075]], cartesian_site_positions=[[0.0, -1.42307679521789, 19.8345042867], [0.0, 0.0, 19.8345044942]], nsites=2, species=[Species(name='C', chemical_symbols=['C'], concentration=[1.0], mass=[12.011], original_name='C', attached=None, nattached=None)], species_at_sites=['C', 'C'], assemblies=None, structure_features=[], _mcloud_ctime='2016-02-27T22:41:09Z')

Which can query by https://aiida.materialscloud.org/2dstructures/optimade/v1/structures?filter=id%3D%2219889%22

@JPBergsma
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Dear unkcpz.

Thank you for the feedback, and sorry for the long wait. Last week, we had the yearly OPTIMADE workshop and we are still quite busy with processing all the comments and suggestions we got there.

I noticed that for the PDB file the lattice information is indeed missing.
I will try to make a patch for this.
I am however also wondering why the original authors @ml-evs and @CasperWA chose to not return the lattice information in this case.

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