Pyscal solid liquid #414
Pyscal solid liquid #414
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| sys.find_neighbors(method="voronoi") | ||
| atoms = sys.atoms | ||
| return np.array([atom.volume for atom in atoms]) | ||
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| def get_system(atoms): |
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I think for consistency we would want to call that pyiron_to_pyscal, similar to pyiron_to_ase and pyiron_to_pymatgen.
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renamed it. I also moved it next to the to_ase, to_pymatgen and to_ovito methods
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| return sys | ||
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| def analyse_find_solids(atoms, neighbor_method="cutoff", |
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This returns the number of atoms that are inside a solid phase? If so it'd cool to also return an index array, that shows which are solid and which are liquid, maybe behind a switch, like the pyscal_adaptive_cna method.
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This only returns the number by default, but when using return_system=True it returns the complete pyscal system object, which allows to get the indices. I thought this is the most simple in the default case and the most flexible approach when using the return_system option.
Alternatively I could change the default to return an array with the indices of all atoms that are identified as solid, so that the len(returned_array) gives the number of solids I guess. But I do not know if the order of the atoms stays the same when converting between pyiron ase and pyscal system, so I am not sure if indices will always be correct
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Ah, I had simply missed that while skimming. Since anything might happen while changing from pyiron to pyscal returning the full system is ok, I suppose.
| return_sys=False, | ||
| ): | ||
| """ | ||
| Get the number of solids or the corresponding pyscal system. |
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Since I misunderstood the method, I thought or should be of or some such... I promise to read more carefully next time. ;)
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Yep, once the h5io is sorted out, go ahead and merge. |
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I fixed the h5io version (for now) in #410, thus, try to rerun the tests :) |
Pull Request Test Coverage Report for Build 1439141654
💛 - Coveralls |
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Cool! We are really getting a lot of pyscal mapped functions -- what about doing a refactor (after this PR, not part of it) so that we nest these bindings, i.e. |
I always tried to type exactly that. |
Adds pyscals ability to find solid and liquid atoms in a structure.
Also adds a get_system convenience function to have easier access to pyscal functionality that is not directly accessible and replaces repetitive code with the get_system function.