Feature Request: Integration with ASE

[ichibha]

It would be greatly appreciated if structures could be obtained as an array of ASE's Atoms. Since VASP is frequently paired with ASE, implementing this feature could lead to wider application of SHRY.

[kousuke-nakano]

Dear @ichibha, thank you for your request. I will try to implement it.

[kousuke-nakano]

Dear @ichibha, I have an idea for implementing this. Would you help me?

I need a function to convert a pymatgen structure to the corresponding ASE atoms such as:

from pymatgen_struct_to_ase_atoms(structure: pymatgen's structure) -> atoms: ASE's atoms

Would you try to implement it?

[ichibha]

@kousuke-nakano Thank you for your willingness to work on this issue. The pymatgen Structure object can be converted into an ASE Atoms object using the following function:

from pymatgen.core import Structure
from ase import Atoms


def pymatgen_struct_to_ase_atoms(structure: Structure) -> Atoms:
    return Atoms(
        symbols=[specie.symbol for specie in structure.species],
        positions=structure.cart_coords,
        cell=structure.lattice.matrix,
        pbc=True,
    )


if __name__ == "__main__":
    for label in ["cartesian", "fractional"]:
        structure = Structure.from_file(f"{label}.vasp")
        atoms = convert_structure_to_atoms(structure)
        atoms.write(f"{label}_converted.vasp")

I attach the files used to verify the code.

submit.zip

[kousuke-nakano]

Dear @ichibha, Thanks. I have implemented it. Would you have a look at my pull request #7? I have added a new example example5.py. I would appreciate if you would confirm that SHRY works as you expected.

[ichibha]

Dear @kousuke-nakano, Thank you for your correspondence. The code works as I expected. I will make a suggestion with my expected behavior from the next time.

[kousuke-nakano]

Dear @ichibha, thanks. We will include this feature to the next release.