diff --git a/src/moxel/utils.py b/src/moxel/utils.py index 13717c0..5c4abd4 100644 --- a/src/moxel/utils.py +++ b/src/moxel/utils.py @@ -117,17 +117,18 @@ def __init__(self, grid_size=25, cutoff=10, epsilon=50, sigma=2.5): self.epsilon = epsilon self.sigma = sigma - def load_structure(self, cif_pathname): + def load_structure(self, pathname): r""" - Load a crystal structure from a ``.cif`` file. + Load a crystal structure from a file in a format supported by pymatgen + (CIF, JSON, etc.) Parameters ---------- - cif_pathname : str - Pathname to the ``.cif`` file. + pathname : str + Pathname to the file. """ - self.structure = Structure.from_file(cif_pathname) - self.structure_name = Path(cif_pathname).stem + self.structure = Structure.from_file(pathname) + self.structure_name = Path(pathname).stem def calculate(self, cubic_box=False, length=30, potential='lj', n_jobs=None): r""" diff --git a/tests/CIFs/MnH28C26(N2Cl)2.json b/tests/CIFs/MnH28C26(N2Cl)2.json new file mode 100644 index 0000000..a3beef4 --- /dev/null +++ b/tests/CIFs/MnH28C26(N2Cl)2.json @@ -0,0 +1 @@ +{"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0, "lattice": {"matrix": [[2.319077576, -15.952689285, 6.114436521], [16.119759785, 3.6009e-05, -6.114639544], [-2.227069811, 16.059340981, 18.435894778]], "pbc": [true, true, true], "a": 17.24101940711739, "b": 17.240518329808083, "c": 24.55085515725636, "alpha": 110.55724094376674, "beta": 110.55679178612553, "gamma": 90.00099777262982, "volume": 6334.205306374938}, "properties": {}, "sites": [{"species": [{"element": "Mn", "occu": 1}], "abc": 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0.31764449717953025], "xyz": [4.29254, 0.16940000000000052, 6.1216800000000005], "properties": {"pbe_ddec_charge": -0.598056}, "label": "Cl"}, {"species": [{"element": "Cl", "occu": 1}], "abc": [0.5085069968372126, 0.051796320977180614, 0.3176152907328825], "xyz": [1.3068600000000001, -3.011359999999999, 8.64804], "properties": {"pbe_ddec_charge": -0.597849}, "label": "Cl"}]} \ No newline at end of file diff --git a/tests/test_utils.py b/tests/test_utils.py index b5e62c1..5356c36 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -159,6 +159,15 @@ def test_batch_clean(self): # Check that the names have been correctly stored. self.assertEqual([names[i] for i in filled_idx], clean_names) + def test_load_file(self): + cif_dir = 'tests/CIFs' + + grid = Grid() + grid.load_structure(f'{cif_dir}/IRMOF-1.cif') + + grid = Grid() + grid.load_structure(f'{cif_dir}/MnH28C26(N2Cl)2.json') + if __name__ == '__main__': unittest.main()