def test_distances(self):
atoms_1 = self.atoms.get_lines()
distances_1 = [float(a[5]) for a in atoms_1]
atoms_2 = Atoms.atoms_string_from_file(os.path.join(test_dir, "ATOMS"))
atoms_2 = atoms_2.splitlines()[3:]
distances_2 = [float(a.split()[5]) for a in atoms_2]
np.testing.assert_allclose(distances_1, distances_2, rtol=1e-5)
def test_distances(self):
atoms_1 = self.atoms.get_lines()
distances_1 = [float(a[5]) for a in atoms_1]
atoms_2 = Atoms.atoms_string_from_file(os.path.join(test_dir, "ATOMS"))
atoms_2 = atoms_2.splitlines()[3:]
distances_2 = [float(a.split()[5]) for a in atoms_2]
np.testing.assert_allclose(distances_1, distances_2)
def test_atoms_from_file(self):
filepath = os.path.join(test_dir, 'ATOMS')
atoms = Atoms.atoms_string_from_file(filepath)
self.assertEqual(atoms.splitlines()[3].split()[4], 'O',
"failed to read ATOMS file")
def test_atoms_from_file(self):
filepath = os.path.join(test_dir, 'ATOMS')
atoms = Atoms.atoms_string_from_file(filepath)
self.assertEqual(atoms.splitlines()[3].split()[4], 'O',
"failed to read ATOMS file")
def test_atoms_from_file(self):
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR, "ATOMS")
atoms = Atoms.atoms_string_from_file(filepath)
self.assertEqual(atoms.splitlines()[3].split()[4], "O",
"failed to read ATOMS file")
],
coords_are_cartesian=False,
tol=1e-9,
)
print(zno_structure)
print(zno_structure.get_space_group_info())
out_file_name = '/home/yugin/PycharmProjects/neurons/data/src/feff.inp.new2'
file_name = '/home/yugin/PycharmProjects/neurons/data/src/feff.inp.old'
atoms_obj = Atoms(zno_structure, 'O', 12)
pprint(atoms_obj.struct.cart_coords)
pprint(atoms_obj.get_lines())
header_obj = Header(struct=zno_structure)
pot_obj = Potential(zno_structure, 'O')
tags_obj = Tags().from_file(filename=file_name)
pprint(tags_obj.as_dict())
pot_obj.pot_string_from_file(filename=file_name)
pprint(pot_obj)
atoms_obj.atoms_string_from_file(filename=file_name)
pprint(atoms_obj.as_dict())
header_obj.write_file(out_file_name)
tags_obj.write_file(out_file_name)
pot_obj.write_file(out_file_name)
atoms_obj.write_file(out_file_name)
# paths_obj = Paths()
# header_obj.from_file(file_name)
print()
