def test_register_with_parent(self):
with self.subTest(msg='test simple case, no additions'):
parent = PerfectZeolite.make('BEA')
child = Zeolite.make('BEA')
child = child.retag_self()
child.register_with_parent(parent)
self.assertEqual(parent.index_mapper, child.index_mapper)
self.assertEqual(parent, child.parent_zeotype)
self.assertIn(child.name, child.index_mapper.names)
with self.subTest(msg='test additions'):
parent = PerfectZeolite.make('BEA')
additions_dict = copy.deepcopy(parent.additions)
child = Zeolite.make('BEA')
child = child.add_atoms(
Atoms("H2", positions=[[0, 0, 0], [1, 1, 1]]),
'H2').delete_atoms([1, 2, 3, 4])
ads_map = child.build_additions_map()
child.additions = additions_dict
child = child.retag_self()
child.register_with_parent(parent, ads_map)
self.assertEqual(parent.index_mapper, child.index_mapper)
self.assertEqual(parent, child.parent_zeotype)
self.assertIn(child.name, child.index_mapper.names)
name_list = []
for key in ads_map:
name_list.extend(list(ads_map[key]))
for name in name_list:
self.assertIn(name, child.index_mapper.names)
def test_build_iz_from_z(self):
tmp_goo = PerfectZeolite.make('GOO')
z = PerfectZeolite.build_from_cif_with_labels('data/GOO.cif')
iz = Zeolite(z)
# tests inheritance
self.assertIsInstance(iz, Zeolite)
self.assertIsInstance(iz, PerfectZeolite)
self.assertIsInstance(iz, Atoms)
# tests empty list attributes
# tests corretly defined parameters
self.assertEqual(iz._site_to_atom_indices, None)
self.assertEqual(iz._atom_indices_to_site, None)
#self.assertEqual(iz.name)
self.assertEqual(iz.parent_zeotype, z)
#tests atoms are there and behave the same
self.assertCountEqual(iz.get_tags(), z.get_tags())
self.assertCountEqual(iz.get_chemical_symbols(),
z.get_chemical_symbols())
self.assertEqual(id(iz.parent_zeotype), id(z.parent_zeotype))
self.assertEqual(id(iz.index_mapper), id(z.index_mapper))
self.assertEqual(id(iz.parent_zeotype), id(z.parent_zeotype))
self.assertNotEqual(iz.index_mapper, None)
self.assertEqual(iz.parent_zeotype, z)
self.assertEqual(iz.index_mapper, z.index_mapper)
self.assertEqual(iz.index_mapper, z.index_mapper)
def test_init_with_zeolite_obj(self):
tmp_goo = PerfectZeolite.make('GOO')
z = PerfectZeolite.build_from_cif_with_labels('data/GOO.cif')
my_zeotype = PerfectZeolite(z)
print(os.getcwd())
# tests inheritance
self.assertIsInstance(my_zeotype, PerfectZeolite)
self.assertIsInstance(my_zeotype, Atoms)
# tests empty list attributes
# tests corretly defined parameters
self.assertEqual(my_zeotype._site_to_atom_indices,
z._site_to_atom_indices)
self.assertEqual(my_zeotype._atom_indices_to_site,
z._atom_indices_to_site)
self.assertEqual(my_zeotype.name, z.name)
self.assertEqual(my_zeotype.parent_zeotype, my_zeotype)
#tests atoms are there and behave the same
self.assertCountEqual(my_zeotype.get_tags(), z.get_tags())
self.assertCountEqual(my_zeotype.get_chemical_symbols(),
z.get_chemical_symbols())
self.assertNotEqual(id(my_zeotype.parent_zeotype),
id(z.parent_zeotype))
self.assertNotEqual(id(my_zeotype.index_mapper), id(z.index_mapper))
self.assertNotEqual(id(my_zeotype.index_mapper), id(z.parent_zeotype))
self.assertNotEqual(my_zeotype.index_mapper, None)
def test_make(self):
z = PerfectZeolite.make('CHA')
cha_site_dict = {
'O1':
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17],
'O2': [
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35
],
'O3': [
36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53
],
'O4': [
54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
70, 71
],
'T1': [
72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,
88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,
103, 104, 105, 106, 107
]
}
self.assertIsInstance(z, PerfectZeolite)
self.assertIs(z, z.parent_zeotype)
self.assertDictEqual(cha_site_dict, z._site_to_atom_indices)
def test_get_hetero_atoms(self):
z = PerfectZeolite.make('CHA')
with self.subTest(msg='testing default arguments'):
z[3].symbol = 'Hf'
z[5].symbol = 'Sn'
self.assertCountEqual([3, 5], z.get_hetero_atoms())
with self.subTest(msg='Custom hetero atoms list'):
# first get a list of O atoms
O_list = []
for atom in z:
if atom.symbol == 'O':
O_list.append(atom.index)
self.assertCountEqual(O_list, z.get_hetero_atoms(['O']))
def test_init_with_atoms_obj(self):
tmp_goo = PerfectZeolite.make('GOO')
my_atoms = read('data/GOO.cif')
my_zeotype = PerfectZeolite(my_atoms)
# tests inheritance
self.assertIsInstance(my_zeotype, PerfectZeolite)
self.assertIsInstance(my_zeotype, Atoms)
# tests empty list attributes
# tests corretly defined parameters
self.assertEqual(my_zeotype._site_to_atom_indices, None)
self.assertEqual(my_zeotype._atom_indices_to_site, None)
self.assertEqual('parent', my_zeotype.name)
self.assertEqual(my_zeotype.parent_zeotype, my_zeotype)
#tests atoms are there and behave the same
self.assertCountEqual(my_zeotype.get_tags(), my_atoms.get_tags())
self.assertCountEqual(my_zeotype.get_chemical_symbols(),
my_atoms.get_chemical_symbols())
def test_get_atom_types(self):
z = PerfectZeolite.make('CHA')
get_atom_types_dict = {
'framework-O': [
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,
66, 67, 68, 69, 70, 71
],
'framework-Si': [
72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87,
88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102,
103, 104, 105, 106, 107
]
}
with self.subTest(msg='test get atom types'):
self.assertDictEqual(z.get_atom_types(), get_atom_types_dict)