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_build_from_cif_with_labels(
self
): # TODO: Write test case for building from CIF file (use rel path)
abs_path = '/Users/dda/Code/MAZE-sim/tests/data/CHA.cif'
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
]
}
z = PerfectZeolite.build_from_cif_with_labels(abs_path)
self.assertIsInstance(z, PerfectZeolite)
self.assertIs(z, z.parent_zeotype)
self.assertDictEqual(cha_site_dict, z._site_to_atom_indices)
def __init__(self,
iza_code=None,
optimized_zeolite_path=None,
user_input_path=None):
""" This is an extra-framework class
:param iza_code: 3 letter code for the zeolite structures (IZA database)
"""
if iza_code is not None:
self.EFzeolite = Zeolite.make(iza_code)
if optimized_zeolite_path is not None:
read_vasp(optimized_zeolite_path, Zeolite.make(iza_code))
if user_input_path is not None:
# self.EFzeolite = read(user_input_path, '0')
self.EFzeolite = Zeolite(
PerfectZeolite.build_from_cif_with_labels(
filepath=user_input_path))
self.t_site_indices = {}
self.t_site_indices_count = {}
self.traj_1Al = []
self.traj_2Al = []
self.count_all_Al_pairs = 0
self.TM_list = ['Pt', 'Cu', 'Co', 'Pd', 'Fe', 'Cr', 'Rh', 'Ru']
self.dict_1Al_replaced = {}
self.dict_2Al_replaced = {}
self.T_site_pair = []
self.T_index_pair = []
def main():
cif_dir = "/Users/dda/Code/MAZE-sim/data/BEA.cif"
zeolite = PerfectZeolite.build_from_cif_with_labels(cif_dir)
print('t_site_to_atom_indices', zeolite._site_to_atom_indices)
print('atom_indices_to_t_site', zeolite._atom_indices_to_site)
atom_types = zeolite.get_atom_types()
for key, val in atom_types.items():
print(key, val)
indices, count = zeolite.count_elements()
print('atom type count', dict(count))
import os
from maze.zeolite import PerfectZeolite
from maze.io_zeolite import *
if __name__ == "__main__":
data_path = '/Users/dda/Code/MAZE-sim/data/'
cif_path = os.path.join(data_path, 'BEA.cif')
output_path = os.path.join(data_path, 'my_first_zeotype')
my_zeotype = PerfectZeolite.build_from_cif_with_labels(cif_path)
print(my_zeotype.index_mapper.main_index)
cluster, od = my_zeotype.get_cluster(1, 10, 10)
# data_dir = os.path.join(Path(os.getcwd()).parent, 'data')
# output_traj = os.path.join(data_dir, 'test.traj')
# cif_dir = os.path.join(data_dir, 'BEA.cif')
# zeolite = Zeotype.build_from_cif_with_labels(cif_dir)
save_zeolites(output_path, [my_zeotype, cluster, od])
new_dict = read_zeotypes(output_path + '.zeo')
print(new_dict)
print(new_dict['parent'])
print(new_dict['parent'].index_mapper.main_index)
# Trajectory(output_traj,'w', zeolite)