def test_write_file(self):
""".
The function is tested by save structure
to a POSCAR file, and then read from it.
Compare the parameters read from to the
origin input parameter. Using almostEqual
"""
bcu_arr = np.array([[[5, 29, 5, 5, 5, 5], [5, 5, 5, 5, 5, 5],
[5, 5, 29, 5, 5, 5]]])
latt = [[0, 0, 20], [1, 0, 0], [0.5, sqrt(3) / 2, 0]]
bcu_stru = CStru.from_array(latt, bcu_arr)
poscar_bcu = VaspPOSCAR(bcu_stru.get_gcell(), zoom=4)
tmp_file = "POSCAR.testing"
poscar_bcu.write(tmp_file)
with open(tmp_file, 'r') as testing_file:
data = testing_file.read()
self.assertEqual(data, str(poscar_bcu))
os.remove(tmp_file)
def test_from_array(self):
ss = CStru.from_array(self.m, self.arr)
self.assertEqual(ss, self.s)
def test_get_string(self):
boron_arr = np.array([[[5, 0, 5, 5, 5, 5], [5, 5, 5, 5, 5, 5],
[5, 5, 0, 5, 5, 5]]])
latt = [[0, 0, 20], [1, 0, 0], [0.5, sqrt(3) / 2, 0]]
boron_stru = CStru.from_array(latt, boron_arr)
poscar = VaspPOSCAR(boron_stru.get_gcell(), zoom=4)
expected_str = '''B16
4
0.000000 0.000000 20.000000
3.000000 0.000000 0.000000
3.000000 5.196152 0.000000
B
16
direct
0.000000 0.000000 0.000000 B
0.000000 0.000000 0.333333 B
0.000000 0.000000 0.500000 B
0.000000 0.000000 0.666667 B
0.000000 0.000000 0.833333 B
0.000000 0.333333 0.000000 B
0.000000 0.333333 0.166667 B
0.000000 0.333333 0.333333 B
0.000000 0.333333 0.500000 B
0.000000 0.333333 0.666667 B
0.000000 0.333333 0.833333 B
0.000000 0.666667 0.000000 B
0.000000 0.666667 0.166667 B
0.000000 0.666667 0.500000 B
0.000000 0.666667 0.666667 B
0.000000 0.666667 0.833333 B
'''
self.assertEqual(str(poscar), expected_str)
bcu_arr = np.array([[[5, 29, 5, 5, 5, 5], [5, 5, 5, 5, 5, 5],
[5, 5, 29, 5, 5, 5]]])
latt = [[0, 0, 20], [1, 0, 0], [0.5, sqrt(3) / 2, 0]]
bcu_stru = CStru.from_array(latt, bcu_arr)
poscar_bcu = VaspPOSCAR(bcu_stru.get_gcell(), zoom=4)
expected_str_bcu = '''B16Cu2
4
0.000000 0.000000 20.000000
3.000000 0.000000 0.000000
3.000000 5.196152 0.000000
B Cu
16 2
direct
0.000000 0.000000 0.000000 B
0.000000 0.000000 0.333333 B
0.000000 0.000000 0.500000 B
0.000000 0.000000 0.666667 B
0.000000 0.000000 0.833333 B
0.000000 0.333333 0.000000 B
0.000000 0.333333 0.166667 B
0.000000 0.333333 0.333333 B
0.000000 0.333333 0.500000 B
0.000000 0.333333 0.666667 B
0.000000 0.333333 0.833333 B
0.000000 0.666667 0.000000 B
0.000000 0.666667 0.166667 B
0.000000 0.666667 0.500000 B
0.000000 0.666667 0.666667 B
0.000000 0.666667 0.833333 B
0.000000 0.000000 0.166667 Cu
0.000000 0.666667 0.333333 Cu
'''
self.assertEqual(str(poscar_bcu), expected_str_bcu)