class TestNaCl(unittest.TestCase):
# Test data is from the Navy's Crystal Lattie Structures website:
# http://cst-www.nrl.navy.mil/lattice/struk.xmol/b1.pos
# All distances are written in Angstroms.
latticevecs = ([0.00000000, 2.81500000, 2.81500000],
[2.81500000, 0.00000000, 2.81500000],
[2.81500000, 2.81500000, 0.00000000])
basis = (('Na', array([0.00000000, 0.00000000, 0.00000000])),
('Cl', array([2.81500000, 2.81500000, 2.81500000])))
# (n1,n2,n3, [Symbol, position, Symbol, position, etc.])
images = ( (1, 0, 0, ['Na', array([ 0. , 2.815, 2.815]),
'Cl', array([ 2.815, 5.63 , 5.63 ])]),
(0, 1, 0, ['Na', array([ 2.815, 0. , 2.815]),
'Cl', array([ 5.63 , 2.815, 5.63 ])]),
(0, 0, 1, ['Na', array([ 2.815, 2.815, 0. ]),
'Cl', array([ 5.63 , 5.63 , 2.815])]),
(-2, 3, -1, ['Na', array([ 5.63 , -8.445, 2.815]),
'Cl', array([ 8.445, -5.63 , 5.63 ])]) )
def setUp(self):
self.crystal = Crystal(self.latticevecs, self.basis)
def test_images(self):
for (n1, n2, n3, solution) in self.images:
computed = self.crystal.cell_n((n1, n2, n3))
print computed[1::2], solution[1::2]
self.assertEqual(computed[0::2], solution[0::2])
assert_array_almost_equal(computed[1::2], solution[1::2], decimal=15)
from periodic.crystal import Crystal
latticevecs = ((4.59373000, 0.00000000, 0.00000000),
(0.00000000, 4.59373000, 0.00000000),
(0.00000000, 0.00000000, 2.95812000))
basis = (('Ti', (0.00000000, 0.00000000, 0.00000000)),
('Ti', (2.29686500, 2.29686500, 1.47906000)),
('O', (1.40246577, 1.40246577, 0.00000000)),
('O', (-1.40246577, -1.40246577, 0.00000000)),
('O', (3.69933077, 0.89439923, 1.47906000)),
('O', (0.89439923, 3.69933077, 1.47906000)))
if __name__ == '__main__':
TiO2 = Crystal(latticevecs, basis)
rcutoff = 2e0
atomlist = TiO2.tile_radially(rcutoff)
filename = 'TiO2_rcut_{0:.2f}.xyz'.format(rcutoff)
with open(filename, 'w') as f:
f.write(str(len(atomlist))+'\n')
f.write('crystal.py-generated xyz file'+'\n')
for (symbol, position) in atomlist:
f.write(symbol+' '+str(position)[1:-1]+'\n')
def setUp(self):
self.crystal = Crystal(self.latticevecs, self.basis)