def test_xsf_symbolparse(self):
"""
Ensure that the same structure is parsed
even if the atomic symbol / number convention
is different.
"""
test_string = """
CRYSTAL
PRIMVEC
11.45191956 0.00000000 0.00000000
5.72596044 9.91765288 0.00000000
-14.31490370 -8.26471287 23.37613199
PRIMCOORD
1 1
H -0.71644986 -0.41364333 1.19898200 0.00181803 0.00084718 0.00804832
"""
structure = XSF.from_string(test_string).structure
self.assertEqual(str(structure.species[0]), 'H')
test_string2 = """
CRYSTAL
PRIMVEC
11.45191956 0.00000000 0.00000000
5.72596044 9.91765288 0.00000000
-14.31490370 -8.26471287 23.37613199
PRIMCOORD
1 1
1 -0.71644986 -0.41364333 1.19898200 0.00181803 0.00084718 0.00804832
"""
structure2 = XSF.from_string(test_string2).structure
self.assertEqual(structure, structure2)
def test_to_string(self):
structure = self.get_structure("Li2O")
xsf = XSF(structure)
s = xsf.to_string()
self.assertEqual(
s,
"""CRYSTAL
# Primitive lattice vectors in Angstrom
PRIMVEC
2.91738857000000 0.09789437000000 1.52000466000000
0.96463406000000 2.75503561000000 1.52000466000000
0.13320635000000 0.09789443000000 3.28691771000000
# Cartesian coordinates in Angstrom.
PRIMCOORD
3 1
O 0.00000000000000 0.00000000000000 0.00000000000000
Li 3.01213761017484 2.21364440998406 4.74632330032018
Li 1.00309136982516 0.73718000001594 1.58060372967982""",
)
s = xsf.to_string(atom_symbol=False)
self.assertEqual(
s,
"""CRYSTAL
# Primitive lattice vectors in Angstrom
PRIMVEC
2.91738857000000 0.09789437000000 1.52000466000000
0.96463406000000 2.75503561000000 1.52000466000000
0.13320635000000 0.09789443000000 3.28691771000000
# Cartesian coordinates in Angstrom.
PRIMCOORD
3 1
8 0.00000000000000 0.00000000000000 0.00000000000000
3 3.01213761017484 2.21364440998406 4.74632330032018
3 1.00309136982516 0.73718000001594 1.58060372967982""",
)
def test_xsf(self):
coords = []
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
structure = Structure(lattice, ["Si", "Si"], coords)
xsf = XSF(structure)
self.assertTrue(structure, xsf.from_string(xsf.to_string()))
def test_xsf(self):
coords = []
coords.append([0, 0, 0])
coords.append([0.75, 0.5, 0.75])
lattice = Lattice([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]])
structure = Structure(lattice, ["Si", "Si"], coords)
xsf = XSF(structure)
self.assertTrue(structure, XSF.from_string(xsf.to_string()))