def test_get_symmetry_operations(self):
fracsymmops = self.sg.get_symmetry_operations()
symmops = self.sg.get_symmetry_operations(True)
self.assertEqual(len(symmops), 8)
latt = self.structure.lattice
for fop, op in zip(fracsymmops, symmops):
for site in self.structure:
newfrac = fop.operate(site.frac_coords)
newcart = op.operate(site.coords)
self.assertTrue(np.allclose(latt.get_fractional_coords(newcart), newfrac))
found = False
newsite = PeriodicSite(site.species_and_occu, newcart, latt, coords_are_cartesian=True)
for testsite in self.structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
def get_primitive_standard_structure(self):
"""
Gives a structure with a primitive cell according to certain standards
the standards are defined in Setyawan, W., & Curtarolo, S. (2010).
High-throughput electronic band structure calculations:
Challenges and tools. Computational Materials Science,
49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010
Returns:
The structure in a primitive standardized cell
"""
conv = self.get_conventional_standard_structure()
lattice = self.get_lattice_type()
if "P" in self.get_spacegroup_symbol() or lattice == "hexagonal":
return conv
if lattice == "rhombohedral":
conv = self.get_refined_structure()
lengths, angles = conv.lattice.lengths_and_angles
a = lengths[0]
alpha = math.pi * angles[0] / 180
new_matrix = [
[a * cos(alpha / 2), -a * sin(alpha / 2), 0],
[a * cos(alpha / 2), a * sin(alpha / 2), 0],
[a * cos(alpha) / cos(alpha / 2), 0,
a * math.sqrt(1 - (cos(alpha) ** 2 / (cos(alpha / 2) ** 2)))]]
new_sites = []
for s in conv.sites:
new_s = PeriodicSite(
s.specie, s.frac_coords, Lattice(new_matrix),
to_unit_cell=True, properties=s.properties)
unique = True
for t in new_sites:
if new_s.is_periodic_image(t):
unique = False
if unique:
new_sites.append(new_s)
return Structure.from_sites(new_sites)
transf = np.eye(3)
if "I" in self.get_spacegroup_symbol():
transf = np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]],
dtype=np.float) / 2
elif "F" in self.get_spacegroup_symbol():
transf = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]],
dtype=np.float) / 2
elif "C" in self.get_spacegroup_symbol():
if self.get_crystal_system() == "monoclinic":
transf = np.array([[1, 1, 0], [-1, 1, 0], [0, 0, 2]],
dtype=np.float) / 2
else:
transf = np.array([[1, -1, 0], [1, 1, 0], [0, 0, 2]],
dtype=np.float) / 2
new_sites = []
for s in conv.sites:
new_s = PeriodicSite(
s.specie, s.coords,
Lattice(np.dot(transf, conv.lattice.matrix)),
to_unit_cell=True, coords_are_cartesian=True,
properties=s.properties)
unique = True
for t in new_sites:
if new_s.is_periodic_image(t):
unique = False
if unique:
new_sites.append(new_s)
return Structure.from_sites(new_sites)
class PeriodicSiteTest(unittest.TestCase):
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", np.array([0.25, 0.35, 0.45]), self.lattice)
self.site2 = PeriodicSite({"Si":0.5}, np.array([0, 0, 0]), self.lattice)
self.assertEquals(self.site2.species_and_occu, {Element('Si'): 0.5}, "Inconsistent site created!")
self.propertied_site = PeriodicSite(Specie("Fe", 2), [0.25, 0.35, 0.45], self.lattice, properties={'magmom':5.1, 'charge':4.2})
def test_properties(self):
"""
Test the properties for a site
"""
self.assertEquals(self.site.a, 0.25)
self.assertEquals(self.site.b, 0.35)
self.assertEquals(self.site.c, 0.45)
self.assertEquals(self.site.x, 2.5)
self.assertEquals(self.site.y, 3.5)
self.assertEquals(self.site.z, 4.5)
self.assertTrue(self.site.is_ordered)
self.assertFalse(self.site2.is_ordered)
self.assertEqual(self.propertied_site.magmom, 5.1)
self.assertEqual(self.propertied_site.charge, 4.2)
def test_distance(self):
other_site = PeriodicSite("Fe", np.array([0, 0, 0]), self.lattice)
self.assertAlmostEquals(self.site.distance(other_site), 6.22494979899, 5)
def test_distance_from_point(self):
self.assertNotAlmostEqual(self.site.distance_from_point(np.array([0.1, 0.1, 0.1])), 6.22494979899, 5)
self.assertAlmostEqual(self.site.distance_from_point(np.array([0.1, 0.1, 0.1])), 6.0564015718906887, 5)
def test_distance_and_image(self):
other_site = PeriodicSite("Fe", np.array([1, 1, 1]), self.lattice)
(distance, image) = self.site.distance_and_image(other_site)
self.assertAlmostEquals(distance, 6.22494979899, 5)
self.assertTrue(([-1, -1, -1] == image).all())
(distance, image) = self.site.distance_and_image(other_site, [1, 0, 0])
self.assertAlmostEquals(distance, 19.461500456028563, 5)
# Test that old and new distance algo give the same ans for "standard lattices"
lattice = Lattice(np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]]))
site1 = PeriodicSite("Fe", np.array([0.01, 0.02, 0.03]), lattice)
site2 = PeriodicSite("Fe", np.array([0.99, 0.98, 0.97]), lattice)
self.assertTrue(site1.distance_and_image_old(site2)[0] == site1.distance_and_image(site2)[0])
lattice = Lattice.from_parameters(1, 0.01, 1, 10, 10, 10)
site1 = PeriodicSite("Fe", np.array([0.01, 0.02, 0.03]), lattice)
site2 = PeriodicSite("Fe", np.array([0.99, 0.98, 0.97]), lattice)
self.assertTrue(site1.distance_and_image_old(site2)[0] > site1.distance_and_image(site2)[0])
site2 = PeriodicSite("Fe", np.random.rand(3), lattice)
(dist_old, jimage_old) = site1.distance_and_image_old(site2)
(dist_new, jimage_new) = site1.distance_and_image(site2)
self.assertTrue(dist_old >= dist_new, "New distance algo should always give smaller answers!")
self.assertFalse((dist_old == dist_new) ^ (jimage_old == jimage_new).all(), "If old dist == new dist, the images returned must be the same!")
def test_is_periodic_image(self):
other = PeriodicSite("Fe", np.array([1.25, 2.35, 4.45]), self.lattice)
self.assertTrue(self.site.is_periodic_image(other), "This other site should be a periodic image.")
other = PeriodicSite("Fe", np.array([1.25, 2.35, 4.46]), self.lattice)
self.assertFalse(self.site.is_periodic_image(other), "This other site should not be a periodic image.")
other = PeriodicSite("Fe", np.array([1.25, 2.35, 4.45]), Lattice.rhombohedral(2))
self.assertFalse(self.site.is_periodic_image(other), "Different lattices should result in different periodic sites.")
def test_equality(self):
other_site = PeriodicSite("Fe", np.array([1, 1, 1]), self.lattice)
self.assertTrue(self.site.__eq__(self.site))
self.assertFalse(other_site.__eq__(self.site))
self.assertFalse(self.site.__ne__(self.site))
self.assertTrue(other_site.__ne__(self.site))
def test_to_from_dict(self):
d = self.site2.to_dict
site = PeriodicSite.from_dict(d)
self.assertEqual(site, self.site2)
self.assertNotEqual(site, self.site)
d = self.propertied_site.to_dict
site = Site.from_dict(d)
self.assertEqual(site.magmom, 5.1)
self.assertEqual(site.charge, 4.2)
