def test_get_symmetry_operations(self):
for sg, structure in [(self.sg, self.structure),
(self.sg4, self.structure4)]:
pgops = sg.get_point_group_operations()
fracsymmops = sg.get_symmetry_operations()
symmops = sg.get_symmetry_operations(True)
latt = structure.lattice
for fop, op, pgop in zip(fracsymmops, symmops, pgops):
self.assertArrayAlmostEqual(fop.rotation_matrix,
pgop.rotation_matrix)
for site in 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 structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
# Make sure this works for any position, not just the atomic
# ones.
random_fcoord = np.random.uniform(size=(3))
random_ccoord = latt.get_cartesian_coords(random_fcoord)
newfrac = fop.operate(random_fcoord)
newcart = op.operate(random_ccoord)
self.assertTrue(np.allclose(latt.get_fractional_coords(newcart),
newfrac))
def test_get_symmetry_operations(self):
for sg, structure in [(self.sg, self.structure), (self.sg4, self.structure4)]:
pgops = sg.get_point_group_operations()
fracsymmops = sg.get_symmetry_operations()
symmops = sg.get_symmetry_operations(True)
latt = structure.lattice
for fop, op, pgop in zip(fracsymmops, symmops, pgops):
# translation vector values should all be 0 or 0.5
t = fop.translation_vector * 2
self.assertArrayAlmostEqual(t - np.round(t), 0)
self.assertArrayAlmostEqual(fop.rotation_matrix, pgop.rotation_matrix)
for site in 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, newcart, latt, coords_are_cartesian=True)
for testsite in structure:
if newsite.is_periodic_image(testsite, 1e-3):
found = True
break
self.assertTrue(found)
# Make sure this works for any position, not just the atomic
# ones.
random_fcoord = np.random.uniform(size=(3))
random_ccoord = latt.get_cartesian_coords(random_fcoord)
newfrac = fop.operate(random_fcoord)
newcart = op.operate(random_ccoord)
self.assertTrue(np.allclose(latt.get_fractional_coords(newcart), newfrac))
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 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)
class PeriodicSiteTest(PymatgenTest):
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", [0.25, 0.35, 0.45], self.lattice)
self.site2 = PeriodicSite({"Si": 0.5}, [0, 0, 0], self.lattice)
self.assertEqual(self.site2.species_and_occu,
Composition({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
})
self.dummy_site = PeriodicSite("X", [0, 0, 0], self.lattice)
def test_properties(self):
"""
Test the properties for a site
"""
self.assertEqual(self.site.a, 0.25)
self.assertEqual(self.site.b, 0.35)
self.assertEqual(self.site.c, 0.45)
self.assertEqual(self.site.x, 2.5)
self.assertEqual(self.site.y, 3.5)
self.assertEqual(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.assertAlmostEqual(self.site.distance(other_site), 6.22494979899,
5)
def test_distance_from_point(self):
self.assertNotAlmostEqual(
self.site.distance_from_point([0.1, 0.1, 0.1]), 6.22494979899, 5)
self.assertAlmostEqual(self.site.distance_from_point([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.assertAlmostEqual(distance, 6.22494979899, 5)
self.assertTrue(([-1, -1, -1] == image).all())
(distance, image) = self.site.distance_and_image(other_site, [1, 0, 0])
self.assertAlmostEqual(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.assertAlmostEqual(
get_distance_and_image_old(site1, 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(
get_distance_and_image_old(site1, site2)[0] >
site1.distance_and_image(site2)[0])
site2 = PeriodicSite("Fe", np.random.rand(3), lattice)
(dist_old, jimage_old) = get_distance_and_image_old(site1, site2)
(dist_new, jimage_new) = site1.distance_and_image(site2)
self.assertTrue(dist_old - dist_new > -1e-8,
"New distance algo should give smaller answers!")
self.assertFalse((abs(dist_old - dist_new) < 1e-8) ^
(jimage_old == jimage_new).all(),
"If old dist == new dist, images must be the same!")
latt = Lattice.from_parameters(3.0, 4.0, 10.0, 3.0, 1.0, 2.0)
site = PeriodicSite("Fe", [0.1, 0.1, 0.1], latt)
site2 = PeriodicSite("Fe", [0.99, 0.99, 0.99], latt)
(dist, img) = site.distance_and_image(site2)
self.assertAlmostEqual(dist, 1.1304420998572722)
self.assertEqual(list(img), [0, -1, -1])
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, 60))
self.assertFalse(self.site.is_periodic_image(other),
"Different lattices should not be periodic images.")
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_as_from_dict(self):
d = self.site2.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site, self.site2)
self.assertNotEqual(site, self.site)
d = self.propertied_site.as_dict()
site3 = PeriodicSite({"Si": 0.5, "Fe": 0.5}, [0, 0, 0], self.lattice)
d = site3.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site.species_and_occu, site3.species_and_occu)
d = self.dummy_site.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site.species_and_occu,
self.dummy_site.species_and_occu)
def test_to_unit_cell(self):
site = PeriodicSite("Fe", np.array([1.25, 2.35, 4.46]), self.lattice)
site = site.to_unit_cell
val = [0.25, 0.35, 0.46]
self.assertArrayAlmostEqual(site.frac_coords, val)
class PeriodicSiteTest(PymatgenTest):
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", [0.25, 0.35, 0.45],
self.lattice)
self.site2 = PeriodicSite({"Si": 0.5}, [0, 0, 0], self.lattice)
self.assertEqual(self.site2.species_and_occu,
Composition({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})
self.dummy_site = PeriodicSite("X", [0, 0, 0], self.lattice)
def test_properties(self):
"""
Test the properties for a site
"""
self.assertEqual(self.site.a, 0.25)
self.assertEqual(self.site.b, 0.35)
self.assertEqual(self.site.c, 0.45)
self.assertEqual(self.site.x, 2.5)
self.assertEqual(self.site.y, 3.5)
self.assertEqual(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.assertAlmostEqual(self.site.distance(other_site), 6.22494979899,
5)
def test_distance_from_point(self):
self.assertNotAlmostEqual(self.site.distance_from_point([0.1, 0.1,
0.1]),
6.22494979899, 5)
self.assertAlmostEqual(self.site.distance_from_point([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.assertAlmostEqual(distance, 6.22494979899, 5)
self.assertTrue(([-1, -1, -1] == image).all())
(distance, image) = self.site.distance_and_image(other_site, [1, 0, 0])
self.assertAlmostEqual(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.assertAlmostEqual(get_distance_and_image_old(site1, 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(get_distance_and_image_old(site1, site2)[0] >
site1.distance_and_image(site2)[0])
site2 = PeriodicSite("Fe", np.random.rand(3), lattice)
(dist_old, jimage_old) = get_distance_and_image_old(site1, site2)
(dist_new, jimage_new) = site1.distance_and_image(site2)
self.assertTrue(dist_old - dist_new > -1e-8,
"New distance algo should give smaller answers!")
self.assertFalse((abs(dist_old - dist_new) < 1e-8) ^
(jimage_old == jimage_new).all(),
"If old dist == new dist, images must be the same!")
latt = Lattice.from_parameters(3.0, 3.1, 10.0, 2.96, 2.0, 1.0)
site = PeriodicSite("Fe", [0.1, 0.1, 0.1], latt)
site2 = PeriodicSite("Fe", [0.99, 0.99, 0.99], latt)
(dist, img) = site.distance_and_image(site2)
self.assertAlmostEqual(dist, 0.15495358379511573)
self.assertEqual(list(img), [-11, 6, 0])
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, 60))
self.assertFalse(self.site.is_periodic_image(other),
"Different lattices should not be periodic images.")
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_as_from_dict(self):
d = self.site2.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site, self.site2)
self.assertNotEqual(site, self.site)
d = self.propertied_site.as_dict()
site3 = PeriodicSite({"Si": 0.5, "Fe": 0.5}, [0, 0, 0], self.lattice)
d = site3.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site.species_and_occu, site3.species_and_occu)
d = self.dummy_site.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site.species_and_occu, self.dummy_site.species_and_occu)
def test_to_unit_cell(self):
site = PeriodicSite("Fe", np.array([1.25, 2.35, 4.46]), self.lattice)
site = site.to_unit_cell
val = [0.25, 0.35, 0.46]
self.assertArrayAlmostEqual(site.frac_coords, val)
class PeriodicSiteTest(PymatgenTest):
def setUp(self):
self.lattice = Lattice.cubic(10.0)
self.si = Element("Si")
self.site = PeriodicSite("Fe", [0.25, 0.35, 0.45], self.lattice)
self.site2 = PeriodicSite({"Si": 0.5}, [0, 0, 0], self.lattice)
self.assertEqual(
self.site2.species,
Composition({Element("Si"): 0.5}),
"Inconsistent site created!",
)
self.propertied_site = PeriodicSite(
Species("Fe", 2),
[0.25, 0.35, 0.45],
self.lattice,
properties={"magmom": 5.1, "charge": 4.2},
)
self.dummy_site = PeriodicSite("X", [0, 0, 0], self.lattice)
def test_properties(self):
"""
Test the properties for a site
"""
self.assertEqual(self.site.a, 0.25)
self.assertEqual(self.site.b, 0.35)
self.assertEqual(self.site.c, 0.45)
self.assertEqual(self.site.x, 2.5)
self.assertEqual(self.site.y, 3.5)
self.assertEqual(self.site.z, 4.5)
self.assertTrue(self.site.is_ordered)
self.assertFalse(self.site2.is_ordered)
self.assertEqual(self.propertied_site.properties["magmom"], 5.1)
self.assertEqual(self.propertied_site.properties["charge"], 4.2)
def test_distance(self):
other_site = PeriodicSite("Fe", np.array([0, 0, 0]), self.lattice)
self.assertAlmostEqual(self.site.distance(other_site), 6.22494979899, 5)
def test_distance_from_point(self):
self.assertNotAlmostEqual(self.site.distance_from_point([0.1, 0.1, 0.1]), 6.22494979899, 5)
self.assertAlmostEqual(self.site.distance_from_point([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.assertAlmostEqual(distance, 6.22494979899, 5)
self.assertTrue(([-1, -1, -1] == image).all())
(distance, image) = self.site.distance_and_image(other_site, [1, 0, 0])
self.assertAlmostEqual(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.assertAlmostEqual(
get_distance_and_image_old(site1, 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(get_distance_and_image_old(site1, site2)[0] > site1.distance_and_image(site2)[0])
site2 = PeriodicSite("Fe", np.random.rand(3), lattice)
(dist_old, jimage_old) = get_distance_and_image_old(site1, site2)
(dist_new, jimage_new) = site1.distance_and_image(site2)
self.assertTrue(
dist_old - dist_new > -1e-8,
"New distance algo should give smaller answers!",
)
self.assertFalse(
(abs(dist_old - dist_new) < 1e-8) ^ (jimage_old == jimage_new).all(),
"If old dist == new dist, images must be the same!",
)
latt = Lattice.from_parameters(3.0, 3.1, 10.0, 2.96, 2.0, 1.0)
site = PeriodicSite("Fe", [0.1, 0.1, 0.1], latt)
site2 = PeriodicSite("Fe", [0.99, 0.99, 0.99], latt)
(dist, img) = site.distance_and_image(site2)
self.assertAlmostEqual(dist, 0.15495358379511573)
self.assertEqual(list(img), [-11, 6, 0])
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, 60))
self.assertFalse(
self.site.is_periodic_image(other),
"Different lattices should not be periodic images.",
)
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_as_from_dict(self):
d = self.site2.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site, self.site2)
self.assertNotEqual(site, self.site)
d = self.propertied_site.as_dict()
site3 = PeriodicSite({"Si": 0.5, "Fe": 0.5}, [0, 0, 0], self.lattice)
d = site3.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site.species, site3.species)
d = self.dummy_site.as_dict()
site = PeriodicSite.from_dict(d)
self.assertEqual(site.species, self.dummy_site.species)
def test_to_unit_cell(self):
site = PeriodicSite("Fe", np.array([1.25, 2.35, 4.46]), self.lattice)
site.to_unit_cell(in_place=True)
val = [0.25, 0.35, 0.46]
self.assertArrayAlmostEqual(site.frac_coords, val)
lattice_pbc = Lattice(self.lattice.matrix, pbc=(True, True, False))
site = PeriodicSite("Fe", np.array([1.25, 2.35, 4.46]), lattice_pbc)
site.to_unit_cell(in_place=True)
val = [0.25, 0.35, 4.46]
self.assertArrayAlmostEqual(site.frac_coords, val)
def test_setters(self):
site = self.propertied_site
site.species = "Cu"
self.assertEqual(site.species, Composition("Cu"))
site.x = 1.25
site.y = 1.35
self.assertEqual(site.coords[0], 1.25)
self.assertEqual(site.coords[1], 1.35)
self.assertEqual(site.a, 0.125)
self.assertEqual(site.b, 0.135)
site.lattice = Lattice.cubic(100)
self.assertEqual(site.x, 12.5)
def set_bad_species():
site.species = {"Cu": 0.5, "Gd": 0.6}
self.assertRaises(ValueError, set_bad_species)
site.frac_coords = [0, 0, 0.1]
self.assertArrayAlmostEqual(site.coords, [0, 0, 10])
site.coords = [1.5, 3.25, 5]
self.assertArrayAlmostEqual(site.frac_coords, [0.015, 0.0325, 0.05])
def test_repr(self):
self.assertEqual(
self.propertied_site.__repr__(),
"PeriodicSite: Fe2+ (2.5000, 3.5000, 4.5000) [0.2500, 0.3500, 0.4500]",
)