def get_period_dis(self, p1, p2):
"""
在考虑周期性的情况下，计算两点之间的距离
:param p1: 分数坐标，例如[0.5，0.5，0.5]
:param p2: 分数坐标
:return: 两点之间的距离，考虑周期性
"""
temp_site1 = PeriodicSite('Ar', p1, self.__struc.lattice)
temp_site2 = PeriodicSite('Ar', p2, self.__struc.lattice)
dis = temp_site1.distance(temp_site2)
return dis
def rediscovery_kdTree(stru, migrate, vorosites, threshold = 0.5):
recover_labels = []
recover_state = {}
migrate_mindis = {}
migrate_pos_frac = np.around(np.array([site.frac_coords for site in stru.sites if migrate in site._atom_site_label], ndmin=2), 3)
# print(migrate_pos_frac)
migrate_pos_frac %= 1.0
migrate_pos_frac %= 1.0
# print(migrate_pos_frac)
# migrate_pos = [site.coords for site in stru.sites if migrate in site._atom_site_label]
# print(migrate_pos)
labels = [site._atom_site_label for site in stru.sites if migrate in site._atom_site_label]
points = np.around(np.array(vorosites[0] + vorosites[1] + vorosites[2], ndmin=2), 3)
# print(points)
points %= 1.0
points %= 1.0
# print(points)
# print(len(points))
vorositesKdTree = cKDTree(points)
min_dis,min_ids = vorositesKdTree.query(migrate_pos_frac,k=1)
# print(labels)
# print(min_dis)
for idx in range(len(min_ids)):
if labels[idx] in recover_labels:
continue
tmp_site1 = PeriodicSite("Ar", migrate_pos_frac[idx], stru.lattice)
tmp_site2 = PeriodicSite("Ar", points[min_ids[idx]], stru.lattice)
pts_len = [len(vorosites[0]), len(vorosites[1]), len(vorosites[2])]
pt_tag = get_point_tag(min_ids[idx], pts_len)
migrate_mindis[str(labels[idx])] = (pt_tag, tmp_site1.distance(tmp_site2))
if tmp_site1.distance(tmp_site2) <= threshold:
recover_state[str(labels[idx])] = pt_tag
recover_labels.append(labels[idx])
else:
recover_state[str(labels[idx])] = None
recover_rate = len(recover_labels) / len(np.unique(labels))
return recover_rate, recover_state, migrate_mindis
def rediscovery(migrate,vorosites,stru):
labels = []
recover_labels = []
recover_state = {}
true_recover_dis = {}
#点类型，分别表示间隙、瓶颈、面心
points_type = ["It","Bn","Fc"]
for k in range(len(stru.sites)):
site = stru.sites[k]
label = site._atom_site_label
if migrate not in label:
continue
#labels记录所有的label
if label not in labels:
labels.append(label)
#recover_labels记录已恢复的label
if label in recover_labels:
continue
for pts_idx, pts in enumerate (vorosites):
cp_tag = np.ones((len(pts), ), dtype=int)
for pt_idx, pt in enumerate (pts):
if cp_tag[pt_idx] != -1:
print("mobile:",site,"label",label)
print("void:",pt)
#以Ar作为临时当前空隙的表示符号
tmp_site = PeriodicSite("Ar",pt,stru.lattice)
print(site.distance(tmp_site))
if site.distance(tmp_site) < 0.5:
#当某空隙位已与结构中的晶格位配对时，将该空隙位以及与该空隙位0.25A半径范围内的所有空隙位移除，后续不再判断。
recover_labels.append(label)
true_recover_dis[str(label)] = (points_type[pts_idx]+str(pt_idx),site.distance(tmp_site))
cp_tag[pt_idx] = -1
for pt_idx2, pt2 in enumerate (pts):
tmp_site2 = PeriodicSite("Ar",list(pt2),stru.lattice)
if tmp_site.distance(tmp_site2) < 0.25:
cp_tag[pt_idx2] = -1
break
#统计当前结构的恢复率
recover_rate = len(recover_labels)/len(labels)
for la in labels:
if la in recover_labels:
recover_state[str(la)] = True
else:
recover_state[str(la)] = False
return recover_rate, recover_state, true_recover_dis
def _supercell_with_defect(self, scaling_matrix, defect_site):
sc = self._structure.copy()
sc.make_supercell(scaling_matrix)
oldf_coords = defect_site.frac_coords
coords = defect_site.lattice.get_cartesian_coords(oldf_coords)
newf_coords = sc.lattice.get_fractional_coords(coords)
sc_defect_site = PeriodicSite(
defect_site.species_and_occu, newf_coords, sc.lattice, properties=defect_site.properties
)
for i in range(len(sc.sites)):
# if sc_defect_site == sc.sites[i]:
if sc_defect_site.distance(sc.sites[i]) < 1e-3:
del sc[i]
return sc
raise ValueError("Something wrong if reached here")
def _supercell_with_defect(self, scaling_matrix, defect_site):
sc = self._structure.copy()
sc.make_supercell(scaling_matrix)
oldf_coords = defect_site.frac_coords
coords = defect_site.lattice.get_cartesian_coords(oldf_coords)
newf_coords = sc.lattice.get_fractional_coords(coords)
sc_defect_site = PeriodicSite(defect_site.species_and_occu,
newf_coords,
sc.lattice,
properties=defect_site.properties)
for i in range(len(sc.sites)):
#if sc_defect_site == sc.sites[i]:
if sc_defect_site.distance(sc.sites[i]) < 1e-3:
del sc[i]
return sc
raise ValueError('Something wrong if reached here')
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)
def rediscovery_byRad_kdTree_onlyVertex(stru, migrate, vorosites, vororad, threshold = 0.5):
recover_labels = []
recover_state = {}
migrate_mindis = {}
# print(stru)
# print("the len of stru.sites:", len(stru.sites))
migrate_pos_frac = np.around(np.array([site.frac_coords for site in stru.sites if migrate in site._atom_site_label], ndmin=2), 3)
migrate_pos_frac %= 1.0
migrate_pos_frac %= 1.0
expand_pos_frac = migrate_pos_frac
# expand the migrant sites to 3*3*3
for a in range(-1, 2):
for b in range(-1, 2):
for c in range(-1, 2):
if a==b==c==0:
continue
else:
expand_pos_frac = np.concatenate((expand_pos_frac,migrate_pos_frac+np.array([a,b,c])),axis=0)
# print(migrate_pos_frac)
# migrate_pos_frac %= 1.0
# migrate_pos_frac %= 1.0
# print(migrate_pos_frac)
# migrate_pos = [site.coords for site in stru.sites if migrate in site._atom_site_label]
# print(migrate_pos)
migrate_labels = [site._atom_site_label for site in stru.sites if migrate in site._atom_site_label]
points = np.around(np.array(vorosites[0], ndmin=2), 3)
points_rad = np.array(vororad[0])
points %= 1.0
points %= 1.0
# print(points)
# print(len(points))
vorositesKdTree = cKDTree(points)
min_dis,min_ids = vorositesKdTree.query(migrate_pos_frac,k=1)
# print(labels)
# print(min_dis)
pts_len = [len(vorosites[0])]
for idx in range(len(migrate_labels)):
if migrate_labels[idx] in recover_labels:
continue
tmp_site1 = PeriodicSite("Ar", migrate_pos_frac[idx], stru.lattice)
tmp_site2 = PeriodicSite("Ar", points[min_ids[idx]], stru.lattice)
pt_tag = get_point_tag_onlyVertex(min_ids[idx], pts_len)
pt_rad = points_rad[min_ids[idx]]
dis_st1_st2 = tmp_site1.distance(tmp_site2)
migrate_mindis[str(migrate_labels[idx])] = (pt_tag, pt_rad, dis_st1_st2)
# if dis_st1_st2 <= threshold or dis_st1_st2 <= pt_rad:
if dis_st1_st2 <= threshold:
recover_state[str(migrate_labels[idx])] = pt_tag
recover_labels.append(migrate_labels[idx])
else:
recover_state[str(migrate_labels[idx])] = None
recover_rate = len(recover_labels) / len(np.unique(migrate_labels))
return recover_rate, recover_state, migrate_mindis
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]",
)
def get_dis(struc, p1, p2):
tmp_siteA = PeriodicSite("Ar", p1, struc.lattice)
tmp_siteB = PeriodicSite("Ar", p2, struc.lattice)
return tmp_siteA.distance(tmp_siteB)
