def test_get_site(self):
lattice = numpy.copy(self.lattice)
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
mcell = MutableCell(lattice, sites=si_sites)
self.assertEqual(mcell.get_site(0), [(-0.125, -0.125, -0.125), "Si"])
self.assertEqual(mcell.get_site(1), [(0.125, 0.125, 0.125), "Si"])
def test_rotate_site_by_z(self):
lattice = numpy.array(
[4.912, 0.000, 0.000, -2.456, 4.254, 0.000, 0.000, 0.000, 16.000])
si_sites = [[(0.0, 0.0, 0.5), "C"], [(0.0, 0.5, 0.5), "C"],
[(0.5, 0.0, 0.5), "C"], [(0.5, 0.5, 0.5), "C"],
[(0.33333, 0.166666, 0.5), "C"],
[(0.33333, 0.666666, 0.5), "C"],
[(0.83333, 0.166666, 0.5), "C"],
[(0.83333, 0.666666, 0.5), "C"]]
mcell = MutableCell(lattice, sites=si_sites)
rotate_sites_in_a_circle_by_z(mcell, (0.416666, 0.5833333, 0.5),
radius=1.0,
degrees=90)
c = mcell.to_cell()
expected_positions = numpy.array([[0., 0., 0.5], [0., 0.5, 0.5],
[0.5, 0., 0.5],
[0.27232809, 0.43899781, 0.5],
[0.33333, 0.166666, 0.5],
[0.56100438, 0.72767076, 0.5],
[0.83333, 0.166666, 0.5],
[0.83333, 0.666666, 0.5]])
numpy.testing.assert_almost_equal(c.positions, expected_positions)
def test_get_car_site(self):
lattice = numpy.copy(numpy.array([0.0, 1.5, 1.5,
1.5, 0.0, 1.5,
1.5, 1.5, 0.0]).reshape(3, 3))
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
mcell = MutableCell(lattice, sites=si_sites)
self.assertEqual(mcell.get_car_site(0), [(-0.375, -0.375, -0.375), "Si"])
self.assertEqual(mcell.get_car_site(1), [(0.375, 0.375, 0.375), "Si"])
def test_remove_site(self):
lattice = numpy.copy(self.lattice)
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
mcell = MutableCell(lattice, sites=si_sites)
mcell.remove_site(1)
self.assertEqual(len(mcell._sites), 2)
self.assertEqual(mcell._sites[0], [(-0.125, -0.125, -0.125), "Si"])
self.assertEqual(mcell._sites[1], [(0.125, 0.125, 0.125), "Vacc"])
def test_to_cell(self):
lattice = numpy.copy(self.lattice)
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
mcell = MutableCell(lattice, sites=si_sites)
c = mcell.to_cell()
self.assertTrue(isinstance(c, Cell))
numpy.testing.assert_almost_equal(c.positions, numpy.array([0.875, 0.875, 0.875,
0.125, 0.125, 0.125]).reshape((2, 3)))
numpy.testing.assert_almost_equal(c.atoms, numpy.array([14, 14]))
def test_init(self):
# 创建空胞
lattice = numpy.copy(self.lattice)
mcell = MutableCell(lattice)
self.assertEqual(len(mcell._sites), 0)
# 创建金刚石Si原胞
lattice = numpy.copy(self.lattice)
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
mcell = MutableCell(lattice, sites=si_sites)
self.assertEqual(len(mcell._sites), 2)
def cell_to_mcell(cell):
lattice = numpy.copy(cell.lattice)
sites = []
for pos, ele in zip(cell.positions.tolist(), cell.atoms.tolist()):
symbol = get_symbol(ele)
sites.append([pos] + [symbol])
return MutableCell(cell.lattice, sites)
def test_add_site(self):
lattice = numpy.copy(self.lattice)
mcell = MutableCell(lattice)
mcell.add_site([(-0.125, -0.125, -0.125), "Zn"])
mcell.add_site([(0.125, 0.125, 0.125), "S"])
self.assertEqual(mcell._sites[0], [(-0.125, -0.125, -0.125), "Zn"])
self.assertEqual(mcell._sites[1], [(0.125, 0.125, 0.125), "S"])
def test_set_site(self):
lattice = numpy.copy(self.lattice)
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
mcell = MutableCell(lattice, sites=si_sites)
mcell.set_site(0, [(-0.125, -0.125, -0.125), "Zn"])
mcell.set_site(1, [(0.126, 0.125, 0.125), "S"])
self.assertEqual(len(mcell._sites), 2)
self.assertEqual(mcell._sites[0], [(-0.125, -0.125, -0.125), "Zn"])
self.assertEqual(mcell._sites[1], [(0.126, 0.125, 0.125), "S"])
def test_from_cell(self):
lattice = numpy.copy(self.lattice)
positions = numpy.array([0.0, 0.0, 0.0,
0.25, 0.25, 0.25]).reshape((2, 3))
atoms = numpy.array([6, 6])
origin_lattice = numpy.copy(lattice)
origin_positions = numpy.copy(positions)
origin_atoms = numpy.copy(atoms)
cell = Cell(lattice, positions, atoms)
mcell = MutableCell.from_cell(cell)
self.assertTrue(isinstance(mcell, MutableCell))
# Make sure mcell modified not change the cell
mcell.remove_site(0)
numpy.testing.assert_almost_equal(cell.lattice, origin_lattice)
numpy.testing.assert_almost_equal(cell.positions, origin_positions)
numpy.testing.assert_almost_equal(cell.atoms, origin_atoms)
def test_perturb(self):
lattice = numpy.copy(self.lattice)
si_sites = [[(-0.125, -0.125, -0.125), "Si"],
[(0.125, 0.125, 0.125), "Si"]]
og_si_sites = copy.deepcopy(si_sites)
mcell = MutableCell(lattice, sites=si_sites)
perturb(mcell, distance=0.01)
self.assertEqual(len(mcell._sites), 2)
for i in range(2):
og_frac_pos = numpy.array(og_si_sites[i][0])
og_car_pos = frac_to_car(lattice, og_frac_pos)
new_frac_pos = numpy.array(mcell._sites[i][0])
new_car_pos = frac_to_car(lattice, new_frac_pos)
numpy.testing.assert_almost_equal(
distance(og_car_pos, new_car_pos), 0.01)
def test_remove_sites_in_a_circle(self):
# 需要测试两类情况，范围内只包含胞内原子的，和范围超出一个胞。
# 原始的晶体
lattice = numpy.array([5.5, 0, 0, 0, 5.5, 0, 0, 0, 11.0]).reshape(
(3, 3))
sites = [[(0.100, 0.100, 0.050), "Zn"], [(0.100, 0.100, 0.550), "Zn"],
[(0.100, 0.600, 0.300), "Zn"], [(0.100, 0.600, 0.800), "Zn"],
[(0.600, 0.100, 0.300), "Zn"], [(0.600, 0.100, 0.800), "Zn"],
[(0.600, 0.600, 0.050), "Zn"], [(0.600, 0.600, 0.550), "Zn"],
[(0.350, 0.350, 0.175), "S"], [(0.350, 0.350, 0.675), "S"],
[(0.850, 0.850, 0.175), "S"], [(0.850, 0.850, 0.675), "S"],
[(0.850, 0.350, 0.425), "S"], [(0.850, 0.350, 0.925), "S"],
[(0.350, 0.850, 0.425), "S"], [(0.350, 0.850, 0.925), "S"]]
# Condition I
mcell = MutableCell(numpy.copy(lattice), sites=copy.deepcopy(sites))
# 只去除包含胞内原子
# [(0.600, 0.600, 0.550), "Zn"] 该位点周围四个S原子都在胞内
# Zn-S 键长2.38157A, 所以选择半径2.5A内作为截断半径
remove_sites_in_a_circle(mcell, (0.6, 0.6, 0.55), 2.5, list_ele=['S'])
# 预期去除以下S原子
# [(0.350, 0.350, 0.675), "S"],
# [(0.850, 0.850, 0.675), "S"],
# [(0.850, 0.350, 0.425), "S"],
# [(0.350, 0.850, 0.425), "S"],
expected_sites = [[(0.100, 0.100, 0.050), "Zn"],
[(0.100, 0.100, 0.550), "Zn"],
[(0.100, 0.600, 0.300), "Zn"],
[(0.100, 0.600, 0.800), "Zn"],
[(0.600, 0.100, 0.300), "Zn"],
[(0.600, 0.100, 0.800), "Zn"],
[(0.600, 0.600, 0.050), "Zn"],
[(0.600, 0.600, 0.550), "Zn"],
[(0.350, 0.350, 0.175), "S"],
[(0.350, 0.350, 0.675), "Vacc"],
[(0.850, 0.850, 0.175), "S"],
[(0.850, 0.850, 0.675), "Vacc"],
[(0.850, 0.350, 0.425), "Vacc"],
[(0.850, 0.350, 0.925), "S"],
[(0.350, 0.850, 0.425), "Vacc"],
[(0.350, 0.850, 0.925), "S"]]
self.assertEqual(mcell._sites, expected_sites)
# Condition II
mcell = MutableCell(numpy.copy(lattice), sites=copy.deepcopy(sites))
# 范围超出一个胞，圆心在晶胞六面体顶点的特殊情况
# 去除最靠近原点的Zn周围的S原子
# [[(0.100, 0.100, 0.050), "Zn"],
remove_sites_in_a_circle(mcell, (0.1, 0.1, 0.05), 2.5, list_ele=['S'])
# 预期去除以下S原子
# [(0.350, 0.350, 0.175), "S"],
# [(0.850, 0.350, 0.925), "S"],
# [(0.350, 0.850, 0.925), "S"],
# [(0.850, 0.850, 0.175), "S"],
expected_sites = [[(0.100, 0.100, 0.050), "Zn"],
[(0.100, 0.100, 0.550), "Zn"],
[(0.100, 0.600, 0.300), "Zn"],
[(0.100, 0.600, 0.800), "Zn"],
[(0.600, 0.100, 0.300), "Zn"],
[(0.600, 0.100, 0.800), "Zn"],
[(0.600, 0.600, 0.050), "Zn"],
[(0.600, 0.600, 0.550), "Zn"],
[(0.350, 0.350, 0.175), "Vacc"],
[(0.350, 0.350, 0.675), "S"],
[(0.850, 0.850, 0.175), "Vacc"],
[(0.850, 0.850, 0.675), "S"],
[(0.850, 0.350, 0.425), "S"],
[(0.850, 0.350, 0.925), "Vacc"],
[(0.350, 0.850, 0.425), "S"],
[(0.350, 0.850, 0.925), "Vacc"]]
self.assertEqual(mcell._sites, expected_sites)