def _is_close_in_radius(lattice, p1, p2, radius):
# 截断圆对应的半径大于距离，说明两点在圆内，需要删除：返回True
# 因为周期性边界条件，首先将原始胞沿着x,y,z三个方向得到27个位置坐标
# TODO: 扩胞为3x3x3是不必要的，可以根据radius和lattice选择性扩胞，
# 若lattice的边或顶点在半径以内才需要选择向该方向扩胞
symprec = 1e-5
trans = numpy.array([i for i in product([-1, 0, 1], repeat=3)])
all_p1 = numpy.array(p1) + trans
car_p2 = frac_to_car(lattice, p2)
for each_p1 in all_p1:
car_p1 = frac_to_car(lattice, each_p1)
if radius - distance(car_p1, car_p2) > symprec:
return True
break
return False
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_distance(self):
p1 = (0, 0, 0)
p2 = (0, 3, 4)
self.assertEqual(distance(p1, p2), 5.0)