def check(self, elements=None, limit=0.1, warn=False):
"""
该方法用于自查对象中的位点是否过近
若过近则抛出一个warning
"""
if elements is None:
origin_cell = self
else:
# 选取要check的元素，构建新的胞
ele_num = [symbol2number(s) for s in elements]
positions = []
atoms = []
for idx, e in enumerate(self.atoms):
if e in ele_num:
positions.append(self.positions[idx])
atoms.append(self.atoms[idx])
origin_cell = self.__class__(self.lattice, positions, atoms)
mat = numpy.diag([3, 3, 3])
periodic_cell = origin_cell.extend(mat)
points = frac_to_car(periodic_cell.lattice, periodic_cell.positions)
if closest_pair(points) < limit:
if warn is True:
import warnings
warnings.warn(
"some atoms are too close(< {:f}), check cell".format(
limit), RuntimeWarning)
return False
else:
return True
def check(self, elements=None, limit=0.1, warn=False):
"""
该方法用于自查对象中的位点是否过近
若过近则抛出一个warning
"""
if elements is None:
mol = self
else:
# 选取要check的元素，构建新的胞
ele_num = [symbol2number(s) for s in elements]
positions = []
atoms = []
for idx, e in enumerate(self.atoms):
if e in ele_num:
positions.append(self.positions[idx])
atoms.append(self.atoms[idx])
mol = self.__class__(positions, atoms)
points = mol.positions
if closest_pair(points) < limit:
if warn is True:
import warnings
warnings.warn(
"some atoms are too close(< {:f}), check cell".format(
limit), RuntimeWarning)
return False
else:
return True
def test_closest_pair(self):
points = numpy.array([0, 0, 0, 0, 3, 4, 3, 60, 6, 10.1, 10.2,
10.3]).reshape((-1, 3))
self.assertEqual(closest_pair(points), 5)