def is_dihedral(self):
""" Whether or not the reflection is a sigma_d
"""
if self.principal_reflection:
return False
for atom in self.molecule:
# If there's an atom in the plane, it's a sigma_v. If there's an atom in the direction of the normal (or it's negative),
# it's sigma_v. Otherwise, it's a sigma_d. If the atom is at the origin, ignore it.
if atom.pos.is_zero():
continue
elif SymmetryOperation.is_same_axis(self.axis, atom.pos):
return False
elif SymmetryOperation.is_perpendicular(self.axis, atom.pos):
return False
return True
def is_dihedral(self):
""" Whether or not the reflection is a sigma_d
"""
if self.principal_reflection:
return False
for atom in self.molecule:
# If there's an atom in the plane, it's a sigma_v. If there's an atom in the direction of the normal (or it's negative),
# it's sigma_v. Otherwise, it's a sigma_d. If the atom is at the origin, ignore it.
if atom.pos.is_zero():
continue
elif SymmetryOperation.is_same_axis(self.axis, atom.pos):
return False
elif SymmetryOperation.is_perpendicular(self.axis, atom.pos):
return False
return True
def _get_name(self):
""" Get the name of the point group
"""
# Using a flow charts from http://www.mineralatlas.com/fga/image007.gif and
# http://capsicum.me.utexas.edu/ChE386K/html/flowchart_point_groups.htm
# If two or more C_n with n > 2...
if len(
[rot for rot in self.rotations if rot.n > 2 and rot.exponent == 1
]) >= 2:
# 12 C5 axes?
if self.num_C_n_axes(5) == 12:
if self.inversion is None:
self.name = 'I'
return
else:
self.name = 'I_h'
return
# 6 C4s?
elif self.num_C_n_axes(4) == 6:
if self.inversion is None:
self.name = 'O'
return
else:
self.name = 'O_h'
return
# 4 C3s?
elif self.num_C_n_axes(3) == 4:
# 8 C3s?
if self.inversion is None:
if len(self.reflections) == 6:
self.name = 'T_d'
return
else:
self.name = 'T'
return
else:
self.name = 'T_h'
return
else:
raise GroupTheoryError(
"Don't know the name of group with classes: " +
str(self.classes) + ". (Perhaps adjust tolerances?)")
elif len(self.rotations) > 0:
highest_Cn = self.rotations[0]
highest_n = highest_Cn.n
highest_axis = highest_Cn.axis
count = 0
for rot in self.rotations:
if rot.n == 2 and SymmetryOperation.is_perpendicular(
highest_axis, rot.axis):
count += 1
if count == highest_n:
if any(ref.is_principal_reflection()
for ref in self.reflections):
self.name = 'D_' + str(highest_n) + 'h'
return
elif len(self.reflections) == highest_n:
self.name = 'D_' + str(highest_n) + 'd'
return
elif len(self.reflections) == 0:
self.name = 'D_' + str(highest_n)
else:
raise GroupTheoryError(
"Don't know the name of group with classes: " +
str(self.classes) + ". (Perhaps adjust tolerances?)")
else:
if any(ref.is_principal_reflection()
for ref in self.reflections):
self.name = 'C_' + str(highest_n) + 'h'
return
elif len(self.reflections) == highest_n:
self.name = 'C_' + str(highest_n) + 'v'
return
elif any(irot.n == 2 * highest_n
for irot in self.improper_rotations):
self.name = 'S_' + str(2 * highest_n)
return
else:
self.name = 'C_' + str(highest_n)
return
else:
if len(self.reflections) == 1:
self.name = 'C_s'
return
elif not self.inversion is None:
self.name = 'C_i'
return
elif len(self) == 1:
self.name = 'C_1'
else:
raise GroupTheoryError(
"Don't know the name of group with classes: " +
str(self.classes) + ". (Perhaps adjust tolerances?)")
def _get_name(self):
""" Get the name of the point group
"""
# Using a flow charts from http://www.mineralatlas.com/fga/image007.gif and
# http://capsicum.me.utexas.edu/ChE386K/html/flowchart_point_groups.htm
# If two or more C_n with n > 2...
if len([rot for rot in self.rotations if rot.n > 2 and rot.exponent == 1 ]) >= 2:
# 12 C5 axes?
if self.num_C_n_axes(5) == 12:
if self.inversion is None:
self.name = 'I'
return
else:
self.name = 'I_h'
return
# 6 C4s?
elif self.num_C_n_axes(4) == 6:
if self.inversion is None:
self.name = 'O'
return
else:
self.name = 'O_h'
return
# 4 C3s?
elif self.num_C_n_axes(3) == 4:
# 8 C3s?
if self.inversion is None:
if len(self.reflections) == 6:
self.name = 'T_d'
return
else:
self.name = 'T'
return
else:
self.name = 'T_h'
return
else:
raise GroupTheoryError("Don't know the name of group with classes: " + str(self.classes)
+ ". (Perhaps adjust tolerances?)")
elif len(self.rotations) > 0:
highest_Cn = self.rotations[0]
highest_n = highest_Cn.n
highest_axis = highest_Cn.axis
count = 0
for rot in self.rotations:
if rot.n == 2 and SymmetryOperation.is_perpendicular(highest_axis, rot.axis):
count += 1
if count == highest_n:
if any(ref.is_principal_reflection() for ref in self.reflections):
self.name = 'D_' + str(highest_n) + 'h'
return
elif len(self.reflections) == highest_n:
self.name = 'D_' + str(highest_n) + 'd'
return
elif len(self.reflections) == 0:
self.name = 'D_' + str(highest_n)
else:
raise GroupTheoryError("Don't know the name of group with classes: " + str(self.classes)
+ ". (Perhaps adjust tolerances?)")
else:
if any(ref.is_principal_reflection() for ref in self.reflections):
self.name = 'C_' + str(highest_n) + 'h'
return
elif len(self.reflections) == highest_n:
self.name = 'C_' + str(highest_n) + 'v'
return
elif any(irot.n == 2*highest_n for irot in self.improper_rotations):
self.name = 'S_' + str(2*highest_n)
return
else:
self.name = 'C_' + str(highest_n)
return
else:
if len(self.reflections) == 1:
self.name = 'C_s'
return
elif not self.inversion is None:
self.name = 'C_i'
return
elif len(self) == 1:
self.name = 'C_1'
else:
raise GroupTheoryError("Don't know the name of group with classes: " + str(self.classes)
+ ". (Perhaps adjust tolerances?)")
