def check_mirror(atoms, normal_vector, debug=False):
com = atoms.get_center_of_mass()
# normalize vector
L = numpy.linalg.norm(normal_vector)
normal_vector /= L
mirrored = mirror_through_plane(atoms, normal_vector, debug=debug)
if debug:
print normal_vector
print atoms.get_positions()
print mirrored
from ice_package.help_methods import get_oxygens
import ase
ase.visualize.view(get_oxygens(mirrored))
ase.visualize.view(atoms)
print normal_vector
raw_input("Continue")
result = get_equals(atoms, mirrored, debug=debug)
if result == None:
return None
return SymmetryOperation('sigma',
result,
None,
vector=normal_vector,
magnitude=1,
order_no=0,
type='sigma')
def check_improper_rotation(atoms,
vector,
angle,
center,
n,
result,
order_no=0):
a = atoms.copy()
a.rotate(vector, a=angle, center=center)
positions = mirror_through_plane(a, vector)
equals = get_equals(atoms, positions)
on = order_no
# n = 2 is equal with inversion operator
if n == 2 or (float(order_no + 1) / float(n)) == 0.5:
return
if equals != None:
operation_name = "S%i" % n
while order_no > 0:
operation_name += "'"
order_no -= 1
result.append(
SymmetryOperation(operation_name,
equals,
None,
vector=vector,
magnitude=n,
type='S',
order_no=on))
def check_inversion_center(atoms):
positions = positions_related_to_center_of_mass(atoms,
atoms.get_positions())
positions = -positions + atoms.get_center_of_mass()
result = get_equals(atoms, positions)
if result == None:
return None
print "Inversion center found"
return SymmetryOperation("i",
result,
None,
type='i',
order_no=0,
magnitude=1)
def check_single_rotation(atoms, vector, angle, center, n, result, order_no=0):
a = atoms.copy()
a.rotate(vector, a=angle, center=center)
positions = a.get_positions()
equals = get_equals(atoms, positions)
on = order_no
if equals != None:
operation_name = "C%i" % n
while order_no > 0:
operation_name += "'"
order_no -= 1
result.append(
SymmetryOperation(operation_name,
equals,
None,
vector=vector,
magnitude=n,
type='C',
order_no=on))
def get_periodic_symmetry_operations(atoms, error_tolerance=0.01, debug=False):
from ase.utils import irotate
from ase.visualize import view
from pyspglib import spglib
#symmetry = spglib.get_symmetry(atoms, symprec=1e-5)
symmetry = spglib.get_symmetry(atoms, symprec=1e-2)
dataset = spglib.get_symmetry_dataset(atoms, symprec=1e-2)
result = []
if debug:
cell, scaled_positions, numbers = spglib.find_primitive(atoms,
symprec=1e-5)
a = Atoms(symbols='O4',
cell=cell,
scaled_positions=scaled_positions,
pbc=True)
#symmetry = spglib.get_symmetry(a, symprec=1e-2)
#dataset = spglib.get_symmetry_dataset(a, symprec=1e-2)
print dataset['equivalent_atoms']
print dataset['international']
print dataset['hall']
print dataset['wyckoffs']
print dataset['transformation_matrix']
print "Number of symmetry operations %i" % len(dataset['rotations'])
for i in range(dataset['rotations'].shape[0]):
new_atoms = atoms.copy()
test = atoms.copy()
rot = dataset['rotations'][i]
trans = dataset['translations'][i]
if debug:
x, y, z = irotate(rot)
#print x, y, z
print "------------------- %i -----------------------" % i
print "Rotation"
print rot
print "Translation"
print trans
new_pos = new_atoms.get_scaled_positions()
for l, pos in enumerate(new_atoms.get_scaled_positions()):
#print new_pos[l]
new_pos[l] = (numpy.dot(rot, pos))
new_pos[l] += trans
#print new_pos[l]
new_atoms.set_scaled_positions(new_pos)
equals = get_equals_periodic(atoms,
new_atoms,
error_tolerance=error_tolerance,
debug=debug)
if equals != None:
so = SymmetryOperation(str(i),
equals,
None,
vector=None,
magnitude=1,
rotation_matrix=rot,
translation_vector=trans)
#if debug:
# print so
result.append(so)
else:
print "Equivalent not found"
#view(test)
#view(new_atoms)
#raw_input()
return result
def get_identity_operator(atoms):
equals = numpy.arange(0, len(atoms), 1)
return SymmetryOperation("Identity", equals, None)
