def __init__(self, gui):
gtk.Window.__init__(self)
angles = irotate(gui.axes)
self.set_title('Rotate')
vbox = gtk.VBox()
pack(vbox, gtk.Label('Rotation angles:'))
self.rotate = [
gtk.Adjustment(value=a,
lower=-360,
upper=360,
step_incr=1,
page_incr=10) for a in angles
]
pack(vbox,
[gtk.SpinButton(a, climb_rate=0, digits=1) for a in self.rotate])
for r in self.rotate:
r.connect('value-changed', self.change)
button = pack(vbox, gtk.Button('Update'))
button.connect('clicked', self.update_angles)
pack(
vbox,
gtk.Label('Note:\nYou can rotate freely\n'
'with the mouse, by holding\n'
'down mouse botton 2.'))
self.add(vbox)
vbox.show()
self.show()
self.gui = gui
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print(xyz)
print(ixyz)
assert abs(a - a2).max() < 1e-10
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print(xyz)
print(ixyz)
assert abs(a - a2).max() < 1e-10
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
print xyz
print ixyz
#print np.around(a-a2, 5)
assert abs(a - a2).max() < 1e-10
def test(xyz):
a = rotate(xyz)
ixyz = '%sx,%sy,%sz' % irotate(a)
a2 = rotate(ixyz)
#print xyz
#print ixyz
#print np.around(a-a2, 5)
assert abs(a-a2).max() < 1e-10
def __init__(self, gui):
gtk.Window.__init__(self)
angles = irotate(gui.axes)
self.set_title(_('Rotate'))
vbox = gtk.VBox()
pack(vbox, gtk.Label(_('Rotation angles:')))
self.rotate = [gtk.Adjustment(value=a, lower=-360, upper=360,
step_incr=1, page_incr=10)
for a in angles]
pack(vbox, [gtk.SpinButton(a, climb_rate=0, digits=1)
for a in self.rotate])
for r in self.rotate:
r.connect('value-changed', self.change)
button = pack(vbox, gtk.Button(_('Update')))
button.connect('clicked', self.update_angles)
pack(vbox, gtk.Label(_('Note:\nYou can rotate freely\n'
'with the mouse, by holding\n'
'down mouse button 2.')))
self.add(vbox)
vbox.show()
self.show()
self.gui = gui
def update_angles(self, button):
angles = irotate(self.gui.axes)
self.update = False
for r, a in zip(self.rotate, angles):
r.value = a
self.update = True
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 update_angles(self):
angles = irotate(self.gui.axes)
for r, a in zip(self.rotate, angles):
r.value = a
def update_angles(self, button):
angles = irotate(self.gui.axes)
self.update = False
for r, a in zip(self.rotate, angles):
r.value = a
self.update = True
def update_angles(self):
angles = irotate(self.gui.axes)
for r, a in zip(self.rotate, angles):
r.value = a
