def do(self):
universe = context.application.cache.node
# first make sure the cell is right handed
if numpy.linalg.det(universe.cell) < 0 and universe.cell_active.sum() == 3:
new_cell = universe.cell.copy()
temp = new_cell[:,0].copy()
new_cell[:,0] = new_cell[:,1]
new_cell[:,1] = temp
primitive.SetProperty(universe, "cell", new_cell)
# then rotate the unit cell box to the normalized frame:
rotation = Rotation()
rotation.r = numpy.array(universe.calc_align_rotation_matrix())
new_cell = numpy.dot(rotation.r, universe.cell)
old_cell_active = universe.cell_active.copy()
universe.cell_active = numpy.array([False, False, False])
primitive.SetProperty(universe, "cell", new_cell)
for child in context.application.cache.transformed_children:
primitive.Transform(child, rotation)
universe.cell_active = old_cell_active
primitive.SetProperty(universe, "cell", new_cell)
def do(self):
cache = context.application.cache
rotation = Rotation()
rotation.r = copy.deepcopy(cache.node.transformation.r)
CenterAlignBase.do(self, cache.parent, cache.transformed_neighbors, rotation)