def operation_matrix_list(self):
op_matrix_list = []
for angle in [
2 * np.pi / self._order * self._exp,
-2 * np.pi / self._order * self._exp
]:
operation1 = rotation(angle, self._axis)
operation2 = reflection(self._axis)
operation = np.dot(operation2, operation1)
op_matrix_list.append(operation)
return op_matrix_list
def get_measure_func(self, op_function, self_similarity, orientation=None):
rotated_axis = self._axis if orientation is None else orientation.apply(
self._axis)
measure_fn = []
for angle in [
2 * np.pi / self._order * self._exp,
-2 * np.pi / self._order * self._exp
]:
operation1 = rotation(angle, rotated_axis)
operation2 = reflection(rotated_axis)
operation = np.dot(operation2, operation1)
op_function_ir = op_function.copy()
op_function_ir.apply_linear_transformation(operation)
measure_fn.append(
(op_function_ir * op_function).integrate / self_similarity)
measure_coor_total = np.average(measure_fn)
return measure_coor_total
def get_measure_pos(self, coordinates, symbols, orientation=None):
rotated_axis = self._axis if orientation is None else orientation.apply(
self._axis)
measure_coor = []
for angle in [
2 * np.pi / self._order * self._exp,
-2 * np.pi / self._order * self._exp
]:
# for angle in np.arange(2*np.pi/self._order, 2*np.pi, 2*np.pi/self._order)[::2]:
operation1 = rotation(angle, rotated_axis)
operation2 = reflection(rotated_axis)
operation = np.dot(operation2, operation1)
mesure_coor, permu = self.get_permutation(operation, coordinates,
symbols)
measure_coor.append(mesure_coor)
measure_coor_total = np.average(measure_coor)
return measure_coor_total
def get_measure(self, coordinates, modes, symbols, orientation=None):
rotated_axis = self._axis if orientation is None else orientation.apply(
self._axis)
measure_mode = []
for angle in [
2 * np.pi / self._order * self._exp,
-2 * np.pi / self._order * self._exp
]:
# for angle in np.arange(2*np.pi/self._order, 2*np.pi, 2*np.pi/self._order)[::2]:
operation1 = rotation(angle, rotated_axis)
operation2 = reflection(rotated_axis)
operation = np.dot(operation2, operation1)
operated_coor = np.dot(operation, coordinates.T).T
mesure_coor, permu = self.get_permutation(operation, coordinates,
symbols)
measure_mode_list = []
for mode in modes:
operated_mode = np.dot(
operation,
prepare_vector(coordinates, mode).T).T - operated_coor
norm = np.linalg.norm(mode)
permu_mode = np.array(operated_mode)[permu]
measure_mode_list.append(
np.trace(np.dot(mode, permu_mode.T)) / norm)
measure_mode.append(measure_mode_list)
measure_mode_total = np.average(measure_mode, axis=0)
return measure_mode_total
#print(optimization_function(res.x))
#rotmol = R.from_euler('zyx', res.x, degrees=True)
#operation = Rotation(label='C3', axis=[0, 0, 1], order=3)
#rotmol = R.from_euler('zyx', [0, 0, 0], degrees=True)
#mode_m, coor_m = operation.get_measure(np.array(coordinates), modes, symbols, orientation=rotmol)
#print('measure', coor_m)
#rotmol = R.from_euler('zyx', [360./3, 0, 0], degrees=True)
#print('---')
print(Structure(coordinates, symbols))
# rotations
rotated_axis = rotmol.apply([0, 0, 1])
operation = rotation(2 * np.pi / 2, rotated_axis)
print('axis', rotated_axis)
# reflection
#rotated_axis_r = rotmol.apply([0, 1, 0])
#operation = reflection(rotated_axis_r)
#print('axis_r', rotated_axis_r)
# C2 rotation
# rotated_axis_i = rotmol.apply([(np.sqrt(8 / 9))/2, 0, (1-1 / 3)/2])
# S4 rotation
#rotated_axis_i = rotmol.apply([np.sqrt(2 / 9), 0, 1 / 3])
#operation1 = rotation(2*np.pi/4, rotated_axis_i)
#operation2 = reflection(rotated_axis_i)
#operation = np.dot(operation2, operation1)