def align_with_plane(self, axis=2, round_decimals=14):
a = self.cell[1]
if axis == 0:
p1 = np.array([0, 1, 0])
p2 = np.array([0, 0, 1])
elif axis == 1:
p1 = np.array([0, 0, 1])
p2 = np.array([1, 0, 0])
elif axis == 2:
p1 = np.array([1, 0, 0])
p2 = np.array([0, 1, 0])
else:
raise ValueError('Axis must be an integer in (0,1,2)')
if np.linalg.norm(np.cross(p1, a)) < 1E-10:
return
c = unit_vector(np.cross(p1, a))
# print c
# A vector perpendicular to the plane
vector_plane = unit_vector(np.cross(p1, p2))
v1_u = unit_vector(vector_plane)
v2_u = unit_vector(c)
proj = np.dot(v1_u, v2_u)
# print 'Projection', proj
av = np.arccos(proj)
# import math
# print 'Angle=', math.degrees(av)
rotation_matrix = rotation_matrix_around_axis_angle(p1, -av)
cell = np.dot(rotation_matrix, self.cell.T).T.round(round_decimals)
# print '-->',cell[1], vector_plane
# print 'PROJECTION', np.dot(cell[1], vector_plane)
if np.abs(np.dot(cell[1], vector_plane)) > 1E-10:
# print 'Failed projection', np.dot(cell[1], vector_plane)
# print cell
rotation_matrix = rotation_matrix_around_axis_angle(p1, av)
cell = np.dot(rotation_matrix, self.cell.T).T.round(round_decimals)
if np.dot(cell[1], vector_plane) > 1E-10:
# print 'Failed projection', np.dot(cell[1], vector_plane)
# print cell
pass
self._cell = cell
def align_with_plane(self, axis=2, round_decimals=14):
a = self.cell[1]
if axis == 0:
p1 = np.array([0, 1, 0])
p2 = np.array([0, 0, 1])
elif axis == 1:
p1 = np.array([0, 0, 1])
p2 = np.array([1, 0, 0])
elif axis == 2:
p1 = np.array([1, 0, 0])
p2 = np.array([0, 1, 0])
else:
raise ValueError('Axis must be an integer in (0,1,2)')
if np.linalg.norm(np.cross(p1, a)) < 1E-10:
return
c = unit_vector(np.cross(p1, a))
# print c
# A vector perpendicular to the plane
vector_plane = unit_vector(np.cross(p1, p2))
v1_u = unit_vector(vector_plane)
v2_u = unit_vector(c)
proj = np.dot(v1_u, v2_u)
# print 'Projection', proj
av = np.arccos(proj)
# import math
# print 'Angle=', math.degrees(av)
rotation_matrix = rotation_matrix_around_axis_angle(p1, -av)
cell = np.dot(rotation_matrix, self.cell.T).T.round(round_decimals)
# print '-->',cell[1], vector_plane
# print 'PROJECTION', np.dot(cell[1], vector_plane)
if np.abs(np.dot(cell[1], vector_plane)) > 1E-10:
# print 'Failed projection', np.dot(cell[1], vector_plane)
# print cell
rotation_matrix = rotation_matrix_around_axis_angle(p1, av)
cell = np.dot(rotation_matrix, self.cell.T).T.round(round_decimals)
if np.dot(cell[1], vector_plane) > 1E-10:
# print 'Failed projection', np.dot(cell[1], vector_plane)
# print cell
pass
self._cell = cell
def align_with_axis(self, axis=0, round_decimals=14):
a = self.cell[0]
if axis == 0:
b = np.array([1, 0, 0])
elif axis == 1:
b = np.array([0, 1, 0])
elif axis == 2:
b = np.array([0, 0, 1])
else:
raise ValueError('Axis must be an integer in (0,1,2)')
if np.linalg.norm(np.cross(a, b)) < 1E-10:
return
c = unit_vector(np.cross(a, b))
av = angle_vector(a, b)
rotation_matrix = rotation_matrix_around_axis_angle(c, av)
self._cell = np.dot(rotation_matrix, self.cell.T).T.round(round_decimals)
def align_with_axis(self, axis=0, round_decimals=14):
a = self.cell[0]
if axis == 0:
b = np.array([1, 0, 0])
elif axis == 1:
b = np.array([0, 1, 0])
elif axis == 2:
b = np.array([0, 0, 1])
else:
raise ValueError('Axis must be an integer in (0,1,2)')
if np.linalg.norm(np.cross(a, b)) < 1E-10:
return
c = unit_vector(np.cross(a, b))
av = angle_vector(a, b)
rotation_matrix = rotation_matrix_around_axis_angle(c, av)
self._cell = np.dot(rotation_matrix, self.cell.T).T.round(round_decimals)