def set_miller(self, miller, miller_angle=0.0, orient=[0., 0., 1.]):
lattice_vectors = self.lattice_vectors
direction = numpy.array(orient, dtype=float)
miller = numpy.array(miller)
# normal vector to the desired miller plane (miller vector)
lattice_vectors_sum = numpy.sum(lattice_vectors, axis=0)
miller = numpy.array([miller[0], miller[1],
miller[2]]) * lattice_vectors_sum
rotation_vector = numpy.cross(miller, direction)
rotation_vector = rotation_vector / numpy.linalg.norm(rotation_vector)
rotation_angle = math.acos(numpy.dot(miller, direction) /
(numpy.linalg.norm(miller) *
numpy.linalg.norm(direction)))
rmatrix = math_tools.rotation_matrix(rotation_vector, rotation_angle)
rmatrix_main = math_tools.rotation_matrix(direction, miller_angle)
lattice_final = [None]*3
for i in xrange(3):
lattice_final[i] = numpy.dot(rmatrix_main,
numpy.dot(rmatrix, lattice_vectors[i]))
self.set_lattice_vectors(numpy.array(lattice_final))
def rotate(self, axis, theta, center=[0, 0, 0]):
rotation_matrix = math_tools.rotation_matrix(axis, theta)
rotation_center = numpy.array([center[0], center[1], center[2]],
dtype=float)
log.info("Rotating molecule around [%f, %f, %f] by %f radians"
% (axis[0], axis[1], axis[2], theta))
coords = self.coords
for i in xrange(len(coords)):
atom_position = numpy.copy(coords[i])
atom_position -= rotation_center
atom_position = numpy.dot(rotation_matrix, atom_position)
atom_position += rotation_center
coords[i] = atom_position
