def alignment_c(self):
"""Computes the rotation matrix that aligns the unit cell with the
Cartesian axes, starting with cell vector c.
* c parallel to z
* b in zy-plane with b_y positive
* a with a_x positive
"""
from molmod.transformations import Rotation
new_z = self.matrix[:, 2].copy()
new_z /= np.linalg.norm(new_z)
new_x = np.cross(self.matrix[:, 1], new_z)
new_x /= np.linalg.norm(new_x)
new_y = np.cross(new_z, new_x)
new_y /= np.linalg.norm(new_y)
return Rotation(np.array([new_x, new_y, new_z]))
def alignment_a(self):
"""Computes the rotation matrix that aligns the unit cell with the
Cartesian axes, starting with cell vector a.
* a parallel to x
* b in xy-plane with b_y positive
* c with c_z positive
"""
from molmod.transformations import Rotation
new_x = self.matrix[:, 0].copy()
new_x /= numpy.linalg.norm(new_x)
new_z = numpy.cross(new_x, self.matrix[:, 1])
new_z /= numpy.linalg.norm(new_z)
new_y = numpy.cross(new_z, new_x)
new_y /= numpy.linalg.norm(new_y)
return Rotation(numpy.array([new_x, new_y, new_z]))
