masses for the atoms (has to have length ``mode.shape[1] // 3``
Returns
-------
numpy.ndarray
displacements per mode with final dimension ``(mode.shape[0], 3)``, the displacements are in Ang
"""
if mode.ndim == 1:
return displacement(mode.reshape(1, -1), hw, mass).reshape(-1, 3)
return _displacement(mode, hw, mass)
# Electron rest mass in units of proton mass (the units we use for the atoms)
_displacement_const = (2 * units('Ry', 'eV') *
constant.m_e('amu'))**0.5 * units('Bohr', 'Ang')
def _displacement(mode, hw, mass):
""" Real space displacements """
idx = (hw < 0).nonzero()[0]
U = mode.copy()
U[idx, :] = 0.
# Now create the remaining displacements
idx = np.delete(_a.arangei(mode.shape[0]), idx)
# Generate displacement factor
factor = _displacement_const / hw[idx].reshape(-1, 1)**0.5
U.shape = (mode.shape[0], -1, 3)
mass : array_like
masses for the atoms (has to have length ``mode.shape[1] // 3``
Returns
-------
numpy.ndarray
displacements per mode with final dimension ``(mode.shape[0], 3)``, displacements are in Ang
"""
if mode.ndim == 1:
return displacement(mode.reshape(1, -1), hw, mass)[0]
return _displacement(mode, hw, mass)
# Rest mass in units of proton mass (the units we use for the atoms)
_displacement_const = (2 * units('Ry', 'eV') * constant.m_e('amu')) ** 0.5 * units('Bohr', 'Ang')
def _displacement(mode, hw, mass):
""" Real space displacements """
idx = (hw == 0).nonzero()[0]
U = mode.copy()
U[idx, :] = 0.
# Now create the remaining displacements
idx = delete(_a.arangei(mode.shape[0]), idx)
# Generate displacement factor
factor = _displacement_const / fabs(hw[idx]).reshape(-1, 1) ** 0.5
U.shape = (mode.shape[0], -1, 3)