Because nuclei are much heavier than the electrons, one usually assumes that the Born-Oppenheimer (BO) approximation holds and that the full wave function factorizes in the electronic and the nuclear wave function. This approximation hugely simplifies the computation of the full wave function and its properties, but the approximation can break down when there is significant vibronic coupling. Traditionally, vibronic coupling is evaluated with complex mathematical machinery, which often yields unrealistic results for large systems. However, if one relaxes the BO approximation and assumes that the electrons experience the moving nuclei as a perturbation of the potential, the full Hamiltonian can be approximated by a Taylor expansion with the adiabatic states at equilibrium and the quantized vibrational modes. This approach is widely used in solid state calculations for modeling electron/phonon transport properties (see  for more discussions).
PySCF supports the calculation of the first-order electron-phonon (e-ph) coupling matrix by either coupled perturbed Kohn-Sham/Hartree-Fock (CPKS/CPHF) or finite differences. In periodic systems, only FFTDF-based Gamma-point calculations are supported with finite differences. In both cases, a geometrically relaxed structure is required or the structural instability could lead to imaginary vibrational frequencies.
A minimal example of analytical e-ph matrix calculation is as follows:
from pyscf import gto, scf, eph mol = gto.M( atom = [['O', [0.000000000000, -0.000000000775, 0.923671924285]], ['H', [-0.00000000000, -1.432564848017, 2.125164039823]], ['H', [0.000000000000, 1.432564848792, 2.125164035930]]], basis = 'sto3g', unit = 'Bohr' ) # Note that this is a pre-computed relaxed molecule mf = scf.RHF(mol).run() myeph = eph.EPH(mf) ephmat, omega = myeph.kernel() print('eph matrix', ephmat) print('phonon frequencies', omega)
Alternatively, one can compute the matrix elements using finite difference:
from pyscf import gto, scf, eph mol = gto.M( atom = [['O', [0.000000000000, -0.000000000775, 0.923671924285]], ['H', [-0.000000000000, -1.432564848017, 2.125164039823]], ['H', [0.000000000000, 1.432564848792, 2.125164035930]]], basis = 'sto3g', unit = 'Bohr' ) mf = scf.RHF(mol).run() ephmat, omega = eph.eph_df.kernel(mf, disp=1e-4) print('eph matrix', ephmat) print('phonon frequencies', omega)
eph module in PySCF supports mean field methods including Hartree Fock and DFT using either spin-restricted or spin-unrestricted reference.
Analytical eph matrix elements¶
eph.EPH(mf) constructor can infer the correct method based
on the type of the mf argument. For more explicit
control or inspection, the respective classes and functions can be found in
For example, a spin-unrestricted calculation can be performed as follows:
mf = scf.UHF(mol).run() myeph = eph.uhf.EPH(mf) ephmat, omega = myeph.kernel() print('eph matrix', ephmat) print('phonon frequencies', omega)
The finite difference kernel function
eph.eph_fd.kernel can handle all the supported mean field methods above.
Filtering noisy frequencies¶
The diagonalization of the mass-weighted hessian can sometimes yield unphysical vibrational modes that correspond to imaginary frequencies or to non-zero frequencies which should strictly vanish. These unphysical modes may arise either from the use of not fully relaxed geometries, the use of insufficiently accurate density functional quadrature, or simply numerical noise. By default, modes below 80 cm-1 are filtered out in PySCF; note that this also includes any negative frequencies.
One can specify a different cutoff frequency (in cm-1) when constructing the EPH object as follows:
myeph = eph.EPH(mf, cutoff_frequency=60) ephmat, omega = myeph.kernel()
Similarly, to keep the imaginary frequencies, one can set keep_imag_frequency to True when initializing the object:
myeph = eph.EPH(mf, keep_imag_frequency=True) ephmat, omega = myeph.kernel()
Matrix element representation¶
The eph matrix is computed in the atomic orbital (AO) basis by default. One can also request it in the MO basis as follows:
myeph = eph.EPH(mf) ephmat, omega = myeph.kernel(mo_rep=True)
Feliciano Giustino. Electron-phonon interactions from first principles. Rev. Mod. Phys., 89:015003, 2017.