def ase_phonon_calc(
struct,
calc=None,
kpoints=[1, 1, 1],
ftol=0.01,
force_clean=False,
name="asephonon",
):
"""Calculate phonon modes of a molecule using ASE and a given calculator.
The system will be geometry optimized before calculating the modes. A
report of the phonon modes will be written to a file and arrays of the
eigenvectors and eigenvalues returned.
| Args:
| struct (ase.Atoms): Atoms object with to calculate modes for.
| calc (ase.Calculator): Calculator for energies and forces (if not
| present, use the one from struct)
| kpoints (np.ndarray): Kpoint grid for phonon calculation. If None, just
| do a Vibration modes calculation (default is [1,1,1])
| ftol (float): Tolerance for geometry optimisation (default
| is 0.01 eV/Ang)
| force_clean (bool): If True, force a deletion of all phonon files
| and recalculate them
| Returns:
| evals (float[k-points][modes]): Eigenvalues of phonon modes
| evecs (float[k-points][modes][ions][3]): Eigenvectors of phonon modes
| struct (ase.Atoms): Optimised structure
"""
N = len(struct)
if calc is None:
calc = struct.calc
struct = struct.copy()
calc.atoms = struct
struct.calc = calc
dyn = BFGS(struct, trajectory="geom_opt.traj")
dyn.run(fmax=ftol)
# Calculate phonon modes
vib_pbc = kpoints is not None
if vib_pbc:
vib = Phonons(struct, calc, name=name)
else:
vib = Vibrations(struct, name=name)
if force_clean:
vib.clean()
vib.run()
if vib_pbc:
vib.read(acoustic=True)
path = monkhorst_pack(kpoints)
evals, evecs = vib.band_structure(path, True)
else:
vib.read()
path = np.zeros((1, 3))
# One axis added since it's like the gamma point
evals = np.real(vib.get_energies()[None])
evecs = np.array([vib.get_mode(i) for i in range(3 * N)])[None]
# eV to cm^-1
evals *= ((cnst.electron_volt / cnst.h) / cnst.c) / 100.0
# Normalise eigenvectors
evecs /= np.linalg.norm(evecs, axis=(2, 3))[:, :, None, None]
return ASEPhononData(evals, evecs, path, struct)
