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Fix Eigenvector normalization problem in Raman workflow #777

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Fix Eigenvector normalization problem in Raman workflow #777

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13 changes: 7 additions & 6 deletions atomate/vasp/firetasks/parse_outputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -472,12 +472,11 @@ class RamanTensorToDb(FiretaskBase):
def run_task(self, fw_spec):
nm_eigenvecs = np.array(fw_spec["normalmodes"]["eigenvecs"])
nm_eigenvals = np.array(fw_spec["normalmodes"]["eigenvals"])
nm_norms = np.linalg.norm(nm_eigenvecs, axis=2)

structure = fw_spec["normalmodes"]["structure"]
masses = np.array([site.specie.data["Atomic mass"] for site in structure])
nm_norms = nm_norms / np.sqrt(
masses
) # eigenvectors in vasprun.xml are not divided by sqrt(M_i)

# eigenvectors in vasprun.xml are not divided by sqrt(M_i)
# To get the actual eigenvals, the values read from vasprun.xml must be multiplied by -1.
# frequency_i = sqrt(-e_i)
# To convert the frequency to THZ: multiply sqrt(-e_i) by 15.633
Expand Down Expand Up @@ -507,14 +506,16 @@ def run_task(self, fw_spec):

# raman tensor = finite difference derivative of epsilon wrt displacement.
raman_tensor_dict = {}
scale = np.sqrt(structure.volume / 2.0) / 4.0 / np.pi
scale = structure.volume / 4.0 / np.pi
for k, v in modes_eps_dict.items():
nm_eigenvec_sqm = nm_eigenvecs[k, :, :] / np.sqrt(masses[:, np.newaxis])
nm_norms = np.linalg.norm(nm_eigenvec_sqm)
raman_tensor = (np.array(v[0][1]) - np.array(v[1][1])) / (v[0][0] - v[1][0])
# frequency in cm^-1
omega = nm_frequencies[k]
if nm_eigenvals[k] > 0:
logger.warning(f"Mode: {k} is UNSTABLE. Freq(cm^-1) = {-omega}")
raman_tensor = scale * raman_tensor * np.sum(nm_norms[k]) / np.sqrt(omega)
raman_tensor = scale * raman_tensor * nm_norms
raman_tensor_dict[str(k)] = raman_tensor.tolist()

d["raman_tensor"] = raman_tensor_dict
Expand Down
10 changes: 4 additions & 6 deletions atomate/vasp/firetasks/write_inputs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -691,14 +691,12 @@ def run_task(self, fw_spec):
mode = self["mode"]
disp = self["displacement"]
structure = Structure.from_file("POSCAR")
masses = np.array([site.specie.data['Atomic mass'] for site in structure])
nm_eigenvecs = np.array(fw_spec["normalmodes"]["eigenvecs"])
nm_norms = np.linalg.norm(nm_eigenvecs, axis=2)
nm_eigenvec_sqm = nm_eigenvecs[mode, :, :] / np.sqrt(masses[:, np.newaxis])
nm_norms = np.linalg.norm(nm_eigenvec_sqm)
nm_displacement = (nm_eigenvec_sqm * disp / nm_norms)

# displace the sites along the given normal mode: displacement vector
# for each site = normalized eigen vector * amount of displacement
nm_displacement = (
nm_eigenvecs[mode, :, :] * disp / nm_norms[mode, :, np.newaxis]
)
for i, vec in enumerate(nm_displacement):
structure.translate_sites(i, vec, frac_coords=False)

Expand Down