def load_polarization(self, path):
"""
This function tries to read Berry phase calculations from three files:
filename+'_berry_1' filename+'_berry_2' filename+'_berry_3'
If the files are not readable, no polarization attribute is set.
On successful run this method fills the following attributes:
- self.polarization - polarization as calculated from the three files, in cartesian coordinates (3 e/A**2)
- self.ev_phase - expectation value reported by VASP for each of the three directions (3x3 -e*A)
- self.ev_recip - the mean of the expectation value projected to internal coordinates (3 -e)
- self.berry_phase - berry phases of all strings in each of the directions (3xN 1)
- self.polarization_quant - polarization quant for the calculation (3x3 e/A**2)
- self.i_polarization_quant - inverse of polarization quant
"""
self.berry_phase = 3 * [None]
self.berry_ev = 3 * [None]
self.berry_ion = 3 * [None]
self.num_per_type = []
# Noncollinear calculations are officially numspin==1, but they do contain separate electrons, not electron pairs,
# Therefore, they should be treated as numspin==2 for calculation of polarizations.
self.numspin = 2
# Extract information from OUTCAR file in each of 3 directions.
for kdirection in range(1, 4):
fname = os.path.join(path, 'Berry_%d/OUTCAR' % kdirection)
if os.access(fname, os.R_OK):
# open and read OUTCAR file
outcar = Outcar(fname)
# berry phase
outcar.read_pattern(
{
'berry_phase':
r"Im\s+ln\[Det\|M_k\|\]=\s+([+-]?\d+\.\d+)\s"
},
terminate_on_match=False,
postprocess=float)
bphase = [
item for sublist in outcar.data.get("berry_phase")
for item in sublist
]
# k-point weights
outcar.read_pattern(
{
'kpoint_weights':
r"K-point string #\s+\S+\s+weight=\s+([+-]?\d+\.\d+)\s"
},
terminate_on_match=False,
postprocess=float)
kpoint_weights = [
item for sublist in outcar.data.get("kpoint_weights")
for item in sublist
]
self.berry_phase[kdirection - 1] = np.array(
[list(x) for x in zip(bphase, kpoint_weights)])
#self.berry_ev[kdirection-1] = self.read_berry_ev(fname)
# alternative way to read berry_ev from Outcar
self.berry_ev[kdirection - 1] = self.read_berry_ev_old(fname)
outcar.read_lcalcpol()
else:
# Make sure, we have 0,0,0 as polarisation in case there is no berry phase output available
print('No file with polarization')
self.berry_phase = 3 * [np.zeros((1, 2))]
self.berry_ev = 3 * [np.zeros((3))]
self.berry_ion = 3 * [[[0., 0., 0.]]]
self.polarization_quant = self.unit_cell.copy() / self.volume
self.berry_multiplier = 1.
self.polarization_quant *= self.berry_multiplier
self.i_polarization_quant = np.linalg.inv(
self.polarization_quant)
self.ev_recip = np.dot(np.mean(self.berry_ev, axis=0),
self.recip_cell)
self.recalculate_polarization()
return
self.polarization_quant = self.unit_cell.copy() / self.volume
# In case of nonpolarised calculations, we have two electrons per each Berry string
# So the quantum needs to be doubled.
self.berry_multiplier = 3 - self.numspin
self.polarization_quant *= self.berry_multiplier
self.i_polarization_quant = np.linalg.inv(self.polarization_quant)
self.ev_recip = np.dot(np.mean(self.berry_ev, axis=0), self.recip_cell)
self.recalculate_polarization()
