Source code for pyprocar.io.bxsf
__author__ = "Logan Lang"
__maintainer__ = "Logan Lang"
__email__ = "lllang@mix.wvu.edu"
__date__ = "March 31, 2020"
import re
import numpy as np
from pyprocar.core import ElectronicBandStructure
[docs]
class BxsfParser:
"""
The class is used to parse the information inside bxsf files
Parameters
----------
infiles : list, optional
This is a list of .bxsf filenames to parse through.
It is a list because in some codes there can be multiple .bsxf files representing spin-up and spin-sown bands
,by default ["in.bxsf"]
"""
[docs]
def __init__(self, infiles = ["in.bxsf"]):
self.reciprocal_lattice = None
self.origin = None
self.nkfs_dim = None
self.nkfs = None
self.nk_dim = None
self.nk = None
self.kpoints=None
self.band_labels = None
self.n_bands = None
self.bands = None
self.parse_bxsf(infiles = infiles)
self.ebs = ElectronicBandStructure(
kpoints=self.kpoints,
bands=self.bands,
projected=None,
efermi=self.e_fermi,
kpath=None,
projected_phase=None,
labels=None,
reciprocal_lattice=self.reciprocal_lattice,
interpolation_factor=None,
)
return None
[docs]
def parse_bxsf(self, infiles):
"""A Helper method to parse bxsf files
Parameters
----------
infiles : List
This is a list of .bxsf filenames to parse through.
"""
band_labels = []
# If 2 bxsf files search for total number of bands in both files
for ispin, infile in enumerate(infiles):
with open(infile,'r') as f:
data = f.read()
band_labels_spin = re.findall("BAND\:\s*(.*)", data)
band_labels_spin = [int(band_label) for band_label in band_labels_spin]
raw_nkfs = re.findall("BEGIN\_BLOCK\_BANDGRID\_3D\n.*\n.*\n.*\n(.*)", data)[0]
self.nkfs_dim = np.array([int(x) for x in raw_nkfs.split()])
self.nkfs = np.product(self.nkfs_dim)
band_labels.extend(band_labels_spin)
self.n_bands = max(band_labels)
self.bands = np.zeros(shape = [self.nkfs_dim[0]*self.nkfs_dim[1]*self.nkfs_dim[2], self.n_bands , 2])
# populates bands array and kpoints
for ispin, infile in enumerate(infiles):
with open(infile,'r') as f:
data = f.read()
self.e_fermi = float(re.findall("Fermi\sEnergy:\s*([\d.]*)", data)[0])
self.origin = re.findall("BEGIN\_BLOCK\_BANDGRID\_3D\n.*\n.*\n.*\n.*\n(.*)", data)[0].split()
self.origin = np.array([float(x) for x in self.origin])
self.reciprocal_lattice = re.findall("BEGIN\_BLOCK\_BANDGRID\_3D\n.*\n.*\n.*\n.*\n.*\n" + 3 * "\s*(.*)\s*\n", data)[0]
self.reciprocal_lattice = np.array([[float(y) for y in x.split()] for x in self.reciprocal_lattice ])
# Bxsf format adds extra redundant +1 dimension-size nkfs is including this dimension
raw_nkfs = re.findall("BEGIN\_BLOCK\_BANDGRID\_3D\n.*\n.*\n.*\n(.*)", data)[0]
self.nkfs_dim = np.array([int(x) for x in raw_nkfs.split()])
self.nkfs = np.product(self.nkfs_dim)
# Bxsf format adds extra redundant +1 dimension-size, nk is excluding this dimension
self.nk_dim = np.array([int(x) - 1 for x in raw_nkfs.split()])
self.nk = np.product(self.nk_dim)
self.band_labels = re.findall("BAND\:\s*(.*)", data)
# Number of bands
self.n_bands = int(re.findall("BEGIN\_BLOCK\_BANDGRID\_3D\n.*\n.*\n\s*(\d*)", data)[0])
band_labels = re.findall("BAND\:\s*(.*)", data)
band_labels = [int(band_label) for band_label in band_labels_spin]
if ispin==0:
self.kpoints = np.zeros(shape = [self.nkfs_dim[0]*self.nkfs_dim[1]*self.nkfs_dim[2],3])
# 2 for spin
band_blocks = re.findall('(?<=BAND:).*\n([\s\S]*?)(?=[A-Za-z])', data)
for i, (band_label,band_block) in enumerate(zip(band_labels,band_blocks)):
band_energies = band_block.split()
band_energies = [float(energy) for energy in band_energies]
i_kpoint=0
iband = band_label -1
extra_band_energy_indices = []
for i in range(self.nkfs_dim[0]):
for j in range(self.nkfs_dim[1]):
for k in range(self.nkfs_dim[2]):
self.bands[i_kpoint, iband,ispin] = band_energies[i_kpoint]
self.kpoints[i_kpoint,:] = np.array([(i)/(self.nkfs_dim[0]-1),(j)/(self.nkfs_dim[1]-1),(k)/(self.nkfs_dim[2]-1)])
if i == self.nkfs_dim[0]-1 or j == self.nkfs_dim[1]-1 or k == self.nkfs_dim[2]-1:
extra_band_energy_indices.append(i_kpoint)
i_kpoint += 1
# Deletes extra kpoints
self.kpoints = np.delete(self.kpoints, extra_band_energy_indices, axis = 0)
# self.kpoints = np.around(self.kpoints.dot(np.linalg.inv(self.reciprocal_lattice)),decimals=8)
# Deletes extra band energies
self.bands = np.delete(self.bands, extra_band_energy_indices , axis = 0)
return None