"""
Interface to irrep.
"""
import warnings
import os
from os import path
import subprocess
import re
from monty.json import MSONable
from monty.dev import requires
from monty.os.path import which
import numpy as np
__author__ = "Jason Munro, Nathan C. Frey"
__copyright__ = "MIT License"
__version__ = "0.0.1"
__maintainer__ = "Jason Munro, Nathan C. Frey, "
__email__ = "jmunro@lbl.gov, ncfrey@lbl.gov,"
__status__ = "Development"
__date__ = "Feb 2021"
IRREPEXE = which("irrep")
class IrrepCaller:
@requires(
IRREPEXE,
"IRREPCaller requires irrep to be in the path.\n"
"Please follow the instructions in https://pypi.org/project/irrep and https://arxiv.org/pdf/2009.01764.pdf ",
)
def __init__(self, folder_name, code="vasp", enable_spinor=True, add_args={}):
"""
Run irrep to compute irreducible representations (irreps) of electronic states from wavefunctions and
symmetry operations determined from an input structure.
For running with vasp (default), it requires a calculation with LWAVE=.TRUE. This does NOT use the symmetry
operations found in the OUTCAR file.
Something like "phonopy --tolerance 0.01 --symmetry -c POSCAR" should be used to ensure
the crystal is in a standard setting before the calculation.
Args:
folder_name (str): Path to directory with input data at kpts where irreps should be computed.
code (str): The code to run with. Default is vasp.
enable_spinor (bool): Whether to include the '-spinor' flag when calling irrep.
add_args (dict): Dictionary of additional arguments (i.e. {-Ecut: 50}).
"""
# Check for POSCAR and WAVECAR if using vasp
if code == "vasp":
if not path.isfile(folder_name + "/WAVECAR") or not path.isfile(
folder_name + "/POSCAR"
):
raise FileNotFoundError()
os.chdir(folder_name)
# Call irrep
cmd_list = ["irrep", "-code", code]
if enable_spinor:
cmd_list += ["-spinor"]
for arg, val in add_args.items():
cmd_list += [str(arg), str(val)]
with open("outir.txt", "w") as out, open("err.txt", "w") as err:
process = subprocess.Popen(cmd_list, stdout=out, stderr=err)
process.communicate() # pause while irrep is executing
self.output = None
# Process output
if path.isfile("outir.txt"):
self.output = IrrepOutput("outir.txt")
else:
raise FileNotFoundError()
[docs]class IrrepOutput(MSONable):
def __init__(
self,
irrep_output,
efermi=None,
saved_bands=None,
starting_band=None,
energy_cutoff=None,
spacegroup_no=None,
spin_polarized=None,
parity_eigenvals=None,
):
"""
This class processes results from irrep to get irreps of electronic states.
Refer to https://arxiv.org/pdf/2009.01764.pdf for further explanation of parameters.
Args:
irvsp_output (txt file): output from irvsp.
efermi (float): Supplied fermi energy used to shift band energies.
saved_bands (int): Number of bands saved in output.
starting_band (int): Starting band number.
energy_cutoff (int): Plane-wave energy cutoff in eV used to generate g-vectors.
spacegroup_no (int): Space group number detected.
parity_eigenvals (dict): band index, band degeneracy, energy eigenval, Re(parity eigenval)
"""
self._irrep_output = irrep_output
self.efermi = efermi
self.saved_bands = saved_bands
self.starting_band = starting_band
self.energy_cutoff = energy_cutoff
self.spacegroup_no = spacegroup_no
self.spin_polarized = spin_polarized
self.parity_eigenvals = parity_eigenvals
self._parse_stdout(irrep_output)
def _parse_stdout(self, irrep_output):
try:
with open(irrep_output, "r") as file:
lines = file.readlines()
for idx, line in enumerate(lines):
if "Efermi" in line:
e = line.split()[3]
self.efermi = float(e) if e != "None" else None
init_block_start = idx
break
band_line = lines[init_block_start + 2].split()
self.saved_bands = int(band_line[1])
self.starting_band = int(band_line[5])
encut_line = lines[init_block_start + 4].split()
self.energy_cutoff = float(encut_line[5])
trunc_lines = lines[init_block_start:]
# Define TRIM labels in units of primitive reciprocal vectors
trim_labels = ["gamma", "x", "y", "z", "s", "t", "u", "r"]
trim_pts = [
(0.0, 0.0, 0.0),
(0.5, 0.0, 0.0),
(0.0, 0.5, 0.0),
(0.0, 0.0, 0.5),
(0.5, 0.5, 0.0),
(0.0, 0.5, 0.5),
(0.5, 0.0, 0.5),
(0.5, 0.5, 0.5),
]
trim_dict = {pt: label for (pt, label) in zip(trim_pts, trim_labels)}
# Dicts with kvec index as keys
parity_eigenvals = {}
# Start of symm. op. and irrep trace info
for idx, line in enumerate(trunc_lines):
if "INFORMATION ABOUT THE SPACE GROUP" in line:
symm_block_start = idx
break
sg_line = trunc_lines[symm_block_start + 3].split()
self.spacegroup_no = int(sg_line[3])
# Find inv symm. op.
for idx, line in enumerate(trunc_lines):
if "angle = 0 , inversion : True" in line:
inv_num = int(trunc_lines[idx + 1].split()[1]) - 1
if "k-point 1" in line:
irrep_block_start = idx
break
# Find parity eigenvalues
trace_start = False
for line in trunc_lines[irrep_block_start:]:
if line.startswith("k-point"): # New kvec
line_list = re.findall("\\[(.*)\\]", line)[0].split()
kvec = tuple([float(i) for i in line_list])
trim_label = trim_dict[kvec]
ndgs = []
bnd_evs = []
inv_evs = []
if "Energy | multiplicity | irreps | sym. operations" in line:
trace_start = True
col_check = False
continue
if trace_start:
if "|" in line and not col_check:
inv_col = line.split().index(str(inv_num)) - 3
col_check = True
elif "|" in line:
line_list = line.split()
bnd_evs.append(float(line_list[0]))
ndgs.append(int(line_list[2]))
inv_ev = complex(line_list[inv_col + 6])
if inv_ev.imag != 0.0:
warnings.warn("Found complex parity eigenvalues!")
inv_evs.append(inv_ev)
else:
if not np.isclose(
inv_ev.real % 1.0, 0.0, rtol=0, atol=0.03
) or not np.isclose(
inv_ev.real % 1.0, 1.0, rtol=0, atol=0.03
):
warnings.warn(
"Irrep output data has non-integer parity eigenvalues!"
)
inv_evs.append(inv_ev.real)
else:
trace_start = False
kvec_data = {
"band_degeneracy": ndgs,
"band_eigenval": bnd_evs,
"inversion_eigenval": inv_evs,
}
parity_eigenvals[trim_label] = kvec_data
continue
self.parity_eigenvals = parity_eigenvals
except FileNotFoundError:
warnings.warn(
"Irrep output not found. Setting instance attributes from direct inputs!"
)
