Source code for pytopomat.vasp2trace_caller
"""
Interface to vasp2trace.
"""
import warnings
import os
from os import path
import subprocess
import numpy as np
from monty.json import MSONable
from monty.dev import requires
from monty.os.path import which
__author__ = "Nathan C. Frey, Jason Munro"
__copyright__ = "MIT License"
__version__ = "0.0.1"
__maintainer__ = "Nathan C. Frey, Jason, Munro"
__email__ = "ncfrey@lbl.gov, jmunro@lbl.gov"
__status__ = "Development"
__date__ = "August 2019"
VASP2TRACEEXE = which("vasp2trace")
VASP2TRACE2EXE = which("vasp2trace2")
class Vasp2TraceCaller:
@requires(
VASP2TRACEEXE,
"Vasp2TraceCaller requires vasp2trace to be in the path."
"Please follow the instructions at http://www.cryst.ehu.es/cgi-bin/cryst/programs/topological.pl.",
)
def __init__(self, folder_name):
"""
Run vasp2trace to find the set of irreducible representations at each maximal k-vec of a space group, given the eigenvalues.
vasp2trace requires a self-consistent VASP run with the flags ISTART=0 and ICHARG=2; followed by a band structure calculation with ICHARG=11, ISYM=2, LWAVE=.True.
High-symmetry kpts that must be included in the band structure path for a given spacegroup can be found in the max_KPOINTS_VASP folder in the vasp2trace directory.
Args:
folder_name (str): Path to directory with OUTCAR and WAVECAR of band structure run with wavefunctions at the high-symmetry kpts.
"""
# Check for OUTCAR and WAVECAR
if not path.isfile(folder_name + "/OUTCAR") or not path.isfile(
folder_name + "/WAVECAR"
):
raise FileNotFoundError()
# Call vasp2trace
os.chdir(folder_name)
process = subprocess.Popen(
["vasp2trace"], stdout=subprocess.PIPE, stderr=subprocess.PIPE
)
stdout, stderr = process.communicate()
stdout = stdout.decode()
if stderr:
stderr = stderr.decode()
warnings.warn(stderr)
if process.returncode != 0:
raise RuntimeError(
"vasp2trace exited with return code {}.".format(process.returncode)
)
self._stdout = stdout
self._stderr = stderr
self.output = None
# Process output
if path.isfile("trace.txt"):
self.output = {}
self.output["up"] = Vasp2TraceOutput("trace.txt")
else:
raise FileNotFoundError()
class Vasp2Trace2Caller:
@requires(
VASP2TRACE2EXE,
"Vasp2Trace2Caller requires vasp2trace2 to be in the path."
"Please install from https://github.com/zjwang11/irvsp",
)
def __init__(self, folder_name):
"""
Run vasp2trace_v2 to find the set of irreducible representations at each maximal k-vec of a space group, given the eigenvalues.
version2 of vasp2trace is for spin-polarized calculations. The executable is renamed "vasp2trace2" to avoid conflict with v1.
vasp2trace requires a self-consistent VASP run with the flags ISTART=0 and ICHARG=2; followed by a band structure calculation with ICHARG=11, ISYM=2, LWAVE=.True.
High-symmetry kpts that must be included in the band structure path for a given spacegroup can be found in the max_KPOINTS_VASP folder in the vasp2trace directory.
Args:
folder_name (str): Path to directory with OUTCAR and WAVECAR of band structure run with wavefunctions at the high-symmetry kpts.
"""
# Check for OUTCAR and WAVECAR
if not path.isfile(folder_name + "/OUTCAR") or not path.isfile(
folder_name + "/WAVECAR"
):
raise FileNotFoundError()
# Call vasp2trace
os.chdir(folder_name)
process = subprocess.Popen(
["vasp2trace2"], stdout=subprocess.PIPE, stderr=subprocess.PIPE
)
stdout, stderr = process.communicate()
stdout = stdout.decode()
if stderr:
stderr = stderr.decode()
warnings.warn(stderr)
if process.returncode != 0:
raise RuntimeError(
"vasp2trace2 exited with return code {}.".format(process.returncode)
)
self._stdout = stdout
self._stderr = stderr
self.output = None
# Process spin-polarized output
if path.isfile("trace_up.txt") and path.isfile("trace_dn.txt"):
self.output = {}
if path.isfile("trace_up.txt"):
self.output["up"] = Vasp2TraceOutput("trace_up.txt")
if path.isfile("trace_dn.txt"):
self.output["down"] = Vasp2TraceOutput("trace_dn.txt")
else:
raise FileNotFoundError()
[docs]class Vasp2TraceOutput(MSONable):
def __init__(
self,
vasp2trace_output,
num_occ_bands=None,
soc=None,
num_symm_ops=None,
symm_ops=None,
num_max_kvec=None,
kvecs=None,
num_kvec_symm_ops=None,
symm_ops_in_little_cogroup=None,
traces=None,
):
"""
This class processes results from vasp2trace to classify material band topology and give topological invariants.
Refer to http://www.cryst.ehu.es/html/cryst/topological/File_Description.txt for further explanation of parameters.
Args:
vasp2trace_stdout (txt file): stdout from running vasp2trace.
num_occ_bands (int): Number of occupied bands.
soc (int): 0: no spin-orbit, 1: yes spin-orbit
num_symm_ops (int): Number of symmetry operations.
symm_ops (list): Each row is a symmetry operation (with spinor components if soc is enabled)
num_max_kvec (int): Number of maximal k-vectors.
kvecs (list): Each row is a k-vector.
num_kvec_symm_ops (dict): {kvec_index: number of symm operations in the little cogroup of the kvec}.
symm_ops_in_little_cogroup (dict): {kvec_index: int indices that correspond to symm_ops}
traces (dict): band index, band degeneracy, energy eigenval, Re eigenval, Im eigenval for each symm op in the little cogroup
"""
self._vasp2trace_output = vasp2trace_output
self.num_occ_bands = num_occ_bands
self.soc = soc
self.num_symm_ops = num_symm_ops
self.symm_ops = symm_ops
self.num_max_kvec = num_max_kvec
self.kvecs = kvecs
self.num_kvec_symm_ops = num_kvec_symm_ops
self.symm_ops_in_little_cogroup = symm_ops_in_little_cogroup
self.traces = traces
self._parse_stdout(vasp2trace_output)
def _parse_stdout(self, vasp2trace_output):
try:
with open(vasp2trace_output, "r") as file:
lines = file.readlines()
# Get header info
num_occ_bands = int(lines[0])
soc = int(lines[1]) # No: 0, Yes: 1
num_symm_ops = int(lines[2])
symm_ops = np.ndarray.tolist(np.loadtxt(lines[3 : 3 + num_symm_ops]))
num_max_kvec = int(lines[3 + num_symm_ops])
kvecs = np.ndarray.tolist(
np.loadtxt(
lines[4 + num_symm_ops : 4 + num_symm_ops + num_max_kvec]
)
)
# Dicts with kvec index as keys
num_kvec_symm_ops = {}
symm_ops_in_little_cogroup = {}
traces = {}
# Start of trace info
trace_start = 5 + num_max_kvec + num_symm_ops
start_block = 0 # Start of this block
# Block start line #s
block_starts = []
for jdx, line in enumerate(lines[trace_start - 1 :], trace_start - 1):
# Parse input lines
line = [i for i in line.split(" ") if i]
if len(line) == 1: # A single entry <-> new block
block_starts.append(jdx)
# Loop over blocks of kvec data
for idx, kpt in enumerate(kvecs):
start_block = block_starts[idx]
if idx < num_max_kvec - 1:
next_block = block_starts[idx + 1]
trace_str = lines[start_block + 2 : next_block]
else:
trace_str = lines[start_block + 2 :]
# Populate dicts
num_kvec_symm_ops[str(idx)] = int(lines[start_block])
soilcg = [
int(i.strip("\n"))
for i in lines[start_block + 1].split(" ")
if i.strip("\n")
]
symm_ops_in_little_cogroup[str(idx)] = soilcg
trace = np.ndarray.tolist(np.loadtxt(trace_str))
traces[str(idx)] = trace
self.num_occ_bands = num_occ_bands
self.soc = soc
self.num_symm_ops = num_symm_ops
self.symm_ops = symm_ops
self.num_max_kvec = num_max_kvec
self.kvecs = kvecs
self.num_kvec_symm_ops = num_kvec_symm_ops
self.symm_ops_in_little_cogroup = symm_ops_in_little_cogroup
self.traces = traces
except Exception as error:
print(error)
warnings.warn(
"Vasp2trace output not found. Setting instance attributes from direct inputs!"
)
