Source code for pymatgen.ext.jhu
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module creates an interface to the JHU kpoints servlet,
see http://muellergroup.jhu.edu/K-Points.html.
"""
import requests
import tempfile
import shutil
import os
from pymatgen.io.vasp.inputs import Kpoints
__author__ = "Joseph Montoya"
__copyright__ = "Copyright 2017, The Materials Project"
__maintainer__ = "Joseph Montoya"
__email__ = "montoyjh@lbl.gov"
__date__ = "June 22, 2017"
[docs]def get_kpoints(structure, min_distance=0, min_total_kpoints=1,
kppra=None, gap_distance=7, remove_symmetry=None,
include_gamma="auto", header="simple", incar=None):
"""
Get kpoints object from JHU servlet, per Wisesa-McGill-Mueller
methodology. Refer to http://muellergroup.jhu.edu/K-Points.html
and P. Wisesa, K. A. McGill, T. Mueller, Phys. Rev. B 93,
155109 (2016)
Args:
structure (Structure): structure object
min_distance (float): The minimum allowed distance
between lattice points on the real-space superlattice
min_total_kpoints (int): The minimum allowed number of
total k-points in the Brillouin zone.
kppra (float): minimum k-points per reciprocal atom.
gap_distance (float): auto-detection threshold for
non-periodicity (in slabs, nanowires, etc.)
remove_symmetry (string): optional flag to control
symmetry options, can be none, structural,
time_reversal, or all
include_gamma (string or bool): whether to include
gamma point
header (string): "verbose" or "simple", denotes
the verbosity of the header
incar (Incar): incar object to upload
"""
config = locals()
config.pop("structure", "incar")
# Generate PRECALC string
precalc = ''.join(["{}={}\n".format(k, v) for k, v in config.items()])
precalc = precalc.replace('_', '').upper()
precalc = precalc.replace('REMOVESYMMETRY', 'REMOVE_SYMMETRY')
precalc = precalc.replace('TIMEREVERSAL', 'TIME_REVERSAL')
url = "http://muellergroup.jhu.edu:8080/PreCalcServer/PreCalcServlet"
temp_dir_name = tempfile.mkdtemp()
cwd = os.getcwd()
os.chdir(temp_dir_name)
precalc_file = open("PRECALC", 'w+')
poscar_file = open("POSCAR", 'w+')
incar_file = open("INCAR", 'w+')
precalc_file.write(precalc)
poscar_file.write(structure.to("POSCAR"))
files = [("fileupload", precalc_file),
("fileupload", poscar_file)]
if incar:
incar_file.write(incar.get_string())
files.append(("fileupload", incar_file))
precalc_file.seek(0)
poscar_file.seek(0)
incar_file.seek(0)
r = requests.post(url, files=files)
precalc_file.close()
poscar_file.close()
incar_file.close()
kpoints = Kpoints.from_string(r.text)
os.chdir(cwd)
shutil.rmtree(temp_dir_name)
return kpoints