pymatgen.ext.jhu — pymatgen 2020.7.3 documentation

# 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"

    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