pymatgen.command_line.aconvasp_caller — pymatgen 2020.7.3 documentation

# Source code for pymatgen.command_line.aconvasp_caller

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    Interface with command line aconvasp. http://aflowlib.org/
    Only tested on Linux. Inspired by Shyue"s qhull_caller
    WARNING: you need to have a convasp in your path for this to work
    """

    __author__ = "Geoffroy Hautier"
    __copyright__ = "Copyright 2011, The Materials Project"
    __version__ = "1.0"
    __maintainer__ = "Geoffroy Hautier"
    __email__ = "geoffroy.hautier@uclouvain.be"
    __status__ = "Production"
    __date__ = "$Nov 22, 2011M$"

    import subprocess

    from pymatgen.io.vasp.inputs import Poscar

    def run_aconvasp_command(command, structure):
        """
        Helper function for calling aconvasp with different arguments
        """
        poscar = Poscar(structure)
        p = subprocess.Popen(command, stdout=subprocess.PIPE,
                             stdin=subprocess.PIPE,
                             stderr=subprocess.PIPE)
        output = p.communicate(input=poscar.get_string())
        return output

    def get_num_division_kpoints(structure, kppa):
        """
        Get kpoint divisions for a given k-point density (per reciprocal-atom):
        kppa and a given structure
        """
        output = run_aconvasp_command(["aconvasp", "--kpoints", str(kppa)],
                                      structure)
        tmp = output[0].rsplit("\n")[6].rsplit(" ")
        return [int(tmp[5]), int(tmp[6]), int(tmp[7])]

    def get_minkowski_red(structure):
        """
        Get a minkowski reduced structure
        """
        output = run_aconvasp_command(["aconvasp", "--kpath"], structure)
        started = False
        poscar_string = ""
        if "ERROR" in output[1]:
            raise AconvaspError(output[1])
        for line in output[0].split("\n"):
            if started or line.find("KPOINTS TO RUN") != -1:
                poscar_string = poscar_string + line + "\n"
            if line.find("STRUCTURE TO RUN") != -1:
                started = True
            if line.find("KPOINTS TO RUN") != -1:
                started = False
        return Poscar.from_string(poscar_string).structure

    def get_conv_struct(structure):
        """
        Get a minkowski reduced structure
        """
        output = run_aconvasp_command(["aconvasp", "--std_conv"], structure)
        if "ERROR" in output[1]:
            raise AconvaspError(output[1])
        tmp = Poscar.from_string(output[0])
        return {'struct': tmp.structure, 'comm': tmp.comment}

    def get_prim_struct(structure):
        """
        Get standard primitive
        """
        output = run_aconvasp_command(["aconvasp", "--std_prim"], structure)
        if "ERROR" in output[1]:
            raise AconvaspError(output[1])
        tmp = Poscar.from_string(output[0])
        return {'struct': tmp.structure, 'comm': tmp.comment}

    def get_vasp_kpoint_file_sym(structure):
        """
        get a kpoint file ready to be ran in VASP along the symmetry lines of the
        Brillouin Zone
        """
        output = run_aconvasp_command(["aconvasp", "--kpath"], structure)
        if "ERROR" in output[1]:
            raise AconvaspError(output[1])
        started = False
        kpoints_string = ""
        for line in output[0].split("\n"):
            # print line
            if started or line.find("END") != -1:
                kpoints_string = kpoints_string + line + "\n"
            if line.find("KPOINTS TO RUN") != -1:
                started = True
            if line.find("END") != -1:
                started = False
        return kpoints_string

    class AconvaspError(Exception):
        """
        Exception class for aconvasp.
        Raised when the aconvasp gives an error
        """

        def __init__(self, msg):
            """
            Args:
                msg (str): Error message
            """
            self.msg = msg

        def __str__(self):
            return "AconvaspError : " + self.msg