pymatgen — pymatgen 2020.7.3 documentation

# Source code for pymatgen

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

    """
    Pymatgen (Python Materials Genomics) is a robust, open-source Python library
    for materials analysis. This is the root package.
    """

    # Useful aliases for commonly used objects and modules.
    # Allows from pymatgen import <class> for quick usage.
    import os
    import warnings
    import ruamel.yaml as yaml
    from fnmatch import fnmatch

    __author__ = "Pymatgen Development Team"
    __email__ = "pymatgen@googlegroups.com"
    __maintainer__ = "Shyue Ping Ong"
    __maintainer_email__ = "shyuep@gmail.com"
    __version__ = "2020.7.3"

    SETTINGS_FILE = os.path.join(os.path.expanduser("~"), ".pmgrc.yaml")

    def _load_pmg_settings():
        try:
            with open(SETTINGS_FILE, "rt") as f:
                d = yaml.safe_load(f)
        except IOError:
            # If there are any errors, default to using environment variables
            # if present.
            d = {}
            for k, v in os.environ.items():
                if k.startswith("PMG_"):
                    d[k] = v
                elif k in ["VASP_PSP_DIR", "MAPI_KEY", "DEFAULT_FUNCTIONAL"]:
                    d["PMG_" + k] = v
        d = d or {}
        return dict(d)

    SETTINGS = _load_pmg_settings()

    from .core.periodic_table import Element, Specie, DummySpecie
    from .core.composition import Composition
    from .core.structure import Structure, IStructure, Molecule, IMolecule
    from .core.lattice import Lattice
    from .core.sites import Site, PeriodicSite
    from .core.operations import SymmOp
    from .core.units import Unit, FloatWithUnit, ArrayWithUnit
    from .electronic_structure.core import Spin, Orbital
    from .ext.matproj import MPRester
    from monty.json import MontyEncoder, MontyDecoder, MSONable

    def get_structure_from_mp(formula):
        """
        Convenience method to get a crystal from the Materials Project database via
        the API. Requires PMG_MAPI_KEY to be set.

        Args:
            formula (str): A formula

        Returns:
            (Structure) The lowest energy structure in Materials Project with that
                formula.
        """
        m = MPRester()
        entries = m.get_entries(formula, inc_structure="final")
        if len(entries) == 0:
            raise ValueError("No structure with formula %s in Materials Project!" %
                             formula)
        elif len(entries) > 1:
            warnings.warn("%d structures with formula %s found in Materials "
                          "Project. The lowest energy structure will be returned." %
                          (len(entries), formula))
        return min(entries, key=lambda e: e.energy_per_atom).structure

    def loadfn(fname):
        """
        Convenience method to perform quick loading of data from a filename. The
        type of object returned depends the file type.

        Args:
            fname (string): A filename.

        Returns:
            Note that fname is matched using unix-style, i.e., fnmatch.
            (Structure) if *POSCAR*/*CONTCAR*/*.cif
            (Vasprun) *vasprun*
            (obj) if *json* (passthrough to monty.serialization.loadfn)
        """
        if (fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or
                ".cif" in fname.lower()) or fnmatch(fname, "*.vasp"):
            return Structure.from_file(fname)
        elif fnmatch(fname, "*vasprun*"):
            from pymatgen.io.vasp import Vasprun
            return Vasprun(fname)
        elif fnmatch(fname, "*.json*"):
            from monty.serialization import loadfn
            return loadfn(fname)