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)