Source code for pymatgen

import sys
import os
import warnings
import ruamel.yaml as yaml
from fnmatch import fnmatch

__author__ = "Pymatgen Development Team"
__email__ =""
__maintainer__ = "Shyue Ping Ong"
__maintainer_email__ =""
__version__ = "2019.8.14"

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

def _load_pmg_settings():
        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
    return dict(d)

SETTINGS = _load_pmg_settings()

# Order of imports is important on some systems to avoid
# failures when loading shared libraries.
# import spglib
# from . import optimization, util
# del(spglib, optimization, util)

# Useful aliases for commonly used objects and modules.
# Allows from pymatgen import <class> for quick usage.

from pymatgen.core import *
from .electronic_structure.core import Spin, Orbital
from .ext.matproj import MPRester
from monty.json import MontyEncoder, MontyDecoder, MSONable

[docs]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
if sys.version_info < (3, 5): warnings.warn(""" Pymatgen will drop Py2k support from v2019.1.1. Pls consult the documentation at for more details.""")
[docs]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 import Vasprun return Vasprun(fname) elif fnmatch(fname, "*.json*"): from monty.serialization import loadfn return loadfn(fname)