pymatgen.entries — pymatgen 2020.7.3 documentation

# Source code for pymatgen.entries

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

    """
    Entries are containers for calculated information, which is used in
    many analyses. This module contains entry related tools and implements
    the base Entry class, which is the basic entity that can be used to
    store calculated information. Other Entry classes such as ComputedEntry
    and PDEntry inherit from this class.
    """

    from pymatgen.core.composition import Composition
    from monty.json import MSONable
    from abc import ABCMeta, abstractmethod

    __author__ = "Shyue Ping Ong, Anubhav Jain, Ayush Gupta"
    __copyright__ = "Copyright 2020, The Materials Project"
    __version__ = "1.1"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "shyuep@gmail.com"
    __status__ = "Production"
    __date__ = "Mar 03, 2020"

    class Entry(MSONable, metaclass=ABCMeta):
        """
        A lightweight object containing the energy associated with
        a specific chemical composition. This base class is not
        intended to be instantiated directly. Note that classes
        which inherit from Entry must define a .energy property.

        """

        def __init__(self,
                     composition: Composition,
                     energy: float):
            """
            Initializes an Entry.

            Args:
                composition (Composition): Composition of the entry. For
                    flexibility, this can take the form of all the typical input
                    taken by a Composition, including a {symbol: amt} dict,
                    a string formula, and others.
                energy (float): Energy of the entry.
            """
            self._energy = energy
            self.composition = Composition(composition)

        @property
        def is_element(self) -> bool:
            """
            :return: Whether composition of entry is an element.
            """
            return self.composition.is_element

        @property
        @abstractmethod
        def energy(self) -> float:
            """
            :return: the energy of the entry.
            """

        @property
        def energy_per_atom(self) -> float:
            """
            :return: the energy per atom of the entry.
            """
            return self.energy / self.composition.num_atoms

        def __str__(self):
            return self.__repr__()

        def normalize(self, mode: str = "formula_unit") -> None:
            """
            Normalize the entry's composition and energy.

            Args:
                mode: "formula_unit" is the default, which normalizes to
                    composition.reduced_formula. The other option is "atom", which
                    normalizes such that the composition amounts sum to 1.
            """
            factor = self._normalization_factor(mode)
            self.composition /= factor
            self._energy /= factor

        def _normalization_factor(self, mode: str = "formula_unit") -> float:
            if mode == "atom":
                factor = self.composition.num_atoms
            else:
                comp, factor = self.composition.get_reduced_composition_and_factor()
            return factor

        def as_dict(self) -> dict:
            """
            :return: MSONable dict.
            """
            return {"@module": self.__class__.__module__,
                    "@class": self.__class__.__name__,
                    "energy": self._energy,
                    "composition": self.composition.as_dict()}