Source code for pymatgen.entries.computed_entries

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

from __future__ import unicode_literals

import json

from monty.json import MontyEncoder, MontyDecoder

from pymatgen.core.composition import Composition
from monty.json import MSONable

"""
This module implements equivalents of the basic ComputedEntry objects, which
is the basic entity that can be used to perform many analyses. ComputedEntries
contain calculated information, typically from VASP or other electronic
structure codes. For example, ComputedEntries can be used as inputs for phase
diagram analysis.
"""

__author__ = "Shyue Ping Ong, Anubhav Jain"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "1.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__status__ = "Production"
__date__ = "Apr 30, 2012"


[docs]class ComputedEntry(MSONable): """ An lightweight ComputedEntry object containing key computed data for many purposes. Extends a PDEntry so that it can be used for phase diagram generation. The difference between a ComputedEntry and a standard PDEntry is that it includes additional parameters like a correction and run_parameters. """ def __init__(self, composition, energy, correction=0.0, parameters=None, data=None, entry_id=None, attribute=None): """ Initializes a ComputedEntry. 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. Usually the final calculated energy from VASP or other electronic structure codes. correction (float): A correction to be applied to the energy. This is used to modify the energy for certain analyses. Defaults to 0.0. parameters (dict): An optional dict of parameters associated with the entry. Defaults to None. data (dict): An optional dict of any additional data associated with the entry. Defaults to None. entry_id (obj): An optional id to uniquely identify the entry. attribute: Optional attribute of the entry. This can be used to specify that the entry is a newly found compound, or to specify a particular label for the entry, or else ... Used for further analysis and plotting purposes. An attribute can be anything but must be MSONable. """ self.uncorrected_energy = energy self.composition = Composition(composition) self.correction = correction self.parameters = parameters if parameters else {} self.data = data if data else {} self.entry_id = entry_id self.name = self.composition.reduced_formula self.attribute = attribute @property def is_element(self): return self.composition.num_atoms == 1 @property def energy(self): """ Returns the *corrected* energy of the entry. """ return self.uncorrected_energy + self.correction @property def energy_per_atom(self): return self.energy / self.composition.num_atoms def __repr__(self): output = ["ComputedEntry {}".format(self.composition.formula), "Energy = {:.4f}".format(self.uncorrected_energy), "Correction = {:.4f}".format(self.correction), "Parameters:"] for k, v in self.parameters.items(): output.append("{} = {}".format(k, v)) output.append("Data:") for k, v in self.data.items(): output.append("{} = {}".format(k, v)) return "\n".join(output) def __str__(self): return self.__repr__()
[docs] @classmethod def from_dict(cls, d): dec = MontyDecoder() return cls(d["composition"], d["energy"], d["correction"], dec.process_decoded(d.get("parameters", {})), dec.process_decoded(d.get("data", {})), entry_id=d.get("entry_id", None), attribute=d["attribute"] if "attribute" in d else None)
[docs] def as_dict(self): return {"@module": self.__class__.__module__, "@class": self.__class__.__name__, "energy": self.uncorrected_energy, "composition": self.composition.as_dict(), "correction": self.correction, "parameters": json.loads(json.dumps(self.parameters, cls=MontyEncoder)), "data": json.loads(json.dumps(self.data, cls=MontyEncoder)), "entry_id": self.entry_id, "attribute": self.attribute}
[docs]class ComputedStructureEntry(ComputedEntry): """ A heavier version of ComputedEntry which contains a structure as well. The structure is needed for some analyses. """ def __init__(self, structure, energy, correction=0.0, parameters=None, data=None, entry_id=None): """ Initializes a ComputedStructureEntry. Args: structure (Structure): The actual structure of an entry. energy (float): Energy of the entry. Usually the final calculated energy from VASP or other electronic structure codes. correction (float): A correction to be applied to the energy. This is used to modify the energy for certain analyses. Defaults to 0.0. parameters (dict): An optional dict of parameters associated with the entry. Defaults to None. data (dict): An optional dict of any additional data associated with the entry. Defaults to None. entry_id (obj): An optional id to uniquely identify the entry. """ super(ComputedStructureEntry, self).__init__( structure.composition, energy, correction=correction, parameters=parameters, data=data, entry_id=entry_id) self.structure = structure def __repr__(self): output = ["ComputedStructureEntry {}".format(self.composition.formula), "Energy = {:.4f}".format(self.uncorrected_energy), "Correction = {:.4f}".format(self.correction), "Parameters:"] for k, v in self.parameters.items(): output.append("{} = {}".format(k, v)) output.append("Data:") for k, v in self.data.items(): output.append("{} = {}".format(k, v)) return "\n".join(output) def __str__(self): return self.__repr__()
[docs] def as_dict(self): d = super(ComputedStructureEntry, self).as_dict() d["@module"] = self.__class__.__module__ d["@class"] = self.__class__.__name__ d["structure"] = self.structure.as_dict() return d
[docs] @classmethod def from_dict(cls, d): dec = MontyDecoder() return cls(dec.process_decoded(d["structure"]), d["energy"], d["correction"], dec.process_decoded(d.get("parameters", {})), dec.process_decoded(d.get("data", {})), entry_id=d.get("entry_id", None))