def cpd():
return ChemPotDiag([
CompositionEnergy(Composition('O8'), -39.58364375, "mp-1"),
CompositionEnergy(Composition('Mg3'), -4.79068775, "mp-2"),
CompositionEnergy(Composition('Mg1O1'), -11.96742144, "mp-3")
],
target=Composition("MgO"))
def cpd_plot_info_2d():
energies = [
CompositionEnergy(Composition("H"), 0.0, ""),
CompositionEnergy(Composition("O"), 1.0, ""),
CompositionEnergy(Composition("H4O2"), -4.0, "")
]
cpd = ChemPotDiag(energies, target=Composition("H2O"))
return CpdPlotInfo(cpd, min_range=-10)
def comp_energies():
return CompositionEnergies({
Composition('O8'):
CompositionEnergy(-39.58364375, "mp-1"),
Composition('Mg3'):
CompositionEnergy(-4.79068775, "mp-2"),
Composition('Mg1O1'):
CompositionEnergy(-11.96742144, "mp-3")
})
def comp_energies_corr():
return CompositionEnergies({
Composition('O8'):
CompositionEnergy(-39.58364375 + diff["O"] * 8, "mp-1"),
Composition('Mg3'):
CompositionEnergy(-4.79068775 + diff["Mg"] * 3, "mp-2"),
Composition('Mg1O1'):
CompositionEnergy(-11.96742144 + diff["Mg"] + diff["O"], "mp-3")
})
def cpd_corr():
return ChemPotDiag([
CompositionEnergy(Composition('O8'), -39.58364375 + diff["O"] * 8,
"mp-1"),
CompositionEnergy(Composition('Mg3'), -4.79068775 + diff["Mg"] * 3,
"mp-2"),
CompositionEnergy(Composition('Mg1O1'),
-11.96742144 + diff["Mg"] + diff["O"], "mp-3")
],
target=Composition("MgO"))
def cpd2():
energies_here = [
CompositionEnergy(Composition("H"), 0.0, "a"),
CompositionEnergy(Composition("H4O2"), -4.0, "c"),
CompositionEnergy(Composition("O"), 1.0, "b"),
CompositionEnergy(Composition("Cl2"), 3.0, "e"),
]
return ChemPotDiag(energies_here,
target=Composition("H2O"),
vertex_elements=[Element.H, Element.O])
def test_remove_higher_energy_comp():
comp_es = CompositionEnergies(
{Composition('Mg1'): CompositionEnergy(-1.9, "mp-2"),
Composition('Mg2'): CompositionEnergy(-4.0, "mp-3"),
Composition('O2'): CompositionEnergy(-4.0, "mp-4")})
actual = remove_higher_energy_comp(comp_es)
expected = CompositionEnergies(
{Composition('Mg2'): CompositionEnergy(-4.0, "mp-3"),
Composition('O2'): CompositionEnergy(-4.0, "mp-4"),})
assert actual == expected
def test_remove_higher_energy_comp():
comp_es = [
CompositionEnergy(Composition('O2'), -2.1, "mp-1"),
CompositionEnergy(Composition('O4'), -4.0, "mp-2"),
CompositionEnergy(Composition('Mg1'), -10, "mp-3")
]
actual = remove_higher_energy_comp(comp_es)
expected = [
CompositionEnergy(Composition('O2'), -2.1, "mp-1"),
CompositionEnergy(Composition('Mg1'), -10, "mp-3")
]
assert actual == expected
def make_chem_pot_diag_from_mp(target: Union[Composition, str],
additional_elements: List[str] = None,
vertex_elements: List[str] = None,
atom_energy_yaml: Optional[str] = None):
"""Obtain the energies from Materials Project."""
properties = ["task_id", "full_formula", "final_energy"]
target = target if isinstance(target, Composition) else Composition(target)
elements = target.chemical_system.split("-")
vertex_elements = vertex_elements or elements
vertex_elements = [Element(e) for e in vertex_elements]
if additional_elements:
elements.extend(additional_elements)
query = MpQuery(elements, properties=properties)
comp_es = []
if atom_energy_yaml:
if ".yaml" in atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
else:
logger.info(f"Atom energy set for {atom_energy_yaml} is used.")
energies = AtomEnergyType.from_string(atom_energy_yaml).energies
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = None
for m in query.materials:
energy = m["final_energy"]
if diff:
for k, v in Composition(m["full_formula"]).as_dict().items():
energy += diff[k] * v
comp_es.append(
CompositionEnergy(Composition(m["full_formula"]), energy,
m["task_id"]))
comp_es = remove_higher_energy_comp(comp_es)
return ChemPotDiag(comp_es, target, vertex_elements)
def make_composition_energies_from_mp(
elements: List[str],
atom_energy_yaml: Optional[str] = None,
) -> CompositionEnergies:
"""Obtain the energies from Materials Project.
When the atom_energy_yaml is provided, the total energies are aligned
via atom energies.
"""
properties = ["task_id", "full_formula", "final_energy"]
query = MpQuery(elements, properties=properties)
comp_es = {}
if atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = {e: 0.0 for e in elements}
for m in query.materials:
key = Composition(m["full_formula"])
energy = m["final_energy"]
for k, v in key.as_dict().items():
energy += diff[k] * v
comp_es[key] = CompositionEnergy(energy, m["task_id"])
print(comp_es)
comp_es = remove_higher_energy_comp(comp_es)
print(comp_es)
return CompositionEnergies(comp_es)
def make_composition_energies(args):
if args.yaml_file:
composition_energies = CompositionEnergies.from_yaml(args.yaml_file)
else:
composition_energies = CompositionEnergies()
for d in args.dirs:
vasprun = Vasprun(d / defaults.vasprun)
composition = vasprun.final_structure.composition
energy = float(vasprun.final_energy) # original type is FloatWithUnit
composition_energies[composition] = CompositionEnergy(energy, "local")
composition_energies.to_yaml_file()
def make_composition_energies(args):
if args.yaml_file:
composition_energies = CompositionEnergies.from_yaml(args.yaml_file)
else:
composition_energies = CompositionEnergies()
for d in args.dirs:
outcar = Outcar(d / defaults.outcar)
composition = Structure.from_file(d / defaults.contcar).composition
energy = float(outcar.final_energy) # original type is FloatWithUnit
composition_energies[composition] = CompositionEnergy(energy, "local")
composition_energies.to_yaml_file()
def test_host_ele_abs_energies_per_atom_2():
energies_with_cl = deepcopy(energies)
energies_with_cl.append(CompositionEnergy(Composition("Cl"), 10.0, "z"))
cpd = ChemPotDiag(energies_with_cl,
target=Composition("H2O"),
vertex_elements=[Element.H, Element.O, Element.Cl])
assert cpd.vertex_elements_abs_energies_per_atom == {
Composition("H2"): 0.0,
Composition("O2"): 1.0,
Composition("H2O"): -2 / 3,
Composition("ClO"): 1.5,
Composition("ClO2"): 1.0,
Composition("Cl2"): 10.0
}
def test_composition_energies_from_mp(mocker, tmpdir):
tmpdir.chdir()
args = Namespace(elements=["H"], atom_energy_yaml="a.yaml")
mock = mocker.patch(
"pydefect.cli.main_util_functions.make_composition_energies_from_mp")
mock.return_value = CompositionEnergies(
{Composition("H"): CompositionEnergy(1.0, "mp-1")})
composition_energies_from_mp(args)
mock.assert_called_once_with(elements=["H"], atom_energy_yaml="a.yaml")
actual = Path("composition_energies.yaml").read_text()
expected = """H1:
energy: 1.0
source: mp-1
"""
assert actual == expected
def test_make_standard_and_relative_energies(mocker, tmpdir):
tmpdir.chdir()
args = Namespace(composition_energies_yaml="a.yaml")
mock = mocker.patch("pydefect.cli.main_functions.CompositionEnergies")
mock.from_yaml.return_value = CompositionEnergies({
Composition("H"):
CompositionEnergy(-1.0),
Composition("He"):
CompositionEnergy(-2.0),
Composition("HHe"):
CompositionEnergy(-5.0)
})
make_standard_and_relative_energies(args)
mock.from_yaml.assert_called_once_with("a.yaml")
actual = Path("standard_energies.yaml").read_text()
expected = """H: -1.0
He: -2.0
"""
assert actual == expected
actual = Path("relative_energies.yaml").read_text()
expected = """HHe: -1.0
"""
assert actual == expected
def cpd_3d_info():
energies = [
CompositionEnergy(Composition("H"), 0.0, ""),
CompositionEnergy(Composition("O"), 1.0, ""),
CompositionEnergy(Composition("H4O2"), -4.0, ""),
CompositionEnergy(Composition("MgH2O"), -10.0, ""),
CompositionEnergy(Composition("Mg"), 0.0, ""),
CompositionEnergy(Composition("MgO"), -3.0, "")
]
cpd = ChemPotDiag(energies, target=Composition("MgH2O"))
return CpdPlotInfo(cpd)
def test_replace_comp_energy():
cpd = ChemPotDiag([
CompositionEnergy(Composition("H"), 0.0, "a"),
CompositionEnergy(Composition("O"), 1.0, "b"),
CompositionEnergy(Composition("F"), 1.0, "c")
],
target={"H": 1})
replace_comp_energy(cpd, [
CompositionEnergy(Composition("H"), -1.0, "x"),
CompositionEnergy(Composition("O"), 0.0, "y")
])
expected = ChemPotDiag([
CompositionEnergy(Composition("H"), -1.0, "x"),
CompositionEnergy(Composition("O"), 0.0, "y"),
CompositionEnergy(Composition("F"), 1.0, "c")
],
target={"H": 1})
assert cpd == expected
def make_chem_pot_diag(args) -> None:
if args.elements:
cpd = make_chem_pot_diag_from_mp(additional_elements=args.elements,
target=args.target,
atom_energy_yaml=args.atom_energy_yaml)
else:
comp_es = []
for d in args.dirs:
vasprun = Vasprun(d / defaults.vasprun)
composition = vasprun.final_structure.composition
energy = float(vasprun.final_energy) # type is FloatWithUnit
comp_es.append(CompositionEnergy(composition, energy, "local"))
if args.update:
cpd = ChemPotDiag.from_yaml(args.yaml)
replace_comp_energy(cpd, comp_es)
else:
cpd = ChemPotDiag(comp_es, args.target)
cpd.to_yaml(args.yaml)
def composition_energies():
return CompositionEnergies({
Composition("H"):
CompositionEnergy(0.0, "a"),
Composition("H4O2"):
CompositionEnergy(-4.0, "c"),
Composition("O"):
CompositionEnergy(1.0, "b"),
Composition("Cl"):
CompositionEnergy(12.0, "f"),
Composition("O2Cl"):
CompositionEnergy(3.0, "e"),
Composition("O2Cl2"):
CompositionEnergy(6.0, "d")
})
def make_composition_energies_from_mp(elements: List[str],
atom_energy_yaml: Optional[str] = None,
) -> CompositionEnergies:
"""Obtain the energies from Materials Project.
When the atom_energy_yaml is provided, the total energies are aligned
via atom energies.
"""
entries: List[ComputedEntry] = MpEntries(elements).materials
comp_es = {}
if atom_energy_yaml:
energies = loadfn(atom_energy_yaml)
diff = {e: energies[e] - mp_energies[e] for e in elements}
else:
diff = {e: 0.0 for e in elements}
for e in entries:
key = e.composition
energy = e.energy
for k, v in key.as_dict().items():
energy += diff[k] * v
comp_es[key] = CompositionEnergy(energy, e.entry_id)
comp_es = remove_higher_energy_comp(comp_es)
return CompositionEnergies(comp_es)
# -*- coding: utf-8 -*-
# Copyright (c) 2020. Distributed under the terms of the MIT License.
from copy import deepcopy
from pathlib import Path
import numpy as np
import pandas as pd
import pytest
from pydefect.chem_pot_diag.chem_pot_diag import ChemPotDiag, CpdPlotInfo, \
NoElementEnergyError, CompositionEnergy, replace_comp_energy
# When same keys are inserted, only the latter one is accepted.
from pydefect.tests.helpers.assertion import assert_msonable
from pymatgen import Composition, Element
energies = [
CompositionEnergy(Composition("H"), 0.0, "a"),
CompositionEnergy(Composition("H4O2"), -4.0, "c"),
CompositionEnergy(Composition("O"), 1.0, "b"),
CompositionEnergy(Composition("O2Cl"), 3.0, "e"),
CompositionEnergy(Composition("O2Cl2"), 6.0, "d"),
]
@pytest.fixture
def cpd():
return ChemPotDiag(energies,
target=Composition("H2O"),
vertex_elements=[Element.H, Element.O])
def test_print(cpd):
def test_impurity_rel_energy(cpd_h2o):
expected = CompositionEnergy(Composition("Cl2O2"), 6.0, 'd'), -7.0
assert cpd_h2o.impurity_rel_energy(Element.Cl, "A") == expected
def test_cpd_plot_info_lacking_element_data():
new_energies = deepcopy(energies)
new_energies.append(CompositionEnergy(Composition("MgO"), -3.0, "f"))
with pytest.raises(NoElementEnergyError):
ChemPotDiag(new_energies, target={"Mg": 1, "O": 1}).offset_to_abs
def test_impurity_abs_energy(cpd):
expected = CompositionEnergy(Composition("Cl2O2"), 6.0, 'd'), 5.0
assert cpd.impurity_abs_energy(Element.Cl, "A") == expected
from pydefect.analyzer.dash_components.cpd_energy_dash import CpdEnergyComponent
from pydefect.chem_pot_diag.chem_pot_diag import ChemPotDiag, CpdPlotInfo, CompositionEnergy
from pydefect.corrections.manual_correction import ManualCorrection
from pydefect.input_maker.defect_entry import DefectEntry
from pymatgen import Composition, Structure, Lattice, Element
import dash_html_components as html
import crystal_toolkit.components as ctc
from dash.dependencies import Input, Output, State
import json
app = JupyterDash(suppress_callback_exceptions=True,
assets_folder=SETTINGS.ASSETS_PATH)
from vise.analyzer.band_edge_properties import BandEdge
comp_energies = [
CompositionEnergy(Composition("Mg"), 0.0, "a"),
CompositionEnergy(Composition("Ca"), 0.0, "a"),
CompositionEnergy(Composition("Sr"), 0.0, "a"),
CompositionEnergy(Composition("O"), 0.0, "a"),
CompositionEnergy(Composition("H"), 0.0, "a"),
# CompositionEnergy(Composition("MgCaO3"), -100.0, "a"),
CompositionEnergy(Composition("MgCaSrO3"), -100.0, "a"),
]
#cpd = ChemPotDiag(comp_energies, target=Composition("MgCaO3"))
cpd = ChemPotDiag(comp_energies, target=Composition("MgCaSrO3"))
cpd_plot_info = CpdPlotInfo(cpd)
# In[2]:
def test_composition_energies_from_dict():
actual = CompositionEnergies.from_dict({"Mg": -1.0})
expected = CompositionEnergies(
{Composition("Mg"): CompositionEnergy(-1.0)})
assert actual == expected
actual = actual.std_rel_energies
def test_impurity_abs_energy2(cpd2):
expected = CompositionEnergy(Composition("Cl2"), 3.0, 'e'), 1.5
assert cpd2.impurity_abs_energy(Element.Cl, "A") == expected
def test_composition_roundtrip(cpd):
comp_e = CompositionEnergy(Composition("H"), 0.0, "a")
rounded_comp_e = comp_e.__class__.from_dict(comp_e.as_dict())
assert comp_e == rounded_comp_e