def test_make_cpd_and_vertices(mocker, tmpdir):
tmpdir.chdir()
mock = mocker.patch("pydefect.cli.main_functions.RelativeEnergies")
mock.from_yaml.return_value = RelativeEnergies({"HHe": -1.0})
args = Namespace(rel_energy_yaml="a.yaml", target="HHe", elements=None)
make_cpd_and_vertices(args)
actual = Path("target_vertices.yaml").read_text()
expected = """target: HHe
A:
chem_pot:
H: 0.0
He: -2.0
competing_phases:
- H
impurity_phases: []
B:
chem_pot:
H: -2.0
He: 0.0
competing_phases:
- He
impurity_phases: []
"""
assert actual == expected
def test_std_rel_energies(composition_energies):
actual = composition_energies.std_rel_energies
expected_ref = StandardEnergies({"H": 0.0, "O": 1.0, "Cl": 12.0})
expected_rel = RelativeEnergies({
'ClO': -5.0,
'ClO2': -3.666666666666667,
'H2O': -1.0
})
assert actual[0] == expected_ref
assert actual[1] == expected_rel
def make_cpd_and_vertices(args):
rel_energies = RelativeEnergies.from_yaml(args.rel_energy_yaml)
if args.target:
elements = args.elements or \
Composition(args.target).chemical_system.split("-")
else:
elements = args.elements or list(rel_energies.all_element_set)
cpd_maker = ChemPotDiagMaker(rel_energies, elements, args.target)
cpd = cpd_maker.chem_pot_diag
cpd.to_json_file()
cpd.to_target_vertices.to_yaml_file()
def relative_energies():
return RelativeEnergies({"MgO2": -3.0, "MgAlO2": -1.0})
def cpd_maker():
return ChemPotDiagMaker(RelativeEnergies({
"MgO2": -3.0,
"MgAlO2": -2.5
}),
elements=["Mg", "O"])
import crystal_toolkit.components as ctc
import dash_html_components as html
from crystal_toolkit.settings import SETTINGS
from jupyter_dash import JupyterDash
from pydefect.analyzer.dash_components.cpd_energy_dash import CpdEnergyComponent
from pydefect.analyzer.defect_energy import DefectEnergySummary, DefectEnergies, \
DefectEnergy
from pydefect.chem_pot_diag.chem_pot_diag import RelativeEnergies, \
ChemPotDiagMaker
if __name__ == "__main__":
app = JupyterDash(suppress_callback_exceptions=True,
assets_folder=SETTINGS.ASSETS_PATH)
# relative_energies = RelativeEnergies({"MgCaO2": -100.0})
relative_energies = RelativeEnergies({"MgCaBaO2": -100.0})
# cpd = ChemPotDiagMaker(relative_energies,
# elements=["Mg", "Ca", "O"],
# target="MgCaO2").chem_pot_diag
cpd = ChemPotDiagMaker(relative_energies,
elements=["Mg", "Ca", "Ba", "O"],
target="MgCaBaO2").chem_pot_diag
energy = DefectEnergy(0.0, {"corr": 1.0}, is_shallow=False)
defect_energy_summary = DefectEnergySummary(
title="test",
defect_energies={
"Va_O1":
DefectEnergies(atom_io={"O": -1},
charges=[0],
defect_energies=[energy])