def featurize(self, comp):
"""
Args:
comp: (Composition)
pymatgen Composition object
Returns:
HOMO_character: (str) orbital symbol ('s', 'p', 'd', or 'f')
HOMO_element: (str) symbol of element for H**O
HOMO_energy: (float in eV) absolute energy of H**O
LUMO_character: (str) orbital symbol ('s', 'p', 'd', or 'f')
LUMO_element: (str) symbol of element for LUMO
LUMO_energy: (float in eV) absolute energy of LUMO
gap_AO: (float in eV)
the estimated bandgap from H**O and LUMO energeis
"""
integer_comp, factor = comp.get_integer_formula_and_factor()
# warning message if composition is dilute and truncated
if not (len(Composition(comp).elements) == len(
Composition(integer_comp).elements)):
warn('AtomicOrbitals: {} truncated to {}'.format(
comp, integer_comp))
homo_lumo = MolecularOrbitals(integer_comp).band_edges
feat = collections.OrderedDict()
for edge in ['H**O', 'LUMO']:
if homo_lumo[edge] is not None:
feat['{}_character'.format(edge)] = homo_lumo[edge][1][-1]
feat['{}_element'.format(edge)] = homo_lumo[edge][0]
feat['{}_energy'.format(edge)] = homo_lumo[edge][2]
else:
#if LUMO is None
feat['{}_character'.format(edge)] = 'na'
feat['{}_element'.format(edge)] = 'na'
#unclear what this value should be. Arbitrarily set to 0. Don't want NaN for modeling
feat['{}_energy'.format(edge)] = 0
feat['gap_AO'] = feat['LUMO_energy'] - feat['HOMO_energy']
return list(feat.values())
def featurize(self, comp):
"""
Args:
comp: (Composition)
pymatgen Composition object
Returns:
HOMO_character: (str) orbital symbol ('s', 'p', 'd', or 'f')
HOMO_element: (str) symbol of element for H**O
HOMO_energy: (float in eV) absolute energy of H**O
LUMO_character: (str) orbital symbol ('s', 'p', 'd', or 'f')
LUMO_element: (str) symbol of element for LUMO
LUMO_energy: (float in eV) absolute energy of LUMO
gap_AO: (float in eV)
the estimated bandgap from H**O and LUMO energeis
"""
# NOTE comprhys: factor is unused
# integer_comp, factor = comp.get_integer_formula_and_factor()
integer_comp, _ = comp.get_integer_formula_and_factor()
# warning message if composition is dilute and truncated
if not (len(Composition(comp).elements) == len(
Composition(integer_comp).elements)):
warn(f"AtomicOrbitals: {comp} truncated to {integer_comp}")
homo_lumo = MolecularOrbitals(integer_comp).band_edges
feat = collections.OrderedDict()
for edge in ['H**O', 'LUMO']:
feat[f"{edge}_character"] = homo_lumo[edge][1][-1]
feat[f"{edge}_element"] = homo_lumo[edge][0]
feat[f"{edge}_energy"] = homo_lumo[edge][2]
feat['gap_AO'] = feat['LUMO_energy'] - feat['HOMO_energy']
return list(feat.values())
def test_fractional_compositions(self):
self.assertRaises(ValueError, lambda: MolecularOrbitals('Na0.5Cl0.5'))
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.molecular_orbitals import MolecularOrbitals
test_case = MolecularOrbitals('NaCl')
class MolecularOrbitalTestCase(PymatgenTest):
def test_max_electronegativity(self):
test_elec_neg = 2.23
self.assertEqual(test_elec_neg, test_case.max_electronegativity())
def test_aos_as_list(self):
test_list = [['Cl', '1s', -100.369229], ['Na', '1s', -37.719975],
['Cl', '2s', -9.187993], ['Cl', '2p', -7.039982],
['Na', '2s', -2.063401], ['Na', '2p', -1.060636],
['Cl', '3s', -0.754458], ['Cl', '3p', -0.32038],
['Na', '3s', -0.103415]]
self.assertEqual(test_list, test_case.aos_as_list())
def test_obtain_band_edges(self):
test_edges = {'H**O': ['Cl', '3p', -0.32038],
'LUMO': ['Na', '3s', -0.103415],
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.core.molecular_orbitals import MolecularOrbitals
from pymatgen.util.testing import PymatgenTest
test_case = MolecularOrbitals("NaCl")
class MolecularOrbitalTestCase(PymatgenTest):
def test_max_electronegativity(self):
test_elec_neg = 2.23
self.assertEqual(test_elec_neg, test_case.max_electronegativity())
def test_aos_as_list(self):
test_list = [
["Cl", "1s", -100.369229],
["Na", "1s", -37.719975],
["Cl", "2s", -9.187993],
["Cl", "2p", -7.039982],
["Na", "2s", -2.063401],
["Na", "2p", -1.060636],
["Cl", "3s", -0.754458],
["Cl", "3p", -0.32038],
["Na", "3s", -0.103415],
]
self.assertEqual(test_list, test_case.aos_as_list())
def test_obtain_band_edges(self):