def setUp(self):
# without spin polarization:
are_coops = False
is_spin_polarized = False
list_atom2 = ['K2', 'K2', 'K2', 'K2', 'K2', 'K2']
list_icohp = [{Spin.up: -0.40075}, {Spin.up: -0.40074}, {Spin.up: -0.40079}, {Spin.up: -0.40079},
{Spin.up: -0.40074}, {Spin.up: -0.40075}]
list_icoop = [{Spin.up: 0.02342}, {Spin.up: 0.02342}, {Spin.up: 0.02343}, {Spin.up: 0.02343},
{Spin.up: 0.02342}, {Spin.up: 0.02342}]
list_labels = ['1', '2', '3', '4', '5', '6']
list_length = [2.71199, 2.71199, 2.71199, 2.71199, 2.71199, 2.71199]
list_num = [1, 1, 1, 1, 1, 1]
list_atom1 = ['F1', 'F1', 'F1', 'F1', 'F1', 'F1']
list_translation = [[0, -1, -1], [-1, 0, -1], [0, 0, -1], [-1, -1, 0], [0, -1, 0], [-1, 0, 0]]
self.icohpcollection_KF = IcohpCollection(is_spin_polarized=is_spin_polarized, are_coops=are_coops,
list_labels=list_labels, list_atom1=list_atom1, list_atom2=list_atom2,
list_length=list_length, list_translation=list_translation,
list_num=list_num, list_icohp=list_icohp)
self.icoopcollection_KF = IcohpCollection(is_spin_polarized=is_spin_polarized, are_coops=True,
list_labels=list_labels, list_atom1=list_atom1, list_atom2=list_atom2,
list_length=list_length, list_translation=list_translation,
list_num=list_num, list_icohp=list_icoop)
# with spin polarization:
list_atom2_sp = ['Fe7', 'Fe9']
list_labels_sp = ['1', '2']
list_translation_sp = [[0, 0, 0], [0, 0, 0]]
list_length_sp = [2.83189, 2.45249]
list_atom1_sp = ['Fe8', 'Fe8']
is_spin_polarized_sp = True
are_coops_sp = False
list_num_sp = [2, 1]
list_icohp_sp = [{Spin.up: -0.10218, Spin.down: -0.19701}, {Spin.up: -0.28485, Spin.down: -0.58279}]
list_icoop_sp = [{Spin.up: -0.11389, Spin.down: -0.20828}, {Spin.up: -0.04087, Spin.down: -0.05756}]
self.icohpcollection_Fe = IcohpCollection(is_spin_polarized=is_spin_polarized_sp, are_coops=are_coops_sp,
list_labels=list_labels_sp, list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp, list_length=list_length_sp,
list_translation=list_translation_sp, list_num=list_num_sp,
list_icohp=list_icohp_sp)
self.icoopcollection_Fe = IcohpCollection(is_spin_polarized=is_spin_polarized_sp, are_coops=True,
list_labels=list_labels_sp, list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp, list_length=list_length_sp,
list_translation=list_translation_sp, list_num=list_num_sp,
list_icohp=list_icoop_sp)
def setUp(self):
# without spin polarization:
are_coops = False
is_spin_polarized = False
list_atom2 = ['K2', 'K2', 'K2', 'K2', 'K2', 'K2']
list_icohp = [{Spin.up: -0.40075}, {Spin.up: -0.40074}, {Spin.up: -0.40079}, {Spin.up: -0.40079},
{Spin.up: -0.40074}, {Spin.up: -0.40075}]
list_icoop = [{Spin.up: 0.02342}, {Spin.up: 0.02342}, {Spin.up: 0.02343}, {Spin.up: 0.02343},
{Spin.up: 0.02342}, {Spin.up: 0.02342}]
list_labels = ['1', '2', '3', '4', '5', '6']
list_length = [2.71199, 2.71199, 2.71199, 2.71199, 2.71199, 2.71199]
list_num = [1, 1, 1, 1, 1, 1]
list_atom1 = ['F1', 'F1', 'F1', 'F1', 'F1', 'F1']
list_translation = [[0, -1, -1], [-1, 0, -1], [0, 0, -1], [-1, -1, 0], [0, -1, 0], [-1, 0, 0]]
self.icohpcollection_KF = IcohpCollection(is_spin_polarized=is_spin_polarized, are_coops=are_coops,
list_labels=list_labels, list_atom1=list_atom1, list_atom2=list_atom2,
list_length=list_length, list_translation=list_translation,
list_num=list_num, list_icohp=list_icohp)
self.icoopcollection_KF = IcohpCollection(is_spin_polarized=is_spin_polarized, are_coops=True,
list_labels=list_labels, list_atom1=list_atom1, list_atom2=list_atom2,
list_length=list_length, list_translation=list_translation,
list_num=list_num, list_icohp=list_icoop)
# with spin polarization:
list_atom2_sp = ['Fe7', 'Fe9']
list_labels_sp = ['1', '2']
list_translation_sp = [[0, 0, 0], [0, 0, 0]]
list_length_sp = [2.83189, 2.45249]
list_atom1_sp = ['Fe8', 'Fe8']
is_spin_polarized_sp = True
are_coops_sp = False
list_num_sp = [2, 1]
list_icohp_sp = [{Spin.up: -0.10218, Spin.down: -0.19701}, {Spin.up: -0.28485, Spin.down: -0.58279}]
list_icoop_sp = [{Spin.up: -0.11389, Spin.down: -0.20828}, {Spin.up: -0.04087, Spin.down: -0.05756}]
self.icohpcollection_Fe = IcohpCollection(is_spin_polarized=is_spin_polarized_sp, are_coops=are_coops_sp,
list_labels=list_labels_sp, list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp, list_length=list_length_sp,
list_translation=list_translation_sp, list_num=list_num_sp,
list_icohp=list_icohp_sp)
self.icoopcollection_Fe = IcohpCollection(is_spin_polarized=is_spin_polarized_sp, are_coops=True,
list_labels=list_labels_sp, list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp, list_length=list_length_sp,
list_translation=list_translation_sp, list_num=list_num_sp,
list_icohp=list_icoop_sp)
def setUp(self):
# without spin polarization:
are_coops = False
is_spin_polarized = False
list_atom2 = ["K2", "K2", "K2", "K2", "K2", "K2"]
list_icohp = [
{Spin.up: -0.40075},
{Spin.up: -0.40074},
{Spin.up: -0.40079},
{Spin.up: -0.40079},
{Spin.up: -0.40074},
{Spin.up: -0.40075},
]
list_icoop = [
{Spin.up: 0.02342},
{Spin.up: 0.02342},
{Spin.up: 0.02343},
{Spin.up: 0.02343},
{Spin.up: 0.02342},
{Spin.up: 0.02342},
]
list_labels = ["1", "2", "3", "4", "5", "6"]
list_length = [2.71199, 2.71199, 2.71199, 2.71199, 2.71199, 2.71199]
list_num = [1, 1, 1, 1, 1, 1]
list_atom1 = ["F1", "F1", "F1", "F1", "F1", "F1"]
list_translation = [
[0, -1, -1],
[-1, 0, -1],
[0, 0, -1],
[-1, -1, 0],
[0, -1, 0],
[-1, 0, 0],
]
self.icohpcollection_KF = IcohpCollection(
is_spin_polarized=is_spin_polarized,
are_coops=are_coops,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icohp,
)
self.icoopcollection_KF = IcohpCollection(
is_spin_polarized=is_spin_polarized,
are_coops=True,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icoop,
)
# with spin polarization:
list_atom2_sp = ["Fe7", "Fe9"]
list_labels_sp = ["1", "2"]
list_translation_sp = [[0, 0, 0], [0, 0, 0]]
list_length_sp = [2.83189, 2.45249]
list_atom1_sp = ["Fe8", "Fe8"]
is_spin_polarized_sp = True
are_coops_sp = False
list_num_sp = [2, 1]
list_icohp_sp = [
{Spin.up: -0.10218, Spin.down: -0.19701},
{Spin.up: -0.28485, Spin.down: -0.58279},
]
list_icoop_sp = [
{Spin.up: -0.11389, Spin.down: -0.20828},
{Spin.up: -0.04087, Spin.down: -0.05756},
]
self.icohpcollection_Fe = IcohpCollection(
is_spin_polarized=is_spin_polarized_sp,
are_coops=are_coops_sp,
list_labels=list_labels_sp,
list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp,
list_length=list_length_sp,
list_translation=list_translation_sp,
list_num=list_num_sp,
list_icohp=list_icohp_sp,
)
self.icoopcollection_Fe = IcohpCollection(
is_spin_polarized=is_spin_polarized_sp,
are_coops=True,
list_labels=list_labels_sp,
list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp,
list_length=list_length_sp,
list_translation=list_translation_sp,
list_num=list_num_sp,
list_icohp=list_icoop_sp,
)
class CombinedIcohpTest(unittest.TestCase):
def setUp(self):
# without spin polarization:
are_coops = False
is_spin_polarized = False
list_atom2 = ["K2", "K2", "K2", "K2", "K2", "K2"]
list_icohp = [
{Spin.up: -0.40075},
{Spin.up: -0.40074},
{Spin.up: -0.40079},
{Spin.up: -0.40079},
{Spin.up: -0.40074},
{Spin.up: -0.40075},
]
list_icoop = [
{Spin.up: 0.02342},
{Spin.up: 0.02342},
{Spin.up: 0.02343},
{Spin.up: 0.02343},
{Spin.up: 0.02342},
{Spin.up: 0.02342},
]
list_labels = ["1", "2", "3", "4", "5", "6"]
list_length = [2.71199, 2.71199, 2.71199, 2.71199, 2.71199, 2.71199]
list_num = [1, 1, 1, 1, 1, 1]
list_atom1 = ["F1", "F1", "F1", "F1", "F1", "F1"]
list_translation = [
[0, -1, -1],
[-1, 0, -1],
[0, 0, -1],
[-1, -1, 0],
[0, -1, 0],
[-1, 0, 0],
]
self.icohpcollection_KF = IcohpCollection(
is_spin_polarized=is_spin_polarized,
are_coops=are_coops,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icohp,
)
self.icoopcollection_KF = IcohpCollection(
is_spin_polarized=is_spin_polarized,
are_coops=True,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icoop,
)
# with spin polarization:
list_atom2_sp = ["Fe7", "Fe9"]
list_labels_sp = ["1", "2"]
list_translation_sp = [[0, 0, 0], [0, 0, 0]]
list_length_sp = [2.83189, 2.45249]
list_atom1_sp = ["Fe8", "Fe8"]
is_spin_polarized_sp = True
are_coops_sp = False
list_num_sp = [2, 1]
list_icohp_sp = [
{Spin.up: -0.10218, Spin.down: -0.19701},
{Spin.up: -0.28485, Spin.down: -0.58279},
]
list_icoop_sp = [
{Spin.up: -0.11389, Spin.down: -0.20828},
{Spin.up: -0.04087, Spin.down: -0.05756},
]
self.icohpcollection_Fe = IcohpCollection(
is_spin_polarized=is_spin_polarized_sp,
are_coops=are_coops_sp,
list_labels=list_labels_sp,
list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp,
list_length=list_length_sp,
list_translation=list_translation_sp,
list_num=list_num_sp,
list_icohp=list_icohp_sp,
)
self.icoopcollection_Fe = IcohpCollection(
is_spin_polarized=is_spin_polarized_sp,
are_coops=True,
list_labels=list_labels_sp,
list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp,
list_length=list_length_sp,
list_translation=list_translation_sp,
list_num=list_num_sp,
list_icohp=list_icoop_sp,
)
def test_get_icohp_by_label(self):
# without spin polarization
# ICOHPs
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("1"), -0.40075)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("2"), -0.40074)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("3"), -0.40079)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("4"), -0.40079)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("5"), -0.40074)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("6"), -0.40075)
# with spin polarization
# summed spin
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label("1"), -0.10218 - 0.19701
)
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label("2"), -0.28485 - 0.58279
)
# Spin up
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label("1", summed_spin_channels=False),
-0.10218,
)
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label("2", summed_spin_channels=False),
-0.28485,
)
# Spin down
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label(
"1", summed_spin_channels=False, spin=Spin.down
),
-0.19701,
)
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label(
"2", summed_spin_channels=False, spin=Spin.down
),
-0.58279,
)
def test_get_summed_icohp_by_label_list(self):
# without spin polarization
self.assertAlmostEqual(
self.icohpcollection_KF.get_summed_icohp_by_label_list(
["1", "2", "3", "4", "5", "6"], divisor=6.0
),
-0.40076,
)
# with spin polarization
sum1 = (-0.10218 - 0.19701 - 0.28485 - 0.58279) / 2.0
sum2 = (-0.10218 - 0.28485) / 2.0
sum3 = (-0.19701 - 0.58279) / 2.0
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_label_list(
["1", "2"], divisor=2.0
),
sum1,
)
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_label_list(
["1", "2"], summed_spin_channels=False, divisor=2.0
),
sum2,
)
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_label_list(
["1", "2"], summed_spin_channels=False, spin=Spin.down, divisor=2.0
),
sum3,
)
def test_get_icohp_dict_by_bondlengths(self):
# without spin polarization
icohpvalue = {}
icohpvalue["1"] = {
"@module": "pymatgen.electronic_structure.cohp",
"num": 1,
"length": 2.71199,
"icohp": {Spin.up: -0.40075},
"are_coops": False,
"label": "1",
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"translation": [0, -1, -1],
}
icohpvalue["2"] = {
"@module": "pymatgen.electronic_structure.cohp",
"num": 1,
"length": 2.71199,
"icohp": {Spin.up: -0.40074},
"are_coops": False,
"label": "2",
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"translation": [-1, 0, -1],
}
icohpvalue["3"] = {
"@module": "pymatgen.electronic_structure.cohp",
"num": 1,
"length": 2.71199,
"icohp": {Spin.up: -0.40079},
"are_coops": False,
"label": "3",
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"translation": [0, 0, -1],
}
icohpvalue["4"] = {
"@module": "pymatgen.electronic_structure.cohp",
"num": 1,
"length": 2.71199,
"icohp": {Spin.up: -0.40079},
"are_coops": False,
"label": "4",
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"translation": [-1, -1, 0],
}
icohpvalue["5"] = {
"@module": "pymatgen.electronic_structure.cohp",
"num": 1,
"length": 2.71199,
"icohp": {Spin.up: -0.40074},
"are_coops": False,
"label": "5",
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"translation": [0, -1, 0],
}
icohpvalue["6"] = {
"@module": "pymatgen.electronic_structure.cohp",
"num": 1,
"length": 2.71199,
"icohp": {Spin.up: -0.40075},
"are_coops": False,
"label": "6",
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"translation": [-1, 0, 0],
}
dict_KF = self.icohpcollection_KF.get_icohp_dict_by_bondlengths(
minbondlength=0.0, maxbondlength=8.0
)
for key, value in sorted(dict_KF.items()):
v = value.as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohpvalue[key])
self.assertDictEqual(
{},
self.icohpcollection_KF.get_icohp_dict_by_bondlengths(
minbondlength=0.0, maxbondlength=1.0
),
)
# with spin polarization
icohpvalue_spin = {}
icohpvalue_spin["1"] = {
"num": 2,
"atom2": "Fe7",
"translation": [0, 0, 0],
"@module": "pymatgen.electronic_structure.cohp",
"are_coops": False,
"atom1": "Fe8",
"label": "1",
"length": 2.83189,
"@class": "IcohpValue",
"icohp": {Spin.up: -0.10218, Spin.down: -0.19701},
}
icohpvalue_spin["2"] = {
"num": 1,
"atom2": "Fe9",
"translation": [0, 0, 0],
"@module": "pymatgen.electronic_structure.cohp",
"are_coops": False,
"atom1": "Fe8",
"label": "2",
"length": 2.45249,
"@class": "IcohpValue",
"icohp": {Spin.up: -0.28485, Spin.down: -0.58279},
}
dict_Fe = self.icohpcollection_Fe.get_icohp_dict_by_bondlengths(
minbondlength=0.0, maxbondlength=8.0
)
for key, value in sorted(dict_Fe.items()):
v = value.as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohpvalue_spin[key])
dict_Fe2 = self.icohpcollection_Fe.get_icohp_dict_by_bondlengths(
minbondlength=2.5, maxbondlength=2.9
)
self.assertEqual(len(dict_Fe2), 1)
for key, value in sorted(dict_Fe2.items()):
v = value.as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohpvalue_spin[key])
def test_get_icohp_dict_of_site(self):
# without spin polarization
icohpvalue = {}
icohpvalue["1"] = {
"translation": [0, -1, -1],
"are_coops": False,
"@module": "pymatgen.electronic_structure.cohp",
"length": 2.71199,
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"num": 1,
"label": "1",
"icohp": {Spin.up: -0.40075},
}
icohpvalue["2"] = {
"translation": [-1, 0, -1],
"are_coops": False,
"@module": "pymatgen.electronic_structure.cohp",
"length": 2.71199,
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"num": 1,
"label": "2",
"icohp": {Spin.up: -0.40074},
}
icohpvalue["3"] = {
"translation": [0, 0, -1],
"are_coops": False,
"@module": "pymatgen.electronic_structure.cohp",
"length": 2.71199,
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"num": 1,
"label": "3",
"icohp": {Spin.up: -0.40079},
}
icohpvalue["4"] = {
"translation": [-1, -1, 0],
"are_coops": False,
"@module": "pymatgen.electronic_structure.cohp",
"length": 2.71199,
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"num": 1,
"label": "4",
"icohp": {Spin.up: -0.40079},
}
icohpvalue["5"] = {
"translation": [0, -1, 0],
"are_coops": False,
"@module": "pymatgen.electronic_structure.cohp",
"length": 2.71199,
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"num": 1,
"label": "5",
"icohp": {Spin.up: -0.40074},
}
icohpvalue["6"] = {
"translation": [-1, 0, 0],
"are_coops": False,
"@module": "pymatgen.electronic_structure.cohp",
"length": 2.71199,
"atom2": "K2",
"@class": "IcohpValue",
"atom1": "F1",
"num": 1,
"label": "6",
"icohp": {Spin.up: -0.40075},
}
dict_KF = self.icohpcollection_KF.get_icohp_dict_of_site(site=0)
for key, value in sorted(dict_KF.items()):
v = value.as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohpvalue[key])
# compare number of results dependent on minsummedicohp, maxsummedicohp,minbondlength, maxbondlength, and
# only_bonds_to
dict_KF_2 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=0,
minsummedicohp=None,
maxsummedicohp=-0.0,
minbondlength=0.0,
maxbondlength=8.0,
)
dict_KF_3 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=0,
minsummedicohp=None,
maxsummedicohp=-0.5,
minbondlength=0.0,
maxbondlength=8.0,
)
dict_KF_4 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=0,
minsummedicohp=0.0,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=8.0,
)
dict_KF_5 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=0,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=2.0,
)
dict_KF_6 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=0,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=3.0,
maxbondlength=8.0,
)
dict_KF_7 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=0, only_bonds_to=["K"]
)
dict_KF_8 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=1, only_bonds_to=["K"]
)
dict_KF_9 = self.icohpcollection_KF.get_icohp_dict_of_site(
site=1, only_bonds_to=["F"]
)
self.assertEqual(len(dict_KF_2), 6)
self.assertEqual(len(dict_KF_3), 0)
self.assertEqual(len(dict_KF_4), 0)
self.assertEqual(len(dict_KF_5), 0)
self.assertEqual(len(dict_KF_6), 0)
self.assertEqual(len(dict_KF_7), 6)
self.assertEqual(len(dict_KF_8), 0)
self.assertEqual(len(dict_KF_9), 6)
# spin polarization
dict_Fe = self.icohpcollection_Fe.get_icohp_dict_of_site(site=0)
self.assertEqual(len(dict_Fe), 0)
# Fe8
dict_Fe2 = self.icohpcollection_Fe.get_icohp_dict_of_site(site=7)
self.assertEqual(len(dict_Fe2), 2)
# Test the values
icohplist_Fe = {}
icohplist_Fe["1"] = {
"are_coops": False,
"translation": [0, 0, 0],
"icohp": {Spin.down: -0.19701, Spin.up: -0.10218},
"length": 2.83189,
"@module": "pymatgen.electronic_structure.cohp",
"atom1": "Fe8",
"atom2": "Fe7",
"label": "1",
"@class": "IcohpValue",
"num": 2,
}
icohplist_Fe["2"] = {
"are_coops": False,
"translation": [0, 0, 0],
"icohp": {Spin.down: -0.58279, Spin.up: -0.28485},
"length": 2.45249,
"@module": "pymatgen.electronic_structure.cohp",
"atom1": "Fe8",
"atom2": "Fe9",
"label": "2",
"@class": "IcohpValue",
"num": 1,
}
for key, value in sorted(dict_Fe2.items()):
v = value.as_dict()
if "@version" in v:
v.pop("@version")
self.assertEqual(v, icohplist_Fe[key])
# Fe9
dict_Fe3 = self.icohpcollection_Fe.get_icohp_dict_of_site(site=8)
self.assertEqual(len(dict_Fe3), 1)
# compare number of results dependent on minsummedicohp, maxsummedicohp,minbondlength, maxbondlength
# Fe8
dict_Fe4 = self.icohpcollection_Fe.get_icohp_dict_of_site(
site=7,
minsummedicohp=-0.3,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=8.0,
)
self.assertEqual(len(dict_Fe4), 1)
values = []
for key, value in dict_Fe4.items():
values.append(value)
v = values[0].as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohplist_Fe["1"])
dict_Fe5 = self.icohpcollection_Fe.get_icohp_dict_of_site(
site=7,
minsummedicohp=None,
maxsummedicohp=-0.3,
minbondlength=0.0,
maxbondlength=8.0,
)
self.assertEqual(len(dict_Fe5), 1)
values = []
for key, value in dict_Fe5.items():
values.append(value)
v = values[0].as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohplist_Fe["2"])
dict_Fe6 = self.icohpcollection_Fe.get_icohp_dict_of_site(
site=7,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=2.5,
)
self.assertEqual(len(dict_Fe6), 1)
values = []
for key, value in dict_Fe6.items():
values.append(value)
v = values[0].as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohplist_Fe["2"])
dict_Fe7 = self.icohpcollection_Fe.get_icohp_dict_of_site(
site=7,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=2.5,
maxbondlength=8.0,
)
self.assertEqual(len(dict_Fe7), 1)
values = []
for key, value in dict_Fe7.items():
values.append(value)
v = values[0].as_dict()
if "@version" in v:
v.pop("@version")
self.assertDictEqual(v, icohplist_Fe["1"])
def test_extremum_icohpvalue(self):
# without spin polarization
# ICOHPs
self.assertEqual(self.icohpcollection_KF.extremum_icohpvalue(), -0.40079)
# ICOOPs
self.assertEqual(self.icoopcollection_KF.extremum_icohpvalue(), 0.02343)
# with spin polarization
# summed spin
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.extremum_icohpvalue(), -0.86764)
self.assertAlmostEqual(
self.icoopcollection_Fe.extremum_icohpvalue(), -0.09842999999999999
)
# ICOOPs
# spin up
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.extremum_icohpvalue(summed_spin_channels=False),
-0.28485,
)
# ICOOPs
self.assertEqual(
self.icoopcollection_Fe.extremum_icohpvalue(summed_spin_channels=False),
-0.04087,
)
# spin down
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.extremum_icohpvalue(
summed_spin_channels=False, spin=Spin.down
),
-0.58279,
)
# ICOOPs
self.assertEqual(
self.icoopcollection_Fe.extremum_icohpvalue(
summed_spin_channels=False, spin=Spin.down
),
-0.05756,
)
def __init__(self, are_coops=False, filename=None):
self.are_coops = are_coops
if filename is None:
filename = "ICOOPLIST.lobster" if are_coops \
else "ICOHPLIST.lobster"
# LOBSTER list files have an extra trailing blank line
# and we don't need the header.
with zopen(filename) as f:
data = f.read().split("\n")[1:-1]
if len(data) == 0:
raise IOError("ICOHPLIST file contains no data.")
# Which Lobster version?
if len(data[0].split()) == 8:
version = '3.1.1'
elif len(data[0].split()) == 6:
version = '2.2.1'
warnings.warn(
'Please consider using the new Lobster version. See www.cohp.de.'
)
else:
raise ValueError
# If the calculation is spin polarized, the line in the middle
# of the file will be another header line.
if "distance" in data[len(data) // 2]:
num_bonds = len(data) // 2
if num_bonds == 0:
raise IOError("ICOHPLIST file contains no data.")
self.is_spin_polarized = True
else:
num_bonds = len(data)
self.is_spin_polarized = False
list_labels = []
list_atom1 = []
list_atom2 = []
list_length = []
list_translation = []
list_num = []
list_icohp = []
for bond in range(num_bonds):
line = data[bond].split()
icohp = {}
if version == '2.2.1':
label = "%s" % (line[0])
atom1 = str(line[1])
atom2 = str(line[2])
length = float(line[3])
icohp[Spin.up] = float(line[4])
num = int(line[5])
translation = [0, 0, 0]
if self.is_spin_polarized:
icohp[Spin.down] = float(data[bond + num_bonds +
1].split()[4])
elif version == '3.1.1':
label = "%s" % (line[0])
atom1 = str(line[1])
atom2 = str(line[2])
length = float(line[3])
translation = [int(line[4]), int(line[5]), int(line[6])]
icohp[Spin.up] = float(line[7])
num = int(1)
if self.is_spin_polarized:
icohp[Spin.down] = float(data[bond + num_bonds +
1].split()[7])
list_labels.append(label)
list_atom1.append(atom1)
list_atom2.append(atom2)
list_length.append(length)
list_translation.append(translation)
list_num.append(num)
list_icohp.append(icohp)
# to avoid circular dependencies
from pymatgen.electronic_structure.cohp import IcohpCollection
self._icohpcollection = IcohpCollection(
are_coops=are_coops,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icohp,
is_spin_polarized=self.is_spin_polarized)
class CombinedIcohpTest(unittest.TestCase):
def setUp(self):
# without spin polarization:
are_coops = False
is_spin_polarized = False
list_atom2 = ['K2', 'K2', 'K2', 'K2', 'K2', 'K2']
list_icohp = [{
Spin.up: -0.40075
}, {
Spin.up: -0.40074
}, {
Spin.up: -0.40079
}, {
Spin.up: -0.40079
}, {
Spin.up: -0.40074
}, {
Spin.up: -0.40075
}]
list_icoop = [{
Spin.up: 0.02342
}, {
Spin.up: 0.02342
}, {
Spin.up: 0.02343
}, {
Spin.up: 0.02343
}, {
Spin.up: 0.02342
}, {
Spin.up: 0.02342
}]
list_labels = ['1', '2', '3', '4', '5', '6']
list_length = [2.71199, 2.71199, 2.71199, 2.71199, 2.71199, 2.71199]
list_num = [1, 1, 1, 1, 1, 1]
list_atom1 = ['F1', 'F1', 'F1', 'F1', 'F1', 'F1']
list_translation = [[0, -1, -1], [-1, 0, -1], [0, 0, -1], [-1, -1, 0],
[0, -1, 0], [-1, 0, 0]]
self.icohpcollection_KF = IcohpCollection(
is_spin_polarized=is_spin_polarized,
are_coops=are_coops,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icohp)
self.icoopcollection_KF = IcohpCollection(
is_spin_polarized=is_spin_polarized,
are_coops=True,
list_labels=list_labels,
list_atom1=list_atom1,
list_atom2=list_atom2,
list_length=list_length,
list_translation=list_translation,
list_num=list_num,
list_icohp=list_icoop)
# with spin polarization:
list_atom2_sp = ['Fe7', 'Fe9']
list_labels_sp = ['1', '2']
list_translation_sp = [[0, 0, 0], [0, 0, 0]]
list_length_sp = [2.83189, 2.45249]
list_atom1_sp = ['Fe8', 'Fe8']
is_spin_polarized_sp = True
are_coops_sp = False
list_num_sp = [2, 1]
list_icohp_sp = [{
Spin.up: -0.10218,
Spin.down: -0.19701
}, {
Spin.up: -0.28485,
Spin.down: -0.58279
}]
list_icoop_sp = [{
Spin.up: -0.11389,
Spin.down: -0.20828
}, {
Spin.up: -0.04087,
Spin.down: -0.05756
}]
self.icohpcollection_Fe = IcohpCollection(
is_spin_polarized=is_spin_polarized_sp,
are_coops=are_coops_sp,
list_labels=list_labels_sp,
list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp,
list_length=list_length_sp,
list_translation=list_translation_sp,
list_num=list_num_sp,
list_icohp=list_icohp_sp)
self.icoopcollection_Fe = IcohpCollection(
is_spin_polarized=is_spin_polarized_sp,
are_coops=True,
list_labels=list_labels_sp,
list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp,
list_length=list_length_sp,
list_translation=list_translation_sp,
list_num=list_num_sp,
list_icohp=list_icoop_sp)
def test_get_icohp_by_label(self):
# without spin polarization
# ICOHPs
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("1"),
-0.40075)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("2"),
-0.40074)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("3"),
-0.40079)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("4"),
-0.40079)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("5"),
-0.40074)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("6"),
-0.40075)
# with spin polarization
# summed spin
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("1"),
-0.10218 - 0.19701)
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("2"),
-0.28485 - 0.58279)
# Spin up
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label(
"1", summed_spin_channels=False), -0.10218)
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label(
"2", summed_spin_channels=False), -0.28485)
# Spin down
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label(
"1", summed_spin_channels=False, spin=Spin.down), -0.19701)
self.assertEqual(
self.icohpcollection_Fe.get_icohp_by_label(
"2", summed_spin_channels=False, spin=Spin.down), -0.58279)
def test_get_summed_icohp_by_labellist(self):
# without spin polarization
self.assertAlmostEqual(
self.icohpcollection_KF.get_summed_icohp_by_labellist(
["1", "2", "3", "4", "5", "6"], divisor=6.0), -0.40076)
# with spin polarization
sum1 = (-0.10218 - 0.19701 - 0.28485 - 0.58279) / 2.0
sum2 = (-0.10218 - 0.28485) / 2.0
sum3 = (-0.19701 - 0.58279) / 2.0
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_labellist(["1", "2"],
divisor=2.0),
sum1)
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_labellist(
["1", "2"], summed_spin_channels=False, divisor=2.0), sum2)
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_labellist(
["1", "2"],
summed_spin_channels=False,
spin=Spin.down,
divisor=2.0), sum3)
def test_get_icohp_dict_by_bondlengths(self):
# without spin polarization
icohpvalue = {}
icohpvalue["1"] = {
'@module': 'pymatgen.electronic_structure.cohp',
'num': 1,
'length': 2.71199,
'icohp': {
Spin.up: -0.40075
},
'are_coops': False,
'label': '1',
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'translation': [0, -1, -1]
}
icohpvalue["2"] = {
'@module': 'pymatgen.electronic_structure.cohp',
'num': 1,
'length': 2.71199,
'icohp': {
Spin.up: -0.40074
},
'are_coops': False,
'label': '2',
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'translation': [-1, 0, -1]
}
icohpvalue["3"] = {
'@module': 'pymatgen.electronic_structure.cohp',
'num': 1,
'length': 2.71199,
'icohp': {
Spin.up: -0.40079
},
'are_coops': False,
'label': '3',
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'translation': [0, 0, -1]
}
icohpvalue["4"] = {
'@module': 'pymatgen.electronic_structure.cohp',
'num': 1,
'length': 2.71199,
'icohp': {
Spin.up: -0.40079
},
'are_coops': False,
'label': '4',
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'translation': [-1, -1, 0]
}
icohpvalue["5"] = {
'@module': 'pymatgen.electronic_structure.cohp',
'num': 1,
'length': 2.71199,
'icohp': {
Spin.up: -0.40074
},
'are_coops': False,
'label': '5',
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'translation': [0, -1, 0]
}
icohpvalue["6"] = {
'@module': 'pymatgen.electronic_structure.cohp',
'num': 1,
'length': 2.71199,
'icohp': {
Spin.up: -0.40075
},
'are_coops': False,
'label': '6',
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'translation': [-1, 0, 0]
}
dict_KF = self.icohpcollection_KF.get_icohp_dict_by_bondlengths(
minbondlength=0.0, maxbondlength=8.0)
for key, value in sorted(dict_KF.items()):
self.assertDictEqual(value.as_dict(), icohpvalue[key])
self.assertDictEqual(
{},
self.icohpcollection_KF.get_icohp_dict_by_bondlengths(
minbondlength=0.0, maxbondlength=1.0))
# with spin polarization
icohpvalue_spin = {}
icohpvalue_spin["1"] = {
'num': 2,
'atom2': 'Fe7',
'translation': [0, 0, 0],
'@module': 'pymatgen.electronic_structure.cohp',
'are_coops': False,
'atom1': 'Fe8',
'label': '1',
'length': 2.83189,
'@class': 'IcohpValue',
'icohp': {
Spin.up: -0.10218,
Spin.down: -0.19701
}
}
icohpvalue_spin["2"] = {
'num': 1,
'atom2': 'Fe9',
'translation': [0, 0, 0],
'@module': 'pymatgen.electronic_structure.cohp',
'are_coops': False,
'atom1': 'Fe8',
'label': '2',
'length': 2.45249,
'@class': 'IcohpValue',
'icohp': {
Spin.up: -0.28485,
Spin.down: -0.58279
}
}
dict_Fe = self.icohpcollection_Fe.get_icohp_dict_by_bondlengths(
minbondlength=0.0, maxbondlength=8.0)
for key, value in sorted(dict_Fe.items()):
self.assertDictEqual(value.as_dict(), icohpvalue_spin[key])
dict_Fe2 = self.icohpcollection_Fe.get_icohp_dict_by_bondlengths(
minbondlength=2.5, maxbondlength=2.9)
self.assertEqual(len(dict_Fe2), 1)
for key, value in sorted(dict_Fe2.items()):
self.assertDictEqual(value.as_dict(), icohpvalue_spin[key])
def test_get_icohp_dict_of_certain_site(self):
# without spin polarization
icohpvalue = {}
icohpvalue["1"] = {
'translation': [0, -1, -1],
'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp',
'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'num': 1,
'label': '1',
'icohp': {
Spin.up: -0.40075
}
}
icohpvalue["2"] = {
'translation': [-1, 0, -1],
'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp',
'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'num': 1,
'label': '2',
'icohp': {
Spin.up: -0.40074
}
}
icohpvalue["3"] = {
'translation': [0, 0, -1],
'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp',
'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'num': 1,
'label': '3',
'icohp': {
Spin.up: -0.40079
}
}
icohpvalue["4"] = {
'translation': [-1, -1, 0],
'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp',
'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'num': 1,
'label': '4',
'icohp': {
Spin.up: -0.40079
}
}
icohpvalue["5"] = {
'translation': [0, -1, 0],
'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp',
'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'num': 1,
'label': '5',
'icohp': {
Spin.up: -0.40074
}
}
icohpvalue["6"] = {
'translation': [-1, 0, 0],
'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp',
'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue',
'atom1': 'F1',
'num': 1,
'label': '6',
'icohp': {
Spin.up: -0.40075
}
}
dict_KF = self.icohpcollection_KF.get_icohp_dict_of_certain_site(
site=0)
for key, value in sorted(dict_KF.items()):
self.assertDictEqual(value.as_dict(), icohpvalue[key])
# compare number of results dependent on minsummedicohp, maxsummedicohp,minbondlength, maxbondlength
dict_KF_2 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(
site=0,
minsummedicohp=None,
maxsummedicohp=-0.0,
minbondlength=0.0,
maxbondlength=8.0)
dict_KF_3 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(
site=0,
minsummedicohp=None,
maxsummedicohp=-0.5,
minbondlength=0.0,
maxbondlength=8.0)
dict_KF_4 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(
site=0,
minsummedicohp=0.0,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=8.0)
dict_KF_5 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(
site=0,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=2.0)
dict_KF_6 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(
site=0,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=3.0,
maxbondlength=8.0)
self.assertEqual(len(dict_KF_2), 6)
self.assertEqual(len(dict_KF_3), 0)
self.assertEqual(len(dict_KF_4), 0)
self.assertEqual(len(dict_KF_5), 0)
self.assertEqual(len(dict_KF_6), 0)
# spin polarization
dict_Fe = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=0)
self.assertEqual(len(dict_Fe), 0)
# Fe8
dict_Fe2 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=7)
self.assertEqual(len(dict_Fe2), 2)
# Test the values
icohplist_Fe = {}
icohplist_Fe["1"] = {
'are_coops': False,
'translation': [0, 0, 0],
'icohp': {
Spin.down: -0.19701,
Spin.up: -0.10218
},
'length': 2.83189,
'@module': 'pymatgen.electronic_structure.cohp',
'atom1': 'Fe8',
'atom2': 'Fe7',
'label': '1',
'@class': 'IcohpValue',
'num': 2
}
icohplist_Fe["2"] = {
'are_coops': False,
'translation': [0, 0, 0],
'icohp': {
Spin.down: -0.58279,
Spin.up: -0.28485
},
'length': 2.45249,
'@module': 'pymatgen.electronic_structure.cohp',
'atom1': 'Fe8',
'atom2': 'Fe9',
'label': '2',
'@class': 'IcohpValue',
'num': 1
}
for key, value in sorted(dict_Fe2.items()):
self.assertEqual(value.as_dict(), icohplist_Fe[key])
# Fe9
dict_Fe3 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=8)
self.assertEqual(len(dict_Fe3), 1)
# compare number of results dependent on minsummedicohp, maxsummedicohp,minbondlength, maxbondlength
# Fe8
dict_Fe4 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=7,
minsummedicohp=-0.3,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=8.0)
self.assertEqual(len(dict_Fe4), 1)
values = []
for key, value in dict_Fe4.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["1"])
dict_Fe5 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=7,
minsummedicohp=None,
maxsummedicohp=-0.3,
minbondlength=0.0,
maxbondlength=8.0)
self.assertEqual(len(dict_Fe5), 1)
values = []
for key, value in dict_Fe5.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["2"])
dict_Fe6 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=7,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=0.0,
maxbondlength=2.5)
self.assertEqual(len(dict_Fe6), 1)
values = []
for key, value in dict_Fe6.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["2"])
dict_Fe7 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(
site=7,
minsummedicohp=None,
maxsummedicohp=None,
minbondlength=2.5,
maxbondlength=8.0)
self.assertEqual(len(dict_Fe7), 1)
values = []
for key, value in dict_Fe7.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["1"])
def test_extremum_icohpvalue(self):
# without spin polarization
# ICOHPs
self.assertEqual(self.icohpcollection_KF.extremum_icohpvalue(),
-0.40079)
# ICOOPs
self.assertEqual(self.icoopcollection_KF.extremum_icohpvalue(),
0.02343)
# with spin polarization
# summed spin
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.extremum_icohpvalue(),
-0.86764)
self.assertAlmostEqual(self.icoopcollection_Fe.extremum_icohpvalue(),
-0.09842999999999999)
# ICOOPs
# spin up
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.extremum_icohpvalue(
summed_spin_channels=False), -0.28485)
# ICOOPs
self.assertEqual(
self.icoopcollection_Fe.extremum_icohpvalue(
summed_spin_channels=False), -0.04087)
# spin down
# ICOHPs
self.assertEqual(
self.icohpcollection_Fe.extremum_icohpvalue(
summed_spin_channels=False, spin=Spin.down), -0.58279)
# ICOOPs
self.assertEqual(
self.icoopcollection_Fe.extremum_icohpvalue(
summed_spin_channels=False, spin=Spin.down), -0.05756)
class CombinedIcohpTest(unittest.TestCase):
def setUp(self):
# without spin polarization:
are_coops = False
is_spin_polarized = False
list_atom2 = ['K2', 'K2', 'K2', 'K2', 'K2', 'K2']
list_icohp = [{Spin.up: -0.40075}, {Spin.up: -0.40074}, {Spin.up: -0.40079}, {Spin.up: -0.40079},
{Spin.up: -0.40074}, {Spin.up: -0.40075}]
list_icoop = [{Spin.up: 0.02342}, {Spin.up: 0.02342}, {Spin.up: 0.02343}, {Spin.up: 0.02343},
{Spin.up: 0.02342}, {Spin.up: 0.02342}]
list_labels = ['1', '2', '3', '4', '5', '6']
list_length = [2.71199, 2.71199, 2.71199, 2.71199, 2.71199, 2.71199]
list_num = [1, 1, 1, 1, 1, 1]
list_atom1 = ['F1', 'F1', 'F1', 'F1', 'F1', 'F1']
list_translation = [[0, -1, -1], [-1, 0, -1], [0, 0, -1], [-1, -1, 0], [0, -1, 0], [-1, 0, 0]]
self.icohpcollection_KF = IcohpCollection(is_spin_polarized=is_spin_polarized, are_coops=are_coops,
list_labels=list_labels, list_atom1=list_atom1, list_atom2=list_atom2,
list_length=list_length, list_translation=list_translation,
list_num=list_num, list_icohp=list_icohp)
self.icoopcollection_KF = IcohpCollection(is_spin_polarized=is_spin_polarized, are_coops=True,
list_labels=list_labels, list_atom1=list_atom1, list_atom2=list_atom2,
list_length=list_length, list_translation=list_translation,
list_num=list_num, list_icohp=list_icoop)
# with spin polarization:
list_atom2_sp = ['Fe7', 'Fe9']
list_labels_sp = ['1', '2']
list_translation_sp = [[0, 0, 0], [0, 0, 0]]
list_length_sp = [2.83189, 2.45249]
list_atom1_sp = ['Fe8', 'Fe8']
is_spin_polarized_sp = True
are_coops_sp = False
list_num_sp = [2, 1]
list_icohp_sp = [{Spin.up: -0.10218, Spin.down: -0.19701}, {Spin.up: -0.28485, Spin.down: -0.58279}]
list_icoop_sp = [{Spin.up: -0.11389, Spin.down: -0.20828}, {Spin.up: -0.04087, Spin.down: -0.05756}]
self.icohpcollection_Fe = IcohpCollection(is_spin_polarized=is_spin_polarized_sp, are_coops=are_coops_sp,
list_labels=list_labels_sp, list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp, list_length=list_length_sp,
list_translation=list_translation_sp, list_num=list_num_sp,
list_icohp=list_icohp_sp)
self.icoopcollection_Fe = IcohpCollection(is_spin_polarized=is_spin_polarized_sp, are_coops=True,
list_labels=list_labels_sp, list_atom1=list_atom1_sp,
list_atom2=list_atom2_sp, list_length=list_length_sp,
list_translation=list_translation_sp, list_num=list_num_sp,
list_icohp=list_icoop_sp)
def test_get_icohp_by_label(self):
# without spin polarization
# ICOHPs
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("1"), -0.40075)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("2"), -0.40074)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("3"), -0.40079)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("4"), -0.40079)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("5"), -0.40074)
self.assertEqual(self.icohpcollection_KF.get_icohp_by_label("6"), -0.40075)
# with spin polarization
# summed spin
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("1"), -0.10218 - 0.19701)
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("2"), -0.28485 - 0.58279)
# Spin up
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("1", summed_spin_channels=False), -0.10218)
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("2", summed_spin_channels=False), -0.28485)
# Spin down
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("1", summed_spin_channels=False, spin=Spin.down),
-0.19701)
self.assertEqual(self.icohpcollection_Fe.get_icohp_by_label("2", summed_spin_channels=False, spin=Spin.down),
-0.58279)
def test_get_summed_icohp_by_labellist(self):
# without spin polarization
self.assertAlmostEqual(
self.icohpcollection_KF.get_summed_icohp_by_labellist(["1", "2", "3", "4", "5", "6"], divisor=6.0),
-0.40076)
# with spin polarization
sum1 = (-0.10218 - 0.19701 - 0.28485 - 0.58279) / 2.0
sum2 = (-0.10218 - 0.28485) / 2.0
sum3 = (-0.19701 - 0.58279) / 2.0
self.assertAlmostEqual(self.icohpcollection_Fe.get_summed_icohp_by_labellist(["1", "2"], divisor=2.0), sum1)
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_labellist(["1", "2"], summed_spin_channels=False, divisor=2.0),
sum2)
self.assertAlmostEqual(
self.icohpcollection_Fe.get_summed_icohp_by_labellist(["1", "2"], summed_spin_channels=False,
spin=Spin.down, divisor=2.0), sum3)
def test_get_icohp_dict_by_bondlengths(self):
# without spin polarization
icohpvalue = {}
icohpvalue["1"] = {'@module': 'pymatgen.electronic_structure.cohp', 'num': 1, 'length': 2.71199,
'icohp': {Spin.up: -0.40075},
'are_coops': False, 'label': '1', 'atom2': 'K2', '@class': 'IcohpValue', 'atom1': 'F1',
'translation': [0, -1, -1]}
icohpvalue["2"] = {'@module': 'pymatgen.electronic_structure.cohp', 'num': 1, 'length': 2.71199,
'icohp': {Spin.up: -0.40074},
'are_coops': False, 'label': '2', 'atom2': 'K2', '@class': 'IcohpValue', 'atom1': 'F1',
'translation': [-1, 0, -1]}
icohpvalue["3"] = {'@module': 'pymatgen.electronic_structure.cohp', 'num': 1, 'length': 2.71199,
'icohp': {Spin.up: -0.40079},
'are_coops': False, 'label': '3', 'atom2': 'K2', '@class': 'IcohpValue', 'atom1': 'F1',
'translation': [0, 0, -1]}
icohpvalue["4"] = {'@module': 'pymatgen.electronic_structure.cohp', 'num': 1, 'length': 2.71199,
'icohp': {Spin.up: -0.40079},
'are_coops': False, 'label': '4', 'atom2': 'K2', '@class': 'IcohpValue', 'atom1': 'F1',
'translation': [-1, -1, 0]}
icohpvalue["5"] = {'@module': 'pymatgen.electronic_structure.cohp', 'num': 1, 'length': 2.71199,
'icohp': {Spin.up: -0.40074},
'are_coops': False, 'label': '5', 'atom2': 'K2', '@class': 'IcohpValue', 'atom1': 'F1',
'translation': [0, -1, 0]}
icohpvalue["6"] = {'@module': 'pymatgen.electronic_structure.cohp', 'num': 1, 'length': 2.71199,
'icohp': {Spin.up: -0.40075},
'are_coops': False, 'label': '6', 'atom2': 'K2', '@class': 'IcohpValue', 'atom1': 'F1',
'translation': [-1, 0, 0]}
dict_KF = self.icohpcollection_KF.get_icohp_dict_by_bondlengths(minbondlength=0.0, maxbondlength=8.0)
for key, value in sorted(dict_KF.items()):
self.assertDictEqual(value.as_dict(), icohpvalue[key])
self.assertDictEqual({}, self.icohpcollection_KF.get_icohp_dict_by_bondlengths(minbondlength=0.0,
maxbondlength=1.0))
# with spin polarization
icohpvalue_spin = {}
icohpvalue_spin["1"] = {'num': 2, 'atom2': 'Fe7', 'translation': [0, 0, 0],
'@module': 'pymatgen.electronic_structure.cohp',
'are_coops': False, 'atom1': 'Fe8',
'label': '1', 'length': 2.83189, '@class': 'IcohpValue',
'icohp': {Spin.up: -0.10218, Spin.down: -0.19701}}
icohpvalue_spin["2"] = {'num': 1, 'atom2': 'Fe9', 'translation': [0, 0, 0],
'@module': 'pymatgen.electronic_structure.cohp',
'are_coops': False, 'atom1': 'Fe8',
'label': '2', 'length': 2.45249, '@class': 'IcohpValue',
'icohp': {Spin.up: -0.28485, Spin.down: -0.58279}}
dict_Fe = self.icohpcollection_Fe.get_icohp_dict_by_bondlengths(minbondlength=0.0, maxbondlength=8.0)
for key, value in sorted(dict_Fe.items()):
self.assertDictEqual(value.as_dict(), icohpvalue_spin[key])
dict_Fe2 = self.icohpcollection_Fe.get_icohp_dict_by_bondlengths(minbondlength=2.5, maxbondlength=2.9)
self.assertEqual(len(dict_Fe2), 1)
for key, value in sorted(dict_Fe2.items()):
self.assertDictEqual(value.as_dict(), icohpvalue_spin[key])
def test_get_icohp_dict_of_certain_site(self):
# without spin polarization
icohpvalue = {}
icohpvalue["1"] = {'translation': [0, -1, -1], 'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp', 'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue', 'atom1': 'F1', 'num': 1, 'label': '1', 'icohp': {Spin.up: -0.40075}}
icohpvalue["2"] = {'translation': [-1, 0, -1], 'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp', 'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue', 'atom1': 'F1', 'num': 1, 'label': '2', 'icohp': {Spin.up: -0.40074}}
icohpvalue["3"] = {'translation': [0, 0, -1], 'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp', 'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue', 'atom1': 'F1', 'num': 1, 'label': '3', 'icohp': {Spin.up: -0.40079}}
icohpvalue["4"] = {'translation': [-1, -1, 0], 'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp', 'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue', 'atom1': 'F1', 'num': 1, 'label': '4', 'icohp': {Spin.up: -0.40079}}
icohpvalue["5"] = {'translation': [0, -1, 0], 'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp', 'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue', 'atom1': 'F1', 'num': 1, 'label': '5', 'icohp': {Spin.up: -0.40074}}
icohpvalue["6"] = {'translation': [-1, 0, 0], 'are_coops': False,
'@module': 'pymatgen.electronic_structure.cohp', 'length': 2.71199,
'atom2': 'K2',
'@class': 'IcohpValue', 'atom1': 'F1', 'num': 1, 'label': '6', 'icohp': {Spin.up: -0.40075}}
dict_KF = self.icohpcollection_KF.get_icohp_dict_of_certain_site(site=0)
for key, value in sorted(dict_KF.items()):
self.assertDictEqual(value.as_dict(), icohpvalue[key])
# compare number of results dependent on minsummedicohp, maxsummedicohp,minbondlength, maxbondlength
dict_KF_2 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(site=0, minsummedicohp=None,
maxsummedicohp=-0.0, minbondlength=0.0,
maxbondlength=8.0)
dict_KF_3 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(site=0, minsummedicohp=None,
maxsummedicohp=-0.5, minbondlength=0.0,
maxbondlength=8.0)
dict_KF_4 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(site=0, minsummedicohp=0.0,
maxsummedicohp=None, minbondlength=0.0,
maxbondlength=8.0)
dict_KF_5 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(site=0, minsummedicohp=None,
maxsummedicohp=None, minbondlength=0.0,
maxbondlength=2.0)
dict_KF_6 = self.icohpcollection_KF.get_icohp_dict_of_certain_site(site=0, minsummedicohp=None,
maxsummedicohp=None, minbondlength=3.0,
maxbondlength=8.0)
self.assertEqual(len(dict_KF_2), 6)
self.assertEqual(len(dict_KF_3), 0)
self.assertEqual(len(dict_KF_4), 0)
self.assertEqual(len(dict_KF_5), 0)
self.assertEqual(len(dict_KF_6), 0)
# spin polarization
dict_Fe = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=0)
self.assertEqual(len(dict_Fe), 0)
# Fe8
dict_Fe2 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=7)
self.assertEqual(len(dict_Fe2), 2)
# Test the values
icohplist_Fe = {}
icohplist_Fe["1"] = {'are_coops': False, 'translation': [0, 0, 0],
'icohp': {Spin.down: -0.19701, Spin.up: -0.10218}, 'length': 2.83189,
'@module': 'pymatgen.electronic_structure.cohp', 'atom1': 'Fe8', 'atom2': 'Fe7',
'label': '1',
'@class': 'IcohpValue', 'num': 2}
icohplist_Fe["2"] = {'are_coops': False, 'translation': [0, 0, 0],
'icohp': {Spin.down: -0.58279, Spin.up: -0.28485}, 'length': 2.45249,
'@module': 'pymatgen.electronic_structure.cohp', 'atom1': 'Fe8', 'atom2': 'Fe9',
'label': '2',
'@class': 'IcohpValue', 'num': 1}
for key, value in sorted(dict_Fe2.items()):
self.assertEqual(value.as_dict(), icohplist_Fe[key])
# Fe9
dict_Fe3 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=8)
self.assertEqual(len(dict_Fe3), 1)
# compare number of results dependent on minsummedicohp, maxsummedicohp,minbondlength, maxbondlength
# Fe8
dict_Fe4 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=7, minsummedicohp=-0.3,
maxsummedicohp=None, minbondlength=0.0,
maxbondlength=8.0)
self.assertEqual(len(dict_Fe4), 1)
values = []
for key, value in dict_Fe4.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["1"])
dict_Fe5 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=7, minsummedicohp=None,
maxsummedicohp=-0.3, minbondlength=0.0,
maxbondlength=8.0)
self.assertEqual(len(dict_Fe5), 1)
values = []
for key, value in dict_Fe5.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["2"])
dict_Fe6 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=7, minsummedicohp=None,
maxsummedicohp=None, minbondlength=0.0,
maxbondlength=2.5)
self.assertEqual(len(dict_Fe6), 1)
values = []
for key, value in dict_Fe6.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["2"])
dict_Fe7 = self.icohpcollection_Fe.get_icohp_dict_of_certain_site(site=7, minsummedicohp=None,
maxsummedicohp=None, minbondlength=2.5,
maxbondlength=8.0)
self.assertEqual(len(dict_Fe7), 1)
values = []
for key, value in dict_Fe7.items():
values.append(value)
self.assertDictEqual(values[0].as_dict(), icohplist_Fe["1"])
def test_extremum_icohpvalue(self):
# without spin polarization
# ICOHPs
self.assertEqual(self.icohpcollection_KF.extremum_icohpvalue(), -0.40079)
# ICOOPs
self.assertEqual(self.icoopcollection_KF.extremum_icohpvalue(), 0.02343)
# with spin polarization
# summed spin
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.extremum_icohpvalue(), -0.86764)
self.assertAlmostEqual(self.icoopcollection_Fe.extremum_icohpvalue(), -0.09842999999999999)
# ICOOPs
# spin up
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.extremum_icohpvalue(summed_spin_channels=False), -0.28485)
# ICOOPs
self.assertEqual(self.icoopcollection_Fe.extremum_icohpvalue(summed_spin_channels=False), -0.04087)
# spin down
# ICOHPs
self.assertEqual(self.icohpcollection_Fe.extremum_icohpvalue(summed_spin_channels=False, spin=Spin.down),
-0.58279)
# ICOOPs
self.assertEqual(self.icoopcollection_Fe.extremum_icohpvalue(summed_spin_channels=False, spin=Spin.down),
-0.05756)