def test_get_sum_icohps_between_neighbors_of_atom(self):
# will only look at icohps between cations or anions
self.chemenvlobster1.get_info_icohps_to_neighbors(isites=[1])
self.assertEqual(
self.chemenvlobster1.get_info_icohps_between_neighbors(
isites=[1])[2], 1)
self.assertAlmostEqual(
self.chemenvlobster1.get_info_icohps_between_neighbors(
isites=[1])[0], -0.05507)
self.assertEqual(
self.chemenvlobster1.get_info_icohps_between_neighbors(
isites=[0])[2], 15)
# use an example where this is easier to test (e.g., linear environment?)
chemenv_here = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp-7000.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp-7000.gz")),
additional_condition=1,
)
self.assertEqual(
len(chemenv_here.get_info_icohps_between_neighbors(isites=[0])[4]),
6)
def test_cation_anion_mode_without_ions(self):
with self.assertRaises(ValueError) as err:
test = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"../ICOHPLIST.lobster"),
structure=Structure.from_file(
os.path.join(test_dir_env, "../POSCAR")),
valences_from_charges=False,
additional_condition=1,
)
self.assertEqual(
str(err.exception),
"Valences cannot be assigned, additional_conditions 1 and 3 and 5 and 6 will not work"
)
with self.assertRaises(ValueError) as err:
test = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"../ICOHPLIST.lobster"),
structure=Structure.from_file(
os.path.join(test_dir_env, "../POSCAR")),
valences_from_charges=False,
additional_condition=1,
valences=[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
)
self.assertEqual(
str(err.exception),
"All valences are equal to 0, additional_conditions 1 and 3 and 5 and 6 will not work"
)
def test_set_limits(self):
test = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env, "ICOHPLIST.lobster.mp_353"),
structure=Structure.from_file(os.path.join(test_dir_env, "POSCAR.mp_353")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env, "CHARGE.lobster.mp-353.gz"),
additional_condition=1,
limits=[-100000, 0],
)
def test_wrong_additional_correction(self):
with self.assertRaises(ValueError):
test = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env, "ICOHPLIST.lobster.mp_353"),
structure=Structure.from_file(os.path.join(test_dir_env, "POSCAR.mp_353")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env, "CHARGE.lobster.mp-353.gz"),
additional_condition=10,
)
def test_get_info_cohps_to_neighbors(self):
chemenvlobster1 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190_2.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=1,
)
self.assertEqual(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"])[0],
"6 x O-Re (per bond)",
)
self.assertEqual(
type(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"],
)[1]),
Cohp,
)
cophthing = chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
)[1]
self.assertAlmostEqual(
np.sum([cophthing.icohp[Spin.up], cophthing.icohp[Spin.down]],
axis=0)[300],
chemenvlobster1.get_info_icohps_to_neighbors(isites=[0])[0],
)
# summed_spin_channel
cophthing = chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
summed_spin_channels=True,
)[1]
self.assertAlmostEqual(
cophthing.icohp[Spin.up][300],
chemenvlobster1.get_info_icohps_to_neighbors(isites=[0])[0])
self.assertEqual(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["Te"],
)[0],
None,
)
self.assertEqual(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["Te"],
)[1],
None,
)
self.assertEqual(
self.chemenvlobster0_NaSi.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.NaSi.gz"),
isites=[8],
onlycation_isites=False,
only_bonds_to=["Na"],
)[0],
"1 x Na-Si (per bond)",
)
self.assertEqual(
self.chemenvlobster0_NaSi.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.NaSi.gz"),
isites=[8],
onlycation_isites=False,
only_bonds_to=["Si"],
)[0],
"3 x Si-Si (per bond)",
)
chemenvlobster1.plot_cohps_of_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"],
summed_spin_channels=True,
)
chemenvlobster1.plot_cohps_of_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"],
summed_spin_channels=True,
xlim=[-10, 10],
ylim=None,
)
with self.assertRaises(ValueError):
# icohplist and cohpcar do not fit together
self.chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
)
with self.assertRaises(ValueError):
# icohplist and cohpcar do not fit together
self.chemenvlobster2.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
)
def setUp(self):
# test additional conditions first
# only consider cation anion bonds
self.chemenvlobster1 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=1,
)
# all bonds
self.chemenvlobster0 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=0,
)
# only cation cation, anion anion bonds
self.chemenvlobster5 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=5,
)
# only cation cation bonds
self.chemenvlobster6 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=6,
)
# 2,3,4 are not tested so far
self.chemenvlobster2 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=2,
)
self.chemenvlobster3 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=3,
)
self.chemenvlobster4 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=4,
)
# search for other testcase where 2,3,4 arrive at different results
self.chemenvlobster0_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=0,
)
self.chemenvlobster1_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=1,
)
self.chemenvlobster2_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=2,
)
self.chemenvlobster5_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=5,
)
self.chemenvlobster5_second_percentage = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=5,
perc_strength_ICOHP=1.0,
)
self.chemenvlobster6_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=6,
)
# TODO: use charge instead of valence
self.chemenvlobster1_charges = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
)
self.chemenvlobster1_charges_loewdin = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
which_charge="Loewdin",
)
self.chemenvlobster6_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=6,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster5_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=5,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster4_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=4,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster3_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=3,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster2_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=2,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster1_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster0_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=0,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster0_NaSi = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.NaSi.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.NaSi.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.NaSi.gz"),
additional_condition=0,
adapt_extremum_to_add_cond=True,
)
class TestLobsterNeighbors(unittest.TestCase):
def setUp(self):
# test additional conditions first
# only consider cation anion bonds
self.chemenvlobster1 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=1,
)
# all bonds
self.chemenvlobster0 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=0,
)
# only cation cation, anion anion bonds
self.chemenvlobster5 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=5,
)
# only cation cation bonds
self.chemenvlobster6 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=6,
)
# 2,3,4 are not tested so far
self.chemenvlobster2 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=2,
)
self.chemenvlobster3 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=3,
)
self.chemenvlobster4 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=4,
)
# search for other testcase where 2,3,4 arrive at different results
self.chemenvlobster0_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=0,
)
self.chemenvlobster1_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=1,
)
self.chemenvlobster2_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=2,
)
self.chemenvlobster5_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=5,
)
self.chemenvlobster5_second_percentage = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=5,
perc_strength_ICOHP=1.0,
)
self.chemenvlobster6_second = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
additional_condition=6,
)
# TODO: use charge instead of valence
self.chemenvlobster1_charges = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
)
self.chemenvlobster1_charges_loewdin = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
which_charge="Loewdin",
)
self.chemenvlobster6_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=6,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster5_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=5,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster4_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=4,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster3_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=3,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster2_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=2,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster1_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster0_charges_additional_condition = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=0,
adapt_extremum_to_add_cond=True,
)
self.chemenvlobster0_NaSi = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.NaSi.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.NaSi.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.NaSi.gz"),
additional_condition=0,
adapt_extremum_to_add_cond=True,
)
def test_use_of_coop(self):
with self.assertRaises(ValueError):
test = LobsterNeighbors(
are_coops=True,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
)
def test_wrong_additional_correction(self):
with self.assertRaises(ValueError):
test = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=10,
)
def test_set_limits(self):
test = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_353.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
valences_from_charges=True,
filename_CHARGE=os.path.join(test_dir_env,
"CHARGE.lobster.mp-353.gz"),
additional_condition=1,
limits=[-100000, 0],
)
self.assertListEqual(test.limits, [-100000, 0])
def test_molecules_allowed(self):
self.chemenvlobster1.molecules_allowed
def test_get_nn_info(self):
# NO_ADDITIONAL_CONDITION = 0
# ONLY_ANION_CATION_BONDS = 1
# NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2
# ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3
# ONLY_ELEMENT_TO_OXYGEN_BONDS = 4
# DO_NOT_CONSIDER_ANION_CATION_BONDS=5
# ONLY_CATION_CATION_BONDS=6
# All bonds
# ReO3
self.assertEqual(
len(
self.chemenvlobster0.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster0.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
2,
)
# ONLY_ANION_CATION_BONDS = 1
self.assertEqual(
len(
self.chemenvlobster1.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster1.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
2,
)
# NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2
self.assertEqual(
len(
self.chemenvlobster2.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster2.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
2,
)
# ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 3
self.assertEqual(
len(
self.chemenvlobster3.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster3.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
2,
)
# ONLY_ELEMENT_TO_OXYGEN_BONDS = 4
self.assertEqual(
len(
self.chemenvlobster4.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster4.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
2,
)
# DO_NOT_CONSIDER_ANION_CATION_BONDS=5
self.assertEqual(
len(
self.chemenvlobster5.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
0,
)
self.assertEqual(
len(
self.chemenvlobster5.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
0,
)
# ONLY_CATION_CATION_BONDS=6
self.assertEqual(
len(
self.chemenvlobster6.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=0)),
0,
)
self.assertEqual(
len(
self.chemenvlobster6.get_nn(structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
n=1)),
0,
)
# All bonds
# mp-353, Ag2O
# all bonds
self.assertEqual(
len(
self.chemenvlobster0_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)),
8,
)
# ONLY_ANION_CATION_BONDS = 1
self.assertEqual(
len(
self.chemenvlobster1_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)),
2,
)
# NO_ELEMENT_TO_SAME_ELEMENT_BONDS = 2
self.assertEqual(
len(
self.chemenvlobster2_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)),
2,
)
self.assertEqual(
len(
self.chemenvlobster2_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=4)),
4,
)
# DO_NOT_CONSIDER_ANION_CATION_BONDS=5
self.assertEqual(
len(
self.chemenvlobster5_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster5_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=4)),
0,
)
# ONLY_CATION_CATION_BONDS=6
self.assertEqual(
len(
self.chemenvlobster6_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)),
6,
)
self.assertEqual(
len(
self.chemenvlobster6_second.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=4)),
0,
)
self.assertEqual(
len(
self.chemenvlobster5_second_percentage.get_nn(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)),
0,
)
def test_structure_graph(self):
sg = self.chemenvlobster1_second.get_bonded_structure(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")))
self.assertEqual(type(sg), StructureGraph)
def test_order_parameter(self):
self.assertAlmostEqual(
self.chemenvlobster1_second.get_local_order_parameters(
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_353.gz")),
n=0)["linear"],
1.0,
)
def test_get_structure_environments(self):
lse = self.chemenvlobster1_second.get_light_structure_environment()
self.assertEqual(lse.coordination_environments[0][0]["ce_symbol"],
"L:2")
self.assertEqual(lse.coordination_environments[5][0]["ce_symbol"],
"T:4")
lse2 = self.chemenvlobster1.get_light_structure_environment()
self.assertEqual(lse2.coordination_environments[0][0]["ce_symbol"],
"O:6")
def test_get_strucuture_environments_further_tests(self):
lse = self.chemenvlobster1_second.get_light_structure_environment()
lse.as_dict()
lse.get_statistics()
self.assertTrue(lse.uniquely_determines_coordination_environments)
def test_get_info_icohps_neighbors(self):
results = self.chemenvlobster1.get_info_icohps_to_neighbors(isites=[0])
self.assertAlmostEqual(results[0], -33.26058)
for bond in results[1]:
self.assertAlmostEqual(bond, -5.54345, 3)
self.assertAlmostEqual(results[2], 6)
self.assertAlmostEqual(results[3],
["27", "30", "48", "49", "64", "73"])
results2 = self.chemenvlobster1.get_info_icohps_to_neighbors(
isites=None)
self.assertAlmostEqual(results2[0], -33.26058)
for bond in results2[1]:
self.assertAlmostEqual(bond, -5.54345, 3)
self.assertAlmostEqual(results2[2], 6)
self.assertAlmostEqual(results2[3],
["27", "30", "48", "49", "64", "73"])
self.assertAlmostEqual(results2[4],
[["Re1", "O2"], ["Re1", "O2"], ["Re1", "O3"],
["Re1", "O3"], ["Re1", "O4"], ["Re1", "O4"]])
def test_get_sum_icohps_between_neighbors_of_atom(self):
# will only look at icohps between cations or anions
self.chemenvlobster1.get_info_icohps_to_neighbors(isites=[1])
self.assertEqual(
self.chemenvlobster1.get_info_icohps_between_neighbors(
isites=[1])[2], 1)
self.assertAlmostEqual(
self.chemenvlobster1.get_info_icohps_between_neighbors(
isites=[1])[0], -0.05507)
self.assertEqual(
self.chemenvlobster1.get_info_icohps_between_neighbors(
isites=[0])[2], 15)
# use an example where this is easier to test (e.g., linear environment?)
chemenv_here = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp-7000.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp-7000.gz")),
additional_condition=1,
)
self.assertEqual(
len(chemenv_here.get_info_icohps_between_neighbors(isites=[0])[4]),
6)
def test_get_plot_label(self):
self.assertEqual(
self.chemenvlobster1._get_plot_label(
atoms=[["Re1", "O2"], ["Re1", "O2"], ["Re1", "O3"],
["Re1", "O3"], ["Re1", "O4"], ["Re1", "O4"]],
per_bond=False,
),
"6 x O-Re",
)
self.assertEqual(
self.chemenvlobster1._get_plot_label(
atoms=[["Re1", "O2"], ["Re1", "O2"], ["Re1", "O3"],
["Re1", "O3"], ["Re1", "O4"], ["Si1", "O4"]],
per_bond=False,
),
"5 x O-Re, 1 x O-Si",
)
self.assertEqual(
self.chemenvlobster1._get_plot_label(
atoms=[["Si1", "O2"], ["Si1", "O2"], ["Si1", "O3"],
["Re1", "O3"], ["Re1", "O4"], ["Si1", "O4"]],
per_bond=False,
),
"4 x O-Si, 2 x O-Re",
)
self.assertEqual(
self.chemenvlobster1._get_plot_label(
atoms=[["Re1", "O2"], ["Re1", "O2"], ["Re1", "O3"],
["Re1", "O3"], ["Re1", "O4"], ["Re1", "O4"]],
per_bond=True,
),
"6 x O-Re (per bond)",
)
def test_get_info_cohps_to_neighbors(self):
chemenvlobster1 = LobsterNeighbors(
are_coops=False,
filename_ICOHP=os.path.join(test_dir_env,
"ICOHPLIST.lobster.mp_190_2.gz"),
structure=Structure.from_file(
os.path.join(test_dir_env, "POSCAR.mp_190.gz")),
additional_condition=1,
)
self.assertEqual(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"])[0],
"6 x O-Re (per bond)",
)
self.assertEqual(
type(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"],
)[1]),
Cohp,
)
cophthing = chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
)[1]
self.assertAlmostEqual(
np.sum([cophthing.icohp[Spin.up], cophthing.icohp[Spin.down]],
axis=0)[300],
chemenvlobster1.get_info_icohps_to_neighbors(isites=[0])[0],
)
# summed_spin_channel
cophthing = chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
summed_spin_channels=True,
)[1]
self.assertAlmostEqual(
cophthing.icohp[Spin.up][300],
chemenvlobster1.get_info_icohps_to_neighbors(isites=[0])[0])
self.assertEqual(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["Te"],
)[0],
None,
)
self.assertEqual(
chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["Te"],
)[1],
None,
)
self.assertEqual(
self.chemenvlobster0_NaSi.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.NaSi.gz"),
isites=[8],
onlycation_isites=False,
only_bonds_to=["Na"],
)[0],
"1 x Na-Si (per bond)",
)
self.assertEqual(
self.chemenvlobster0_NaSi.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.NaSi.gz"),
isites=[8],
onlycation_isites=False,
only_bonds_to=["Si"],
)[0],
"3 x Si-Si (per bond)",
)
chemenvlobster1.plot_cohps_of_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"],
summed_spin_channels=True,
)
chemenvlobster1.plot_cohps_of_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=["O"],
summed_spin_channels=True,
xlim=[-10, 10],
ylim=None,
)
with self.assertRaises(ValueError):
# icohplist and cohpcar do not fit together
self.chemenvlobster1.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
)
with self.assertRaises(ValueError):
# icohplist and cohpcar do not fit together
self.chemenvlobster2.get_info_cohps_to_neighbors(
path_to_COHPCAR=os.path.join(test_dir_env,
"COHPCAR.lobster.mp-190.gz"),
isites=[0],
only_bonds_to=None,
per_bond=False,
)
