def setUp(self):
with open(os.path.join(test_dir, "cohp.json"), "r") as f:
self.cohp = Cohp.from_dict(json.load(f))
self.cohp_only = Cohp(self.cohp.efermi, self.cohp.energies,
self.cohp.cohp)
with open(os.path.join(test_dir, "coop.json"), "r") as f:
self.coop = Cohp.from_dict(json.load(f))
def setUp(self):
with open(os.path.join(test_dir, "cohp.json"), "r") as f:
self.cohp = Cohp.from_dict(json.load(f))
self.cohp_only = Cohp(self.cohp.efermi,
self.cohp.energies,
self.cohp.cohp)
with open(os.path.join(test_dir, "coop.json"), "r") as f:
self.coop = Cohp.from_dict(json.load(f))
class CohpTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "cohp.json"), "r") as f:
self.cohp = Cohp.from_dict(json.load(f))
self.cohp_only = Cohp(self.cohp.efermi, self.cohp.energies, self.cohp.cohp)
with open(os.path.join(test_dir, "coop.json"), "r") as f:
self.coop = Cohp.from_dict(json.load(f))
def test_as_from_dict(self):
with open(os.path.join(test_dir, "cohp.json"), "r") as f:
cohp_dict = json.load(f)
self.assertEqual(self.cohp.as_dict(), cohp_dict)
def test_attributes(self):
self.assertEqual(len(self.cohp.energies), 301)
self.assertEqual(self.cohp.efermi, 9.75576)
self.assertEqual(self.coop.efermi, 5.90043)
self.assertFalse(self.cohp.are_coops)
self.assertTrue(self.coop.are_coops)
def test_get_icohp(self):
self.assertEqual(self.cohp.get_icohp(), self.cohp.get_cohp(integrated=True))
self.assertEqual(None, self.cohp_only.get_icohp())
def test_get_interpolated_value(self):
# icohp_ef are the ICHOP(Ef) values taken from
# the ICOHPLIST.lobster file.
icohp_ef_dict = {Spin.up: -0.10218, Spin.down: -0.19701}
icoop_ef_dict = {Spin.up: 0.24714}
icohp_ef = self.cohp.get_interpolated_value(self.cohp.efermi, integrated=True)
icoop_ef = self.coop.get_interpolated_value(self.coop.efermi, integrated=True)
self.assertAlmostEqual(icohp_ef_dict, icohp_ef)
self.assertAlmostEqual(icoop_ef_dict, icoop_ef)
with self.assertRaises(ValueError):
self.cohp_only.get_interpolated_value(5.0, integrated=True)
def test_str(self):
with open(os.path.join(test_dir, "cohp.str"), "rt") as f:
str_cohp = f.read()
with open(os.path.join(test_dir, "coop.str"), "rt") as f:
str_coop = f.read()
self.assertEqual(self.cohp.__str__(), str_cohp)
self.assertEqual(self.coop.__str__(), str_coop)
def test_antibnd_states_below_efermi(self):
self.assertDictEqual(
self.cohp.has_antibnd_states_below_efermi(spin=None),
{Spin.up: True, Spin.down: True},
)
self.assertDictEqual(
self.cohp.has_antibnd_states_below_efermi(spin=None, limit=0.5),
{Spin.up: False, Spin.down: False},
)
self.assertDictEqual(
self.cohp.has_antibnd_states_below_efermi(spin=Spin.up, limit=0.5),
{Spin.up: False},
)
class CohpTest(unittest.TestCase):
def setUp(self):
with open(os.path.join(test_dir, "cohp.json"), "r") as f:
self.cohp = Cohp.from_dict(json.load(f))
self.cohp_only = Cohp(self.cohp.efermi,
self.cohp.energies,
self.cohp.cohp)
with open(os.path.join(test_dir, "coop.json"), "r") as f:
self.coop = Cohp.from_dict(json.load(f))
def test_as_from_dict(self):
with open(os.path.join(test_dir, "cohp.json"), "r") as f:
cohp_dict = json.load(f)
self.assertEqual(self.cohp.as_dict(), cohp_dict)
def test_attributes(self):
self.assertEqual(len(self.cohp.energies), 301)
self.assertEqual(self.cohp.efermi, 9.75576)
self.assertEqual(self.coop.efermi, 5.90043)
self.assertFalse(self.cohp.are_coops)
self.assertTrue(self.coop.are_coops)
def test_get_icohp(self):
self.assertEqual(self.cohp.get_icohp(),
self.cohp.get_cohp(integrated=True))
self.assertEqual(None, self.cohp_only.get_icohp())
def test_get_interpolated_value(self):
# icohp_ef are the ICHOP(Ef) values taken from
# the ICOHPLIST.lobster file.
icohp_ef_dict = {Spin.up: -0.10218, Spin.down: -0.19701}
icoop_ef_dict = {Spin.up: 0.24714}
icohp_ef = self.cohp.get_interpolated_value(self.cohp.efermi,
integrated=True)
icoop_ef = self.coop.get_interpolated_value(self.coop.efermi,
integrated=True)
self.assertAlmostEqual(icohp_ef_dict, icohp_ef)
self.assertAlmostEqual(icoop_ef_dict, icoop_ef)
with self.assertRaises(ValueError):
self.cohp_only.get_interpolated_value(5.0, integrated=True)
def test_str(self):
with open(os.path.join(test_dir, "cohp.str"), "rt") as f:
str_cohp = f.read()
with open(os.path.join(test_dir, "coop.str"), "rt") as f:
str_coop = f.read()
self.assertEqual(self.cohp.__str__(), str_cohp)
self.assertEqual(self.coop.__str__(), str_coop)
def test_antibnd_states_below_efermi(self):
self.assertDictEqual(self.cohp.has_antibnd_states_below_efermi(spin=None), {Spin.up: True, Spin.down: True})
self.assertDictEqual(self.cohp.has_antibnd_states_below_efermi(spin=None, limit=0.5),
{Spin.up: False, Spin.down: False})
self.assertDictEqual(self.cohp.has_antibnd_states_below_efermi(spin=Spin.up, limit=0.5), {Spin.up: False})
from pymatgen.electronic_structure.cohp import Cohp
from pymatgen.electronic_structure.plotter import CohpPlotter
from pymatgen.io.lobster import Cohpcar
COHPCAR_path = "E:/Python/pymatgen-master/test_files/cohp/COHPCAR.lobster"
cohpcar = Cohpcar(filename=COHPCAR_path)
cdata = cohpcar.cohp_data
cdata_processed = {}
#测试上传是否成功
for key in cdata:
c = cdata[key]
c["efermi"] = 0
c["energies"] = cohpcar.energies
c["are_coops"] = False
cdata_processed[key] = Cohp.from_dict(c)
cp = CohpPlotter()
cp.add_cohp_dict(cdata_processed)
x = cp.get_plot()
x.ylim([-6, 6])
x.show()