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JaGeoJaGeo
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Fix average error (#2986)
1 parent 3dd5300 commit 2f4daf4

28 files changed

+33
-10387
lines changed

‎pymatgen/electronic_structure/cohp.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -786,7 +786,7 @@ def from_file(cls, fmt, filename=None, structure_file=None, are_coops=False, are
786786
efermi,
787787
energies,
788788
cohp_data["average"]["COHP"],
789-
icohp=cohp_data["average"]["COHP"],
789+
icohp=cohp_data["average"]["ICOHP"],
790790
are_coops=are_coops,
791791
are_cobis=are_cobis,
792792
)

‎pymatgen/electronic_structure/tests/test_cohp.py

Lines changed: 16 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -725,21 +725,25 @@ def setUp(self):
725725
filepath = os.path.join(test_dir, "COPL.BiSe")
726726
structure = os.path.join(test_dir, "CTRL.BiSe")
727727
self.cohp_lmto = CompleteCohp.from_file("lmto", filename=filepath, structure_file=structure)
728-
filepath = os.path.join(test_dir, "COHPCAR.lobster")
728+
filepath = os.path.join(test_dir, "COHPCAR.lobster.gz")
729729
structure = os.path.join(test_dir, "POSCAR")
730730
self.cohp_lobster = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure)
731-
filepath = os.path.join(test_dir, "COOPCAR.lobster.BiSe")
731+
# with open(os.path.join(test_dir, "complete_cohp_lobster.json"),'w') as f:
732+
# json.dump(self.cohp_lobster.as_dict(),f)
733+
filepath = os.path.join(test_dir, "COOPCAR.lobster.BiSe.gz")
732734
structure = os.path.join(test_dir, "POSCAR.BiSe")
733735
self.coop_lobster = CompleteCohp.from_file(
734736
"lobster", filename=filepath, structure_file=structure, are_coops=True
735737
)
736-
filepath = os.path.join(test_dir, "COHPCAR.lobster.orbitalwise")
738+
filepath = os.path.join(test_dir, "COHPCAR.lobster.orbitalwise.gz")
737739
structure = os.path.join(test_dir, "POSCAR.orbitalwise")
738740
self.cohp_orb = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure)
739-
filepath = os.path.join(test_dir, "COHPCAR.lobster.notot.orbitalwise")
741+
# with open(os.path.join(test_dir, "complete_cohp_orbitalwise.json"),'w') as f:
742+
# json.dump(self.cohp_orb.as_dict(),f)
743+
filepath = os.path.join(test_dir, "COHPCAR.lobster.notot.orbitalwise.gz")
740744
self.cohp_notot = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure)
741745
# Lobster 3.0
742-
filepath = os.path.join(test_dir, "COHPCAR.lobster.Na2UO4")
746+
filepath = os.path.join(test_dir, "COHPCAR.lobster.Na2UO4.gz")
743747
structure = os.path.join(test_dir, "POSCAR.Na2UO4")
744748
self.cohp_lobster_forb = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure)
745749

@@ -750,12 +754,12 @@ def setUp(self):
750754
"lobster", filename=filepath, structure_file=structure
751755
)
752756
# COBI
753-
filepath = os.path.join(test_dir, "COBICAR.lobster")
757+
filepath = os.path.join(test_dir, "COBICAR.lobster.gz")
754758
structure = os.path.join(test_dir, "POSCAR.COBI")
755759

756760
self.cobi = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure, are_cobis=True)
757761

758-
def test_attiributes(self):
762+
def test_attributes(self):
759763
assert not self.cohp_lobster.are_coops
760764
assert not self.cohp_lobster.are_cobis
761765
assert not self.cohp_lobster_dict.are_coops
@@ -779,6 +783,9 @@ def test_attiributes(self):
779783
assert self.cobi.are_cobis
780784
assert not self.cobi.are_coops
781785

786+
assert self.cohp_lobster_forb.cohp[Spin.up][0] == 0.00000
787+
assert self.cohp_lobster_forb.icohp[Spin.up][0] == -0.09040
788+
782789
def test_dict(self):
783790
# The json files are dict representations of the COHPs from the LMTO
784791
# and LOBSTER calculations and should thus be the same.
@@ -1092,11 +1099,11 @@ def test_orbital_resolved_cohp_summed_spin_channels(self):
10921099

10931100
class MethodTest(unittest.TestCase):
10941101
def setUp(self):
1095-
filepath = os.path.join(test_dir, "COHPCAR.lobster")
1102+
filepath = os.path.join(test_dir, "COHPCAR.lobster.gz")
10961103
structure = os.path.join(test_dir, "POSCAR")
10971104
self.cohp_lobster = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure)
10981105

1099-
filepath = os.path.join(test_dir, "COHPCAR.lobster.orbitalwise")
1106+
filepath = os.path.join(test_dir, "COHPCAR.lobster.orbitalwise.gz")
11001107
structure = os.path.join(test_dir, "POSCAR.orbitalwise")
11011108
self.cohp_orb = CompleteCohp.from_file("lobster", filename=filepath, structure_file=structure)
11021109

‎pymatgen/io/lobster/tests/test_lobster.py

Lines changed: 13 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -44,36 +44,38 @@
4444

4545
class CohpcarTest(PymatgenTest):
4646
def setUp(self):
47-
self.cohp_bise = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.BiSe"))
47+
self.cohp_bise = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.BiSe.gz"))
4848
self.coop_bise = Cohpcar(
49-
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster.BiSe"),
49+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster.BiSe.gz"),
5050
are_coops=True,
5151
)
52-
self.cohp_fe = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster"))
52+
self.cohp_fe = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster.gz"))
5353
self.coop_fe = Cohpcar(
54-
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster"),
54+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster.gz"),
5555
are_coops=True,
5656
)
57-
self.orb = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.orbitalwise"))
57+
self.orb = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.orbitalwise.gz"))
5858
self.orb_notot = Cohpcar(
59-
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.notot.orbitalwise")
59+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.notot.orbitalwise.gz")
6060
)
6161

6262
# Lobster 3.1 (Test data is from prerelease of Lobster 3.1)
63-
self.cohp_KF = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.KF"))
63+
self.cohp_KF = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.KF.gz"))
6464
self.coop_KF = Cohpcar(
65-
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.KF"),
65+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.KF.gz"),
6666
are_coops=True,
6767
)
6868

6969
# example with f electrons
70-
self.cohp_Na2UO4 = Cohpcar(filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.Na2UO4"))
70+
self.cohp_Na2UO4 = Cohpcar(
71+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COHPCAR.lobster.Na2UO4.gz")
72+
)
7173
self.coop_Na2UO4 = Cohpcar(
72-
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster.Na2UO4"),
74+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COOPCAR.lobster.Na2UO4.gz"),
7375
are_coops=True,
7476
)
7577
self.cobi = Cohpcar(
76-
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COBICAR.lobster"),
78+
filename=os.path.join(PymatgenTest.TEST_FILES_DIR, "cohp", "COBICAR.lobster.gz"),
7779
are_cobis=True,
7880
)
7981

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