Skip to content

Commit

Permalink
Update tests (rounding issue on GH Actions)
Browse files Browse the repository at this point in the history
  • Loading branch information
@kavanase
kavanase committed Aug 23, 2023
1 parent 2d96187 commit 5be140a
Show file tree
Hide file tree
Showing 2 changed files with 106 additions and 50 deletions.
1 change: 0 additions & 1 deletion tests/data/lmno_defect_gen.json
View file

Large diffs are not rendered by default.

155 changes: 106 additions & 49 deletions tests/test_generation.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -150,8 +150,7 @@ def setUp(self):
"DefectsGenerator for input composition Li2Mn3NiO8, space group P4_332 with 197 defect "
"entries created."
)
self.lmno_defect_gen_info = (
"""Vacancies Charge States Conv. Cell Coords Wyckoff
self.lmno_defect_gen_info_pt1 = """Vacancies Charge States Conv. Cell Coords Wyckoff
----------- ------------------ ------------------- ---------
v_Li [-1,0,+1] [0.004,0.004,0.004] 8c
v_Mn [-4,-3,-2,-1,0,+1] [0.121,0.129,0.625] 12d
Expand All @@ -176,9 +175,12 @@ def setUp(self):
O_Li [-3,-2,-1,0] [0.004,0.004,0.004] 8c
O_Mn [-6,-5,-4,-3,-2,-1,0] [0.121,0.129,0.625] 12d
O_Ni [-4,-3,-2,-1,0] [0.625,0.625,0.625] 4b
"""

Interstitials Charge States Conv. Cell Coords Wyckoff
------------------- --------------- ------------------- ---------
self.lmno_defect_gen_info_interstitials = (
"Interstitials Charge States Conv. Cell "
"Coords Wyckoff\n"
"""------------------- --------------- ------------------- ---------
Li_i_C1_Li1.75 [0,+1] [0.199,0.303,0.444] 24e
Li_i_C1_O1.72 [0,+1] [0.248,0.480,0.249] 24e
Li_i_C1_O1.78 [0,+1] [0.017,0.261,0.250] 24e
Expand Down Expand Up @@ -208,6 +210,44 @@ def setUp(self):
O_i_C2_Li1.86 [-2,-1,0] [0.086,0.375,0.336] 12d
O_i_C3 [-2,-1,0] [0.497,0.497,0.497] 8c
\n"""
)

self.lmno_defect_gen_info_interstitials_GH = (
"Interstitials Charge States Conv. Cell "
"Coords Wyckoff\n"
"""--------------- --------------- ------------------- ---------
Li_i_C1_Li1.75 [0,+1] [0.199,0.303,0.444] 24e
Li_i_C1_O1.72 [0,+1] [0.248,0.480,0.249] 24e
Li_i_C1_O1.78 [0,+1] [0.017,0.261,0.250] 24e
Li_i_C2_Li1.83 [0,+1] [0.077,0.125,0.173] 12d
Li_i_C2_Li1.84 [0,+1] [0.151,0.375,0.401] 12d
Li_i_C2_Li1.86 [0,+1] [0.086,0.375,0.336] 12d
Li_i_C3 [0,+1] [0.497,0.497,0.497] 8c
Mn_i_C1_Li1.75 [0,+1,+2,+3,+4] [0.199,0.303,0.444] 24e
Mn_i_C1_O1.72 [0,+1,+2,+3,+4] [0.248,0.480,0.249] 24e
Mn_i_C1_O1.78 [0,+1,+2,+3,+4] [0.017,0.261,0.250] 24e
Mn_i_C2_Li1.83 [0,+1,+2,+3,+4] [0.077,0.125,0.173] 12d
Mn_i_C2_Li1.84 [0,+1,+2,+3,+4] [0.151,0.375,0.401] 12d
Mn_i_C2_Li1.86 [0,+1,+2,+3,+4] [0.086,0.375,0.336] 12d
Mn_i_C3 [0,+1,+2,+3,+4] [0.497,0.497,0.497] 8c
Ni_i_C1_Li1.75 [0,+1,+2,+3,+4] [0.199,0.303,0.444] 24e
Ni_i_C1_O1.72 [0,+1,+2,+3,+4] [0.248,0.480,0.249] 24e
Ni_i_C1_O1.78 [0,+1,+2,+3,+4] [0.017,0.261,0.250] 24e
Ni_i_C2_Li1.83 [0,+1,+2,+3,+4] [0.077,0.125,0.173] 12d
Ni_i_C2_Li1.84 [0,+1,+2,+3,+4] [0.151,0.375,0.401] 12d
Ni_i_C2_Li1.86 [0,+1,+2,+3,+4] [0.086,0.375,0.336] 12d
Ni_i_C3 [0,+1,+2,+3,+4] [0.497,0.497,0.497] 8c
O_i_C1_Li1.75 [-2,-1,0] [0.199,0.303,0.444] 24e
O_i_C1_O1.72 [-2,-1,0] [0.248,0.480,0.249] 24e
O_i_C1_O1.78 [-2,-1,0] [0.017,0.261,0.250] 24e
O_i_C2_Li1.83 [-2,-1,0] [0.077,0.125,0.173] 12d
O_i_C2_Li1.84 [-2,-1,0] [0.151,0.375,0.401] 12d
O_i_C2_Li1.86 [-2,-1,0] [0.086,0.375,0.336] 12d
O_i_C3 [-2,-1,0] [0.497,0.497,0.497] 8c
\n"""
)

self.lmno_defect_gen_info_final = (
"The number in the Wyckoff label is the site multiplicity/degeneracy of that defect in the "
"conventional ('conv.') unit cell, which comprises 4 formula unit(s) of Li2Mn3NiO8.\n"
"Note that Wyckoff letters can depend on the ordering of elements in the conventional "
Expand Down Expand Up @@ -1505,7 +1545,7 @@ def test_ytos_supercell_input(self):
self.ytos_defect_gen_check(ytos_defect_gen)
self._load_and_test_defect_gen_jsons(ytos_defect_gen)

ytos_defect_gen.to_json("data/ytos_defect_gen.json") # for testing in test_vasp.py
ytos_defect_gen.to_json(f"{self.data_dir}/ytos_defect_gen.json") # for testing in test_vasp.py

def test_ytos_no_generate_supercell(self):
# tests the case of an input structure which is >10 Å in each direction, has
Expand Down Expand Up @@ -1537,7 +1577,12 @@ def test_ytos_no_generate_supercell(self):
) # for testing in test_vasp.py

def lmno_defect_gen_check(self, lmno_defect_gen, generate_supercell=True):
assert self.lmno_defect_gen_info in lmno_defect_gen._defect_generator_info()
assert self.lmno_defect_gen_info_pt1 in lmno_defect_gen._defect_generator_info()
assert self.lmno_defect_gen_info_final in lmno_defect_gen._defect_generator_info()
assert (
self.lmno_defect_gen_info_interstitials in lmno_defect_gen._defect_generator_info()
or self.lmno_defect_gen_info_interstitials_GH in lmno_defect_gen._defect_generator_info()
)
assert lmno_defect_gen._BilbaoCS_conv_cell_vector_mapping == [0, 1, 2]
# test attributes:
structure_matcher = StructureMatcher(comparator=ElementComparator()) # ignore oxidation states
Expand Down Expand Up @@ -1629,43 +1674,37 @@ def lmno_defect_gen_check(self, lmno_defect_gen, generate_supercell=True):
)
assert dict(lmno_defect_gen.items()) == lmno_defect_gen.defect_entries # __iter__()
assert str(lmno_defect_gen) == self.lmno_defect_gen_string # __str__()
assert ( # __repr__()
repr(lmno_defect_gen)
== self.lmno_defect_gen_string
+ "\n---------------------------------------------------------\n"
+ self.lmno_defect_gen_info
)
# __repr__() tested in other tests, skipped here due to slight difference in rounding behaviour
# between local and GH Actions
assert all(
defect_entry_name in lmno_defect_gen
for defect_entry_name in lmno_defect_gen.defect_entries # __contains__()
)
assert (
lmno_defect_gen["Ni_i_C2_Li1.84O1.94_+2"]
== lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"]
lmno_defect_gen["Ni_i_C1_O1.78_+2"] == lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"]
) # __getitem__()
assert (
lmno_defect_gen.get("Ni_i_C2_Li1.84O1.94_+2")
== lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"]
lmno_defect_gen.get("Ni_i_C1_O1.78_+2") == lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"]
) # get()
defect_entry = lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"]
del lmno_defect_gen["Ni_i_C2_Li1.84O1.94_+2"] # __delitem__()
assert "Ni_i_C2_Li1.84O1.94_+2" not in lmno_defect_gen
lmno_defect_gen["Ni_i_C2_Li1.84O1.94_+2"] = defect_entry # __setitem__()
defect_entry = lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"]
del lmno_defect_gen["Ni_i_C1_O1.78_+2"] # __delitem__()
assert "Ni_i_C1_O1.78_+2" not in lmno_defect_gen
lmno_defect_gen["Ni_i_C1_O1.78_+2"] = defect_entry # __setitem__()
# assert setting something else throws an error
with self.assertRaises(TypeError) as e:
lmno_defect_gen["Ni_i_C2_Li1.84O1.94_+2"] = defect_entry.defect
lmno_defect_gen["Ni_i_C1_O1.78_+2"] = defect_entry.defect
assert "Value must be a DefectEntry object, not Interstitial" in str(e.exception)
with self.assertRaises(ValueError) as e:
fd_up_defect_entry = copy.deepcopy(lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"])
fd_up_defect_entry = copy.deepcopy(lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"])
fd_up_defect_entry.defect.structure = self.cdte_bulk_supercell
lmno_defect_gen["Ni_i_C2_Li1.84O1.94_+2"] = fd_up_defect_entry
lmno_defect_gen["Ni_i_C1_O1.78_+2"] = fd_up_defect_entry
assert "Value must have the same primitive structure as the DefectsGenerator object, " in str(
e.exception
)
with self.assertRaises(ValueError) as e:
fd_up_defect_entry = copy.deepcopy(lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"])
fd_up_defect_entry = copy.deepcopy(lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"])
fd_up_defect_entry.sc_entry = copy.deepcopy(lmno_defect_gen.defect_entries["Li_O_C3_+3"])
lmno_defect_gen["Ni_i_C2_Li1.84O1.94_+2"] = fd_up_defect_entry
lmno_defect_gen["Ni_i_C1_O1.78_+2"] = fd_up_defect_entry
assert "Value must have the same supercell as the DefectsGenerator object," in str(e.exception)
# randomly test one defect entry equivalent supercell sites:
random_name, random_defect_entry = random.choice(list(lmno_defect_gen.defect_entries.items()))
Expand Down Expand Up @@ -1694,56 +1733,55 @@ def lmno_defect_gen_check(self, lmno_defect_gen, generate_supercell=True):
assert np.isclose(min_frac_dist, equiv_min_frac_dist, atol=0.001)

# test defect entry attributes
assert lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].name == "Ni_i_C2_Li1.84O1.94_+2"
assert lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].charge_state == +2
assert lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].name == "Ni_i_C1_O1.78_+2"
assert lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].charge_state == +2
assert (
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect.defect_type
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect.defect_type
== DefectType.Interstitial
)
assert lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].wyckoff == "12d"
assert lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect.wyckoff == "12d"
assert lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].wyckoff == "24e"
assert lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect.wyckoff == "24e"
assert (
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect.multiplicity == 12
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect.multiplicity == 24
) # prim = conv structure in LMNO
if generate_supercell:
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].sc_defect_frac_coords,
np.array([0.4246, 0.4375, 0.5496]), # closest to [0.5, 0.5, 0.5]
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].sc_defect_frac_coords,
np.array([0.494716, 0.616729, 0.500199]), # closest to [0.5, 0.5, 0.5]
rtol=1e-2,
)
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect_supercell_site.frac_coords,
np.array([0.4246, 0.4375, 0.5496]), # closest to [0.5, 0.5, 0.5]
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect_supercell_site.frac_coords,
np.array([0.494716, 0.616729, 0.500199]), # closest to [0.5, 0.5, 0.5]
rtol=1e-2,
)
else:
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].sc_defect_frac_coords,
np.array([0.15074, 0.375, 0.40074]), # closest to [0.5, 0.5, 0.5]
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].sc_defect_frac_coords,
np.array([0.500397, 0.510568, 0.766541]), # closest to [0.5, 0.5, 0.5]
rtol=1e-2,
)
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect_supercell_site.frac_coords,
np.array([0.15074, 0.375, 0.40074]), # closest to [0.5, 0.5, 0.5]
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect_supercell_site.frac_coords,
np.array([0.500397, 0.510568, 0.766541]), # closest to [0.5, 0.5, 0.5]
rtol=1e-2,
)
assert (
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect_supercell_site.specie.symbol
== "Ni"
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect_supercell_site.specie.symbol == "Ni"
)
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].conv_cell_frac_coords,
np.array([0.151, 0.375, 0.401]),
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].conv_cell_frac_coords,
np.array([0.017, 0.261, 0.250]),
atol=1e-3,
)
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect.conv_cell_frac_coords,
np.array([0.151, 0.375, 0.401]),
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect.conv_cell_frac_coords,
np.array([0.017, 0.261, 0.250]),
atol=1e-3,
)
np.testing.assert_allclose(
lmno_defect_gen.defect_entries["Ni_i_C2_Li1.84O1.94_+2"].defect.site.frac_coords,
np.array([0.15074, 0.375, 0.40074]),
lmno_defect_gen.defect_entries["Ni_i_C1_O1.78_+2"].defect.site.frac_coords,
np.array([0.017, 0.261, 0.250]),
atol=1e-3,
)

Expand Down Expand Up @@ -1948,7 +1986,16 @@ def test_lmno(self):
finally:
sys.stdout = original_stdout # Reset standard output to its original value

assert self.lmno_defect_gen_info in output
assert self.lmno_defect_gen_info_pt1 in output
assert self.lmno_defect_gen_info_final in output
assert (
self.lmno_defect_gen_info_interstitials in output
or self.lmno_defect_gen_info_interstitials_GH in output
)
if self.lmno_defect_gen_info_interstitials in output:
print("Original interstitials output printed")
else: # for tracking purposes
print("GH-rounded interstitials output printed")

self._save_defect_gen_jsons(lmno_defect_gen)
self.lmno_defect_gen_check(lmno_defect_gen)
Expand Down Expand Up @@ -1980,7 +2027,17 @@ def test_lmno_no_generate_supercell(self):
finally:
sys.stdout = original_stdout # Reset standard output to its original value.

assert self.lmno_defect_gen_info in output
assert self.lmno_defect_gen_info_pt1 in output
assert self.lmno_defect_gen_info_final in output
assert (
self.lmno_defect_gen_info_interstitials in output
or self.lmno_defect_gen_info_interstitials_GH in output
)

if self.lmno_defect_gen_info_interstitials in output:
print("Original interstitials output printed")
else: # for tracking purposes
print("GH-rounded interstitials output printed")

self._save_defect_gen_jsons(lmno_defect_gen)
self.lmno_defect_gen_check(lmno_defect_gen, generate_supercell=False)
Expand Down

0 comments on commit 5be140a

Please sign in to comment.