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Update tests
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@kavanase
kavanase committed Mar 22, 2024
1 parent fb378ca commit 5263ca5
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Showing 2 changed files with 56 additions and 40 deletions.
2 changes: 1 addition & 1 deletion tests/test_chemical_potentials.py
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Original file line number Diff line number Diff line change
Expand Up @@ -687,7 +687,7 @@ def test_vasp_std_setup(self):
assert Path(path1).is_dir()
with open(f"{path1}/KPOINTS", encoding="utf-8") as file:
contents = file.readlines()
assert contents[0] == "pymatgen with grid density = 1295 / number of atoms\n"
assert "KPOINTS from doped, with reciprocal_density = 64/Å" in contents[0]
assert contents[3] == "4 4 4\n"

with open(f"{path1}/POTCAR.spec", encoding="utf-8") as file:
Expand Down
94 changes: 55 additions & 39 deletions tests/test_vasp.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -144,7 +144,7 @@ def _general_defect_dict_set_check(self, dds, struct, incar_check=True, **dds_kw
]:
assert "PBE" in potcar_functional

potcar_settings = default_potcar_dict["POTCAR"].copy()
potcar_settings = default_potcar_dict.copy()
potcar_settings.update(dds.user_potcar_settings or {})
assert set(dds.potcar.as_dict()["symbols"]) == {
potcar_settings[el_symbol] for el_symbol in dds.structure.symbol_set
Expand Down Expand Up @@ -200,42 +200,55 @@ def _check_potcar_nupdown_dds_warnings(self, w, dds):
)

def _check_dds_incar(self, dds, struct):
# these are the base INCAR settings:
expected_incar_settings = self.neutral_def_incar_min.copy()
expected_incar_settings.update(self.hse06_incar_min) # HSE06 by default
expected_incar_settings.update(dds.user_incar_settings)
if dds.incar.get("IBRION") == -1 or dds.incar.get("NSW") == 0:
_isif = expected_incar_settings.pop("ISIF", None) # ISIF = 2 not set w/static calculations now
expected_incar_settings_w_none_vals = expected_incar_settings.copy()
# remove any entries where value is None:
expected_incar_settings = {k: v for k, v in expected_incar_settings.items() if v is not None}

default_relax_settings = default_defect_relax_set["INCAR"].copy()
default_relax_settings.update(dds.user_incar_settings)
default_relax_settings = {k: v for k, v in default_relax_settings.items() if v is not None}
print(dds.user_incar_settings, dds.incar, default_relax_settings) # for debugging

if dds.incar.get("NSW") == 0:
assert "EDIFFG" not in dds.incar
default_relax_settings.pop("EDIFFG", None) # EDIFFG not set w/static calculations
default_relax_settings.pop("IBRION", None) # IBRION not set w/static calculations now
default_relax_settings.pop("ISIF", None) # ISIF = 2 not set w/static calculations now
default_relax_settings.pop("NSW", None)
assert "ISIF" not in dds.incar
expected_incar_settings.pop("ISIF", None) # ISIF = 2 not set w/static calculations now

print("Comparing expected base INCAR settings with dds.incar")
assert expected_incar_settings.items() <= dds.incar.items()

if dds.incar.get("NSW", 0) > 0:
assert dds.incar["EDIFF"] == scaled_ediff(len(struct))
else:
assert dds.incar["EDIFF"] == 1e-6 # hard set to 1e-6 for static calculations
default_relax_settings.pop("EDIFF_PER_ATOM")

for k, v in default_defect_relax_set["INCAR"].items():
if k in [
"EDIFF_PER_ATOM",
*list(expected_incar_settings_w_none_vals.keys()), # to ensure we skip EDIFFG/POTIM
# -> None in singleshot calcs
"ISIF",
]: # already tested
for k, v in default_relax_settings.items():
if k == "GGA" and dds.incar.get("LHFCALC", False):
assert dds.incar[k] in ["Pe", "PE"] # auto set to PE if LHFCALC = True
continue

assert k in dds.incar
if isinstance(v, str): # DictSet converts all strings to capitalised lowercase
print(k, v, dds.incar[k]) # for debugging
if isinstance(v, str): # DictSet converts all ``user_incar_settings`` strings to capitalised
# lowercase, but not if set as config_dict["INCAR"]
try:
val = float(v[:2])
if k in dds.user_incar_settings: # has been overwritten
assert val != dds.incar[k]
else:
assert val == dds.incar[k]
except ValueError:
except (ValueError, AssertionError):
if k in dds.user_incar_settings:
assert v.lower().capitalize() == dds.user_incar_settings[k]
assert dds.user_incar_settings[k] in [v, v.lower().capitalize(), bool(v[:5])]
else:
assert v.lower().capitalize() == dds.incar[k]
assert dds.incar[k] in [v, v.lower().capitalize(), bool(v[:5])]
elif k in dds.user_incar_settings:
assert dds.incar[k] == dds.user_incar_settings[k]
else:
Expand Down Expand Up @@ -373,6 +386,7 @@ def test_bad_incar_setting(self):
)
_incar_pop = dds.incar # get KPAR warning

print([str(warning.message) for warning in w]) # for debugging
assert any(
"Cannot find Whoops from your user_incar_settings in the list of INCAR flags"
in str(warning.message)
Expand Down Expand Up @@ -471,7 +485,7 @@ def _write_and_check_dds_files(self, dds, **kwargs):

dds.write_input(output_path, **kwargs)

# print(output_path) # to help debug if tests fail
print(output_path) # to help debug if tests fail
assert os.path.exists(output_path)

if _potcars_available() or dds.charge_state == 0: # INCARs should be written
Expand Down Expand Up @@ -600,7 +614,9 @@ def _general_defect_relax_set_check(self, defect_relax_set, **kwargs):
def _check_drs_dds_attribute_transfer(parent_drs, child_dds):
child_incar_settings = child_dds.user_incar_settings.copy()
if "KPAR" in child_incar_settings and "KPAR" not in parent_drs.user_incar_settings:
assert child_incar_settings.pop("KPAR") == 2
assert (
child_incar_settings.pop("KPAR") == 2 or int(child_incar_settings.pop("KPAR")[0]) == 2
)
assert parent_drs.vasp_std
if "LSORBIT" in child_incar_settings and "LSORBIT" not in parent_drs.user_incar_settings:
assert child_incar_settings.pop("LSORBIT") is True
Expand All @@ -618,6 +634,7 @@ def _check_drs_dds_attribute_transfer(parent_drs, child_dds):
for k, v in singleshot_incar_settings.items(): # bulk singleshots
assert child_incar_settings.pop(k) == v

print("Checking incar settings")
assert parent_drs.user_incar_settings == child_incar_settings
assert parent_drs.user_potcar_functional == child_dds.user_potcar_functional or str(
parent_drs.user_potcar_functional[:3]
Expand Down Expand Up @@ -645,29 +662,29 @@ def _check_drs_dds_attribute_transfer(parent_drs, child_dds):
.as_dict(),
]
else:
assert parent_drs.user_kpoints_settings == child_dds.user_kpoints_settings
assert child_dds.user_kpoints_settings in [
parent_drs.user_kpoints_settings,
{"reciprocal_density": 100}, # default
]

for defect_dict_set, type in dds_test_list:
if defect_dict_set is not None:
print(f"Testing {defect_relax_set.defect_entry.name}, {type}")
print("Here")
self.dds_test._check_dds(
defect_dict_set,
defect_relax_set.defect_supercell,
charge_state=defect_relax_set.charge_state,
**kwargs,
)
print("Here")
self.dds_test._write_and_check_dds_files(defect_dict_set)
print("Here")
self.dds_test._write_and_check_dds_files(
defect_dict_set, output_path=f"{defect_relax_set.defect_entry.name}"
)
print("Here")
self.dds_test._write_and_check_dds_files(defect_dict_set, unperturbed_poscar=False)
if defect_relax_set.charge_state == 0:
self.dds_test._write_and_check_dds_files(defect_dict_set, potcar_spec=True)

print("Checking DRS/DDS attribute transfer")
_check_drs_dds_attribute_transfer(defect_relax_set, defect_dict_set)

for defect_dict_set, type in dds_bulk_test_list:
Expand Down Expand Up @@ -710,11 +727,8 @@ def _check_drs_defect_entry_attribute_transfer(parent_drs, input_defect_entry):
assert parent_drs.bulk_supercell == input_defect_entry.bulk_supercell

# test initialising DefectRelaxSet with our generation-tests materials, and writing files to disk
defect_gen_test_list = [
(self.CdTe_defect_gen, "CdTe defect_gen"),
(DefectsGenerator(self.sqs_agsbte2, generate_supercell=False), "SQS AgSbTe2 defect_gen"),
]
for defect_gen_name in [
"CdTe defect_gen",
"ytos_defect_gen",
"ytos_defect_gen_supercell",
"lmno_defect_gen",
Expand All @@ -723,13 +737,16 @@ def _check_drs_defect_entry_attribute_transfer(parent_drs, input_defect_entry):
"cd_i_supercell_defect_gen",
"N_diamond_defect_gen", # input structure for this is unordered (but this checks
# that POSCAR site symbols output should be ordered)
"SQS AgSbTe2 defect_gen",
]:
defect_gen_test_list.append(
(DefectsGenerator.from_json(f"{self.data_dir}/{defect_gen_name}.json"), defect_gen_name)
)

for defect_gen, defect_gen_name in defect_gen_test_list:
print(f"Initialising and testing: {defect_gen_name}")
if defect_gen_name == "CdTe defect_gen":
defect_gen = self.CdTe_defect_gen
elif defect_gen_name == "SQS AgSbTe2 defect_gen":
defect_gen = DefectsGenerator(self.sqs_agsbte2, generate_supercell=False)
else:
defect_gen = DefectsGenerator.from_json(f"{self.data_dir}/{defect_gen_name}.json")

# randomly choose a defect entry from the defect_gen dict:
defect_entry = random.choice(list(defect_gen.values()))

Expand All @@ -739,6 +756,7 @@ def _check_drs_defect_entry_attribute_transfer(parent_drs, input_defect_entry):

_check_drs_defect_entry_attribute_transfer(drs, defect_entry)

print(f"Testing {defect_entry.name} with custom INCAR settings")
custom_drs = DefectRelaxSet(
defect_entry,
user_incar_settings={"ENCUT": 350},
Expand Down Expand Up @@ -1134,17 +1152,15 @@ def check_generated_vasp_inputs(
if check_incar is None:
check_incar = _potcars_available()

if single_defect_dir:
folders = [
"",
]

else:
folders = [
folders = (
[
folder
for folder in os.listdir(data_dir)
if os.path.isdir(f"{data_dir}/{folder}") and ("bulk" not in folder.lower() or bulk)
]
if not single_defect_dir
else [""]
)

for folder in folders:
print(f"{generated_dir}/{folder}") # for debugging
Expand Down

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