def run_task(self, fw_spec):
lobster_cmd = env_chk(self.get("lobster_cmd"), fw_spec)
gzip_output = self.get("gzip_output", True)
gzip_WAVECAR = self.get("gzip_WAVECAR", False)
if gzip_WAVECAR:
add_files_to_gzip = VASP_OUTPUT_FILES
else:
add_files_to_gzip = [f for f in VASP_OUTPUT_FILES if f not in ["WAVECAR"]]
handler_groups = {"default": [], "no_handler": []}
validator_groups = {
"default": [
LobsterFilesValidator(),
EnoughBandsValidator(output_filename="lobsterout"),
],
"strict": [
ChargeSpillingValidator(output_filename="lobsterout"),
LobsterFilesValidator(),
EnoughBandsValidator(output_filename="lobsterout"),
],
"no_validator": [],
}
handler_group = self.get("handler_group", "default")
if isinstance(handler_group, str):
handlers = handler_groups[handler_group]
else:
handlers = handler_group
validator_group = self.get("validator_group", "default")
if isinstance(validator_group, str):
validators = validator_groups[validator_group]
else:
validators = handler_group
# LobsterJob gzips output files, Custodian would gzip all output files (even slurm)
jobs = [
LobsterJob(
lobster_cmd=lobster_cmd,
output_file="lobster.out",
stderr_file="std_err_lobster.txt",
gzipped=gzip_output,
add_files_to_gzip=add_files_to_gzip,
)
]
c = Custodian(
handlers=handlers,
jobs=jobs,
validators=validators,
gzipped_output=False,
max_errors=5,
)
c.run()
if os.path.exists(zpath("custodian.json")):
stored_custodian_data = {"custodian": loadfn(zpath("custodian.json"))}
return FWAction(stored_data=stored_custodian_data)
def test_as_dict(self):
os.chdir(test_files_lobster)
v = LobsterFilesValidator()
d = v.as_dict()
v2 = LobsterFilesValidator.from_dict(d)
self.assertIsInstance(v2, LobsterFilesValidator)
def test_check_and_correct_3(self):
os.chdir(os.path.join(test_files_lobster, "crash"))
v3 = LobsterFilesValidator()
self.assertTrue(v3.check())
def test_check_and_correct_2(self):
os.chdir(os.path.join(test_files_lobster, "../lobsterins"))
v2 = LobsterFilesValidator()
self.assertTrue(v2.check())
def test_check_and_correct_1(self):
os.chdir(test_files_lobster)
v = LobsterFilesValidator()
self.assertFalse(v.check())