def setUp(self):
super(TestLammpsDrone, self).setUp()
self.drone = LammpsDrone()
self.calc_dir = os.path.join(module_dir, "test_files")
self.input_file = os.path.join(self.calc_dir, "lammps.in")
self.data_file = os.path.join(self.calc_dir, "lammps.data")
self.log_file = os.path.join(self.calc_dir, "lammps.log")
def setUp(self):
super(TestLammpsDrone, self).setUp()
self.drone = LammpsDrone()
self.calc_dir = os.path.join(module_dir, "test_files")
self.input_file = os.path.join(self.calc_dir, "lammps.in")
self.data_file = os.path.join(self.calc_dir, "lammps.data")
self.log_file = os.path.join(self.calc_dir, "lammps.log")
class TestLammpsDrone(AtomateTest):
def setUp(self):
super(TestLammpsDrone, self).setUp()
self.drone = LammpsDrone()
self.calc_dir = os.path.join(module_dir, "test_files")
self.input_file = os.path.join(self.calc_dir, "lammps.in")
self.data_file = os.path.join(self.calc_dir, "lammps.data")
self.log_file = os.path.join(self.calc_dir, "lammps.log")
def test_assimilate(self):
doc = self.drone.assimilate(self.calc_dir, input_filename="lammps.in",
log_filename="lammps.log",
data_filename="lammps.data")
lmps_input_set = LammpsInputSet.from_file("lammps", self.input_file,
{}, lammps_data=self.data_file,
data_filename="lammps.data")
# no dump file ==> output is just the log file
lmps_output = LammpsLog(self.log_file)
self.assertDictEqual(doc["input"], lmps_input_set.as_dict())
self.assertDictEqual(doc["output"]["log"], lmps_output.as_dict())
enthalpy = [1906.1958, 1220.2265, 596.51973, 465.01619, 148.91822, 26.160144,
319.27146, 141.35729, 299.04503, 271.19625, 145.4361]
self.assertEqual(lmps_output.as_dict()['thermo_data']['enthalpy'], enthalpy)
class TestLammpsDrone(AtomateTest):
def setUp(self):
super(TestLammpsDrone, self).setUp()
self.drone = LammpsDrone()
self.calc_dir = os.path.join(module_dir, "test_files")
self.input_file = os.path.join(self.calc_dir, "lammps.in")
self.data_file = os.path.join(self.calc_dir, "lammps.data")
self.log_file = os.path.join(self.calc_dir, "lammps.log")
def test_assimilate(self):
doc = self.drone.assimilate(self.calc_dir, input_filename="lammps.in",
log_filename="lammps.log",
data_filename="lammps.data")
lmps_input_set = LammpsInputSet.from_file("lammps", self.input_file,
{}, lammps_data=self.data_file,
data_filename="lammps.data")
# no dump file ==> output is just the log file
lmps_output = LammpsLog(self.log_file)
self.assertDictEqual(doc["input"], lmps_input_set.as_dict())
self.assertDictEqual(doc["output"]["log"], lmps_output.as_dict())
enthalpy = [1906.1958, 1220.2265, 596.51973, 465.01619, 148.91822, 26.160144,
319.27146, 141.35729, 299.04503, 271.19625, 145.4361]
self.assertEqual(lmps_output.as_dict()['thermo_data']['enthalpy'], enthalpy)
def run_task(self, fw_spec):
# get the directory that contains the LAMMPS run parse.
calc_dir = os.getcwd()
if "calc_dir" in self:
calc_dir = self["calc_dir"]
elif self.get("calc_loc"):
calc_dir = get_calc_loc(self["calc_loc"],
fw_spec["calc_locs"])["path"]
# parse the directory
logger.info(f"PARSING DIRECTORY: {calc_dir}")
drone = LammpsDrone(
additional_fields=self.get("additional_fields"),
diffusion_params=self.get("diffusion_params", None),
)
task_doc = drone.assimilate(
calc_dir,
input_filename=self["input_filename"],
log_filename=self.get("log_filename", "log.lammps"),
is_forcefield=self.get("is_forcefield", False),
data_filename=self.get("data_filename", None),
dump_files=self.get("dump_filenames", None),
)
# Check for additional keys to set based on the fw_spec
if self.get("fw_spec_field"):
task_doc.update(fw_spec[self.get("fw_spec_field")])
db_file = env_chk(self.get("db_file"), fw_spec)
# db insertion
if not db_file:
with open("task.json", "w") as f:
f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
else:
mmdb = LammpsCalcDb.from_db_file(db_file)
# insert the task document
t_id = mmdb.insert(task_doc)
logger.info(f"Finished parsing with task_id: {t_id}")
return FWAction(stored_data={"task_id": task_doc.get("task_id", None)})
def run_task(self, fw_spec):
# get the directory that contains the LAMMPS run parse.
calc_dir = os.getcwd()
if "calc_dir" in self:
calc_dir = self["calc_dir"]
elif self.get("calc_loc"):
calc_dir = get_calc_loc(self["calc_loc"], fw_spec["calc_locs"])["path"]
# parse the directory
logger.info("PARSING DIRECTORY: {}".format(calc_dir))
drone = LammpsDrone(additional_fields=self.get("additional_fields"),
diffusion_params=self.get("diffusion_params", None))
task_doc = drone.assimilate(calc_dir, input_filename=self["input_filename"],
log_filename=self.get("log_filename", "log.lammps"),
is_forcefield=self.get("is_forcefield", False),
data_filename=self.get("data_filename", None),
dump_files=self.get("dump_filenames", None))
# Check for additional keys to set based on the fw_spec
if self.get("fw_spec_field"):
task_doc.update(fw_spec[self.get("fw_spec_field")])
db_file = env_chk(self.get('db_file'), fw_spec)
# db insertion
if not db_file:
with open("task.json", "w") as f:
f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
else:
mmdb = LammpsCalcDb.from_db_file(db_file)
# insert the task document
t_id = mmdb.insert(task_doc)
logger.info("Finished parsing with task_id: {}".format(t_id))
return FWAction(stored_data={"task_id": task_doc.get("task_id", None)})