def test_assimilate_freq(self):
drone = QChemDrone()
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "FF_working"),
input_file="test.qin.freq_1",
output_file="test.qout.freq_1",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "freq")
self.assertEqual(doc["output"]["job_type"], "freq")
test_freqs = np.array([
12.52, 45.28, 260.96, 329.08, 531.01, 582.11, 744.91, 779.2,
800.47, 863.15, 928.68, 969., 1092.86, 1124., 1147.64, 1209.1,
1387.39, 1693.97, 1913.05, 3316.2, 3341.73
])
for ii in enumerate(test_freqs):
self.assertEqual(test_freqs[ii[0]], doc["output"]["frequencies"][ii[0]])
self.assertEqual(doc["output"]["enthalpy"], 37.547)
self.assertEqual(doc["output"]["entropy"], 83.81)
self.assertEqual(doc["walltime"], 394.45)
self.assertEqual(doc["cputime"], 997.39)
self.assertEqual(doc["smiles"], "O1[C](O[Li])OC=C1")
self.assertEqual(doc["formula_pretty"], "LiH2(CO)3")
self.assertEqual(doc["formula_anonymous"], "AB2C3D3")
self.assertEqual(doc["chemsys"], "C-H-Li-O")
self.assertEqual(doc["pointgroup"], "Cs")
self.assertIn("custodian", doc)
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 1)
def test_assimilate_opt(self):
drone = QChemDrone()
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "FF_working"),
input_file="test.qin.opt_1",
output_file="test.qout.opt_1",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "opt")
self.assertEqual(doc["output"]["final_energy"], -348.652462579636)
self.assertEqual(doc["walltime"], 62.83)
self.assertEqual(doc["cputime"], 715.76)
self.assertEqual(doc["smiles"], "O1[C](O[Li])OC=C1")
self.assertEqual(doc["formula_pretty"], "LiH2(CO)3")
self.assertEqual(doc["formula_anonymous"], "AB2C3D3")
self.assertEqual(doc["chemsys"], "C-H-Li-O")
self.assertEqual(doc["pointgroup"], "Cs")
self.assertIn("custodian", doc)
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("optimized_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 1)
def test_assimilate_opt_with_hidden_changes_from_handler(self):
drone = QChemDrone(additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "1746_complete"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "freq")
self.assertEqual(doc["output"]["final_energy"], -303.835532370106)
self.assertEqual(doc["smiles"], "O1C(=CC1=O)[CH]")
self.assertEqual(doc["state"], "successful")
self.assertEqual(doc["num_frequencies_flattened"], 0)
self.assertEqual(doc["walltime"], 631.54)
self.assertEqual(doc["cputime"], 7471.17)
self.assertEqual(doc["formula_pretty"], "HC2O")
self.assertEqual(doc["formula_anonymous"], "ABC2")
self.assertEqual(doc["chemsys"], "C-H-O")
self.assertEqual(doc["pointgroup"], "C1")
self.assertEqual(doc["orig"]["rem"], doc["calcs_reversed"][-1]["input"]["rem"])
orig_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["orig"]["molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
initial_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["input"]["initial_molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
self.assertEqual(orig_molgraph.isomorphic_to(initial_molgraph), False)
def test_assimilate_unstable_opt(self):
drone = QChemDrone(
runs=[
"opt_0", "freq_0", "opt_1", "freq_1", "opt_2", "freq_2",
"opt_3", "freq_3"
],
additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "2620_complete"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "opt")
self.assertEqual(doc["output"]["final_energy"], "unstable")
self.assertEqual(doc["smiles"], "[S](=O)[N]S[C]")
self.assertEqual(doc["state"], "unsuccessful")
self.assertEqual(doc["num_frequencies_flattened"], 0)
self.assertEqual(doc["walltime"], None)
self.assertEqual(doc["cputime"], None)
self.assertEqual(doc["formula_pretty"], "CS2NO")
self.assertEqual(doc["formula_anonymous"], "ABCD2")
self.assertEqual(doc["chemsys"], "C-N-O-S")
self.assertEqual(doc["pointgroup"], "C1")
self.assertEqual(doc["orig"]["rem"], doc["calcs_reversed"][-1]["input"]["rem"])
self.assertEqual(doc["orig"]["molecule"], doc["calcs_reversed"][-1]["input"]["molecule"])
orig_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["orig"]["molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
initial_molgraph = MoleculeGraph.with_local_env_strategy(Molecule.from_dict(doc["input"]["initial_molecule"]),
OpenBabelNN(),
reorder=False,
extend_structure=False)
self.assertEqual(orig_molgraph.isomorphic_to(initial_molgraph), True)
def test_assimilate_bad_FF(self):
drone = QChemDrone(additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "launcher_bad_FF"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["special_run_type"], "frequency_flattener")
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "freq")
self.assertEqual(doc["state"], "unsuccessful")
def run_task(self, fw_spec):
# get the directory that contains the QChem dir to 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"]
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
multirun = self.get("multirun", False)
# parse the QChem directory
logger.info("PARSING DIRECTORY: {}".format(calc_dir))
drone = QChemDrone(additional_fields=self.get("additional_fields"))
# assimilate (i.e., parse)
task_doc = drone.assimilate(
path=calc_dir,
input_file=input_file,
output_file=output_file,
multirun=multirun)
# 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")])
# Update fw_spec with final/optimized structure
update_spec = {}
if task_doc.get("output").get("optimized_molecule"):
update_spec["prev_calc_molecule"] = task_doc["output"][
"optimized_molecule"]
# get the database connection
db_file = env_chk(self.get("db_file"), fw_spec)
# db insertion or taskdoc dump
if not db_file:
with open(os.path.join(calc_dir, "task.json"), "w") as f:
f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
else:
mmdb = QChemCalcDb.from_db_file(db_file, admin=True)
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)},
update_spec=update_spec)
def test_assimilate_FF(self):
drone = QChemDrone(
runs=[
"opt_0", "freq_0", "opt_1", "freq_1", "opt_2", "freq_2",
"opt_3", "freq_3"
],
additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "FF_working"),
input_file="test.qin",
output_file="test.qout",
multirun=False)
self.assertEqual(doc["special_run_type"], "frequency_flattener")
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "freq")
test_freqs = np.array([
12.52, 45.28, 260.96, 329.08, 531.01, 582.11, 744.91, 779.2,
800.47, 863.15, 928.68, 969., 1092.86, 1124., 1147.64, 1209.1,
1387.39, 1693.97, 1913.05, 3316.2, 3341.73
])
for ii in enumerate(test_freqs):
self.assertEqual(test_freqs[ii[0]], doc["output"]["frequencies"][ii[0]])
self.assertEqual(doc["output"]["frequencies"][ii[0]],
doc["calcs_reversed"][0]["frequencies"][ii[0]])
self.assertEqual(doc["output"]["enthalpy"], 37.547)
self.assertEqual(doc["output"]["entropy"], 83.81)
self.assertEqual(doc["num_frequencies_flattened"], 1)
self.assertEqual(doc["walltime"], 935.29)
self.assertEqual(doc["cputime"], 3616.6400000000003)
self.assertEqual(doc["smiles"], "O1[C](O[Li])OC=C1")
self.assertEqual(doc["formula_pretty"], "LiH2(CO)3")
self.assertEqual(doc["formula_anonymous"], "AB2C3D3")
self.assertEqual(doc["chemsys"], "C-H-Li-O")
self.assertEqual(doc["pointgroup"], "Cs")
self.assertIn("custodian", doc)
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("optimized_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 4)
self.assertEqual(
list(doc["calcs_reversed"][0].keys()),
list(doc["calcs_reversed"][2].keys()))
self.assertEqual(
list(doc["calcs_reversed"][1].keys()),
list(doc["calcs_reversed"][3].keys()))
def test_assimilate_disconnected_opt(self):
drone = QChemDrone(additional_fields={"special_run_type": "frequency_flattener"})
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "disconnected_but_converged"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "freq")
self.assertEqual(doc["output"]["final_energy"], -303.07602688705)
self.assertEqual(doc["smiles"], "O=C.O=C=O")
self.assertEqual(doc["state"], "successful")
self.assertEqual(doc["num_frequencies_flattened"], 0)
self.assertEqual(doc["walltime"], 492.42999999999995)
self.assertEqual(doc["cputime"], 8825.76)
self.assertEqual(doc["formula_pretty"], "H2C2O3")
self.assertEqual(doc["formula_anonymous"], "A2B2C3")
self.assertEqual(doc["chemsys"], "C-H-O")
self.assertEqual(doc["pointgroup"], "C1")
self.assertEqual(doc["orig"]["rem"], doc["calcs_reversed"][-1]["input"]["rem"])
self.assertEqual(doc["calcs_reversed"][-1]["structure_change"], "unconnected_fragments")
def test_assimilate_sp(self):
drone = QChemDrone()
doc = drone.assimilate(path=os.path.join(module_dir, "..",
"test_files", "launcher_sp"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "sp")
self.assertEqual(doc["output"]["job_type"], "sp")
self.assertEqual(doc["output"]["final_energy"], -75.1151765884)
self.assertEqual(doc["walltime"], 4.69)
self.assertEqual(doc["cputime"], 134.03)
self.assertEqual(doc["smiles"], "[O]")
self.assertEqual(doc["formula_pretty"], "O2")
self.assertEqual(doc["formula_anonymous"], "A")
self.assertEqual(doc["chemsys"], "O")
self.assertEqual(doc["pointgroup"], "Kh")
self.assertIn("custodian", doc)
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 1)
def test_sp_with_orig(self):
drone = QChemDrone()
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "launcher_bad_sp"),
input_file="mol.qin",
output_file="mol.qout",
multirun=False)
self.assertEqual(doc["input"]["job_type"], "sp")
self.assertEqual(doc["output"]["job_type"], "sp")
self.assertEqual(doc["output"]["final_energy"], -74.540726551)
self.assertEqual(doc["walltime"], 3.9)
self.assertEqual(doc["cputime"], 113.27)
self.assertEqual(doc["smiles"], "[O]")
self.assertEqual(doc["formula_pretty"], "O2")
self.assertEqual(doc["formula_anonymous"], "A")
self.assertEqual(doc["chemsys"], "O")
self.assertEqual(doc["pointgroup"], "Kh")
self.assertIn("custodian", doc)
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 1)
def test_multirun(self):
drone = QChemDrone()
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "julian_nt"),
input_file="julian.qin",
output_file="julian.qout",
multirun=True)
self.assertEqual(doc["input"]["job_type"], "optimization")
self.assertEqual(doc["output"]["job_type"], "frequency")
test_freqs = np.array([
-69.17, 117.81, 244.67, 257.93, 530., 579.64, 737.42, 771.1,
787.32, 869.29, 924.77, 962.67, 1084.55, 1117.49, 1143.1, 1196.27,
1378.76, 1696.26, 1860.75, 3321.43
])
for ii in enumerate(test_freqs):
self.assertEqual(test_freqs[ii[0]], doc["output"]["frequencies"][ii[0]])
self.assertEqual(doc["output"]["frequencies"][ii[0]],
doc["calcs_reversed"][0]["frequencies"][ii[0]])
self.assertEqual(doc["output"]["enthalpy"], 36.755)
self.assertEqual(doc["output"]["entropy"], 74.989)
self.assertEqual(doc["walltime"], 684.6300000000001)
self.assertEqual(doc["cputime"], 4039.37)
self.assertEqual(doc["smiles"], "O1[C](O[Li])OC=C1")
self.assertEqual(doc["formula_pretty"], "LiH2(CO)3")
self.assertEqual(doc["formula_anonymous"], "AB2C3D3")
self.assertEqual(doc["chemsys"], "C-H-Li-O")
self.assertEqual(doc["pointgroup"], "C2")
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("optimized_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 3)
self.assertEqual(doc["calcs_reversed"][0]["task"]["name"], "calc2")
self.assertEqual(doc["calcs_reversed"][-1]["task"]["name"], "calc0")
def run_task(self, fw_spec):
# get the directory that contains the QChem dir to 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"]
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
multirun = self.get("multirun", False)
# parse the QChem directory
logger.info("PARSING DIRECTORY: {}".format(calc_dir))
drone = QChemDrone(additional_fields=self.get("additional_fields"))
# assimilate (i.e., parse)
task_doc = drone.assimilate(path=calc_dir,
input_file=input_file,
output_file=output_file,
multirun=multirun)
# 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")])
# Update fw_spec with final/optimized structure
update_spec = {}
if task_doc.get("output").get("optimized_molecule"):
update_spec["prev_calc_molecule"] = task_doc["output"][
"optimized_molecule"]
# get the database connection
db_file = env_chk(self.get("db_file"), fw_spec)
# db insertion or taskdoc dump
if not db_file:
with open(os.path.join(calc_dir, "task.json"), "w") as f:
f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
else:
mmdb = QChemCalcDb.from_db_file(db_file, admin=True)
t_id = mmdb.insert(task_doc)
logger.info("Finished parsing with task_id: {}".format(t_id))
defuse_children = False
if task_doc["state"] != "successful":
defuse_unsuccessful = self.get("defuse_unsuccessful",
DEFUSE_UNSUCCESSFUL)
if defuse_unsuccessful is True:
defuse_children = True
elif defuse_unsuccessful is False:
pass
elif defuse_unsuccessful == "fizzle":
raise RuntimeError(
"QChemToDb indicates that job is not successful "
"(perhaps your job did not converge within the "
"limit of electronic iterations)!")
else:
raise RuntimeError("Unknown option for defuse_unsuccessful: "
"{}".format(defuse_unsuccessful))
return FWAction(stored_data={"task_id": task_doc.get("task_id", None)},
defuse_children=defuse_children,
update_spec=update_spec)
def test_assimilate_FF(self):
drone = QChemDrone(
runs=[
"opt_0",
"freq_0",
"opt_1",
"freq_1",
"opt_2",
"freq_2",
"opt_3",
"freq_3",
],
additional_fields={"special_run_type": "frequency_flattener"},
)
doc = drone.assimilate(
path=os.path.join(module_dir, "..", "test_files", "FF_working"),
input_file="test.qin",
output_file="test.qout",
multirun=False,
)
self.assertEqual(doc["special_run_type"], "frequency_flattener")
self.assertEqual(doc["input"]["job_type"], "opt")
self.assertEqual(doc["output"]["job_type"], "freq")
test_freqs = np.array([
12.52,
45.28,
260.96,
329.08,
531.01,
582.11,
744.91,
779.2,
800.47,
863.15,
928.68,
969.0,
1092.86,
1124.0,
1147.64,
1209.1,
1387.39,
1693.97,
1913.05,
3316.2,
3341.73,
])
for ii in enumerate(test_freqs):
self.assertEqual(test_freqs[ii[0]],
doc["output"]["frequencies"][ii[0]])
self.assertEqual(
doc["output"]["frequencies"][ii[0]],
doc["calcs_reversed"][0]["frequencies"][ii[0]],
)
self.assertEqual(doc["output"]["enthalpy"], 37.547)
self.assertEqual(doc["output"]["entropy"], 83.81)
self.assertEqual(doc["num_frequencies_flattened"], 1)
self.assertEqual(doc["walltime"], 935.29)
self.assertEqual(doc["cputime"], 3616.6400000000003)
self.assertEqual(doc["smiles"], "O1[C](O[Li])OC=C1")
self.assertEqual(doc["formula_pretty"], "LiH2(CO)3")
self.assertEqual(doc["formula_anonymous"], "AB2C3D3")
self.assertEqual(doc["chemsys"], "C-H-Li-O")
self.assertEqual(doc["pointgroup"], "Cs")
self.assertIn("custodian", doc)
self.assertIn("calcs_reversed", doc)
self.assertIn("initial_molecule", doc["input"])
self.assertIn("initial_molecule", doc["output"])
self.assertIn("optimized_molecule", doc["output"])
self.assertIn("last_updated", doc)
self.assertIn("dir_name", doc)
self.assertEqual(len(doc["calcs_reversed"]), 4)
self.assertEqual(list(doc["calcs_reversed"][0].keys()),
list(doc["calcs_reversed"][2].keys()))
self.assertEqual(list(doc["calcs_reversed"][1].keys()),
list(doc["calcs_reversed"][3].keys()))
def run_task(self, fw_spec):
# get the directory that contains the QChem dir to 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"]
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
multirun = self.get("multirun", False)
# parse the QChem directory
logger.info(f"PARSING DIRECTORY: {calc_dir}")
additional_fields = self.get("additional_fields", {})
drone = QChemDrone(additional_fields=additional_fields)
# assimilate (i.e., parse)
task_doc = drone.assimilate(
path=calc_dir,
input_file=input_file,
output_file=output_file,
multirun=multirun,
)
# Check for additional keys to set based on the fw_spec
if self.get("fw_spec_field"):
task_doc.update({
self.get("fw_spec_field"):
fw_spec.get(self.get("fw_spec_field"))
})
# Update fw_spec with final/optimized structure
update_spec = {}
if task_doc.get("output").get("optimized_molecule"):
update_spec["prev_calc_molecule"] = task_doc["output"][
"optimized_molecule"]
update_spec["prev_calc_mulliken"] = task_doc["output"]["mulliken"]
if "RESP" in task_doc["output"]:
update_spec["prev_calc_resp"] = task_doc["output"]["RESP"]
elif "ESP" in task_doc["output"]:
update_spec["prev_calc_esp"] = task_doc["output"]["ESP"]
# get the database connection
db_file = env_chk(self.get("db_file"), fw_spec)
# db insertion or taskdoc dump
if not db_file:
with open(os.path.join(calc_dir, "task.json"), "w") as f:
f.write(json.dumps(task_doc, default=DATETIME_HANDLER))
else:
mmdb = QChemCalcDb.from_db_file(db_file, admin=True)
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)},
update_spec=update_spec,
)
