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janoshjanosh
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black atomate/**/*.py
1 parent b8dc79c commit 06c714a

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8 files changed

+253
-174
lines changed

8 files changed

+253
-174
lines changed

‎atomate/qchem/drones.py‎

Lines changed: 55 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -243,16 +243,30 @@ def generate_doc(self, dir_name, qcinput_files, qcoutput_files, multirun):
243243
else:
244244
if len(d["calcs_reversed"]) > 1:
245245
first_calc = d["calcs_reversed"][-1]["input"]["rem"]["job_type"]
246-
second_calc = d["calcs_reversed"][-2]["input"]["rem"]["job_type"]
247-
if first_calc in ["freq", "frequency"] and second_calc in ["opt", "optimization", "ts"]:
248-
d["output"]["optimized_molecule"] = d_calc_final["initial_molecule"]
249-
d["output"]["final_energy"] = d["calcs_reversed"][1]["final_energy"]
246+
second_calc = d["calcs_reversed"][-2]["input"]["rem"][
247+
"job_type"
248+
]
249+
if first_calc in ["freq", "frequency"] and second_calc in [
250+
"opt",
251+
"optimization",
252+
"ts",
253+
]:
254+
d["output"]["optimized_molecule"] = d_calc_final[
255+
"initial_molecule"
256+
]
257+
d["output"]["final_energy"] = d["calcs_reversed"][1][
258+
"final_energy"
259+
]
250260

251261
if d["output"]["job_type"] == "pes_scan":
252262
d["output"]["scan_energies"] = d_calc_final.get("scan_energies")
253263
d["input"]["scan_variables"] = d_calc_final.get("scan_variables")
254-
d["output"]["scan_geometries"] = d_calc_final.get("optimized_geometries")
255-
d["output"]["scan_molecules"] = d_calc_final.get("molecules_from_optimized_geometries")
264+
d["output"]["scan_geometries"] = d_calc_final.get(
265+
"optimized_geometries"
266+
)
267+
d["output"]["scan_molecules"] = d_calc_final.get(
268+
"molecules_from_optimized_geometries"
269+
)
256270

257271
if d["output"]["job_type"] == "force":
258272
d["output"]["gradients"] = d_calc_final["gradients"][0]
@@ -267,8 +281,8 @@ def generate_doc(self, dir_name, qcinput_files, qcoutput_files, multirun):
267281
for calc in calcs:
268282
job_type = calc["input"]["rem"]["job_type"]
269283
if job_type in ["opt", "optimization", "ts"]:
270-
for ii,geom in enumerate(calc["geometries"]):
271-
site_properties = {"Mulliken":calc["Mulliken"][ii]}
284+
for ii, geom in enumerate(calc["geometries"]):
285+
site_properties = {"Mulliken": calc["Mulliken"][ii]}
272286
if "RESP" in calc:
273287
site_properties["RESP"] = calc["RESP"][ii]
274288
mol = Molecule(
@@ -326,36 +340,59 @@ def generate_doc(self, dir_name, qcinput_files, qcoutput_files, multirun):
326340

327341
d["state"] = "successful" if d_calc_final["completion"] else "unsuccessful"
328342
if "special_run_type" in d:
329-
if d["special_run_type"] in ["frequency_flattener", "ts_frequency_flattener"]:
343+
if d["special_run_type"] in [
344+
"frequency_flattener",
345+
"ts_frequency_flattener",
346+
]:
330347
if d["state"] == "successful":
331348
orig_num_neg_freq = None
332349
for calc in d["calcs_reversed"][::-1]:
333350
if "frequencies" in calc:
334-
orig_num_neg_freq = sum(1 for freq in calc["frequencies"] if freq < 0)
351+
orig_num_neg_freq = sum(
352+
1 for freq in calc["frequencies"] if freq < 0
353+
)
335354
break
336355
orig_energy = None
337356
for calc in d["calcs_reversed"][::-1]:
338357
if "final_energy" in calc:
339358
if calc["final_energy"] is not None:
340359
orig_energy = calc["final_energy"]
341360
break
342-
final_num_neg_freq = sum(1 for freq in d_calc_final["frequencies"] if freq < 0)
361+
final_num_neg_freq = sum(
362+
1 for freq in d_calc_final["frequencies"] if freq < 0
363+
)
343364
final_energy = d["calcs_reversed"][1]["final_energy"]
344365
if orig_num_neg_freq is None:
345366
d["num_frequencies_flattened"] = 0
346367
else:
347-
d["num_frequencies_flattened"] = orig_num_neg_freq - final_num_neg_freq
368+
d["num_frequencies_flattened"] = (
369+
orig_num_neg_freq - final_num_neg_freq
370+
)
348371

349372
if d["special_run_type"] == "frequency_flattener":
350-
if final_num_neg_freq > 0: # If a negative frequency remains,
373+
if (
374+
final_num_neg_freq > 0
375+
): # If a negative frequency remains,
351376
# and it's too large to ignore,
352-
if final_num_neg_freq > 1 or abs(d["output"]["frequencies"][0]) >= 15.0:
353-
d["state"] = "unsuccessful" # then the flattening was unsuccessful
377+
if (
378+
final_num_neg_freq > 1
379+
or abs(d["output"]["frequencies"][0]) >= 15.0
380+
):
381+
d[
382+
"state"
383+
] = "unsuccessful" # then the flattening was unsuccessful
354384
else:
355-
if final_num_neg_freq > 1: # If a negative frequency remains,
385+
if (
386+
final_num_neg_freq > 1
387+
): # If a negative frequency remains,
356388
# and it's too large to ignore,
357-
if final_num_neg_freq > 2 or abs(d["output"]["frequencies"][1]) >= 15.0:
358-
d["state"] = "unsuccessful" # then the flattening was unsuccessful
389+
if (
390+
final_num_neg_freq > 2
391+
or abs(d["output"]["frequencies"][1]) >= 15.0
392+
):
393+
d[
394+
"state"
395+
] = "unsuccessful" # then the flattening was unsuccessful
359396
if final_energy > orig_energy:
360397
d["warnings"]["energy_increased"] = True
361398

‎atomate/qchem/firetasks/geo_transformations.py‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -77,7 +77,9 @@ def run_task(self, fw_spec):
7777
elif fw_spec.get("prev_calc_molecule"):
7878
mol = fw_spec.get("prev_calc_molecule")
7979
else:
80-
raise KeyError("No molecule present; add as an optional param or check fw_spec")
80+
raise KeyError(
81+
"No molecule present; add as an optional param or check fw_spec"
82+
)
8183

8284
if self.get("mode") is not None:
8385
mode = self.get("mode")
@@ -92,4 +94,4 @@ def run_task(self, fw_spec):
9294

9395
update_spec = {"prev_calc_molecule": mol_copy}
9496

95-
return FWAction(update_spec=update_spec)
97+
return FWAction(update_spec=update_spec)

‎atomate/qchem/firetasks/parse_outputs.py‎

Lines changed: 9 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -46,9 +46,15 @@ class QChemToDb(FiretaskBase):
4646
"""
4747

4848
optional_params = [
49-
"calc_dir", "calc_loc", "input_file", "output_file",
50-
"additional_fields", "db_file", "fw_spec_field", "multirun",
51-
"runs"
49+
"calc_dir",
50+
"calc_loc",
51+
"input_file",
52+
"output_file",
53+
"additional_fields",
54+
"db_file",
55+
"fw_spec_field",
56+
"multirun",
57+
"runs",
5258
]
5359

5460
def run_task(self, fw_spec):

‎atomate/qchem/firetasks/run_calc.py‎

Lines changed: 18 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -91,11 +91,24 @@ class RunQChemCustodian(FiretaskBase):
9191

9292
required_params = ["qchem_cmd"]
9393
optional_params = [
94-
"multimode", "input_file", "output_file", "max_cores", "qclog_file",
95-
"suffix", "calc_loc", "save_scratch", "max_errors", "job_type",
96-
"handler_group", "gzipped_output", "backup", "linked",
97-
"max_iterations", "max_molecule_perturb_scale", "freq_before_opt",
98-
"transition_state"
94+
"multimode",
95+
"input_file",
96+
"output_file",
97+
"max_cores",
98+
"qclog_file",
99+
"suffix",
100+
"calc_loc",
101+
"save_scratch",
102+
"max_errors",
103+
"job_type",
104+
"handler_group",
105+
"gzipped_output",
106+
"backup",
107+
"linked",
108+
"max_iterations",
109+
"max_molecule_perturb_scale",
110+
"freq_before_opt",
111+
"transition_state",
99112
]
100113

101114
def run_task(self, fw_spec):

‎atomate/qchem/firetasks/write_inputs.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -71,10 +71,10 @@ def run_task(self, fw_spec):
7171
if self.get("molecule"):
7272
mol = self.get("molecule")
7373
# check if mol and prev_calc_mol are isomorphic
74-
mol_graph = MoleculeGraph.with_local_env_strategy(mol,
75-
OpenBabelNN())
76-
prev_mol_graph = MoleculeGraph.with_local_env_strategy(prev_calc_mol,
77-
OpenBabelNN())
74+
mol_graph = MoleculeGraph.with_local_env_strategy(mol, OpenBabelNN())
75+
prev_mol_graph = MoleculeGraph.with_local_env_strategy(
76+
prev_calc_mol, OpenBabelNN()
77+
)
7878
# If they are isomorphic, aka a previous FW has not changed bonding,
7979
# then we will use prev_calc_mol. If bonding has changed, we will use mol.
8080
if mol_graph.isomorphic_to(prev_mol_graph):
@@ -147,10 +147,10 @@ def run_task(self, fw_spec):
147147
if self.get("molecule"):
148148
mol = self.get("molecule")
149149
# check if mol and prev_calc_mol are isomorphic
150-
mol_graph = MoleculeGraph.with_local_env_strategy(mol,
151-
OpenBabelNN())
152-
prev_mol_graph = MoleculeGraph.with_local_env_strategy(prev_calc_mol,
153-
OpenBabelNN())
150+
mol_graph = MoleculeGraph.with_local_env_strategy(mol, OpenBabelNN())
151+
prev_mol_graph = MoleculeGraph.with_local_env_strategy(
152+
prev_calc_mol, OpenBabelNN()
153+
)
154154
if mol_graph.isomorphic_to(prev_mol_graph):
155155
mol = prev_calc_mol
156156
else:

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