def from_dict(cls, d):
h = QChemErrorHandler(input_file=d["input_file"],
output_file=d["output_file"],
ex_backup_list=d["ex_backup_list"],
rca_gdm_thresh=d["rca_gdm_thresh"],
scf_max_cycles=d["scf_max_cycles"],
geom_max_cycles=d["geom_max_cycles"])
h.outdata = d["outdata"]
h.qcinp = QcInput.from_dict(d["qcinp"]) if d["qcinp"] else None
h.error_step_id = d["error_step_id"]
h.errors = d["errors"]
h.fix_step = QcTask.from_dict(d["fix_step"]) if d["fix_step"] else None
return h
def test_to_and_from_dict(self):
qctask1 = QcTask(mol, title="Test Methane Opt", exchange="B3LYP",
jobtype="Opt", basis_set="6-31+G*")
qctask2 = QcTask(molecule="read", title="Test Methane Frequency",
exchange="B3LYP", jobtype="Freq",
basis_set="6-31+G*")
qctask3 = QcTask(title="Test Methane Single Point Energy",
exchange="B3LYP", jobtype="SP",
basis_set="6-311+G(3df,2p)")
qcinp1 = QcInput(jobs=[qctask1, qctask2, qctask3])
d1 = qcinp1.to_dict
qcinp2 = QcInput.from_dict(d1)
d2 = qcinp2.to_dict
self.assertEqual(d1, d2)
def check(self):
# Checks output file for errors.
self.outdata = QcOutput(self.output_file).data
self.qcinp = QcInput.from_file(self.input_file)
self.error_step_id = None
self.errors = None
self.fix_step = None
for i, od in enumerate(self.outdata):
if od["has_error"]:
self.error_step_id = i
self.fix_step = self.qcinp.jobs[i]
self.errors = sorted(list(set(od["errors"])))
return True
return False
def _set_qchem_memory(self, qcinp=None):
if not qcinp:
qcinp = QcInput.from_file(self.input_file)
if "PBS_JOBID" in os.environ:
if "hopque" in os.environ["PBS_JOBID"]:
# on Hopper
for j in qcinp.jobs:
if self.current_command_name == "general":
if self.large_static_mem:
j.set_memory(total=1100, static=300)
else:
j.set_memory(total=1100, static=100)
elif self.current_command_name == "half_cpus":
if self.large_static_mem:
j.set_memory(total=2200, static=500)
else:
j.set_memory(total=2200, static=100)
elif self.current_command_name == "openmp":
if self.large_static_mem:
j.set_memory(total=28000, static=10000)
else:
j.set_memory(total=28000, static=3000)
elif "edique" in os.environ["PBS_JOBID"]:
# on Edison
for j in qcinp.jobs:
if self.current_command_name == "general":
if self.large_static_mem:
j.set_memory(total=2500, static=500)
else:
j.set_memory(total=2500, static=100)
elif self.current_command_name == "half_cpus":
if self.large_static_mem:
j.set_memory(total=5000, static=1000)
else:
j.set_memory(total=5000, static=200)
elif self.current_command_name == "openmp":
if self.large_static_mem:
j.set_memory(total=60000, static=20000)
else:
j.set_memory(total=60000, static=5000)
qcinp.write_file(self.input_file)
def test_str_and_from_string(self):
ans = '''$comments
Test Methane Opt
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = opt
exchange = b3lyp
basis = 6-31+g*
$end
@@@
$comments
Test Methane Frequency
$end
$molecule
read
$end
$rem
jobtype = freq
exchange = b3lyp
basis = 6-31+g*
$end
@@@
$comments
Test Methane Single Point Energy
$end
$molecule
read
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-311+g(3df,2p)
$end
'''
qctask1 = QcTask(mol, title="Test Methane Opt", exchange="B3LYP",
jobtype="Opt", basis_set="6-31+G*")
qctask2 = QcTask(molecule="read", title="Test Methane Frequency",
exchange="B3LYP", jobtype="Freq", basis_set="6-31+G*")
qctask3 = QcTask(title="Test Methane Single Point Energy",
exchange="B3LYP", jobtype="SP",
basis_set="6-311+G(3df,2p)")
qcinp1 = QcInput(jobs=[qctask1, qctask2, qctask3])
self.assertEqual(str(qcinp1), ans)
qcinp2 = QcInput.from_string(ans)
self.assertEqual(qcinp1.to_dict, qcinp2.to_dict)