def test_not_defaults(self):
with patch("custodian.qchem.jobs.os.putenv") as putenv_patch:
myjob = QCJob(qchem_command="qchem -slurm", multimode="mpi", input_file="different.qin", output_file="not_default.qout", max_cores=12, scratch_dir="/not/default/scratch/", backup=False)
self.assertEqual(myjob.current_command, ["qchem", "-slurm", "-np", "12", "different.qin", "not_default.qout"])
myjob.setup()
self.assertEqual(putenv_patch.call_args_list[0][0][0], "QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1], "/not/default/scratch/")
def test_not_defaults(self):
with patch("custodian.qchem.jobs.os.putenv") as putenv_patch:
myjob = QCJob(qchem_command="qchem -slurm", multimode="mpi", input_file="different.qin", output_file="not_default.qout", max_cores=12, scratch_dir="/not/default/scratch/", backup=False)
self.assertEqual(myjob.current_command, ["qchem", "-slurm", "-np", "12", "different.qin", "not_default.qout"])
myjob.setup()
self.assertEqual(putenv_patch.call_args_list[0][0][0], "QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1], "/not/default/scratch/")
def test_defaults(self):
with patch("custodian.qchem.jobs.shutil.copy") as copy_patch:
myjob = QCJob(qchem_command="qchem", max_cores=32)
self.assertEqual(myjob.current_command, "qchem -nt 32 mol.qin mol.qout scratch")
myjob.setup()
self.assertEqual(copy_patch.call_args_list[0][0][0], "mol.qin")
self.assertEqual(copy_patch.call_args_list[0][0][1], "mol.qin.orig")
self.assertEqual(os.environ["QCSCRATCH"], os.getcwd())
self.assertEqual(os.environ["QCTHREADS"], "32")
self.assertEqual(os.environ["OMP_NUM_THREADS"], "32")
def test_save_scratch(self):
with patch("custodian.qchem.jobs.shutil.copy") as copy_patch:
myjob = QCJob(qchem_command="qchem -slurm", max_cores=32, scratch_dir=os.getcwd(), save_scratch=True, save_name="freq_scratch")
self.assertEqual(myjob.current_command, ' qchem -slurm -nt 32 mol.qin mol.qout freq_scratch')
myjob.setup()
self.assertEqual(copy_patch.call_args_list[0][0][0], "mol.qin")
self.assertEqual(copy_patch.call_args_list[0][0][1], "mol.qin.orig")
self.assertEqual(os.environ["QCSCRATCH"],os.getcwd())
self.assertEqual(os.environ["QCTHREADS"],"32")
self.assertEqual(os.environ["OMP_NUM_THREADS"],"32")
def run_QChem(label,
encode=None,
rem=None,
pcm=None,
solvent=None,
more_info=None,
self_correct=True):
inname = label + '.inp'
outname = label + '.out'
logname = label + '.log'
command = 'qchem'
handlers = [QChemErrorHandler(input_file=inname, output_file=outname)]
"""If no encoding provided, assume this is the first Firework in workflow and that input file is already written.
'label' is the name of the file without the extension (e.g. .inp, .out). otherwise, take encoding,
form new QCInput and write input file, then run.
"""
if encode != None:
qcin = encode_to_QCInput(encode=encode,
rem=rem,
pcm=pcm,
solvent=solvent)
qcin.write_file(inname)
if self_correct:
jobs = [
QCJob(input_file=inname,
output_file=outname,
qchem_command=command,
max_cores=multiprocessing.cpu_count(),
qclog_file=logname)
]
c = Custodian(handlers, jobs, max_errors=10)
c.run()
else:
job = QCJob(input_file=inname,
output_file=outname,
qchem_command=command,
max_cores=multiprocessing.cpu_count(),
qclog_file=logname)
job.setup()
p = job.run()
p.wait()
"""
qclog = open(logname, "w")
current_command = ['qchem', '-nt', '20',inname]
print(current_command)
subprocess.run(current_command, stdout=qclog, shell=True)
"""
try:
output = [QCOutput(filename=outname)]
except:
output = QCOutput.multiple_outputs_from_file(QCOutput, filename)
return QCOutput_to_encode(output, more_info=more_info)
def test_defaults(self):
with patch("custodian.qchem.jobs.os.putenv") as putenv_patch:
with patch("custodian.qchem.jobs.shutil.copy") as copy_patch:
myjob = QCJob(qchem_command="qchem")
self.assertEqual(myjob.current_command, ["qchem", "-nt", "32", "mol.qin", "mol.qout"])
myjob.setup()
self.assertEqual(copy_patch.call_args_list[0][0][0], "mol.qin")
self.assertEqual(copy_patch.call_args_list[0][0][1], "mol.qin.orig")
self.assertEqual(putenv_patch.call_args_list[0][0][0], "QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1], "/dev/shm/qcscratch/")
self.assertEqual(putenv_patch.call_args_list[1][0][0], "QCTHREADS")
self.assertEqual(putenv_patch.call_args_list[1][0][1], "32")
self.assertEqual(putenv_patch.call_args_list[2][0][0], "OMP_NUM_THREADS")
self.assertEqual(putenv_patch.call_args_list[2][0][1], "32")
def test_not_defaults(self):
myjob = QCJob(
qchem_command="qchem -slurm",
multimode="mpi",
input_file="different.qin",
output_file="not_default.qout",
max_cores=12,
calc_loc="/not/default/",
backup=False,
)
self.assertEqual(myjob.current_command, "qchem -slurm -np 12 different.qin not_default.qout scratch")
myjob.setup()
self.assertEqual(os.environ["QCSCRATCH"], os.getcwd())
self.assertEqual(os.environ["QCLOCALSCR"], "/not/default/")
def test_defaults(self):
with patch("custodian.qchem.jobs.os.putenv") as putenv_patch:
with patch("custodian.qchem.jobs.shutil.copy") as copy_patch:
myjob = QCJob(qchem_command="qchem", max_cores=32)
self.assertEqual(myjob.current_command, ["qchem", "-nt", "32", "mol.qin", "mol.qout"])
myjob.setup()
self.assertEqual(copy_patch.call_args_list[0][0][0], "mol.qin")
self.assertEqual(copy_patch.call_args_list[0][0][1], "mol.qin.orig")
self.assertEqual(putenv_patch.call_args_list[0][0][0], "QCSCRATCH")
self.assertEqual(putenv_patch.call_args_list[0][0][1], "/dev/shm/qcscratch/")
self.assertEqual(putenv_patch.call_args_list[1][0][0], "QCTHREADS")
self.assertEqual(putenv_patch.call_args_list[1][0][1], "32")
self.assertEqual(putenv_patch.call_args_list[2][0][0], "OMP_NUM_THREADS")
self.assertEqual(putenv_patch.call_args_list[2][0][1], "32")
def test_not_defaults(self):
myjob = QCJob(qchem_command="qchem -slurm", multimode="mpi", input_file="different.qin", output_file="not_default.qout", max_cores=12, scratch_dir="/not/default/scratch/", backup=False)
self.assertEqual(myjob.current_command, ' qchem -slurm -np 12 different.qin not_default.qout')
myjob.setup()
self.assertEqual(os.environ["QCSCRATCH"],"/not/default/scratch/")