def test_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(
qchem_command="qchem -slurm",
max_cores=32,
input_file="mol.qin",
output_file="mol.qout")
expected_next = QCJob(qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_0",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
expected_next = QCJob(qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_0",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(
os.path.join(
test_dir,
"disconnected_but_converged/mol.qin.freq_0")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict())
self.assertRaises(StopIteration, myjob.__next__)
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_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(
qchem_command="qchem -slurm",
max_cores=32,
input_file="mol.qin",
output_file="mol.qout",
linked=True,
transition_state=True,
freq_before_opt=True,
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_pre",
save_scratch=True,
backup=True,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".ts_0",
save_scratch=True,
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "fftsopt_freqfirst/mol.qin.ts_0")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
shutil.copyfile(
os.path.join(scr_dir, "mol.qin"),
os.path.join(scr_dir, "mol.qin.ts_0"),
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_0",
save_scratch=True,
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "fftsopt_freqfirst/mol.qin.freq_0")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
shutil.copyfile(
os.path.join(scr_dir, "mol.qin"),
os.path.join(scr_dir, "mol.qin.freq_0"),
)
self.assertRaises(StopIteration, myjob.__next__)
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 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_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm", input_file="mol.qin", output_file="mol.qout")
expected_next = QCJob(
qchem_command="qchem -slurm",
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_0",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertRaises(StopIteration,myjob.__next__)
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")
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_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_RunQChemCustodian_using_fw_spec_defaults(self):
with patch("atomate.qchem.firetasks.run_calc.Custodian"
) as custodian_patch:
firetask = RunQChemCustodian(qchem_cmd=">>qchem_cmd<<",
scratch_dir=">>scratch_dir<<",
input_file=os.path.join(
module_dir, "..", "..",
"test_files", "co_qc.in"))
firetask.run_task(
fw_spec={
"_fw_env": {
"qchem_cmd": "qchem -slurm",
"scratch_dir": "/this/is/a/test"
}
})
custodian_patch.assert_called_once()
self.assertEqual(
custodian_patch.call_args[0][0][0].as_dict(),
QChemErrorHandler(input_file=os.path.join(
module_dir, "..", "..", "test_files", "co_qc.in"),
output_file="mol.qout").as_dict())
self.assertEqual(
custodian_patch.call_args[0][1][0].as_dict(),
QCJob(qchem_command="qchem -slurm",
multimode="openmp",
input_file=os.path.join(module_dir, "..", "..",
"test_files", "co_qc.in"),
output_file="mol.qout",
scratch_dir="/this/is/a/test").as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 5,
"gzipped_output": True
})
def test_RunQChemCustodian_basic_defaults(self):
with patch("atomate.qchem.firetasks.run_calc.Custodian"
) as custodian_patch:
firetask = RunQChemCustodian(
qchem_cmd="qchem",
input_file=os.path.join(module_dir, "..", "..", "test_files",
"co_qc.in"),
max_cores=32)
firetask.run_task(fw_spec={})
custodian_patch.assert_called_once()
self.assertEqual(custodian_patch.call_args[0][0][0].as_dict(),
QChemErrorHandler(
input_file=os.path.join(
module_dir, "..", "..", "test_files",
"co_qc.in"),
output_file="mol.qout").as_dict())
self.assertEqual(custodian_patch.call_args[0][1][0].as_dict(),
QCJob(
qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file=os.path.join(
module_dir, "..", "..", "test_files",
"co_qc.in"),
output_file="mol.qout").as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 5,
"gzipped_output": True
})
def test_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm", max_cores=32, input_file="mol.qin", output_file="mol.qout")
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_0",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertRaises(StopIteration,myjob.__next__)
def test_RunQChemCustodian_using_fw_spec_not_defaults(self):
with patch("atomate.qchem.firetasks.run_calc.Custodian"
) as custodian_patch:
firetask = RunQChemCustodian(
qchem_cmd=">>qchem_cmd<<",
calc_loc=">>calc_loc<<",
multimode=">>multimode<<",
input_file=os.path.join(module_dir, "..", "..", "test_files",
"co_qc.in"),
output_file="this_is_a_test.qout",
max_cores=4,
qclog_file="this_is_a_test.qclog",
suffix="bad_idea",
save_scratch=True,
max_errors=137,
gzipped_output=False,
handler_group="no_handler",
)
firetask.run_task(
fw_spec={
"_fw_env": {
"qchem_cmd": "qchem -slurm",
"calc_loc": "/this/is/a/test",
"max_cores": 32,
"multimode": "mpi",
}
})
custodian_patch.assert_called_once()
self.assertEqual(custodian_patch.call_args[0][0], [])
self.assertEqual(
custodian_patch.call_args[0][1][0].as_dict(),
QCJob(
qchem_command="qchem -slurm",
calc_loc="/this/is/a/test",
multimode="mpi",
input_file=os.path.join(module_dir, "..", "..",
"test_files", "co_qc.in"),
output_file="this_is_a_test.qout",
max_cores=4,
qclog_file="this_is_a_test.qclog",
suffix="bad_idea",
save_scratch=True,
).as_dict(),
)
self.assertEqual(
custodian_patch.call_args[1],
{
"max_errors": 137,
"gzipped_output": False
},
)
def test_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem", input_file="test.qin", output_file="test.qout")
expected_next = QCJob(
qchem_command="qchem",
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".opt_0",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
expected_next = QCJob(
qchem_command="qchem",
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".freq_0",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"FF_working/test.qin.freq_0")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"test.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem",
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".opt_1",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"FF_working/test.qin.opt_1")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"test.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem",
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".freq_1",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"FF_working/test.qin.freq_1")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"test.qin")).as_dict())
self.assertRaises(StopIteration,myjob.__next__)
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_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem", max_cores=32, input_file="test.qin", output_file="test.qout")
expected_next = QCJob(
qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".opt_0",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
expected_next = QCJob(
qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".freq_0",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"FF_working/test.qin.freq_0")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"test.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".opt_1",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"FF_working/test.qin.opt_1")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"test.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem",
max_cores=32,
multimode="openmp",
input_file="test.qin",
output_file="test.qout",
suffix=".freq_1",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"FF_working/test.qin.freq_1")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"test.qin")).as_dict())
self.assertRaises(StopIteration,myjob.__next__)
def run_task(self, fw_spec):
# initialize variables
qchem_cmd = env_chk(self["qchem_cmd"], fw_spec)
multimode = env_chk(self.get("multimode"), fw_spec)
if multimode == None:
multimode = "openmp"
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
max_cores = env_chk(self["max_cores"], fw_spec)
qclog_file = self.get("qclog_file", "mol.qclog")
suffix = self.get("suffix", "")
scratch_dir = env_chk(self.get("scratch_dir"), fw_spec)
if scratch_dir == None:
scratch_dir = "/dev/shm/qcscratch/"
save_scratch = self.get("save_scratch", False)
save_name = self.get("save_name", "saved_scratch")
max_errors = self.get("max_errors", 5)
max_iterations = self.get("max_iterations", 10)
linked = self.get("linked", False)
max_molecule_perturb_scale = self.get("max_molecule_perturb_scale",
0.3)
job_type = self.get("job_type", "normal")
gzipped_output = self.get("gzipped_output", True)
handler_groups = {
"default": [
QChemErrorHandler(input_file=input_file,
output_file=output_file)
],
"no_handler": []
}
# construct jobs
if job_type == "normal":
jobs = [
QCJob(qchem_command=qchem_cmd,
max_cores=max_cores,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=suffix,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name)
]
elif job_type == "opt_with_frequency_flattener":
if linked:
jobs = QCJob.opt_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
max_iterations=max_iterations,
linked=linked,
max_cores=max_cores)
else:
jobs = QCJob.opt_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
max_iterations=max_iterations,
linked=linked,
max_molecule_perturb_scale=max_molecule_perturb_scale,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name,
max_cores=max_cores)
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handlers = handler_groups[self.get("handler_group", "default")]
c = Custodian(handlers,
jobs,
max_errors=max_errors,
gzipped_output=gzipped_output)
c.run()
from custodian import Custodian from custodian.qchem.jobs import QCJob from custodian.qchem.handlers import QChemErrorHandler my_input = "mol.qin" my_output = "mol.qout" myjob = QCJob(qchem_command="qchem -slurm",multimode="openmp",input_file=my_input,output_file=my_output,max_cores=12) myhandler = QChemErrorHandler(input_file=my_input,output_file=my_output) c = Custodian([myhandler],[myjob],max_errors_per_job=10,max_errors=10) c.run()
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/")
def run_task(self, fw_spec):
# initialize variables
qchem_cmd = env_chk(self["qchem_cmd"], fw_spec)
multimode = env_chk(self.get("multimode"), fw_spec)
if multimode == None:
multimode = "openmp"
"""
Note that I'm considering hardcoding openmp in the future
because there is basically no reason anyone should ever run
QChem on multiple nodes, aka with multimode = mpi.
"""
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
max_cores = env_chk(self["max_cores"], fw_spec)
qclog_file = self.get("qclog_file", "mol.qclog")
suffix = self.get("suffix", "")
calc_loc = env_chk(self.get("calc_loc"), fw_spec)
save_scratch = self.get("save_scratch", False)
max_errors = self.get("max_errors", 5)
max_iterations = self.get("max_iterations", 10)
linked = self.get("linked", True)
backup = self.get("backup", True)
max_molecule_perturb_scale = self.get("max_molecule_perturb_scale",
0.3)
job_type = self.get("job_type", "normal")
gzipped_output = self.get("gzipped_output", True)
handler_groups = {
"default": [
QChemErrorHandler(input_file=input_file,
output_file=output_file)
],
"no_handler": []
}
# construct jobs
if job_type == "normal":
jobs = [
QCJob(qchem_command=qchem_cmd,
max_cores=max_cores,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=suffix,
calc_loc=calc_loc,
save_scratch=save_scratch,
backup=backup)
]
elif job_type == "opt_with_frequency_flattener":
if linked:
jobs = QCJob.opt_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
max_iterations=max_iterations,
linked=linked,
save_final_scratch=save_scratch,
max_cores=max_cores,
calc_loc=calc_loc)
else:
jobs = QCJob.opt_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
max_iterations=max_iterations,
max_molecule_perturb_scale=max_molecule_perturb_scale,
linked=linked,
save_final_scratch=save_scratch,
max_cores=max_cores,
calc_loc=calc_loc)
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handlers = handler_groups[self.get("handler_group", "default")]
c = Custodian(handlers,
jobs,
max_errors=max_errors,
gzipped_output=gzipped_output)
c.run()
def test_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm", max_cores=32,input_file="mol.qin", output_file="mol.qout", linked=True)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_0",
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=True).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_0",
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"small_neg_freq/mol.qin.freq_0")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"mol.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_1",
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"small_neg_freq/mol.qin.opt_1")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"mol.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_1",
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"small_neg_freq/mol.qin.freq_1")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"mol.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_2",
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"small_neg_freq/mol.qin.opt_2")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"mol.qin")).as_dict())
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_2",
scratch_dir=os.getcwd(),
save_scratch=True,
save_name="chain_scratch",
backup=False).as_dict()
self.assertEqual(next(myjob).as_dict(),expected_next)
self.assertEqual(QCInput.from_file(os.path.join(test_dir,"small_neg_freq/mol.qin.freq_2")).as_dict(),QCInput.from_file(os.path.join(scr_dir,"mol.qin")).as_dict())
self.assertRaises(StopIteration,myjob.__next__)
from custodian import Custodian from custodian.qchem.jobs import QCJob from custodian.qchem.handlers import QChemErrorHandler my_input = "test.qin" my_output = "test.qout" myjob = QCJob.opt_with_frequency_flattener(qchem_command="qchem -slurm",multimode="openmp",input_file=my_input,output_file=my_output,max_iterations=10,max_molecule_perturb_scale=0.3,max_cores=12) myhandler = QChemErrorHandler(input_file=my_input,output_file=my_output) c = Custodian([myhandler],myjob,max_errors_per_job=10,max_errors=10) c.run()
def run_task(self, fw_spec):
# initialize variables
qchem_cmd = env_chk(self["qchem_cmd"], fw_spec)
multimode = env_chk(self.get("multimode"), fw_spec)
if multimode == None:
multimode = "openmp"
input_file = self.get("input_file", "mol.qin")
output_file = self.get("output_file", "mol.qout")
max_cores = env_chk(self["max_cores"], fw_spec)
qclog_file = self.get("qclog_file", "mol.qclog")
suffix = self.get("suffix", "")
scratch_dir = env_chk(self.get("scratch_dir"), fw_spec)
if scratch_dir == None:
scratch_dir = "/dev/shm/qcscratch/"
save_scratch = self.get("save_scratch", False)
save_name = self.get("save_name", "default_save_name")
max_errors = self.get("max_errors", 5)
max_iterations = self.get("max_iterations", 10)
max_molecule_perturb_scale = self.get("max_molecule_perturb_scale",
0.3)
job_type = self.get("job_type", "normal")
gzipped_output = self.get("gzipped_output", True)
handler_groups = {
"default": [
QChemErrorHandler(
input_file=input_file, output_file=output_file)
],
"no_handler": []
}
# construct jobs
if job_type == "normal":
jobs = [
QCJob(
qchem_command=qchem_cmd,
max_cores=max_cores,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
suffix=suffix,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name)
]
elif job_type == "opt_with_frequency_flattener":
jobs = QCJob.opt_with_frequency_flattener(
qchem_command=qchem_cmd,
multimode=multimode,
input_file=input_file,
output_file=output_file,
qclog_file=qclog_file,
max_iterations=max_iterations,
max_molecule_perturb_scale=max_molecule_perturb_scale,
scratch_dir=scratch_dir,
save_scratch=save_scratch,
save_name=save_name,
max_cores=max_cores)
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handlers = handler_groups[self.get("handler_group", "default")]
c = Custodian(
handlers,
jobs,
max_errors=max_errors,
gzipped_output=gzipped_output)
c.run()
def test_OptFF(self):
myjob = QCJob.opt_with_frequency_flattener(
qchem_command="qchem -slurm",
max_cores=32,
input_file="mol.qin",
output_file="mol.qout",
linked=False,
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_0",
backup=True,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_0",
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "5690_frag18/mol.qin.freq_0")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_1",
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "5690_frag18/mol.qin.opt_1")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_1",
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "5690_frag18/mol.qin.freq_1")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".opt_2",
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "5690_frag18/mol.qin.opt_2")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
expected_next = QCJob(
qchem_command="qchem -slurm",
max_cores=32,
multimode="openmp",
input_file="mol.qin",
output_file="mol.qout",
suffix=".freq_2",
backup=False,
).as_dict()
self.assertEqual(next(myjob).as_dict(), expected_next)
self.assertEqual(
QCInput.from_file(os.path.join(test_dir, "5690_frag18/mol.qin.freq_2")).as_dict(),
QCInput.from_file(os.path.join(scr_dir, "mol.qin")).as_dict(),
)
self.assertRaises(Exception, myjob.__next__)
