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_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_FF_basic_defaults(self):
with patch("atomate.qchem.firetasks.run_calc.Custodian"
) as custodian_patch:
with patch(
"atomate.qchem.firetasks.run_calc.QCJob.opt_with_frequency_flattener"
) as FF_patch:
firetask = RunQChemCustodian(
qchem_cmd="qchem",
max_cores=32,
input_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qin"),
output_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qout"),
job_type="opt_with_frequency_flattener",
)
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", "FF_before_run",
"test.qin"),
output_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qout")).as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 5,
"gzipped_output": True
})
self.assertEqual(
FF_patch.call_args[1], {
"qchem_command":
"qchem",
"multimode":
"openmp",
"input_file":
os.path.join(module_dir, "..", "..", "test_files",
"FF_before_run", "test.qin"),
"output_file":
os.path.join(module_dir, "..", "..", "test_files",
"FF_before_run", "test.qout"),
"qclog_file":
"mol.qclog",
"max_iterations":
10,
"max_molecule_perturb_scale":
0.3,
"scratch_dir":
"/dev/shm/qcscratch/",
"save_scratch":
False,
"save_name":
"default_save_name",
"max_cores":
32
})
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_RunQChemCustodian_FF_using_fw_spec_not_defaults(self):
with patch("atomate.qchem.firetasks.run_calc.Custodian"
) as custodian_patch:
with patch(
"atomate.qchem.firetasks.run_calc.QCJob.opt_with_frequency_flattener"
) as FF_patch:
firetask = RunQChemCustodian(
qchem_cmd=">>qchem_cmd<<",
calc_loc=">>calc_loc<<",
input_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qin"),
output_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qout"),
job_type="opt_with_frequency_flattener",
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",
linked=False,
max_iterations=1029,
max_molecule_perturb_scale=0.5,
multimode=">>multimode<<")
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[1], {
"max_errors": 137,
"gzipped_output": False
})
self.assertEqual(
FF_patch.call_args[1], {
"qchem_command":
"qchem -slurm",
"multimode":
"mpi",
"input_file":
os.path.join(module_dir, "..", "..", "test_files",
"FF_before_run", "test.qin"),
"output_file":
os.path.join(module_dir, "..", "..", "test_files",
"FF_before_run", "test.qout"),
"qclog_file":
"this_is_a_test.qclog",
"max_iterations":
1029,
"max_molecule_perturb_scale":
0.5,
"linked":
False,
"calc_loc":
"/this/is/a/test",
"save_final_scratch":
True,
"max_cores":
4
})
def test_RunQChemCustodian_FF_using_fw_spec_defaults(self):
with patch("atomate.qchem.firetasks.run_calc.Custodian"
) as custodian_patch:
with patch(
"atomate.qchem.firetasks.run_calc.QCJob.opt_with_frequency_flattener"
) as FF_patch:
firetask = RunQChemCustodian(
qchem_cmd=">>qchem_cmd<<",
calc_loc=">>calc_loc<<",
max_cores=">>max_cores<<",
multimode=">>multimode<<",
input_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qin"),
output_file=os.path.join(module_dir, "..", "..",
"test_files", "FF_before_run",
"test.qout"),
job_type="opt_with_frequency_flattener")
firetask.run_task(
fw_spec={
"_fw_env": {
"qchem_cmd": "qchem -slurm",
"calc_loc": "/this/is/a/test",
"max_cores": 32,
"multimode": "openmp"
}
})
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",
"FF_before_run", "test.qin"),
output_file=os.path.join(
module_dir, "..", "..", "test_files",
"FF_before_run",
"test.qout")).as_dict())
self.assertEqual(custodian_patch.call_args[1], {
"max_errors": 5,
"gzipped_output": True
})
self.assertEqual(
FF_patch.call_args[1], {
"qchem_command":
"qchem -slurm",
"multimode":
"openmp",
"input_file":
os.path.join(module_dir, "..", "..", "test_files",
"FF_before_run", "test.qin"),
"output_file":
os.path.join(module_dir, "..", "..", "test_files",
"FF_before_run", "test.qout"),
"qclog_file":
"mol.qclog",
"max_iterations":
10,
"linked":
True,
"calc_loc":
"/this/is/a/test",
"save_final_scratch":
False,
"max_cores":
32
})