def test_freq_job_too_small(self):
shutil.copyfile(os.path.join(test_dir, "freq_seg_too_small.qcinp"),
os.path.join(scr_dir, "freq_seg_too_small.qcinp"))
shutil.copyfile(os.path.join(test_dir, "freq_seg_too_small.qcout"),
os.path.join(scr_dir, "freq_seg_too_small.qcout"))
h = QChemErrorHandler(input_file="freq_seg_too_small.qcinp",
output_file="freq_seg_too_small.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Freq Job Too Small'],
'actions': ['use 31 segment in CPSCF']})
with open(os.path.join(test_dir, "freq_seg_too_small_31_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "freq_seg_too_small.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "freq_seg_too_small_31_segments.qcinp"),
os.path.join(scr_dir, "freq_seg_too_small_31_segments.qcinp"))
shutil.copyfile(os.path.join(test_dir, "freq_seg_too_small.qcout"),
os.path.join(scr_dir, "freq_seg_too_small.qcout"))
h = QChemErrorHandler(input_file="freq_seg_too_small_31_segments.qcinp",
output_file="freq_seg_too_small.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Freq Job Too Small'],
'actions': None})
def test_nan_error(self):
shutil.copyfile(os.path.join(test_dir, "thiane_nan.inp"), os.path.join(scr_dir, "thiane_nan.inp"))
shutil.copyfile(os.path.join(test_dir, "thiane_nan.out"), os.path.join(scr_dir, "thiane_nan.out"))
h = QChemErrorHandler(input_file="thiane_nan.inp", output_file="thiane_nan.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["NAN values"], "actions": ["use tighter grid"]})
with open(os.path.join(test_dir, "thiane_nan_dense_grid.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "thiane_nan.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "thiane_nan_dense_grid.inp"), os.path.join(scr_dir, "thiane_nan_dense_grid.inp")
)
shutil.copyfile(os.path.join(test_dir, "thiane_nan.out"), os.path.join(scr_dir, "thiane_nan.out"))
h = QChemErrorHandler(input_file="thiane_nan_dense_grid.inp", output_file="thiane_nan.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["NAN values"], "actions": None})
shutil.copyfile(os.path.join(test_dir, "h2o_nan.qcinp"), os.path.join(scr_dir, "h2o_nan.qcinp"))
shutil.copyfile(os.path.join(test_dir, "h2o_nan.qcout"), os.path.join(scr_dir, "h2o_nan.qcout"))
h = QChemErrorHandler(input_file="h2o_nan.qcinp", output_file="h2o_nan.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["NAN values"], "actions": ["use tighter grid"]})
with open(os.path.join(test_dir, "h2o_nan_dense_grid.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "h2o_nan.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_autoz_error(self):
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcinp"),
os.path.join(scr_dir, "qunino_vinyl.qcinp"))
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcout"),
os.path.join(scr_dir, "qunino_vinyl.qcout"))
h = QChemErrorHandler(input_file="qunino_vinyl.qcinp",
output_file="qunino_vinyl.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found',
'autoz error'],
'actions': ['disable symmetry']})
with open(os.path.join(test_dir, "qunino_vinyl_nosymm.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "qunino_vinyl.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl_nosymm.qcinp"),
os.path.join(scr_dir, "qunino_vinyl_nosymm.qcinp"))
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcout"),
os.path.join(scr_dir, "qunino_vinyl.qcout"))
h = QChemErrorHandler(input_file="qunino_vinyl_nosymm.qcinp",
output_file="qunino_vinyl.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found',
'autoz error'],
'actions': None})
def test_freq_job_too_small(self):
shutil.copyfile(
os.path.join(test_dir, "freq_seg_too_small.qcinp"), os.path.join(scr_dir, "freq_seg_too_small.qcinp")
)
shutil.copyfile(
os.path.join(test_dir, "freq_seg_too_small.qcout"), os.path.join(scr_dir, "freq_seg_too_small.qcout")
)
h = QChemErrorHandler(input_file="freq_seg_too_small.qcinp", output_file="freq_seg_too_small.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Exit Code 134", "Freq Job Too Small"], "actions": ["use 31 segment in CPSCF"]})
with open(os.path.join(test_dir, "freq_seg_too_small_31_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "freq_seg_too_small.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "freq_seg_too_small_31_segments.qcinp"),
os.path.join(scr_dir, "freq_seg_too_small_31_segments.qcinp"),
)
shutil.copyfile(
os.path.join(test_dir, "freq_seg_too_small.qcout"), os.path.join(scr_dir, "freq_seg_too_small.qcout")
)
h = QChemErrorHandler(input_file="freq_seg_too_small_31_segments.qcinp", output_file="freq_seg_too_small.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Exit Code 134", "Freq Job Too Small"], "actions": None})
def test_not_enough_total_memory(self):
old_jobid = os.environ.get("PBS_JOBID", None)
os.environ["PBS_JOBID"] = "hopque473945"
shutil.copyfile(
os.path.join(test_dir, "not_enough_total_memory.qcinp"),
os.path.join(scr_dir, "not_enough_total_memory.qcinp"),
)
shutil.copyfile(
os.path.join(test_dir, "not_enough_total_memory.qcout"),
os.path.join(scr_dir, "not_enough_total_memory.qcout"),
)
h = QChemErrorHandler(input_file="not_enough_total_memory.qcinp", output_file="not_enough_total_memory.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {"errors": ["Exit Code 134", "Not Enough Total Memory"], "actions": ["Use 48 CPSCF segments"]}
)
with open(os.path.join(test_dir, "not_enough_total_memory_48_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "not_enough_total_memory.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "not_enough_total_memory_48_segments.qcinp"),
os.path.join(scr_dir, "not_enough_total_memory_48_segments.qcinp"),
)
shutil.copyfile(
os.path.join(test_dir, "not_enough_total_memory.qcout"),
os.path.join(scr_dir, "not_enough_total_memory.qcout"),
)
qchem_job = QchemJob(
qchem_cmd=["qchem", "-np", "24"],
alt_cmd={"openmp": ["qchem", "-seq", "-nt", "24"], "half_cpus": ["qchem", "-np", "12"]},
input_file="not_enough_total_memory_48_segments.qcinp",
)
h = QChemErrorHandler(
input_file="not_enough_total_memory_48_segments.qcinp",
output_file="not_enough_total_memory.qcout",
qchem_job=qchem_job,
)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Exit Code 134", "Not Enough Total Memory"],
"actions": ["Use half CPUs and 60 CPSCF segments"],
},
)
with open(os.path.join(test_dir, "not_enough_total_memory_60_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "not_enough_total_memory_48_segments.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
if old_jobid is None:
os.environ.pop("PBS_JOBID")
else:
os.environ["PBS_JOBID"] = old_jobid
def test_autoz_error(self):
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcinp"),
os.path.join(scr_dir, "qunino_vinyl.qcinp"))
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcout"),
os.path.join(scr_dir, "qunino_vinyl.qcout"))
h = QChemErrorHandler(input_file="qunino_vinyl.qcinp",
output_file="qunino_vinyl.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found',
'autoz error'],
'actions': ['disable symmetry']})
with open(os.path.join(test_dir, "qunino_vinyl_nosymm.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "qunino_vinyl.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl_nosymm.qcinp"),
os.path.join(scr_dir, "qunino_vinyl_nosymm.qcinp"))
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcout"),
os.path.join(scr_dir, "qunino_vinyl.qcout"))
h = QChemErrorHandler(input_file="qunino_vinyl_nosymm.qcinp",
output_file="qunino_vinyl.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found',
'autoz error'],
'actions': None})
def test_scf_failed_to_converge(self):
for ii in range(3):
shutil.copyfile(
os.path.join(test_dir, "crowd_gradient.qin." + str(ii)),
os.path.join(scr_dir, "crowd_gradient.qin." + str(ii)),
)
shutil.copyfile(
os.path.join(test_dir, "crowd_gradient.qout." + str(ii)),
os.path.join(scr_dir, "crowd_gradient.qout." + str(ii)),
)
h = QChemErrorHandler(input_file="crowd_gradient.qin.0",
output_file="crowd_gradient.qout.0")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["SCF_failed_to_converge"])
self.assertEqual(d["actions"], [{"max_scf_cycles": 200}])
self._check_equivalent_inputs("crowd_gradient.qin.0",
"crowd_gradient.qin.1")
h = QChemErrorHandler(input_file="crowd_gradient.qin.1",
output_file="crowd_gradient.qout.1")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["SCF_failed_to_converge"])
self.assertEqual(d["actions"], [{"thresh": "14"}])
def test_exit_code_134_after_scf_fix(self):
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix.qcinp"),
os.path.join(scr_dir, "exit_134_after_scf_fix.qcinp"))
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix.qcout"),
os.path.join(scr_dir, "exit_134_after_scf_fix.qcout"))
h = QChemErrorHandler(input_file="exit_134_after_scf_fix.qcinp",
output_file="exit_134_after_scf_fix.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors': [
'Bad SCF convergence', 'Exit Code 134',
'Geometry optimization failed',
'Molecular charge is not found'
],
'actions': ['use tight integral threshold']
})
with open(
os.path.join(
test_dir,
"exit_134_after_scf_fix_tight_thresh.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "exit_134_after_scf_fix.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir,
"exit_134_after_scf_fix_tight_thresh.qcinp"),
os.path.join(scr_dir, "exit_134_after_scf_fix_tight_thresh.qcinp"))
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix.qcout"),
os.path.join(scr_dir, "exit_134_after_scf_fix.qcout"))
qchem_job = QchemJob(
qchem_cmd=shlex.split("qchem -np 24"),
input_file="exit_134_after_scf_fix_tight_thresh.qcinp",
output_file="exit_134_after_scf_fix.qcout",
alt_cmd={
"half_cpus": shlex.split("qchem -np 12"),
"openmp": shlex.split("qchem -nt 24")
})
h = QChemErrorHandler(
input_file="exit_134_after_scf_fix_tight_thresh.qcinp",
output_file="exit_134_after_scf_fix.qcout",
qchem_job=qchem_job)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors': [
'Bad SCF convergence', 'Exit Code 134',
'Geometry optimization failed',
'Molecular charge is not found'
],
'actions': ['openmp']
})
def test_opt_failed(self):
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcinp"), os.path.join(scr_dir, "hf_opt_failed.qcinp"))
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"), os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed.qcinp", output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Geometry optimization failed"], "actions": ["increase_iter"]})
with open(os.path.join(test_dir, "hf_opt_failed_tried_0.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_opt_failed.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "hf_opt_failed_tried_0.qcinp"), os.path.join(scr_dir, "hf_opt_failed_tried_0.qcinp")
)
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"), os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed_tried_0.qcinp", output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Geometry optimization failed"], "actions": ["GDIIS"]})
with open(os.path.join(test_dir, "hf_opt_failed_tried_1.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_opt_failed_tried_0.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "hf_opt_failed_tried_1.qcinp"), os.path.join(scr_dir, "hf_opt_failed_tried_1.qcinp")
)
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"), os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed_tried_1.qcinp", output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Geometry optimization failed"], "actions": ["CartCoords"]})
with open(os.path.join(test_dir, "hf_opt_failed_tried_2.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_opt_failed_tried_1.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "hf_opt_failed_tried_2.qcinp"), os.path.join(scr_dir, "hf_opt_failed_tried_2.qcinp")
)
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"), os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed_tried_2.qcinp", output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Geometry optimization failed"], "actions": None})
def test_json_serializable(self):
q1 = QChemErrorHandler()
str1 = json.dumps(q1, cls=MontyEncoder)
q2 = json.loads(str1, cls=MontyDecoder)
self.assertEqual(q1.as_dict(), q2.as_dict())
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcinp"), os.path.join(scr_dir, "qunino_vinyl.qcinp"))
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcout"), os.path.join(scr_dir, "qunino_vinyl.qcout"))
q3 = QChemErrorHandler(input_file="qunino_vinyl.qcinp", output_file="qunino_vinyl.qcout")
q3.check()
q3.correct()
for od in q3.outdata:
od.pop("input")
str3 = json.dumps(q3, cls=MontyEncoder)
q4 = json.loads(str3, cls=MontyDecoder)
self.assertEqual(q3.as_dict(), q4.as_dict())
def test_nan_error(self):
shutil.copyfile(os.path.join(test_dir, "thiane_nan.inp"),
os.path.join(scr_dir, "thiane_nan.inp"))
shutil.copyfile(os.path.join(test_dir, "thiane_nan.out"),
os.path.join(scr_dir, "thiane_nan.out"))
h = QChemErrorHandler(input_file="thiane_nan.inp",
output_file="thiane_nan.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {
'errors': ['NAN values'],
'actions': ['use tighter grid']
})
with open(os.path.join(test_dir, "thiane_nan_dense_grid.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "thiane_nan.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "thiane_nan_dense_grid.inp"),
os.path.join(scr_dir, "thiane_nan_dense_grid.inp"))
shutil.copyfile(os.path.join(test_dir, "thiane_nan.out"),
os.path.join(scr_dir, "thiane_nan.out"))
h = QChemErrorHandler(input_file="thiane_nan_dense_grid.inp",
output_file="thiane_nan.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['NAN values'], 'actions': None})
shutil.copyfile(os.path.join(test_dir, "h2o_nan.qcinp"),
os.path.join(scr_dir, "h2o_nan.qcinp"))
shutil.copyfile(os.path.join(test_dir, "h2o_nan.qcout"),
os.path.join(scr_dir, "h2o_nan.qcout"))
h = QChemErrorHandler(input_file="h2o_nan.qcinp",
output_file="h2o_nan.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {
'errors': ['NAN values'],
'actions': ['use tighter grid']
})
with open(os.path.join(test_dir, "h2o_nan_dense_grid.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "h2o_nan.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_pcm_solvent_deprecated(self):
shutil.copyfile(os.path.join(test_dir, "pcm_solvent_deprecated.qcinp"),
os.path.join(scr_dir, "pcm_solvent_deprecated.qcinp"))
shutil.copyfile(os.path.join(test_dir, "pcm_solvent_deprecated.qcout"),
os.path.join(scr_dir, "pcm_solvent_deprecated.qcout"))
h = QChemErrorHandler(input_file="pcm_solvent_deprecated.qcinp",
output_file="pcm_solvent_deprecated.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors': [
'Bad SCF convergence', 'Molecular charge is not found',
'No input text', 'pcm_solvent deprecated'
],
'actions': ['use keyword solvent instead']
})
with open(
os.path.join(
test_dir,
"pcm_solvent_deprecated_use_qc42_format.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "pcm_solvent_deprecated.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_pcm_solvent_deprecated(self):
shutil.copyfile(
os.path.join(test_dir, "pcm_solvent_deprecated.qcinp"),
os.path.join(scr_dir, "pcm_solvent_deprecated.qcinp"),
)
shutil.copyfile(
os.path.join(test_dir, "pcm_solvent_deprecated.qcout"),
os.path.join(scr_dir, "pcm_solvent_deprecated.qcout"),
)
h = QChemErrorHandler(input_file="pcm_solvent_deprecated.qcinp", output_file="pcm_solvent_deprecated.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": [
"Bad SCF convergence",
"Molecular charge is not found",
"No input text",
"pcm_solvent deprecated",
],
"actions": ["use keyword solvent instead"],
},
)
with open(os.path.join(test_dir, "pcm_solvent_deprecated_use_qc42_format.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "pcm_solvent_deprecated.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_unable_to_determine_lambda(self):
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lambda_in_geom_opt.qcinp"),
os.path.join(scr_dir,
"unable_to_determine_lambda_in_geom_opt.qcinp"))
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lambda_in_geom_opt.qcout"),
os.path.join(scr_dir,
"unable_to_determine_lambda_in_geom_opt.qcout"))
h = QChemErrorHandler(
input_file="unable_to_determine_lambda_in_geom_opt.qcinp",
output_file="unable_to_determine_lambda_in_geom_opt.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors':
['Geometry optimization failed', 'Lamda Determination Failed'],
'actions': ['reset']
})
with open(
os.path.join(
test_dir,
"unable_to_determine_lambda_in_geom_opt_reset.qcinp")
) as f:
ref = [line.strip() for line in f.readlines()]
with open(
os.path.join(
scr_dir,
"unable_to_determine_lambda_in_geom_opt.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_out_of_opt_cycles(self):
shutil.copyfile(
os.path.join(test_dir, "crowd_gradient.qin.2"),
os.path.join(scr_dir, "crowd_gradient.qin.2"),
)
shutil.copyfile(
os.path.join(test_dir, "crowd_gradient.qout.2"),
os.path.join(scr_dir, "crowd_gradient.qout.2"),
)
shutil.copyfile(
os.path.join(test_dir, "crowd_gradient.qin.3"),
os.path.join(scr_dir, "crowd_gradient.qin.3"),
)
h = QChemErrorHandler(input_file="crowd_gradient.qin.2",
output_file="crowd_gradient.qout.2")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["out_of_opt_cycles"])
self.assertEqual(
d["actions"],
[{
"geom_max_cycles:": 200
}, {
"molecule": "molecule_from_last_geometry"
}],
)
self._check_equivalent_inputs("crowd_gradient.qin.2",
"crowd_gradient.qin.3")
def test_advanced_out_of_opt_cycles(self):
shutil.copyfile(
os.path.join(test_dir, "2564_complete/error1/mol.qin"),
os.path.join(scr_dir, "mol.qin"),
)
shutil.copyfile(
os.path.join(test_dir, "2564_complete/error1/mol.qout"),
os.path.join(scr_dir, "mol.qout"),
)
shutil.copyfile(
os.path.join(test_dir, "2564_complete/mol.qin.opt_0"),
os.path.join(scr_dir, "mol.qin.opt_0"),
)
h = QChemErrorHandler(input_file="mol.qin", output_file="mol.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["out_of_opt_cycles"])
self.assertEqual(d["actions"],
[{
"molecule": "molecule_from_last_geometry"
}])
self._check_equivalent_inputs("mol.qin.opt_0", "mol.qin")
self.assertEqual(h.opt_error_history[0], "more_bonds")
shutil.copyfile(
os.path.join(test_dir, "2564_complete/mol.qin.opt_0"),
os.path.join(scr_dir, "mol.qin"),
)
shutil.copyfile(
os.path.join(test_dir, "2564_complete/mol.qout.opt_0"),
os.path.join(scr_dir, "mol.qout"),
)
h.check()
self.assertEqual(h.opt_error_history, [])
def test_OOS_read_hess(self):
shutil.copyfile(
os.path.join(test_dir, "OOS_read_hess.qin"),
os.path.join(scr_dir, "mol.qin"),
)
shutil.copyfile(
os.path.join(test_dir, "OOS_read_hess.qout"),
os.path.join(scr_dir, "mol.qout"),
)
h = QChemErrorHandler(input_file="mol.qin", output_file="mol.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["out_of_opt_cycles"])
self.assertEqual(
d["actions"],
[
{
"molecule": "molecule_from_last_geometry"
},
{
"geom_opt_hessian": "deleted"
},
],
)
self._check_equivalent_inputs(
os.path.join(test_dir, "OOS_read_hess_next.qin"), "mol.qin")
def test_unable_to_determine_lamda(self):
for ii in range(2):
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lamda.qin." + str(ii)),
os.path.join(scr_dir,
"unable_to_determine_lamda.qin." + str(ii)),
)
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lamda.qout." + str(ii)),
os.path.join(scr_dir,
"unable_to_determine_lamda.qout." + str(ii)),
)
h = QChemErrorHandler(
input_file="unable_to_determine_lamda.qin.0",
output_file="unable_to_determine_lamda.qout.0",
)
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["unable_to_determine_lamda"])
self.assertEqual(d["actions"],
[{
"molecule": "molecule_from_last_geometry"
}])
self._check_equivalent_inputs("unable_to_determine_lamda.qin.0",
"unable_to_determine_lamda.qin.1")
def test_linear_dependent_basis(self):
for ii in range(1, 3):
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lamda.qin." + str(ii)),
os.path.join(scr_dir,
"unable_to_determine_lamda.qin." + str(ii)))
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lamda.qout." + str(ii)),
os.path.join(scr_dir,
"unable_to_determine_lamda.qout." + str(ii)))
h = QChemErrorHandler(input_file="unable_to_determine_lamda.qin.1",
output_file="unable_to_determine_lamda.qout.1")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['linear_dependent_basis'])
self.assertEqual(d["actions"], [{"scf_algorithm": "rca_diis"}])
self._check_equivalent_inputs("unable_to_determine_lamda.qin.1",
"unable_to_determine_lamda.qin.2")
h = QChemErrorHandler(input_file="unable_to_determine_lamda.qin.2",
output_file="unable_to_determine_lamda.qout.2")
self.assertEqual(h.check(), False)
def test_failed_to_transform(self):
for ii in range(2):
shutil.copyfile(
os.path.join(test_dir, "qunino_vinyl.qin." + str(ii)),
os.path.join(scr_dir, "qunino_vinyl.qin." + str(ii)),
)
shutil.copyfile(
os.path.join(test_dir, "qunino_vinyl.qout." + str(ii)),
os.path.join(scr_dir, "qunino_vinyl.qout." + str(ii)),
)
h = QChemErrorHandler(input_file="qunino_vinyl.qin.0",
output_file="qunino_vinyl.qout.0")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["failed_to_transform_coords"])
self.assertEqual(d["actions"], [{
"sym_ignore": True
}, {
"symmetry": False
}])
self._check_equivalent_inputs("qunino_vinyl.qin.0",
"qunino_vinyl.qin.1")
h = QChemErrorHandler(input_file="qunino_vinyl.qin.1",
output_file="qunino_vinyl.qout.1")
self.assertEqual(h.check(), False)
def test_not_enough_total_memory(self):
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory.qcinp"),
os.path.join(scr_dir, "not_enough_total_memory.qcinp"))
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory.qcout"),
os.path.join(scr_dir, "not_enough_total_memory.qcout"))
qchem_job = QchemJob(qchem_cmd=shlex.split("qchem -np 24"),
input_file="not_enough_total_memory.qcinp",
output_file="not_enough_total_memory.qcout",
alt_cmd={"half_cpus": shlex.split("qchem -np 12"),
"openmp": shlex.split("qchem -nt 24")},
total_physical_memory=120)
h = QChemErrorHandler(input_file="not_enough_total_memory.qcinp",
output_file="not_enough_total_memory.qcout", qchem_job=qchem_job)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Not Enough Total Memory'],
'actions': ['Use 48 CPSCF segments']})
with open(os.path.join(test_dir, "not_enough_total_memory_48_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "not_enough_total_memory.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory_48_segments.qcinp"),
os.path.join(scr_dir, "not_enough_total_memory_48_segments.qcinp"))
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory.qcout"),
os.path.join(scr_dir, "not_enough_total_memory.qcout"))
qchem_job = QchemJob(qchem_cmd=["qchem", "-np", "24"],
alt_cmd={"openmp": ["qchem", "-seq", "-nt", "24"],
"half_cpus": ["qchem", "-np", "12"]},
input_file="not_enough_total_memory_48_segments.qcinp")
h = QChemErrorHandler(input_file="not_enough_total_memory_48_segments.qcinp",
output_file="not_enough_total_memory.qcout",
qchem_job=qchem_job)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Not Enough Total Memory'],
'actions': ['Use half CPUs and 60 CPSCF segments']})
with open(os.path.join(test_dir, "not_enough_total_memory_60_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "not_enough_total_memory_48_segments.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_negative_eigen(self):
shutil.copyfile(os.path.join(test_dir, "negative_eigen.qcinp"),
os.path.join(scr_dir, "negative_eigen.qcinp"))
shutil.copyfile(os.path.join(test_dir, "negative_eigen.qcout"),
os.path.join(scr_dir, "negative_eigen.qcout"))
h = QChemErrorHandler(input_file="negative_eigen.qcinp",
output_file="negative_eigen.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors': [
'Bad SCF convergence', 'Molecular charge is not found',
'Negative Eigen'
],
'actions': ['use tight integral threshold']
})
with open(os.path.join(test_dir, "negative_eigen_tried_1.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "negative_eigen.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "negative_eigen_tried_1.qcinp"),
os.path.join(scr_dir, "negative_eigen_tried_1.qcinp"))
shutil.copyfile(os.path.join(test_dir, "negative_eigen.qcout"),
os.path.join(scr_dir, "negative_eigen.qcout"))
h = QChemErrorHandler(input_file="negative_eigen_tried_1.qcinp",
output_file="negative_eigen.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors': [
'Bad SCF convergence', 'Molecular charge is not found',
'Negative Eigen'
],
'actions': ['use even tighter integral threshold']
})
with open(os.path.join(test_dir, "negative_eigen_tried_2.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "negative_eigen_tried_1.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_not_enough_total_memory(self):
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory.qcinp"),
os.path.join(scr_dir, "not_enough_total_memory.qcinp"))
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory.qcout"),
os.path.join(scr_dir, "not_enough_total_memory.qcout"))
qchem_job = QchemJob(qchem_cmd=shlex.split("qchem -np 24"),
input_file="not_enough_total_memory.qcinp",
output_file="not_enough_total_memory.qcout",
alt_cmd={"half_cpus": shlex.split("qchem -np 12"),
"openmp": shlex.split("qchem -nt 24")},
total_physical_memory=120)
h = QChemErrorHandler(input_file="not_enough_total_memory.qcinp",
output_file="not_enough_total_memory.qcout", qchem_job=qchem_job)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Not Enough Total Memory'],
'actions': ['Use 48 CPSCF segments']})
with open(os.path.join(test_dir, "not_enough_total_memory_48_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "not_enough_total_memory.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory_48_segments.qcinp"),
os.path.join(scr_dir, "not_enough_total_memory_48_segments.qcinp"))
shutil.copyfile(os.path.join(test_dir, "not_enough_total_memory.qcout"),
os.path.join(scr_dir, "not_enough_total_memory.qcout"))
qchem_job = QchemJob(qchem_cmd=["qchem", "-np", "24"],
alt_cmd={"openmp": ["qchem", "-seq", "-nt", "24"],
"half_cpus": ["qchem", "-np", "12"]},
input_file="not_enough_total_memory_48_segments.qcinp")
h = QChemErrorHandler(input_file="not_enough_total_memory_48_segments.qcinp",
output_file="not_enough_total_memory.qcout",
qchem_job=qchem_job)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Not Enough Total Memory'],
'actions': ['Use half CPUs and 60 CPSCF segments']})
with open(os.path.join(test_dir, "not_enough_total_memory_60_segments.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "not_enough_total_memory_48_segments.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_json_serializable(self):
q1 = QChemErrorHandler()
str1 = json.dumps(q1, cls=MontyEncoder)
q2 = json.loads(str1, cls=MontyDecoder)
self.assertEqual(q1.as_dict(), q2.as_dict())
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcinp"),
os.path.join(scr_dir, "qunino_vinyl.qcinp"))
shutil.copyfile(os.path.join(test_dir, "qunino_vinyl.qcout"),
os.path.join(scr_dir, "qunino_vinyl.qcout"))
q3 = QChemErrorHandler(input_file="qunino_vinyl.qcinp",
output_file="qunino_vinyl.qcout")
q3.check()
q3.correct()
for od in q3.outdata:
od.pop("input")
str3 = json.dumps(q3, cls=MontyEncoder)
q4 = json.loads(str3, cls=MontyDecoder)
self.assertEqual(q3.as_dict(), q4.as_dict())
def test_never_called_qchem_error(self):
shutil.copyfile(os.path.join(test_dir, "mpi_error/mol.qin"),
os.path.join(scr_dir, "mol.qin"))
shutil.copyfile(os.path.join(test_dir, "mpi_error/mol.qout"),
os.path.join(scr_dir, "mol.qout"))
h = QChemErrorHandler(input_file="mol.qin", output_file="mol.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['never_called_qchem'])
self.assertEqual(d["actions"], [{"rerun job as-is"}])
self._check_equivalent_inputs("mol.qin.last", "mol.qin")
def test_input_file_error(self):
shutil.copyfile(os.path.join(test_dir, "bad_input.qin"),
os.path.join(scr_dir, "bad_input.qin"))
shutil.copyfile(os.path.join(test_dir, "bad_input.qout"),
os.path.join(scr_dir, "bad_input.qout"))
h = QChemErrorHandler(input_file="bad_input.qin",
output_file="bad_input.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['input_file_error'])
self.assertEqual(d["actions"], None)
def test_negative_eigen(self):
shutil.copyfile(os.path.join(test_dir, "negative_eigen.qcinp"), os.path.join(scr_dir, "negative_eigen.qcinp"))
shutil.copyfile(os.path.join(test_dir, "negative_eigen.qcout"), os.path.join(scr_dir, "negative_eigen.qcout"))
h = QChemErrorHandler(input_file="negative_eigen.qcinp", output_file="negative_eigen.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Molecular charge is not found", "Negative Eigen"],
"actions": ["use tight integral threshold"],
},
)
with open(os.path.join(test_dir, "negative_eigen_tried_1.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "negative_eigen.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(
os.path.join(test_dir, "negative_eigen_tried_1.qcinp"),
os.path.join(scr_dir, "negative_eigen_tried_1.qcinp"),
)
shutil.copyfile(os.path.join(test_dir, "negative_eigen.qcout"), os.path.join(scr_dir, "negative_eigen.qcout"))
h = QChemErrorHandler(input_file="negative_eigen_tried_1.qcinp", output_file="negative_eigen.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Molecular charge is not found", "Negative Eigen"],
"actions": ["use even tighter integral threshold"],
},
)
with open(os.path.join(test_dir, "negative_eigen_tried_2.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "negative_eigen_tried_1.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_exit_code_134_after_scf_fix(self):
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix.qcinp"),
os.path.join(scr_dir, "exit_134_after_scf_fix.qcinp"))
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix.qcout"),
os.path.join(scr_dir, "exit_134_after_scf_fix.qcout"))
h = QChemErrorHandler(input_file="exit_134_after_scf_fix.qcinp",
output_file="exit_134_after_scf_fix.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Exit Code 134',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['use tight integral threshold']})
with open(os.path.join(test_dir, "exit_134_after_scf_fix_tight_thresh.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "exit_134_after_scf_fix.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix_tight_thresh.qcinp"),
os.path.join(scr_dir, "exit_134_after_scf_fix_tight_thresh.qcinp"))
shutil.copyfile(os.path.join(test_dir, "exit_134_after_scf_fix.qcout"),
os.path.join(scr_dir, "exit_134_after_scf_fix.qcout"))
qchem_job = QchemJob(qchem_cmd="qchem -np 24",
input_file="exit_134_after_scf_fix_tight_thresh.qcinp",
output_file="exit_134_after_scf_fix.qcout",
alt_cmd={"half_cpus": "qchem -np 12",
"openmp": "qchem -nt 24"})
h = QChemErrorHandler(input_file="exit_134_after_scf_fix_tight_thresh.qcinp",
output_file="exit_134_after_scf_fix.qcout",
qchem_job=qchem_job)
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Exit Code 134',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['half_cpus']})
def test_scf_in_aimd_reset(self):
shutil.copyfile(os.path.join(test_dir, "h2o_aimd.qcinp"), os.path.join(scr_dir, "h2o_aimd.qcinp"))
shutil.copyfile(os.path.join(test_dir, "h2o_aimd.qcout"), os.path.join(scr_dir, "h2o_aimd.qcout"))
h = QChemErrorHandler(input_file="h2o_aimd.qcinp", output_file="h2o_aimd.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Bad SCF convergence"], "actions": ["reset"]})
with open(os.path.join(test_dir, "h2o_aimd_reset.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "h2o_aimd.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_scf_reset(self):
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_1.inp"), os.path.join(scr_dir, "hf_scf_reset.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_scf_reset.out"), os.path.join(scr_dir, "hf_scf_reset.out"))
h = QChemErrorHandler(input_file="hf_scf_reset.inp", output_file="hf_scf_reset.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Bad SCF convergence", "Geometry optimization failed"], "actions": ["reset"]})
with open(os.path.join(test_dir, "hf_scf_reset.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_scf_reset.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_failed_to_read_input(self):
shutil.copyfile(os.path.join(test_dir, "unable_lamda_weird.qin"),
os.path.join(scr_dir, "unable_lamda_weird.qin"))
shutil.copyfile(os.path.join(test_dir, "unable_lamda_weird.qout"),
os.path.join(scr_dir, "unable_lamda_weird.qout"))
h = QChemErrorHandler(input_file="unable_lamda_weird.qin",
output_file="unable_lamda_weird.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['failed_to_read_input'])
self.assertEqual(d["actions"], [{"rerun job as-is"}])
self._check_equivalent_inputs("unable_lamda_weird.qin.last",
"unable_lamda_weird.qin")
def test_ts_opt(self):
shutil.copyfile(os.path.join(test_dir, "ts_cf3_leave.qcinp"), os.path.join(scr_dir, "ts_cf3_leave.qcinp"))
shutil.copyfile(os.path.join(test_dir, "ts_cf3_leave.qcout"), os.path.join(scr_dir, "ts_cf3_leave.qcout"))
h = QChemErrorHandler(input_file="ts_cf3_leave.qcinp", output_file="ts_cf3_leave.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {"errors": ["Exit Code 134", "Geometry optimization failed"], "actions": ["increase_iter"]})
with open(os.path.join(test_dir, "ts_cf3_leave_reset_first_step_mol.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "ts_cf3_leave.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_read_error(self):
shutil.copyfile(
os.path.join(test_dir, "molecule_read_error/mol.qin"),
os.path.join(scr_dir, "mol.qin"),
)
shutil.copyfile(
os.path.join(test_dir, "molecule_read_error/mol.qout"),
os.path.join(scr_dir, "mol.qout"),
)
h = QChemErrorHandler(input_file="mol.qin", output_file="mol.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["read_molecule_error"])
self.assertEqual(d["actions"], [{"rerun_job_no_changes": True}])
self._check_equivalent_inputs("mol.qin.last", "mol.qin")
def test_NLebdevPts(self):
shutil.copyfile(
os.path.join(test_dir, "lebdevpts.qin"),
os.path.join(scr_dir, "lebdevpts.qin"),
)
shutil.copyfile(
os.path.join(test_dir, "lebdevpts.qout"),
os.path.join(scr_dir, "lebdevpts.qout"),
)
h = QChemErrorHandler(input_file="lebdevpts.qin",
output_file="lebdevpts.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["NLebdevPts"])
self.assertEqual(d["actions"], [{"esp_surface_density": "250"}])
def test_basis_not_supported(self):
shutil.copyfile(
os.path.join(test_dir, "basis_not_supported.qin"),
os.path.join(scr_dir, "basis_not_supported.qin"),
)
shutil.copyfile(
os.path.join(test_dir, "basis_not_supported.qout"),
os.path.join(scr_dir, "basis_not_supported.qout"),
)
h = QChemErrorHandler(input_file="basis_not_supported.qin",
output_file="basis_not_supported.qout")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["basis_not_supported"])
self.assertEqual(d["actions"], None)
def test_scf_in_aimd_reset(self):
shutil.copyfile(os.path.join(test_dir, "h2o_aimd.qcinp"),
os.path.join(scr_dir, "h2o_aimd.qcinp"))
shutil.copyfile(os.path.join(test_dir, "h2o_aimd.qcout"),
os.path.join(scr_dir, "h2o_aimd.qcout"))
h = QChemErrorHandler(input_file="h2o_aimd.qcinp",
output_file="h2o_aimd.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence'],
'actions': ['reset']})
with open(os.path.join(test_dir, "h2o_aimd_reset.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "h2o_aimd.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_scf_reset(self):
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_1.inp"),
os.path.join(scr_dir, "hf_scf_reset.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_scf_reset.out"),
os.path.join(scr_dir, "hf_scf_reset.out"))
h = QChemErrorHandler(input_file="hf_scf_reset.inp",
output_file="hf_scf_reset.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed'],
'actions': ['reset']})
with open(os.path.join(test_dir, "hf_scf_reset.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_scf_reset.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_ts_opt(self):
shutil.copyfile(os.path.join(test_dir, "ts_cf3_leave.qcinp"),
os.path.join(scr_dir, "ts_cf3_leave.qcinp"))
shutil.copyfile(os.path.join(test_dir, "ts_cf3_leave.qcout"),
os.path.join(scr_dir, "ts_cf3_leave.qcout"))
h = QChemErrorHandler(input_file="ts_cf3_leave.qcinp",
output_file="ts_cf3_leave.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Exit Code 134',
'Geometry optimization failed'],
'actions': ['increase_iter']})
with open(os.path.join(test_dir, "ts_cf3_leave_reset_first_step_mol.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "ts_cf3_leave.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_unable_to_determine_lambda(self):
shutil.copyfile(os.path.join(test_dir, "unable_to_determine_lambda_in_geom_opt.qcinp"),
os.path.join(scr_dir, "unable_to_determine_lambda_in_geom_opt.qcinp"))
shutil.copyfile(os.path.join(test_dir, "unable_to_determine_lambda_in_geom_opt.qcout"),
os.path.join(scr_dir, "unable_to_determine_lambda_in_geom_opt.qcout"))
h = QChemErrorHandler(input_file="unable_to_determine_lambda_in_geom_opt.qcinp",
output_file="unable_to_determine_lambda_in_geom_opt.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Geometry optimization failed',
'Lamda Determination Failed'],
'actions': ['reset']})
with open(os.path.join(test_dir, "unable_to_determine_lambda_in_geom_opt_reset.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "unable_to_determine_lambda_in_geom_opt.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_exit_code_134(self):
shutil.copyfile(os.path.join(test_dir, "exit_code_134.qcinp"), os.path.join(scr_dir, "exit_code_134.qcinp"))
shutil.copyfile(os.path.join(test_dir, "exit_code_134.qcout"), os.path.join(scr_dir, "exit_code_134.qcout"))
h = QChemErrorHandler(input_file="exit_code_134.qcinp", output_file="exit_code_134.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Exit Code 134", "Molecular charge is not found"],
"actions": ["use tight integral threshold"],
},
)
with open(os.path.join(test_dir, "exit_code_134_tight_thresh.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "exit_code_134.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_no_input_text(self):
shutil.copyfile(os.path.join(test_dir, "no_reading.qcinp"), os.path.join(scr_dir, "no_reading.qcinp"))
shutil.copyfile(os.path.join(test_dir, "no_reading.qcout"), os.path.join(scr_dir, "no_reading.qcout"))
h = QChemErrorHandler(input_file="no_reading.qcinp", output_file="no_reading.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Exit Code 134", "Molecular charge is not found", "No input text"],
"actions": ["disable symmetry"],
},
)
with open(os.path.join(test_dir, "no_reading_nosymm.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "no_reading.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_scf_fon(self):
shutil.copyfile(os.path.join(test_dir, "hf_rca_hit_5.inp"),
os.path.join(scr_dir, "hf_rca_hit_5.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_hit_5.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['fon']})
with open(os.path.join(test_dir, "hf_rca_hit_5_fon.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_hit_5.inp")) as f:
ans = [line.strip() for line in f.readlines()]
ans = self._revert_scf_fix_strategy_to_version(ans, fix_version="2.0")
self.assertEqual(ref, ans)
def test_no_input_text(self):
shutil.copyfile(os.path.join(test_dir, "no_reading.qcinp"),
os.path.join(scr_dir, "no_reading.qcinp"))
shutil.copyfile(os.path.join(test_dir, "no_reading.qcout"),
os.path.join(scr_dir, "no_reading.qcout"))
h = QChemErrorHandler(input_file="no_reading.qcinp",
output_file="no_reading.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Exit Code 134',
'Molecular charge is not found',
'No input text'],
'actions': ['disable symmetry']})
with open(os.path.join(test_dir, "no_reading_nosymm.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "no_reading.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_exit_code_134(self):
shutil.copyfile(os.path.join(test_dir, "exit_code_134.qcinp"),
os.path.join(scr_dir, "exit_code_134.qcinp"))
shutil.copyfile(os.path.join(test_dir, "exit_code_134.qcout"),
os.path.join(scr_dir, "exit_code_134.qcout"))
h = QChemErrorHandler(input_file="exit_code_134.qcinp",
output_file="exit_code_134.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Exit Code 134',
'Molecular charge is not found'],
'actions': ['use tight integral threshold']})
with open(os.path.join(test_dir, "exit_code_134_tight_thresh.qcinp"))\
as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "exit_code_134.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
def test_scf_fon(self):
shutil.copyfile(os.path.join(test_dir, "hf_rca_hit_5.inp"), os.path.join(scr_dir, "hf_rca_hit_5.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_hit_5.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["fon"],
},
)
with open(os.path.join(test_dir, "hf_rca_hit_5_fon.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_hit_5.inp")) as f:
ans = [line.strip() for line in f.readlines()]
ans = self._revert_scf_fix_strategy_to_version(ans, fix_version="2.0")
self.assertEqual(ref, ans)
def test_linear_dependent_basis_and_FileMan(self):
for ii in range(1, 3):
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lamda.qin." + str(ii)),
os.path.join(scr_dir,
"unable_to_determine_lamda.qin." + str(ii)))
shutil.copyfile(
os.path.join(test_dir,
"unable_to_determine_lamda.qout." + str(ii)),
os.path.join(scr_dir,
"unable_to_determine_lamda.qout." + str(ii)))
h = QChemErrorHandler(
input_file="unable_to_determine_lamda.qin.1",
output_file="unable_to_determine_lamda.qout.1")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['premature_end_FileMan_error'])
self.assertEqual(d["warnings"]["linear_dependence"], True)
self.assertEqual(d["actions"], [{"thresh": "14"}])
def test_scf_rca(self):
shutil.copyfile(os.path.join(test_dir, "hf_rca.inp"), os.path.join(scr_dir, "hf_rca.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["increase_iter"],
},
)
with open(os.path.join(test_dir, "hf_rca_tried_0.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca.inp")) as f:
ans = [line.strip() for line in f.readlines()]
ans = self._revert_scf_fix_strategy_to_version(ans, fix_version="1.0")
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_0.inp"), os.path.join(scr_dir, "hf_rca_tried_0.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_0.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["rca_diis"],
},
)
with open(os.path.join(test_dir, "hf_rca_tried_1.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_0.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_1.inp"), os.path.join(scr_dir, "hf_rca_tried_1.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_1.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["gwh"],
},
)
with open(os.path.join(test_dir, "hf_rca_tried_2.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_1.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_2.inp"), os.path.join(scr_dir, "hf_rca_tried_2.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_2.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["gdm"],
},
)
with open(os.path.join(test_dir, "hf_rca_tried_3.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_2.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_3.inp"), os.path.join(scr_dir, "hf_rca_tried_3.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_3.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["rca"],
},
)
with open(os.path.join(test_dir, "hf_rca_tried_4.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_3.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_4.inp"), os.path.join(scr_dir, "hf_rca_tried_4.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_4.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": ["core+rca"],
},
)
with open(os.path.join(test_dir, "hf_rca_tried_5.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_4.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_5.inp"), os.path.join(scr_dir, "hf_rca_tried_5.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"), os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_5.inp", output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d,
{
"errors": ["Bad SCF convergence", "Geometry optimization failed", "Molecular charge is not found"],
"actions": None,
},
)
def test_opt_failed(self):
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcinp"),
os.path.join(scr_dir, "hf_opt_failed.qcinp"))
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"),
os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed.qcinp",
output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(
d, {
'errors': ['Geometry optimization failed'],
'actions': ['increase_iter']
})
with open(os.path.join(test_dir, "hf_opt_failed_tried_0.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_opt_failed.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed_tried_0.qcinp"),
os.path.join(scr_dir, "hf_opt_failed_tried_0.qcinp"))
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"),
os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed_tried_0.qcinp",
output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {
'errors': ['Geometry optimization failed'],
'actions': ['GDIIS']
})
with open(os.path.join(test_dir, "hf_opt_failed_tried_1.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_opt_failed_tried_0.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed_tried_1.qcinp"),
os.path.join(scr_dir, "hf_opt_failed_tried_1.qcinp"))
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"),
os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed_tried_1.qcinp",
output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {
'errors': ['Geometry optimization failed'],
'actions': ['CartCoords']
})
with open(os.path.join(test_dir, "hf_opt_failed_tried_2.qcinp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_opt_failed_tried_1.qcinp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed_tried_2.qcinp"),
os.path.join(scr_dir, "hf_opt_failed_tried_2.qcinp"))
shutil.copyfile(os.path.join(test_dir, "hf_opt_failed.qcout"),
os.path.join(scr_dir, "hf_opt_failed.qcout"))
h = QChemErrorHandler(input_file="hf_opt_failed_tried_2.qcinp",
output_file="hf_opt_failed.qcout")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {
'errors': ['Geometry optimization failed'],
'actions': None
})
def test_scf_rca(self):
shutil.copyfile(os.path.join(test_dir, "hf_rca.inp"),
os.path.join(scr_dir, "hf_rca.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['increase_iter']})
with open(os.path.join(test_dir, "hf_rca_tried_0.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_0.inp"),
os.path.join(scr_dir, "hf_rca_tried_0.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_0.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['rca_diis']})
with open(os.path.join(test_dir, "hf_rca_tried_1.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_0.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_1.inp"),
os.path.join(scr_dir, "hf_rca_tried_1.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_1.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['gwh']})
with open(os.path.join(test_dir, "hf_rca_tried_2.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_1.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_2.inp"),
os.path.join(scr_dir, "hf_rca_tried_2.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_2.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['gdm']})
with open(os.path.join(test_dir, "hf_rca_tried_3.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_2.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_3.inp"),
os.path.join(scr_dir, "hf_rca_tried_3.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_3.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['rca']})
with open(os.path.join(test_dir, "hf_rca_tried_4.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_3.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_4.inp"),
os.path.join(scr_dir, "hf_rca_tried_4.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_4.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': ['core+rca']})
with open(os.path.join(test_dir, "hf_rca_tried_5.inp")) as f:
ref = [line.strip() for line in f.readlines()]
with open(os.path.join(scr_dir, "hf_rca_tried_4.inp")) as f:
ans = [line.strip() for line in f.readlines()]
self.assertEqual(ref, ans)
shutil.copyfile(os.path.join(test_dir, "hf_rca_tried_5.inp"),
os.path.join(scr_dir, "hf_rca_tried_5.inp"))
shutil.copyfile(os.path.join(test_dir, "hf_rca.out"),
os.path.join(scr_dir, "hf_rca.out"))
h = QChemErrorHandler(input_file="hf_rca_tried_5.inp",
output_file="hf_rca.out")
has_error = h.check()
self.assertTrue(has_error)
d = h.correct()
self.assertEqual(d, {'errors': ['Bad SCF convergence',
'Geometry optimization failed',
'Molecular charge is not found'],
'actions': None})