def validate_transitionstate(self,
transitionstate,
calculator,
vibrational_analysis=True):
validated = False
if vibrational_analysis:
vib = VibrationalAnalysis(ts=transitionstate,
scratch=calculator.scratch)
validated = vib.validate_ts()
if not validated:
logging.info("Running an IRC to validate")
irc_calc = calculator.get_irc_calc(ts=transitionstate)
label = self.submit_transitionstate(transitionstate, irc_calc,
"general")
while not self.check_complete(label):
time.sleep(15)
result = calculator.validate_irc(calc=irc_calc)
if result:
logging.info("Validated via IRC")
return True
else:
logging.info(
"Could not validate this conformer... trying the next lowest energy conformer"
)
return False
else:
logging.info("Validated via Vibrational Analysis")
return True
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction.get_labeled_reaction()
self.ts = self.reaction.ts["forward"][0]
self.ts.get_molecules()
directory = os.path.expandvars("$AUTOTST/test")
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
"conformers")):
os.makedirs(
os.path.join(directory, "ts", self.reaction.label,
"conformers"))
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
self.reaction.label + "_forward_0.log"),
os.path.join(directory, "ts", self.reaction.label,
"conformers",
self.reaction.label + "_forward_0.log"))
self.directory = directory
self.vibrational_analysis = VibrationalAnalysis(
transitionstate=self.ts, directory=self.directory)
def validate_transitionstate(self,
transitionstate,
vibrational_analysis=True):
validated = False
if vibrational_analysis:
vib = VibrationalAnalysis(transitionstate=transitionstate,
directory=self.directory)
validated = vib.validate_ts()
if not validated:
logging.info(
"Could not validate with Vibrational Analysis... Running an IRC to validate instead..."
)
label = self.submit_transitionstate(transitionstate,
opt_type="irc")
while not self.check_complete(label):
time.sleep(15)
result = self.calculator.validate_irc(calc=irc_calc)
if result:
logging.info("Validated via IRC")
return True
else:
logging.info(
"Could not validate this conformer... trying the next lowest energy conformer"
)
return False
else:
logging.info("Validated via Vibrational Analysis")
return True
class VibrationalAnalysisTest(unittest.TestCase):
def setUp(self):
self.reaction = Reaction("CC+[O]O_[CH2]C+OO")
self.reaction.get_labeled_reaction()
self.ts = self.reaction.ts["forward"][0]
self.ts.get_molecules()
directory = os.path.expandvars("$AUTOTST/test")
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
"conformers")):
os.makedirs(
os.path.join(directory, "ts", self.reaction.label,
"conformers"))
if not os.path.exists(
os.path.join(directory, "ts", self.reaction.label,
self.reaction.label + ".log")):
shutil.copy(
os.path.join(directory, "bin", "log-files",
self.reaction.label + "_forward_0.log"),
os.path.join(directory, "ts", self.reaction.label,
"conformers",
self.reaction.label + "_forward_0.log"))
self.directory = directory
self.vibrational_analysis = VibrationalAnalysis(
transitionstate=self.ts, directory=self.directory)
def tearDown(self):
directory = os.path.expandvars("$AUTOTST/test")
if os.path.exists(os.path.join(directory, "ts")):
shutil.rmtree(os.path.join(directory, "ts"))
for head, _, files in os.walk(os.path.expandvars("$AUTOTST")):
for fi in files:
if fi.endswith(".symm"):
os.remove(os.path.join(head, fi))
def test_get_log_file(self):
log_file = self.vibrational_analysis.get_log_file()
actual_path = os.path.join(
self.directory, "ts", self.ts.reaction_label, "conformers",
"{}_{}_{}.log".format(self.ts.reaction_label, self.ts.direction,
self.ts.index))
self.assertEqual(log_file, actual_path)
def test_parse_vibrations(self):
vibrations = self.vibrational_analysis.parse_vibrations()
self.assertIsInstance(vibrations, list)
self.assertEqual(len(vibrations), 27)
def test_obtain_geometries(self):
vibrations = self.vibrational_analysis.parse_vibrations()
symbol_dict = {
17: "Cl",
9: "F",
8: "O",
7: "N",
6: "C",
1: "H",
}
atoms = []
parser = ccread(self.vibrational_analysis.log_file)
for atom_num, coords in zip(parser.atomnos, parser.atomcoords[-1]):
atoms.append(Atom(symbol=symbol_dict[atom_num], position=coords))
test_pre_geometry = Atoms(atoms)
test_post_geometry = test_pre_geometry.copy()
for vib, displacement in vibrations:
if vib < 0:
test_post_geometry.arrays["positions"] -= displacement
pre_geometry, post_geometry = self.vibrational_analysis.obtain_geometries(
)
for i, positions in enumerate(test_pre_geometry.arrays["positions"]):
for j, x in enumerate(positions):
self.assertEqual(x, pre_geometry.arrays["positions"][i][j])
for i, positions in enumerate(test_post_geometry.arrays["positions"]):
for j, x in enumerate(positions):
self.assertEqual(x, post_geometry.arrays["positions"][i][j])
def test_validate_ts(self):
self.assertTrue(self.vibrational_analysis.validate_ts())