class TestScrewer(unittest.TestCase):
"""Tests the Jobset Class"""
def setUp(self):
self.screwer = Screwer("5")
def test_setup_screwer(self):
"""Test setting up screwer"""
self.assertEqual(self.screwer.mode, "5")
def test_exit_screwer(self):
"""Test exit code"""
self.assertEqual(self.screwer._end_screwer(), -99)
def ensure_not_ts(job):
"""
This runs to read out the vibrational modes. If there are negatives, runs
screwer to adjust the geometry along the imaginary coordinate, and
resubmits job.
"""
if job.freqopt == 'numforce':
newdir = os.path.join(job.indir, 'numforce')
else:
newdir = job.indir
filetoread = os.path.join(newdir, 'control')
controlfile = turbogo_helpers.read_clean_file(filetoread)
vib1 = False
for i in range(len(controlfile)):
if '$vibrational spectrum' in controlfile[i]:
for j in range (i+3, len(controlfile)):
col = controlfile[j][15:34].strip()
if not (col == '0.00' or col == '-0.00'):
try:
vib1 = float(col)
except ValueError:
pass
else:
mode = controlfile[j][:6].strip()
break
if vib1:
break
if vib1:
if job.firstfreq == vib1:
#Found the same TS as before. End job.
return 'same'
job.firstfreq = vib1
if vib1 < 0:
os.chdir(newdir)
screwer = Screwer(mode)
try:
screwer.run_screwer()
except Exception as e:
logging.warning("Error '{}' running screwer on job {}.".format(
e, job.name))
os.chdir(TOPDIR)
return "error"
control = turbogo_helpers.read_clean_file('control')
newcoord = list()
readin = False
for line in control:
if '$newcoord' in line:
readin = -1
elif '$end' in line:
readin = False
if readin:
newcoord.append(line)
elif readin == -1:
readin = True
if job.freqopt == 'numforce':
os.chdir(os.pardir)
turbogo_helpers.write_file('coord', newcoord)
try: # Better to remove numforce, if not no biggie
os.remove(os.path.join(os.curdir, 'control'))
shutil.rmtree(os.path.join(os.curdir, 'numforce'))
except OSError:
pass
try:
job.jobid, job.freqopt, job.name, job.jobtype = jobrunner(job=self.job)
job.curstart = time()
except Exception as e:
logging.warning("Error {} resubmitting job {}.".format(
e, job.name))
os.chdir(TOPDIR)
return 'error'
os.chdir(TOPDIR)
return 'opt'
else:
return 'completed'
else:
logging.warning(
'Error getting vibrational frequencies from job {}.'.format(
job.name
))
return 'error'
def setUp(self):
self.screwer = Screwer("5")