def check_freq(job):
"""
Check if a freq job is done or crashed, if done: check for imaginary and
send for adjustment if required.
Return a status string
"""
if job.freqopt == 'numforce':
filetoread = os.path.join(job.indir, 'numforce', 'aoforce.out')
endfile = 'numforce.out'
else:
filetoread = os.path.join(job.indir, 'aoforce.out')
endfile = 'aoforce.out'
try:
with open(filetoread, 'r') as f:
endstatus = f.readlines()[-5]
except (OSError, IOError) as e:
endstatus = ''
logging.info(
"Error {} reading aoforce.out for {}".format(
e, job.indir))
else:
if " **** force : all done ****" in endstatus:
freqtime = turbogo_helpers.get_calc_time(job.indir, endfile)
if freqtime:
job.ftime += freqtime
else:
job.ftime += (time() - job.curstart)
logging.info('Job {} completed frequency.'.format(job.name))
job.status = "Completed Freq"
if not job.ts:
status = ensure_not_ts(job)
else:
status = ensure_ts(job)
if status == 'completed':
if job.freeh:
logging.debug('Do Freeh')
do_freeh(job)
return 'completed'
elif status == 'error':
return 'ocrashed'
elif status == 'opt':
return 'opt'
elif status == 'same':
return 'same'
elif status == 'imaginary':
return 'imaginary'
elif status == 'ts':
return 'ts'
else:
job.status = "Freq Crashed"
return 'fcrashed'
def check_opt(job):
"""
Check if an opt job is done or crashed, if done: resubmit to queue if freq
is required. Return a status string
"""
if turbogo_helpers.check_files_exist([
os.path.join(job.indir, 'GEO_OPT_CONVERGED')]):
#Job converged
logging.info('Job {} completed optimization.'.format(job.name))
if job.jobtype == 'opt' or job.jobtype == 'optfreq':
opttime = turbogo_helpers.get_calc_time(job.indir, 'opt.out')
elif job.jobtype == 'ts':
opttime = turbogo_helpers.get_calc_time(job.indir, 'ts.out')
elif job.jobtype == 'sp':
opttime = turbogo_helpers.get_calc_time(job.indir, 'sp.out')
else:
opttime = False
if opttime:
job.otime += opttime
else:
job.otime += (time() - job.curstart)
if job.freqopt != None:
newid = freq_submit(job)
if newid != -99:
job.curstart = time()
job.jobid = newid
job.status = "Freq Submitted"
return 'freq'
else:
job.status = "Freq Setup Failed"
return 'fcrashed'
else:
if reformat:
convert_filetype(os.path.join(job.indir, 'finalgeometry.xyz'),
os.path.join(job.indir, 'finalgeometry.mol'))
return 'completed'
else:
logging.warning("Job {} crashed in optimization."
.format(job.name))
job.status = "Opt Crashed"
return 'ocrashed'