def jobrunner(infile=None, job=None):
"""
run the job prep and submit from a specific file or supplied prepared job
"""
starttime = time.time()
if not job:
if infile:
job = jobsetup(infile)
logging.debug("Job setup complete.")
else:
logging.critical("Job input file or prepared job must be supplied.")
raise JobLogicError("No input file or supplied prepared job to submit.")
logging.debug("Working with {}.".format(job.name))
write_coord(job)
logging.debug("coord written")
if (
job.jobtype == "opt"
or job.jobtype == "optfreq"
or job.jobtype == "ts"
or job.jobtype == "sp"
or job.jobtype == "prep"
):
defstart = time.time()
run_define(job)
logging.debug("define complete.")
defend = time.time()
logging.debug("define ended in {0:.2f}s".format(defend - defstart))
if job.cosmo != None:
try:
run_cosmo(job)
except Exception as e:
logging.warn("Some error in cosmo running: {}".format(e))
elif job.jobtype == "aoforce" or job.jobtype == "numforce":
if not turbogo_helpers.check_files_exist(["GEO_OPT_CONVERGED", "converged"]):
logging.warning("Convergence required before {} job.".format(job.jobtype))
raise JobLogicError("Convergence required before {} job.".format(job.jobtype))
if job.control_remove or job.control_add:
control_edit(job)
logging.debug("control file editing complete.")
else:
logging.debug("No control file edits")
script = submit_script_prepare(job)
logging.debug("Submit script written.")
if job.jobtype != "prep":
jobid = submit_job(job, script)
else:
logging.info("Job not submitted - prep flag in input.")
logging.debug("Submitted in {0:.2f} seconds.".format(time.time() - starttime))
return jobid, job.freqopts, job.name, job.jobtype
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'
def main():
"""Manages the code"""
logging.basicConfig(
format=("%(asctime)s - %(name)s - [%(levelname)s] - %(message)s"), filename="turbogo.log", level=logging.DEBUG
)
logging.info("Started")
parser = argparse.ArgumentParser("Usage: %prog [options]")
parser.add_argument("file", help="Read input from gaussian-type input FILE")
group = parser.add_mutually_exclusive_group()
group.add_argument("-v", "--verbose", action="store_true", help="Run more verbose (show debugging info)")
group.add_argument("-q", "--quiet", action="store_true", help="Run less verbose (show only warnings)")
args = parser.parse_args()
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.INFO)
if args.verbose:
ch.setLevel(logging.DEBUG)
elif args.quiet:
ch.setLevel(logging.WARNING)
logging.getLogger().setLevel(logging.INFO)
formatter = logging.Formatter("%(asctime)s - %(name)s - [%(levelname)s] - %(message)s")
ch.setFormatter(formatter)
logging.getLogger().addHandler(ch)
infile = args.file
logging.debug("Specified file {} in args".format(infile))
# check file exists, if not request file.
ifile = turbogo_helpers.check_files_exist([infile])
if not ifile:
logging.critical("Input file {} does not exist.".format(infile))
exit()
# file is good. let's go!
jobid, freqopts, _name, _type = jobrunner(infile=infile)
if not args.verbose:
try:
os.remove(os.path.join(os.path.curdir, "define.log"))
except (OSError, IOError):
pass
logging.debug("Jobid: {}\nFreqStatus: {}".format(jobid, freqopts))
exit()
def write_freeh(job):
"""
Writes a line to the freeh file for each job that completes successfully
with freeh requested.
"""
if not turbogo_helpers.check_files_exist(['freeh.txt']):
#write the header to the file
try:
with open('freeh.txt', 'w') as f:
f.write("{name:^16}{directory:^20}{zpe:^14}{t:^10}" \
"{p:^11}{qtrans:^12}{qrot:^10}" \
"{pot:^14}{eng:^14}{entr:^20}{cv:^14}{cp:^14}{enth:^14}\n"
.format(
name='Name',
directory = 'Directory',
zpe = 'ZPE (kJ/mol)',
t = 'Temp (K)',
p = 'p (MPa)',
qtrans = 'ln(qtrans)',
qrot = 'ln(qrot)',
qvib = 'ln(qvib)',
pot = 'Pot (kJ/mol)',
eng = 'Eng (kJ/mol)',
entr = 'Entropy (kJ/mol/K)',
cv = 'Cv (kJ/molK)',
cp = 'Cp (kJ/molK)',
enth = 'Enthalpy (kJ/mol)'
))
logging.debug("Wrote freeh titles")
except IOError as e:
logging.warning("Error preparing freeh file: {}".format(e))
except Exception as e:
logging.warning("Unknown error {}".format(e))
name = job.name
directory = os.path.join(job.indir, job.infile)
zpe = job.data['zpe']
t = job.data['t']
p = job.data['p']
qtrans = job.data['qtrans']
qrot = job.data['qrot']
qvib = job.data['qvib']
pot = job.data['pot']
eng = job.data['eng']
entr = job.data['entr']
cv = job.data['cv']
cp = job.data['cp']
enth = job.data['enth']
try:
with open('freeh.txt', 'a') as f:
f.write("{name:^16}{directory:^20}{zpe:^14}{t:^10}" \
"{p:^11}{qtrans:^12}{qrot:^10}" \
"{pot:^14}{eng:^14}{entr:^20}{cv:^14}{cp:^14}{enth:^14}\n"
.format(
name=name,
directory = directory,
zpe = zpe,
t = t[0],
p = p[0],
qtrans = qtrans[0],
qrot = qrot[0],
qvib = qvib[0],
pot = pot[0],
eng = eng[0],
entr = entr[0],
cv = cv[0],
cp = cp[0],
enth = enth[0]
))
if len(t) > 1: #don't rewrite name/zpe for each line
for i in range(1, len(t)):
f.write("{name:^16}{directory:^20}{zpe:^14}{t:^8}" \
"{p:^11}{qtrans:^12}{qrot:^10}" \
"{pot:^14}{eng:^14}{entr:^20}{cv:^14}{cp:^14}{enth:^14}\n"
.format(
name='',
directory = '',
zpe = '',
t = t[i],
p = p[i],
qtrans = qtrans[i],
qrot = qrot[i],
qvib = qvib[i],
pot = pot[i],
eng = eng[i],
entr = entr[i],
cv = cv[i],
cp = cp[i],
enth = enth[i]
))
except (OSError, IOError) as e:
logging.warning("Error writing freeh file: {}".format(e))
def write_stats(job):
"""
Writes a line to the stats file for each job that completes successfully.
"""
if not turbogo_helpers.check_files_exist(['stats.txt']):
#write the header to the file
try:
with open('stats.txt', 'w') as f:
f.write("{name:^16}{directory:^20}{optsteps:^10}{opttime:^12}" \
"{freqtime:^12}{tottime:^12}{firstfreq:^16}{energy:^16}"
.format(
name='Name',
directory = 'Directory',
optsteps = 'Opt Steps',
opttime = 'Opt Time',
freqtime = 'Freq Time',
tottime = 'Total Time',
firstfreq = '1st Frequency',
energy = 'Energy',
))
f.write('\n')
except IOError as e:
logging.warning("Error preparing stats file: {}".format(e))
except Exception as e:
logging.warning("Unknown error {}".format(e))
name = job.name
directory = os.path.join(job.indir, job.infile)
try:
with open(os.path.join(job.indir, 'energy')) as f:
lines = f.readlines()
except IOError as e:
logging.warning("Error reading energy file for stats: {}".format(e))
optsteps = '?'
energy = '?'
except Exception as e:
logging.warning("Unknown error {}.".format(e))
else:
optsteps = lines[-2][:6].strip()
energy = lines[-2][6:22].strip()
opttime = turbogo_helpers.time_readable(job.otime)
freqtime = turbogo_helpers.time_readable(job.ftime)
tottime = turbogo_helpers.time_readable(job.otime + job.ftime)
firstfreq = job.firstfreq
try:
with open('stats.txt', 'a') as f:
f.write("{name:^16.16}{directory:^20.20}{optsteps:^10.10}" \
"{opttime:^12.12}{freqtime:^12.12}{tottime:^12.12}" \
"{firstfreq:^16.16}{energy:^16.16}"
.format(
name=name,
directory = directory,
optsteps = optsteps,
opttime = opttime,
freqtime = freqtime,
tottime = tottime,
firstfreq = firstfreq,
energy = energy,
))
f.write('\n')
except (OSError, IOError) as e:
logging.warning("Error writing stats file: {}".format(e))
