def submit_job(job, script=None):
"""Submit the specified job to queue for calculation"""
logging.debug("Submitting job to queue")
if not script:
try:
script = turbogo_helpers.read_clean_file("submitscript.sge")
except turbogo_helpers.FileAccessError:
raise turbogo_helpers.FileAccessError
# submit job in Popen pipe and get job number back.
p = Popen("qsub", stdin=PIPE, stdout=PIPE)
poutput, perr = p.communicate(input=script)
if "has been submitted" in poutput:
jobid = poutput.split("\n")[0].split(" ")[2]
if turbogo_helpers.is_int(jobid):
job.jobid = jobid
logging.info("Job {} with job id {} submitted".format(job.name, jobid))
turbogo_helpers.write_file("jobid", ["{}: {}".format(job.jobtype, jobid)])
else:
job.jobid = None
logging.warning("Job id unknown.")
else:
job.jobid = None
logging.warning("Error starting job. qsub output: \n{}".format(poutput))
return job.jobid
def ensure_ts(job):
"""
This runs to read out the vibrational modes. If there are more than one negative,
run 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
vib2 = False
for i in range(len(controlfile)):
if '$vibrational spectrum' in controlfile[i]:
for j in range (i+3, len(controlfile)):
col = controlfile[j][15:34].strip()
if col != '0.00':
try:
if not vib1:
vib1 = float(col)
elif not vib2:
vib2 = float(col)
except ValueError:
pass
else:
mode = controlfile[j][:6].strip()
if vib2:
break
if vib1 and vib2:
if vib1 < 0 and vib2 > 0:
return 'ts'
elif vib1 > 0:
return 'opt'
elif vib2 < 0:
return 'imaginary' # itvc = 1 SHOULD only ever return 1 img. freq
else:
logging.warning(
'Error getting vibrational frequencies from job {}.'.format(
job.name
))
return 'error'
def ensure_not_ts(job):
"""
This runs to read out the vibrational modes. If there are negatives, runs
screwer to adjust the geometry along the imaginary coordinate, and
resubmits job.
"""
if job.freqopt == 'numforce':
newdir = os.path.join(job.indir, 'numforce')
else:
newdir = job.indir
filetoread = os.path.join(newdir, 'control')
controlfile = turbogo_helpers.read_clean_file(filetoread)
vib1 = False
for i in range(len(controlfile)):
if '$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 jobsetup(infile):
"""
Read the input file, get the keyword flags & geometry. Utilizes a gaussian
type input file.
"""
lines = turbogo_helpers.read_clean_file(infile)
iargs = list()
igeom = list()
control_add = list()
control_remove = list()
# first parse %args from top of file
lines.reverse()
moreargs = True
while moreargs:
if lines[-1][0] == "%":
iargs.append(lines.pop())
else:
moreargs = False
args = turbogo_helpers.check_args(iargs)
logging.debug("{} args processed".format(len(args)))
# immediately following %args is the #route card
if not lines[-1][0] == "#":
logging.error(
"""Syntax error at route. Must immediately follow
arguements ('%') and start with #"""
)
raise InputSyntaxError(
str(lines[0]),
"""Syntax error at route.
Must immediately follow arguements ('%') and
start with #""",
)
else:
iroute = lines.pop()
logging.debug("Parsing input route card.")
route = turbogo_helpers.check_route(iroute)
logging.debug("{} Route parameters processed".format(len(route)))
# specs from gaussian: blank line required
if not lines[-1] == "":
logging.error(
"""Syntax error after route. Blank line required before
title"""
)
raise InputSyntaxError(
str(lines[0]),
"""Syntax error after route.
Blank line required before title""",
)
else:
del lines[-1]
# Now is the job title.
title = str(lines[-1])
logging.debug("Title: {}".format(title))
del lines[-1]
# Gaussian spec another blank line
if not lines[-1] == "":
logging.error(
"""Syntax error after title. Blank line required before
charge & spin"""
)
raise InputSyntaxError(
str(lines[0]),
"""Syntax error after title.
Blank line required before charge & spin""",
)
else:
del lines[-1]
# Charge and spin (0 1)
ichspin = lines[-1]
ch_spin = turbogo_helpers.check_chspin(ichspin)
logging.debug("Charge of {} and spin of {}.".format(ch_spin["ch"], ch_spin["spin"]))
del lines[-1]
# Input Geometry in xyz cartesian format
moregeom = True
while moregeom:
if not lines[-1][:1] == "":
igeom.append(lines.pop())
else:
moregeom = False
geom = turbogo_helpers.check_geom(igeom)
logging.debug("{} lines of geometry processed".format(len(geom)))
# gaussian spec blankline
if not lines[-1] == "":
logging.error("Syntax error after geometry. Blank line required.")
raise InputSyntaxError(
str(lines[0]),
"""Syntax error after geometry.
Blank line required.""",
)
else:
del lines[-1]
# new spec: manual add or subtract from control file with:
# $opt to add, or:
# -$opt to remove
if len(lines) > 0:
logging.debug("Parsing additional control arguements")
morelines = True
while morelines:
try:
if lines[-1][0] == "$" or lines[-1][0] == "-" and lines[-1][1] == "$":
if lines[-1][0] == "$":
control_add.append(lines.pop())
else:
control_remove.append(lines.pop())
else:
morelines = False
except IndexError:
morelines = False
logging.debug("{} additional lines processed".format(len(control_add)))
# Set up job.class
logging.debug("Setting up Job with collected information.")
job = Job()
job.name = title
job.charge = ch_spin["ch"]
job.spin = ch_spin["spin"]
if "basis" in route:
job.basis = route["basis"]
if "functional" in route:
job.functional = route["functional"]
if "jobtype" in route:
job.jobtype = route["jobtype"]
else:
job.jobtype = "sp"
if job.jobtype == "opt" or job.jobtype == "optfreq":
# one atom checking - can't opt one atom, so single point it.
if len(geom) == 1:
logging.debug("One atom job changed to SP")
job.jobtype = "sp"
if "freqopts" in route and job.jobtype != "sp":
job.freqopts = route["freqopts"]
elif job.jobtype == "freq" and not "freqopts" in route:
job.freqopts = DEFAULT_FREQ
elif job.jobtype == "ts" and not "freqopts" in route:
job.freqopts = DEFAULT_FREQ
if "ri" in route:
job.ri = True
else:
job.ri = False
if "marij" in route and "ri" in route:
job.marij = True
else:
job.ri = False
if "disp" in route or job.functional == "b97-d":
job.disp = True
if "freeh" in route:
job.freeh = True
if job.freeh:
job.freqopts += "+freeh"
if "iterations" in args:
job.iterations = int(args["iterations"])
elif "maxcycles" in args:
job.iterations = int(args["maxcycles"])
if "nproc" in args:
job.nproc = int(args["nproc"])
if "cosmo" in args:
job.cosmo = args["cosmo"]
if "rt" in args:
job.rt = "{}:00:00".format(args["rt"])
if job.jobtype != "freq":
if "arch" in args:
job.para_arch = args["arch"]
else:
job.para_arch = "SMP"
if "mod" in args and not args["mod"]:
logging.debug("No mod of control requested")
else:
control_add = turbogo_helpers.auto_control_mod(control_add, job)
job.control_add = control_add
job.control_remove = control_remove
job.geometry = geom
return job