cmd_str = ("%s -i %s.min.mdin -p %s -c %s -r %s.min.rst7 -o %s.min.mdout " + "-inf %s.min.mdinfo -suffix %s") % (
prog_str,
prefix,
args[0],
args[1],
prefix,
prefix,
prefix,
prefix,
)
if opt.rst_wt:
cmd_str += " -ref %s" % args[1]
pbs_job.add_command(cmd_str)
# If we just want to print the jobfile
if opt.jobfile:
pbs_job.print_submit(opt.jobfile)
elif opt.ask:
pbs_job.submit_ask(after_job=opt.jobid)
else:
pbs_job.submit(after_job=opt.jobid)
else:
cmd_str = ("%s -i %s.min.mdin -p %s -c %s -r %s.min.rst7 -o %s.min.mdout " + "-inf %s.min.mdinfo -suffix %s") % (
prog_str,
prefix,
# Set walltime
pbs_job.set_walltime(opt.walltime)
cmd_str = ("%s -i %s.%s.mdin -p %s -c %s -r %s.%s.rst7 -o %s.%s." +
"mdout -inf %s.%s.mdinfo -x %s.%s.nc -suffix %s") % (prog_str,
prefix, opt.label, args[0], args[1], prefix, opt.label, prefix,
opt.label, prefix, opt.label, prefix, opt.label, prefix)
if opt.rst_wt:
cmd_str += " -ref %s" % args[1]
if len(args) == 3:
cmd_str += " -cpin %s -cpout %s.%s.cpout -cprestrt %s.%s.cpin" % (args[2],
prefix, opt.label, prefix, opt.label)
pbs_job.add_command(cmd_str)
# If we just want to print the jobfile
if opt.jobfile:
pbs_job.print_submit(opt.jobfile)
elif opt.ask:
pbs_job.submit_ask(after_job=opt.jobid)
else:
pbs_job.submit(after_job=opt.jobid)
else:
cmd_str = ("%s -i %s.%s.mdin -p %s -c %s -r %s.%s.rst7 -o %s.%s." +
"mdout -inf %s.%s.mdinfo -x %s.%s.nc -suffix %s") % (prog_str,
prefix, opt.label, args[0], args[1], prefix, opt.label, prefix,
opt.path = path.join(getenv('%sroot' % opt.version))
if not path.exists(args[0]):
print >> sys.stderr, "Error: Gaussian input file %s doesn't exist!" % args[
1]
sys.exit()
# Create the gaussian PBSjob instance
gaussjob = PBS_Script(name=opt.name, template=opt.template)
gaussjob.set_proc_count([1])
# Source the resource file
if not path.exists(path.join(opt.path, 'bsd', '%s.profile' % opt.version)):
print >> sys.stderr, 'Error: Missing %sprofile script! Looked in %s' % (
opt.version, path.join(opt.path, 'bsd'))
sys.exit(1)
gaussjob.add_command('source %s' %
(path.join(opt.path, 'bsd', '%s.profile' % opt.version)))
gaussjob.add_command(opt.version + ' ' + args[0])
# Set a random name if no name had been set
if not opt.name: gaussjob.set_name()
# Do we ask permission before submitting the job or just submit it?
if opt.jobfile: gaussjob.print_submit(opt.jobfile)
elif not opt.force: gaussjob.submit_ask()
else:
gaussjob.submit()
if not opt.path:
opt.path = path.join(getenv('%sroot' % opt.version))
if not path.exists(args[0]):
print >> sys.stderr, "Error: Gaussian input file %s doesn't exist!" % args[1]
sys.exit()
# Create the gaussian PBSjob instance
gaussjob = PBS_Script(name=opt.name, template=opt.template)
gaussjob.set_proc_count([1])
# Source the resource file
if not path.exists(path.join(opt.path, 'bsd', '%s.profile' % opt.version)):
print >> sys.stderr, 'Error: Missing %sprofile script! Looked in %s' % (
opt.version, path.join(opt.path, 'bsd'))
sys.exit(1)
gaussjob.add_command('source %s' % (path.join(opt.path, 'bsd', '%s.profile' %
opt.version)))
gaussjob.add_command(opt.version + ' ' + args[0])
# Set a random name if no name had been set
if not opt.name: gaussjob.set_name()
# Do we ask permission before submitting the job or just submit it?
if opt.jobfile: gaussjob.print_submit(opt.jobfile)
elif not opt.force: gaussjob.submit_ask()
else: gaussjob.submit()
