pbs_job.queue = opt.pbs_queue
# Set the PBS job name
pbs_job.set_name(opt.job_name)
# Determine processor count
nproc = opt.nproc.split(",")
nproc = [int(i) for i in nproc]
if not opt.pbs_nproc:
pbs_nproc = nproc[:]
else:
pbs_nproc = opt.pbs_nproc.split(",")
pbs_nproc = [int(i) for i in pbs_nproc]
pbs_job.set_proc_count(pbs_nproc)
# Set walltime
pbs_job.set_walltime(opt.walltime)
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,
)
# Change the queue if desired
if opt.pbs_queue: pbs_job.queue = opt.pbs_queue
# Set the PBS job name
pbs_job.set_name(opt.job_name)
# Determine processor count
nproc = opt.nproc.split(',')
nproc = [int(i) for i in nproc]
if not opt.pbs_nproc: pbs_nproc = nproc[:]
else:
pbs_nproc = opt.pbs_nproc.split(',')
pbs_nproc = [int(i) for i in pbs_nproc]
pbs_job.set_proc_count(pbs_nproc)
# 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)
if not opt.version in ('g09', 'g03'):
print >> sys.stderr, 'Error: Gaussian version must be g03 or g09!'
sys.exit(1)
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()
sys.exit(1)
if not opt.version in ('g09', 'g03'):
print >> sys.stderr, 'Error: Gaussian version must be g03 or g09!'
sys.exit(1)
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()
