def setUp(self):
self.freeh = Freeh(modvals={"tstart": "200", "tend": "250"})
self.freehfile = """ ------------------
your wishes are :
------------------
pstart= 0.1000E+00 pend= 0.1000E+00 nump= 1
tstart= 298.1 tend= 298.1 numt= 1
zero point vibrational energy
-----------------------------
zpe= 481.3 kJ/mol
T p ln(qtrans) ln(qrot) ln(qvib) chem.pot. energy entropy
(K) (MPa) (kJ/mol) (kJ/mol) (kJ/mol/K)
298.15 0.1000000 19.81 15.66 15.89 353.99 530.06 0.59886
T P Cv Cp enthalpy
(K) (MPa) (kJ/mol-K) (kJ/mol-K) (kJ/mol)
298.15 0.1000000 0.2849985 0.2933128 532.54
"""
write_file("testfreeh", self.freehfile.split("\n"))
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_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 setUp(self):
os.mkdir("testdir")
os.chdir("testdir")
os.mkdir("indir-good1")
os.mkdir("indir-good2")
os.mkdir("indir-badfile3")
os.mkdir("indir-nofile4")
os.mkdir("indir-twofile5")
os.mkdir("indir-deep")
os.mkdir(os.path.join("indir-deep", "deepdir"))
self.infile = """%nproc=8
%mem=100MW
%arch=GA
%maxcycles=200
# Opt ri marij b3-lyp/TZVP
Test Infile
0 1
C -10.14896312689057 1.75782324146904 -0.2949862481115
C -8.99358457406949 2.76561418392812 1.85268749294372
C -6.82890329788933 1.622707823532 2.83855761235287
C -5.82243516371775 -0.51249372509826 1.62856597451948
$ricore 0
$ricore_slave 1
-$marij
"""
os.chdir("indir-good1")
write_file("input1.in", self.infile.split("\n"))
os.chdir(os.pardir)
os.chdir("indir-good2")
write_file("input2.in", self.infile.split("\n"))
os.chdir(os.pardir)
os.chdir("indir-badfile3")
write_file("input3.in", ["this is a bad file", "booya"])
os.chdir(os.pardir)
os.chdir("indir-twofile5")
write_file("input5a.in", self.infile.split("\n"))
write_file("input5b.in", self.infile.split("\n"))
os.chdir(os.pardir)
os.chdir("indir-deep")
os.chdir("deepdir")
write_file("input6.in", self.infile.split("\n"))
os.chdir(os.pardir)
os.chdir(os.pardir)
def submit_script_prepare(job, filename="submitscript.sge"):
"""Write a submit script for gridengine for the job."""
logging.debug("Preparing gridengine submit script")
# NPROC has to be one less for MPI jobs
nproc = job.nproc
if job.para_arch == "MPI":
nproc = nproc - 1
env_mod = ""
# env = turbogo_helpers.check_env()
# if env:
# logging.warn("Env vars not set. Attempting to fix via submit script")
# for key in env:
# env_mod += "export {}={}\n".format(key, env[key])
# Set up the parallel preamble. No parallel arch info if numforce
if job.jobtype != "numforce":
preamble_template = """export PARA_ARCH={para_arch}\n""".format(para_arch=job.para_arch)
else:
preamble_template = ""
preamble_template += """export MPI_IC_ORDER="TCP"
export PARNODES={nproc}
cat $PE_HOSTFILE | awk '{{for(i=0;i<$2;i++) print $1}}' > hosts_file
export HOSTS_FILE=`readlink -f hosts_file`
""".format(
nproc=nproc
)
if job.nproc > 1:
parallel_preamble = preamble_template
else:
parallel_preamble = ""
# set up the job command call itself
if job.jobtype == "opt" or job.jobtype == "optfreq":
jobcommand = "jobex"
jobcommand += " -c {}".format(job.iterations)
if job.ri:
jobcommand += " -ri"
# add making xyz sp geom and opt trajectory xyz files after jobex
jobcommand += " > opt.out"
jobcommand += "\nt2x > optimization.xyz\nt2x -c > final_geometry.xyz"
elif job.jobtype == "aoforce":
jobcommand = "aoforce"
jobcommand += " > aoforce.out"
elif job.jobtype == "numforce":
jobcommand = "NumForce -central"
if job.ri:
jobcommand += " -ri"
if job.nproc > 1:
jobcommand += " -mfile hosts_file"
jobcommand += " > numforce.out"
elif job.jobtype == "sp":
if job.ri:
jobcommand = "ridft"
else:
jobcommand = "dscf"
jobcommand += " > sp.out"
elif job.jobtype == "ts":
if job.ri:
jobcommand = "ridft\nrdgrad\njobex -trans -ri"
else:
jobcommand = "dscf\ngrad\njobex -trans"
if job.iterations:
jobcommand += " -c {}".format(job.iterations)
jobcommand += " > ts.out"
jobcommand += "\nt2x > optimization.xyz\nt2x -c > final_geometry.xyz"
logging.debug("Job submit script: {} completed.".format(jobcommand.replace("\n", " & ")))
# make one big sumbit script
# runs the jobcommand
submit_script = """#!/bin/bash
#$ -cwd
#$ -V
#$ -j y
#$ -o {jobname}.stdout
#$ -N tm.{jobname}
#$ -l h_rt={rt}
#$ -R y
#$ -pe threaded {nproc}
{env_mod}
{parallel_preamble}
source $TURBODIR/Config_turbo_env
ulimit -s unlimited
touch startfile
{jobcommand}
""".format(
jobname=turbogo_helpers.slug(job.name),
nproc=job.nproc,
parallel_preamble=parallel_preamble,
jobcommand=jobcommand,
env_mod=env_mod,
rt=job.rt,
)
# listify script by lines and write lines to file
try:
turbogo_helpers.write_file(filename, submit_script.split("\n"))
except turbogo_helpers.FileAccessError:
logging.warning("Error writing submit script to file.")
logging.debug("Submit script generated at {}.".format(filename))
return submit_script
def write_coord(job, filename="coord"):
"""Write the coord file"""
job.geometry.insert(0, "$coord")
job.geometry.append("$end")
turbogo_helpers.write_file(filename, job.geometry)
logging.debug("File {} written.".format(filename))
