def setup(self, initdir, settings):
""" mv all files and directories (besides initdir) into initdir """
print "Moving files into initial run directory:", initdir
initdir = os.path.abspath(initdir)
for p in os.listdir(self.relaxdir):
if (p in (io.VASP_INPUT_FILE_LIST +
self.settings["extra_input_files"])) and (os.path.join(
self.relaxdir, p) != initdir):
os.rename(os.path.join(self.relaxdir, p),
os.path.join(initdir, p))
print ""
sys.stdout.flush()
# Keep a backup copy of the base INCAR
shutil.copyfile(os.path.join(initdir, "INCAR"),
os.path.join(self.relaxdir, "INCAR.base"))
# If an initial incar is called for, copy it in and set the appropriate flag
if (self.settings["initial"] != None) and (os.path.isfile(
os.path.join(self.relaxdir, self.settings["initial"]))):
new_values = io.Incar(
os.path.join(self.relaxdir, self.settings["initial"])).tags
io.set_incar_tag(new_values, initdir)
print " Set INCAR tags:", new_values, "\n"
sys.stdout.flush()
def fix(self, err_jobdir, new_jobdir, settings):
""" Try to fix the error by increasing the number of bands"""
continue_job(err_jobdir, new_jobdir, settings)
with open(os.path.join(err_jobdir, "OUTCAR")) as f:
err_outcar = f.read().splitlines()
nbands_line = []
for line in err_outcar:
if "NBANDS" in line:
nbands_line.append(line)
if len(nbands_line) < 1:
print "SERIOUS WARNING : "
print " Couldn't find any reference to nbands in the OUTCAR. Continuing without fixing"
else:
for l in nbands_line:
if "k-points" in l.strip().split():
print " Set NBANDS = " + str(int(1.1 * float(l.strip().split()[-1])))
sys.stdout.flush()
io.set_incar_tag({"NBANDS": int(1.1 * float(l.strip().split()[-1]))}, jobdir=new_jobdir)
break
def setup(self, initdir, settings):
""" mv all files and directories (besides initdir) into initdir """
print "Moving files into initial run directory:", initdir
initdir = os.path.abspath(initdir)
for p in os.listdir(self.relaxdir):
if (p in (io.VASP_INPUT_FILE_LIST + self.settings["extra_input_files"])) and (os.path.join(self.relaxdir, p) != initdir):
os.rename(os.path.join(self.relaxdir,p), os.path.join(initdir,p))
print ""
sys.stdout.flush()
# Keep a backup copy of the base INCAR
shutil.copyfile(os.path.join(initdir,"INCAR"),os.path.join(self.relaxdir,"INCAR.base"))
# If an initial incar is called for, copy it in and set the appropriate flag
if (self.settings["initial"] != None) and (os.path.isfile(os.path.join(self.relaxdir,self.settings["initial"]))):
new_values = io.Incar(os.path.join(self.relaxdir,self.settings["initial"])).tags
io.set_incar_tag(new_values, initdir)
print " Set INCAR tags:", new_values, "\n"
sys.stdout.flush()
def fix(self, err_jobdir, new_jobdir, settings):
""" First attempt:
Set ALGO = VeryFast
Unset IALGO
Second attempt:
Set IBRION = 1 and POTIM = 0.1
Final attempt:
Set LREAD = .FALSE.
"""
continue_job(err_jobdir, new_jobdir, settings)
if io.get_incar_tag("ALGO", jobdir=new_jobdir) != "VeryFast":
print " Set Algo = VeryFast, and Unset IALGO"
io.set_incar_tag({
"IALGO": None,
"ALGO": "VeryFast"
},
jobdir=new_jobdir)
elif io.get_incar_tag("IBRION", jobdir=new_jobdir) != 1:
print " Set IBRION = 1 and POTIM = 0.1"
sys.stdout.flush()
io.set_incar_tag({"IBRION": 1, "POTIM": 0.1}, jobdir=new_jobdir)
elif io.get_incar_tag("LREAL", jobdir=new_jobdir) != False:
print " Set LREAL = .FALSE."
sys.stdout.flush()
io.set_incar_tag({"LREAL": False}, jobdir=new_jobdir)
def fix(self, err_jobdir, new_jobdir, settings):
""" Try to fix the error by increasing the number of bands"""
continue_job(err_jobdir, new_jobdir, settings)
with open(os.path.join(err_jobdir, 'OUTCAR')) as f:
err_outcar = f.read().splitlines()
nbands_line = []
for line in err_outcar:
if "NBANDS" in line:
nbands_line.append(line)
if len(nbands_line) < 1:
print "SERIOUS WARNING : "
print " Couldn't find any reference to nbands in the OUTCAR. Continuing without fixing"
else:
for l in nbands_line:
if 'k-points' in l.strip().split():
print " Set NBANDS = " + str(
int(1.1 * float(l.strip().split()[-1])))
sys.stdout.flush()
io.set_incar_tag(
{"NBANDS": int(1.1 * float(l.strip().split()[-1]))},
jobdir=new_jobdir)
break
def fix(self, err_jobdir, new_jobdir, settings):
""" First attempt:
Set ALGO = VeryFast
Unset IALGO
Second attempt:
Set IBRION = 1 and POTIM = 0.1
Final attempt:
Set LREAD = .FALSE.
"""
continue_job(err_jobdir, new_jobdir, settings)
if io.get_incar_tag("ALGO", jobdir=new_jobdir) != "VeryFast":
print " Set Algo = VeryFast, and Unset IALGO"
io.set_incar_tag({"IALGO": None, "ALGO": "VeryFast"}, jobdir=new_jobdir)
elif io.get_incar_tag("IBRION", jobdir=new_jobdir) != 1:
print " Set IBRION = 1 and POTIM = 0.1"
sys.stdout.flush()
io.set_incar_tag({"IBRION": 1, "POTIM": 0.1}, jobdir=new_jobdir)
elif io.get_incar_tag("LREAL", jobdir=new_jobdir) != False:
print " Set LREAL = .FALSE."
sys.stdout.flush()
io.set_incar_tag({"LREAL": False}, jobdir=new_jobdir)
def run(self):
""" Perform a series of vasp jobs to relax a structure. Performs a series of vasp calculations until
convergence is reached according to the criteria in 'status()'. Then performs a final constant volume run
{"ISIF":2, "ISMEAR":-5, "NSW":0, "IBRION":-1}.
"""
print "Begin VASP relaxation run"
sys.stdout.flush()
# get current status of the relaxation:
(status, task) = self.status()
print "\n++ status:", status, " next task:", task
sys.stdout.flush()
while status == "incomplete":
if task == "setup":
self.add_rundir()
self.setup(self.rundir[-1], self.settings)
elif task == "relax":
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
shutil.copyfile(os.path.join(self.relaxdir, "INCAR.base"),
os.path.join(self.rundir[-1], "INCAR"))
elif task == "constant":
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
# set INCAR to ISIF = 2, ISMEAR = -5, NSW = 0, IBRION = -1
if (self.settings["final"] != None) and (os.path.isfile(
os.path.join(self.relaxdir, self.settings["final"]))):
new_values = io.Incar(
os.path.join(self.relaxdir,
self.settings["final"])).tags
else:
new_values = {
"ISIF": 2,
"ISMEAR": -5,
"NSW": 0,
"IBRION": -1
}
# set INCAR system tag to denote 'final'
if io.get_incar_tag("SYSTEM", self.rundir[-1]) is None:
new_values["SYSTEM"] = "final"
else:
new_values["SYSTEM"] = io.get_incar_tag(
"SYSTEM", self.rundir[-1]) + " final"
io.set_incar_tag(new_values, self.rundir[-1])
print " Set INCAR tags:", new_values, "\n"
sys.stdout.flush()
else:
# probably hit walltime
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
while True:
# run vasp
result = vasp.run(self.rundir[-1],
npar=self.settings["npar"],
ncore=self.settings["ncore"],
command=self.settings["vasp_cmd"],
ncpus=self.settings["ncpus"],
kpar=self.settings["kpar"])
# if no errors, continue
if result == None or self.not_converging():
break
# else, attempt to fix first error
self.add_errdir()
os.mkdir(self.rundir[-1])
# self.add_rundir()
err = result.itervalues().next()
print "\n++ status:", "error", " next task:", "fix_error"
sys.stdout.flush()
print "Attempting to fix error:", str(err)
err.fix(self.errdir[-1], self.rundir[-1], self.settings)
print ""
sys.stdout.flush()
if (self.settings["backup"] != None) and len(self.rundir) > 1:
print "Restoring from backups:"
for f in self.settings["backup"]:
if os.path.isfile(
os.path.join(self.rundir[-2],
f + "_BACKUP.gz")):
f_in = gzip.open(
os.path.join(self.rundir[-2], f + "_BACKUP.gz",
'rb'))
f_out = open(os.path.join(self.rundir[-1], f,
'wb'))
f_out.write(f_in.read())
f_in.close()
f_out.close()
print f, " restored!"
sys.stdout.flush()
(status, task) = self.status()
print "\n++ status:", status, " next task:", task
sys.stdout.flush()
if status == "complete":
if not os.path.isdir(self.finaldir):
# mv final results to relax.final
print "mv", os.path.basename(
self.rundir[-1]), os.path.basename(self.finaldir)
sys.stdout.flush()
os.rename(self.rundir[-1], self.finaldir)
self.rundir.pop()
vasp.complete_job(self.finaldir, self.settings)
return (status, task)
def run(jobdir=None,
stdout="std.out",
stderr="std.err",
npar=None,
ncore=None,
command=None,
ncpus=None,
kpar=None,
poll_check_time=5.0,
err_check_time=60.0):
""" Run vasp using subprocess.
The 'command' is executed in the directory 'jobdir'.
Args:
jobdir: directory to run vasp. If jobdir == None, the current directory is used.
stdout: filename to write to. If stdout == None, "std.out" is used.
stderr: filename to write to. If stderr == None, "std.err" is used.
npar: (int or None) VASP INCAR NPAR setting. If npar == None, then NPAR is removed from INCAR
kpar: (int or None) VASP INCAR KPAR setting. If kpar == None, then KPAR is removed from INCAR
ncore: (int or None) VASP INCAR NCORE setting. If not npar == None or ncore == None, then NCORE is removed from INCAR
command: (str or None) vasp execution command
If command != None: then 'command' is run in a subprocess
Else, if ncpus == 1, then command = "vasp"
Else, command = "mpirun -np {NCPUS} vasp"
ncpus: (int) if '{NCPUS}' is in 'command' string, then 'ncpus' is substituted in the command.
if ncpus==None, $PBS_NP is used if it exists, else 1
poll_check_time: how frequently to check if the vasp job is completed
err_check_time: how frequently to parse vasp output to check for errors
"""
print "Begin vasp run:"
sys.stdout.flush()
if jobdir == None:
jobdir = os.getcwd()
currdir = os.getcwd()
os.chdir(jobdir)
if ncpus == None:
if "PBS_NP" in os.environ:
ncpus = os.environ["PBS_NP"]
else:
ncpus = 1
if command == None:
if ncpus == 1:
command = "vasp"
else:
command = "mpirun -np {NCPUS} vasp"
if re.search("\{NCPUS\}", command):
command = command.format(NCPUS=str(ncpus))
if not npar == None:
ncore = None
io.set_incar_tag({"NPAR": npar, "NCORE": ncore, "KPAR": kpar}, jobdir)
print " jobdir:", jobdir
print " exec:", command
sys.stdout.flush()
sout = open(os.path.join(jobdir, stdout), 'w')
serr = open(os.path.join(jobdir, stderr), 'w')
err = None
p = subprocess.Popen(command.split(), stdout=sout, stderr=serr)
# wait for process to end, and periodically check for errors
poll = p.poll()
last_check = time.time()
stopcar_time = None
while poll == None:
time.sleep(poll_check_time)
if time.time() - last_check > err_check_time:
last_check = time.time()
err = error_check(jobdir, os.path.join(jobdir, stdout))
if err != None:
# FreezeErrors are fatal and usually not helped with STOPCAR
if "FreezeError" in err.keys():
print " VASP is frozen, killing job"
sys.stdout.flush()
p.kill()
# Other errors can be killed with STOPCAR, which is safer
elif stopcar_time == None:
print " Found errors:",
for e in err:
print e,
print "\n Killing job with STOPCAR"
sys.stdout.flush()
io.write_stopcar('e', jobdir)
stopcar_time = time.time()
# If the STOPCAR exists, wait 5 min before manually killing the job
elif time.time() - stopcar_time > 300:
print " VASP is non-responsive, killing job"
sys.stdout.flush()
p.kill()
poll = p.poll()
# close output files
sout.close()
serr.close()
os.chdir(currdir)
print "Run complete"
sys.stdout.flush()
# check finished job for errors
if err == None:
err = error_check(jobdir, os.path.join(jobdir, stdout))
if err != None:
print " Found errors:",
for e in err:
print e,
print "\n"
return err
def run(self):
""" Perform a series of vasp jobs to relax a structure. Performs a series of vasp calculations until
convergence is reached according to the criteria in 'status()'. Then performs a final constant volume run
{"ISIF":2, "ISMEAR":-5, "NSW":0, "IBRION":-1}.
"""
print "Begin VASP relaxation run"
sys.stdout.flush()
# get current status of the relaxation:
(status, task) = self.status()
print "\n++ status:", status, " next task:", task
sys.stdout.flush()
while status == "incomplete":
if task == "setup":
self.add_rundir()
self.setup(self.rundir[-1], self.settings)
elif task == "relax":
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings)
shutil.copyfile(os.path.join(self.relaxdir,"INCAR.base"),os.path.join(self.rundir[-1],"INCAR"))
elif task == "constant":
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings)
# set INCAR to ISIF = 2, ISMEAR = -5, NSW = 0, IBRION = -1
if (self.settings["final"] != None) and (os.path.isfile(os.path.join(self.relaxdir,self.settings["final"]))):
new_values = io.Incar(os.path.join(self.relaxdir, self.settings["final"])).tags
else:
new_values = {"ISIF":2, "ISMEAR":-5, "NSW":0, "IBRION":-1}
# set INCAR system tag to denote 'final'
if io.get_incar_tag("SYSTEM", self.rundir[-1]) is None:
new_values["SYSTEM"] = "final"
else:
new_values["SYSTEM"] = io.get_incar_tag("SYSTEM", self.rundir[-1]) + " final"
io.set_incar_tag( new_values, self.rundir[-1])
print " Set INCAR tags:", new_values, "\n"
sys.stdout.flush()
else:
# probably hit walltime
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings)
while True:
# run vasp
result = vasp.run(self.rundir[-1],npar=self.settings["npar"],ncore=self.settings["ncore"],command=self.settings["vasp_cmd"],ncpus=self.settings["ncpus"],kpar=self.settings["kpar"],err_types=self.settings["err_types"])
# if no errors, continue
if result is None or self.not_converging():
break
# else, attempt to fix first error
self.add_errdir()
os.mkdir(self.rundir[-1])
# self.add_rundir()
err = result.itervalues().next()
print "\n++ status:", "error", " next task:", "fix_error"
sys.stdout.flush()
print "Attempting to fix error:", str(err)
err.fix(self.errdir[-1],self.rundir[-1], self.settings)
print ""
sys.stdout.flush()
if (self.settings["backup"] != None) and len(self.rundir) > 1:
print "Restoring from backups:"
for f in self.settings["backup"]:
if os.path.isfile(os.path.join(self.rundir[-2], f + "_BACKUP.gz")):
f_in = gzip.open(os.path.join(self.rundir[-2], f + "_BACKUP.gz", 'rb'))
f_out = open(os.path.join(self.rundir[-1], f, 'wb'))
f_out.write(f_in.read())
f_in.close()
f_out.close()
print f, " restored!"
sys.stdout.flush()
(status, task) = self.status()
print "\n++ status:", status, " next task:", task
sys.stdout.flush()
if status == "complete":
if not os.path.isdir(self.finaldir):
# mv final results to relax.final
print "mv", os.path.basename(self.rundir[-1]), os.path.basename(self.finaldir)
sys.stdout.flush()
os.rename(self.rundir[-1], self.finaldir)
self.rundir.pop()
vasp.complete_job(self.finaldir, self.settings)
return (status, task)
def run(
jobdir=None,
stdout="std.out",
stderr="std.err",
npar=None,
ncore=None,
command=None,
ncpus=None,
kpar=None,
poll_check_time=5.0,
err_check_time=60.0,
):
""" Run vasp using subprocess.
The 'command' is executed in the directory 'jobdir'.
Args:
jobdir: directory to run vasp. If jobdir == None, the current directory is used.
stdout: filename to write to. If stdout == None, "std.out" is used.
stderr: filename to write to. If stderr == None, "std.err" is used.
npar: (int or None) VASP INCAR NPAR setting. If npar == None, then NPAR is removed from INCAR
kpar: (int or None) VASP INCAR KPAR setting. If kpar == None, then KPAR is removed from INCAR
ncore: (int or None) VASP INCAR NCORE setting. If not npar == None or ncore == None, then NCORE is removed from INCAR
command: (str or None) vasp execution command
If command != None: then 'command' is run in a subprocess
Else, if ncpus == 1, then command = "vasp"
Else, command = "mpirun -np {NCPUS} vasp"
ncpus: (int) if '{NCPUS}' is in 'command' string, then 'ncpus' is substituted in the command.
if ncpus==None, $PBS_NP is used if it exists, else 1
poll_check_time: how frequently to check if the vasp job is completed
err_check_time: how frequently to parse vasp output to check for errors
"""
print "Begin vasp run:"
sys.stdout.flush()
if jobdir == None:
jobdir = os.getcwd()
currdir = os.getcwd()
os.chdir(jobdir)
if ncpus == None:
if "PBS_NP" in os.environ:
ncpus = os.environ["PBS_NP"]
else:
ncpus = 1
if command == None:
if ncpus == 1:
command = "vasp"
else:
command = "mpirun -np {NCPUS} vasp"
if re.search("\{NCPUS\}", command):
command = command.format(NCPUS=str(ncpus))
if not npar == None:
ncore = None
io.set_incar_tag({"NPAR": npar, "NCORE": ncore, "KPAR": kpar}, jobdir)
print " jobdir:", jobdir
print " exec:", command
sys.stdout.flush()
sout = open(os.path.join(jobdir, stdout), "w")
serr = open(os.path.join(jobdir, stderr), "w")
err = None
p = subprocess.Popen(command.split(), stdout=sout, stderr=serr)
# wait for process to end, and periodically check for errors
poll = p.poll()
last_check = time.time()
stopcar_time = None
while poll == None:
time.sleep(poll_check_time)
if time.time() - last_check > err_check_time:
last_check = time.time()
err = error_check(jobdir, os.path.join(jobdir, stdout))
if err != None:
# FreezeErrors are fatal and usually not helped with STOPCAR
if "FreezeError" in err.keys():
print " VASP is frozen, killing job"
sys.stdout.flush()
p.kill()
# Other errors can be killed with STOPCAR, which is safer
elif stopcar_time == None:
print " Found errors:",
for e in err:
print e,
print "\n Killing job with STOPCAR"
sys.stdout.flush()
io.write_stopcar("e", jobdir)
stopcar_time = time.time()
# If the STOPCAR exists, wait 5 min before manually killing the job
elif time.time() - stopcar_time > 300:
print " VASP is non-responsive, killing job"
sys.stdout.flush()
p.kill()
poll = p.poll()
# close output files
sout.close()
serr.close()
os.chdir(currdir)
print "Run complete"
sys.stdout.flush()
# check finished job for errors
if err == None:
err = error_check(jobdir, os.path.join(jobdir, stdout))
if err != None:
print " Found errors:",
for e in err:
print e,
print "\n"
return err
