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 status(self):
""" Determine the status of a vasp relaxation series of runs. Individual runs in the series
are in directories labeled "run.0", "run.1", etc.
Returns a tuple: (status = "incomplete" or "complete" or "not_converging",
task = continuedir or "relax" or "constant" or None)
The first value is the status of the entire relaxation.
The second value is the current task, where 'continuedir' is the path to a
vasp job directory that is not yet completed, "relax" indicates another
volume relaxation job is required, and "constant" that a constant volume run is required.
"""
# check if all complete
if io.job_complete(self.finaldir):
return ("complete", None)
# check status of relaxation runs
self.update_rundir()
# if not yet started
if len(self.rundir) == 0:
return ("incomplete", "setup")
# if the latest run is complete:
if io.job_complete(self.rundir[-1]):
# if it is a final constant volume run
if io.get_incar_tag("SYSTEM", self.rundir[-1]) != None:
if io.get_incar_tag("NSW", self.rundir[-1]) == 0 and \
io.get_incar_tag("SYSTEM", self.rundir[-1]).split()[-1].strip().lower() == "final":
# if io.get_incar_tag("ISIF", self.rundir[-1]) == 2 and \
# io.get_incar_tag("NSW", self.rundir[-1]) == 0 and \
# io.get_incar_tag("ISMEAR", self.rundir[-1]) == -5:
return ("complete", None)
# elif constant volume run (but not the final one)
if io.get_incar_tag("ISIF", self.rundir[-1]) in [0, 1, 2]:
return ("incomplete", "constant")
# elif convergence criteria met
if self.converged():
return ("incomplete", "constant")
# elif not converging, return 'not_converging' error
if self.not_converging():
return ("not_converging", None)
# else continue relaxing
else:
return ("incomplete", "relax")
# elif not converging, return 'not_converging' error
elif self.not_converging():
return ("not_converging", None)
# else if the latest run is not complete, continue running it
return ("incomplete", self.rundir[-1])
def status(self):
""" Determine the status of a vasp relaxation series of runs. Individual runs in the series
are in directories labeled "run.0", "run.1", etc.
Returns a tuple: (status = "incomplete" or "complete" or "not_converging",
task = continuedir or "relax" or "constant" or None)
The first value is the status of the entire relaxation.
The second value is the current task, where 'continuedir' is the path to a
vasp job directory that is not yet completed, "relax" indicates another
volume relaxation job is required, and "constant" that a constant volume run is required.
"""
# check if all complete
if io.job_complete(self.finaldir):
return ("complete",None)
# check status of relaxation runs
self.update_rundir()
# if not yet started
if len(self.rundir) == 0:
return ("incomplete", "setup")
# if the latest run is complete:
if io.job_complete(self.rundir[-1]):
# if it is a final constant volume run
if io.get_incar_tag("SYSTEM", self.rundir[-1]) != None:
if io.get_incar_tag("NSW", self.rundir[-1]) == 0 and \
io.get_incar_tag("SYSTEM", self.rundir[-1]).split()[-1].strip().lower() == "final":
# if io.get_incar_tag("ISIF", self.rundir[-1]) == 2 and \
# io.get_incar_tag("NSW", self.rundir[-1]) == 0 and \
# io.get_incar_tag("ISMEAR", self.rundir[-1]) == -5:
return ("complete", None)
# elif constant volume run (but not the final one)
if io.get_incar_tag("ISIF", self.rundir[-1]) in [0,1,2]:
return ("incomplete", "constant")
# elif convergence criteria met
if self.converged():
return ("incomplete", "constant")
# elif not converging, return 'not_converging' error
if self.not_converging():
return ("not_converging", None)
# else continue relaxing
else:
return ("incomplete", "relax")
# elif not converging, return 'not_converging' error
elif self.not_converging():
return ("not_converging", None)
# else if the latest run is not complete, continue running it
return ("incomplete", self.rundir[-1])
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(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)
