def fix(self, err_jobdir, new_jobdir, settings):
""" Try to fix by making kpoints subdivisions odd or changing kpoint length"""
continue_job(err_jobdir, new_jobdir, settings)
kpt = io.Kpoints(os.path.join(new_jobdir, "KPOINTS"))
if kpt.automode[0].lower() == "a":
old_kpt = kpt.subdivisions[0]
ocr = io.Outcar(os.path.join(err_jobdir, "OUTCAR"))
max_k = max(ocr.kpts)
kpt.automode = "GAMMA"
kpt.subdivisions = [max_k, max_k, max_k]
kpt.shift = [0.0, 0.0, 0.0]
print " Changed KPOINTS from AUTO (%s) to GAMMA (%s)" % (
old_kpt, kpt.subdivisions)
# kpt.subdivisions[0]+=1
# print " Increased KPOINTS length from ", kpt.subdivisions[0]-1, " to ", kpt.subdivisions[0]
kpt.write(os.path.join(new_jobdir, "KPOINTS"))
else:
odd = True
for i in range(len(kpt.subdivisions)):
if kpt.subdivisions[i] % 2 == 0:
odd = False
kpt.subdivisions[i] += 1
if odd == False:
print " Set KPOINTS subdivision to be odd:", kpt.subdivisions, "and mode to Gamma"
kpt.automode = "Gamma"
kpt.write(os.path.join(new_jobdir, "KPOINTS"))
def complete(self):
"""Check if the VASP relaxation is complete.
Completion criteria: .../config/vasp/relax/run.final/OUTCAR exists and is complete
"""
outcarfile = os.path.join(self.finaldir, "OUTCAR")
if not os.path.isfile(outcarfile):
return False
if not io.Outcar(outcarfile).complete():
return False
return True
def complete(self):
"""Check if the VASP convergence is complete.
Completion criteria: .../config/calctype/prop/prop_value/run.final/OUTCAR exists and is complete
"""
outcarfile = os.path.join(self.finaldir, "OUTCAR")
if not os.path.isfile(outcarfile):
return False
if not io.Outcar(outcarfile).complete():
return False
return True
def error(self, line=None, jobdir=None):
""" Check if VASP appears frozen
Returns true if:
1) no file has been modified for 5 minutes
2) 'LOOP+' exists in OUTCAR and no output file has been modified
in 5x the time for the slowest loop
"""
# Check if any files modified in last 300 s
most_recent = None
most_recent_file = None
for f in os.listdir(jobdir):
t = time.time() - os.path.getmtime(os.path.join(jobdir, f))
if most_recent == None:
most_recent = t
most_recent_file = f
elif t < most_recent:
most_recent = t
most_recent_file = f
print "Most recent file output (" + f + "):", most_recent, " seconds ago."
sys.stdout.flush()
if t < 300:
return False
outcar = io.Outcar(os.path.join(jobdir, "OUTCAR"))
if outcar.complete:
print "outcar.complete:", outcar.complete
sys.stdout.flush()
return False
elif outcar.slowest_loop != None and most_recent > 5.0 * outcar.slowest_loop:
print "slowest_loop:", outcar.slowest_loop
print "5.0*slowest_loop:", 5.0 * outcar.slowest_loop
print "most_recent:", most_recent
sys.stdout.flush()
return True
return False
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 convergence 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])
elif task == "relax":
self.add_rundir()
vasp.continue_job(self.rundir[-2], self.rundir[-1], self.settings)
shutil.copyfile(os.path.join(self.propdir, "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.propdir, self.settings["final"]))):
new_values = io.Incar(os.path.join(self.propdir, 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():
# Check for actions that should be taken after the initial run
if len(self.rundir) == 1:
if self.settings["fine_ngx"]:
outcarfile = os.path.join(self.rundir[-1], "OUTCAR")
if not os.path.isfile(outcarfile):
# This is an error but I'm not sure what to do about it
pass
else:
init_outcar = io.Outcar(outcarfile)
if not init_outcar.complete:
# This is an error but I'm not sure what to do about it
pass
elif (init_outcar.ngx is None or
init_outcar.ngy is None or
init_outcar.ngz is None):
# This is an error but I'm not sure what to do about it
pass
else:
ng_tags = {
"ngx" : init_outcar.ngx*2,
"ngy" : init_outcar.ngy*2,
"ngz" : init_outcar.ngz*2}
print ng_tags
io.set_incar_tag(ng_tags, self.propdir, "INCAR.base")
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 my_file in self.settings["backup"]:
if os.path.isfile(os.path.join(self.rundir[-2], my_file + "_BACKUP.gz")):
f_in = gzip.open(os.path.join(self.rundir[-2], my_file + "_BACKUP.gz", 'rb'))
f_out = open(os.path.join(self.rundir[-1], my_file, 'wb'))
f_out.write(f_in.read())
f_in.close()
f_out.close()
print my_file, " 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)