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.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 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 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 calculation is complete.
Completion criteria: self.calcdir/self.rundir[-1]/OUTCAR exists and is complete
"""
## test if this gives write output when job is still running
for img in range(1, self.settings["n_images"] + 1):
outcarfile = os.path.join(self.rundir[-1],
str(img).zfill(2), "OUTCAR")
if not os.path.isfile(outcarfile):
return False
if not io.Outcar(outcarfile).complete(): ## check this
return False
return True
def crash_check(jobdir, stdoutfile, crash_types):
""" Check vasp stdout for evidence of a crash """
err = None
possible = [i_err() for i_err in _CrashError.__subclasses__()]
ocar = io.Outcar(os.path.join(jobdir, "OUTCAR"))
if ocar.complete:
return None
# Error to check line by line, only track most-recent error
sout = open(stdoutfile, 'r')
for line in sout:
for p in possible:
if p.error(line=line, jobdir=jobdir):
err = p
sout.close()
if err is None:
return None
else:
return {err.__class__.__name__: err}
def error(line=None, jobdir=None): #pylint: disable=unused-argument
""" 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 is None:
most_recent = t
most_recent_file = f
elif t < most_recent:
most_recent = t
most_recent_file = f
print("Most recent file output (" + most_recent_file + "):",
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()
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()
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()
continue_job(self.rundir[-2], self.rundir[-1], self.settings)
while True:
# run vasp
result = 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()
complete_job(self.finaldir, self.settings)
return (status, task)
