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 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)