def setup(self, initdir):
""" mv all files and directories (besides initdir) into initdir """
print("Moving files into initial run directory:", initdir)
initdir = os.path.abspath(initdir)
for my_prop in os.listdir(self.propdir):
if (my_prop in io.VASP_INPUT_FILE_LIST +
self.settings["extra_input_files"]) and (os.path.join(
self.propdir, my_prop) != initdir):
os.rename(os.path.join(self.propdir, my_prop),
os.path.join(initdir, my_prop))
print("")
sys.stdout.flush()
# Keep a backup copy of the base INCAR
shutil.copyfile(os.path.join(initdir, "INCAR"),
os.path.join(self.propdir, "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.propdir, self.settings["initial"]))):
new_values = io.Incar(
os.path.join(self.propdir, self.settings["initial"])).tags
io.set_incar_tag(new_values, initdir)
print(" Set INCAR tags:", new_values, "\n")
sys.stdout.flush()
def setup(self, initdir, settings):
""" mv all files and directories (besides initdir) into initdir """
### still has to handle the images
print("Moving files and directories into initial run directory:",
initdir)
initdir = os.path.abspath(initdir)
for p in os.listdir(self.calcdir):
if (p in (io.VASP_INPUT_FILE_LIST +
self.settings["extra_input_files"])) and (os.path.join(
self.calcdir, p) != initdir):
os.rename(os.path.join(self.calcdir, p),
os.path.join(initdir, p))
## copying the folders with image poscars into initdir
for i in range(settings["n_images"] + 2):
folder_name = str(i).zfill(
2) #max(2, len(str(settings["n_images"]))+1 )) ##too fancy!!!
shutil.copytree(os.path.join(self.calcdir, "poscars", folder_name),
os.path.join(initdir, folder_name))
print("")
sys.stdout.flush()
# Keep a backup copy of the base INCAR
shutil.copyfile(os.path.join(initdir, "INCAR"),
os.path.join(self.calcdir, "INCAR.base"))
os.rename(os.path.join(initdir, "POSCAR"),
os.path.join(self.calcdir, "POSCAR.start"))
# 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.calcdir, self.settings["initial"]))):
new_values = io.Incar(
os.path.join(self.calcdir, 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 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)
def run(self):
""" Perform a series of vasp jobs to run calculations. Performs a series of vasp calculations until
convergence is reached according to the criteria in 'status()'.
"""
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 == "new_run":
self.add_rundir()
# if "n_images" in settings then image CONTCARs will be copied
casm.vasp.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
shutil.copyfile(
os.path.join(self.calcdir, "INCAR.base"),
os.path.join(self.rundir[-1],
"INCAR")) ## should it be enforced??
elif task == "constant":
self.add_rundir()
# if "n_images" in settings then image CONTCARs will be copied
casm.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.calcdir, self.settings["final"]))):
new_values = io.Incar(
os.path.join(self.calcdir,
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: ## redundent
self.add_rundir()
casm.vasp.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
while True:
# run vasp
result = casm.vasp.run(self.rundir[-1],
stdout="stdout",
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"],
is_neb=True)
# 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()
(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()
casm.vasp.complete_job(self.finaldir, self.settings)
return (status, task)
