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 fix(self, err_jobdir, new_jobdir, settings):
""" Up symprec, or turn off symmetry"""
continue_job(err_jobdir, new_jobdir, settings)
symprec = io.get_incar_tag("SYMPREC", jobdir=new_jobdir)
if symprec is None or symprec > 1.1e-8:
print(" Set SYMPREC = 1e-8")
io.set_incar_tag({"SYMPREC": 1e-8}, jobdir=new_jobdir)
elif io.get_incar_tag("ISYM", jobdir=new_jobdir) != 0:
print(" Set ISYM = 0")
io.set_incar_tag({"ISYM": 0}, jobdir=new_jobdir)
def fix(self, err_jobdir, new_jobdir, settings):
""" Try to fix the error by changing the algo"""
continue_job(err_jobdir, new_jobdir, settings)
# Replace the potentially bad POSCAR
shutil.copyfile(os.path.join(err_jobdir, "POSCAR"),
os.path.join(new_jobdir, "POSCAR"))
# First, see if a change of ALGO helps
curr_algo = io.get_incar_tag("ALGO", new_jobdir).upper()
if curr_algo == 'FAST':
io.set_incar_tag({
"ALGO": "Normal",
"IALGO": None
},
jobdir=new_jobdir)
print(" Set ALGO = Normal")
elif curr_algo == 'NORMAL':
io.set_incar_tag({"ALGO": "All", "IALGO": None}, jobdir=new_jobdir)
print(" Set ALGO = All")
elif curr_algo == 'ALL':
io.set_incar_tag({
"ALGO": "Damped",
"IALGO": None
},
jobdir=new_jobdir)
io.set_incar_tag({"TIME": "0.4"}, jobdir=new_jobdir)
print(" Set ALGO = Damped, TIME = 0.4")
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 LREAL = .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)
else:
print(" Set Algo = Normal, and Unset IALGO")
sys.stdout.flush()
io.set_incar_tag({
"IALGO": None,
"ALGO": "Normal"
},
jobdir=new_jobdir)
def fix(self, err_jobdir, new_jobdir, settings):
""" Try to fix the error by increasing the number of bands"""
continue_job(err_jobdir, new_jobdir, settings)
with open(os.path.join(err_jobdir, 'OUTCAR')) as f:
err_outcar = f.read().splitlines()
nbands_line = []
for line in err_outcar:
if "NBANDS" in line:
nbands_line.append(line)
if len(nbands_line) < 1:
print("SERIOUS WARNING : ")
print(
" Couldn't find any reference to nbands in the OUTCAR. Continuing without fixing"
)
else:
for l in nbands_line:
if 'k-points' in l.strip().split():
print(" Set NBANDS = " +
str(int(1.1 * float(l.strip().split()[-1]))))
sys.stdout.flush()
io.set_incar_tag(
{"NBANDS": int(1.1 * float(l.strip().split()[-1]))},
jobdir=new_jobdir)
break
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 fix(self, err_jobdir, new_jobdir, settings):
""" First attempt:
Set IBRION = 2
Second attempt:
Reduce POTIM to 0.1
Final attempt:
Reduce POTIM to 0.01
"""
continue_job(err_jobdir, new_jobdir, settings)
if io.get_incar_tag("IBRION", jobdir=new_jobdir) != 2:
print(" Set IBRION = 2")
io.set_incar_tag({"IBRION": 2}, jobdir=new_jobdir)
elif io.get_incar_tag("POTIM", jobdir=new_jobdir) > 0.1:
print(" Set POTIM = 0.1")
sys.stdout.flush()
io.set_incar_tag({"POTIM": 0.1}, jobdir=new_jobdir)
elif io.get_incar_tag("POTIM", jobdir=new_jobdir) > 0.01:
print(" Set POTIM = 0.01")
sys.stdout.flush()
io.set_incar_tag({"POTIM": 0.01}, jobdir=new_jobdir)
def run(jobdir=None,
stdout="std.out",
stderr="std.err",
npar=None,
ncore=None,
command=None,
ncpus=None,
kpar=None,
poll_check_time=5.0,
err_check_time=60.0,
err_types=None,
is_neb=False):
""" Run vasp using subprocess.
The 'command' is executed in the directory 'jobdir'.
Args:
jobdir: directory to run vasp. If jobdir is None, the current directory is used.
stdout: filename to write to. If stdout is None, "std.out" is used.
stderr: filename to write to. If stderr is None, "std.err" is used.
npar: (int or None) VASP INCAR NPAR setting. If npar is None, then NPAR is removed from INCAR
kpar: (int or None) VASP INCAR KPAR setting. If kpar is None, then KPAR is removed from INCAR
ncore: (int or None) VASP INCAR NCORE setting. If not npar is None or ncore is None, then NCORE is removed from INCAR
command: (str or None) vasp execution command
If command != None: then 'command' is run in a subprocess
Else, if ncpus == 1, then command = "vasp"
Else, command = "mpirun -np {NCPUS} vasp"
ncpus: (int) if '{NCPUS}' is in 'command' string, then 'ncpus' is substituted in the command.
if ncpus==None, $PBS_NP is used if it exists, else 1
poll_check_time: how frequently to check if the vasp job is completed
err_check_time: how frequently to parse vasp output to check for errors
err_types: List of error types to check for. Supported errors: 'IbzkptError', 'SubSpaceMatrixError', 'NbandsError'. Default: None, in which case only SubSpaceMatrixErrors are checked.
"""
print("Begin vasp run:")
sys.stdout.flush()
if jobdir is None:
jobdir = os.getcwd()
currdir = os.getcwd()
os.chdir(jobdir)
if ncpus is None:
if "PBS_NP" in os.environ:
ncpus = os.environ["PBS_NP"]
elif "SLURM_NTASKS" in os.environ:
ncpus = os.environ["SLURM_NTASKS"]
else:
ncpus = 1
if command is None:
if ncpus == 1:
command = "vasp"
else:
command = "mpirun -np {NCPUS} vasp"
if re.search("\{NCPUS\}", command):
command = command.format(NCPUS=str(ncpus))
### Expand remaining environment variables
command = os.path.expandvars(command)
if npar is not None:
ncore = None
if npar is not None or ncore is not None:
io.set_incar_tag({"NPAR": npar, "NCORE": ncore}, jobdir)
if kpar is not None:
io.set_incar_tag({"KPAR": kpar}, jobdir)
print(" jobdir:", jobdir)
print(" exec:", command)
sys.stdout.flush()
if is_neb:
# checkdir = os.path.join(jobdir, "01")
sout = open(os.path.join(jobdir, stdout), 'w')
else:
# checkdir = jobdir
sout = open(os.path.join(jobdir, stdout), 'w')
serr = open(os.path.join(jobdir, stderr), 'w')
err = None
p = subprocess.Popen(command.split(), stdout=sout, stderr=serr)
# wait for process to end, and periodically check for errors
poll = p.poll()
last_check = time.time()
stopcar_time = None
while poll is None:
time.sleep(poll_check_time)
if time.time() - last_check > err_check_time:
last_check = time.time()
if is_neb:
err = error_check_neb(jobdir, os.path.join(jobdir, stdout),
err_types)
else:
err = error_check(jobdir, os.path.join(jobdir, stdout),
err_types)
if err != None:
# FreezeErrors are fatal and usually not helped with STOPCAR
if "FreezeError" in err.keys():
print(" VASP is frozen, killing job")
sys.stdout.flush()
# Sometimes p.kill doesn't work if the process is on multiple nodes
os.kill(p.pid, signal.SIGKILL)
p.kill()
# If the job is re-invoked (e.g. via mpirun or srun) too quickly
# after the previous job ended, infinitiband clusters can have
# some issues with resource allocation. A 30s sleep solves this.
time.sleep(30)
# Other errors can be killed with STOPCAR, which is safer
elif stopcar_time is None:
print(" Found errors:", end='')
for e in err:
print(e, end='')
print("\n Killing job with STOPCAR")
sys.stdout.flush()
io.write_stopcar('e', jobdir)
stopcar_time = time.time()
time.sleep(30)
# If the STOPCAR exists, wait 5 min before manually killing the job
elif time.time() - stopcar_time > 300:
print(" VASP is non-responsive, killing job")
sys.stdout.flush()
os.kill(p.pid, signal.SIGKILL)
p.kill()
# If the job is re-invoked (e.g. via mpirun or srun) too quickly
# after the previous job ended, infinitiband clusters can have
# some issues with resource allocation. A 30s sleep solves this.
time.sleep(30)
poll = p.poll()
# close output files
sout.close()
serr.close()
os.chdir(currdir)
print("Run complete")
sys.stdout.flush()
# check finished job for errors
if err is None:
# Crash-type errors take priority over any other error that may show up
if is_neb: #if its neb it checks for crashes in the first image
err = crash_check(os.path.join(jobdir, "01"),
os.path.join(jobdir, stdout), err_types)
else:
err = crash_check(jobdir, os.path.join(jobdir, stdout), err_types)
if err is None:
if is_neb:
err = error_check_neb(jobdir, os.path.join(jobdir, stdout),
err_types)
else:
err = error_check(jobdir, os.path.join(jobdir, stdout),
err_types)
if err != None:
print(" Found errors:", end='')
for e in err:
print(e, end='')
print("\n")
sys.stdout.flush()
return err
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)
