def test_check_and_correct(self):
os.chdir(os.path.join(test_dir, "bad_vasprun"))
h = VasprunXMLValidator()
self.assertTrue(h.check())
#Unconverged still has a valid vasprun.
os.chdir(os.path.join(test_dir, "unconverged"))
self.assertFalse(h.check())
def test_check_and_correct(self):
os.chdir(os.path.join(test_dir, "bad_vasprun"))
h = VasprunXMLValidator()
self.assertTrue(h.check())
#Unconverged still has a valid vasprun.
os.chdir(os.path.join(test_dir, "unconverged"))
self.assertFalse(h.check())
def test_check_and_correct(self):
os.chdir(os.path.join(test_dir, "bad_vasprun"))
h = VasprunXMLValidator()
self.assertTrue(h.check())
# Unconverged still has a valid vasprun.
os.chdir(os.path.join(test_dir, "unconverged"))
shutil.copy("vasprun.xml.electronic", "vasprun.xml")
self.assertFalse(h.check())
os.remove("vasprun.xml")
def test_check_and_correct(self):
os.chdir(os.path.join(test_dir, "bad_vasprun"))
h = VasprunXMLValidator()
self.assertTrue(h.check())
# Unconverged still has a valid vasprun.
os.chdir(os.path.join(test_dir, "unconverged"))
shutil.copy("vasprun.xml.electronic", "vasprun.xml")
self.assertFalse(h.check())
os.remove("vasprun.xml")
def run_task(self, fw_spec):
dec = MontyDecoder()
jobs = dec.process_decoded(self["jobs"])
fw_env = fw_spec.get("_fw_env", {})
#Override VASP and gamma VASP commands using fw_env
if fw_env.get("vasp_cmd"):
for j in jobs:
j.vasp_cmd = os.path.expandvars(fw_env["vasp_cmd"])
j.gamma_vasp_cmd = j.gamma_vasp_cmd
logging.info("Vasp command is {}".format(j.vasp_cmd))
if fw_env.get("gamma_vasp_cmd"):
for j in jobs:
j.gamma_vasp_cmd = os.path.expandvars(fw_env["gamma_vasp_cmd"])
logging.info("Vasp gamma command is {}".format(
j.gamma_vasp_cmd))
#Override custodian scratch dir.
cust_params = self.get("custodian_params", {})
if fw_env.get("scratch_root"):
cust_params["scratch_dir"] = os.path.expandvars(
fw_env["scratch_root"])
logging.info("Running with custodian params %s" % cust_params)
handlers = [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler()
]
validators = [VasprunXMLValidator()]
c = Custodian(handlers=[h.as_dict() for h in handlers],
jobs=jobs,
validators=[v.as_dict() for v in validators],
**cust_params)
output = c.run()
return FWAction(stored_data=output)
def test_as_dict(self):
h = VasprunXMLValidator()
d = h.as_dict()
h2 = VasprunXMLValidator.from_dict(d)
self.assertIsInstance(h2, VasprunXMLValidator)
from custodian.vasp.handlers import VaspErrorHandler,UnconvergedErrorHandler, \
NonConvergingErrorHandler,FrozenJobErrorHandler,StdErrHandler,\
WalltimeHandler,PositiveEnergyErrorHandler
from custodian import Custodian
import argparse
handlers = [
VaspErrorHandler(),
FrozenJobErrorHandler(),
StdErrHandler(),
NonConvergingErrorHandler(),
WalltimeHandler(),
PositiveEnergyErrorHandler(),
UnconvergedErrorHandler()
]
validators = [VaspFilesValidator(), VasprunXMLValidator()]
def runvasp(cmd,
opt=False,
max_errors=3,
backup=False,
auto_gamma=False,
auto_npar=False,
ediffg=-.05):
"""
cmd example:
cmd=['mpirun', '-np', '32' , '-machinefile', 'hosts','vasp_std']
"""
if opt:
jobs = cvj.full_opt_run(cmd,
def run_task(self, fw_spec):
handler_groups = {
"default": [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(),
StdErrHandler(),
DriftErrorHandler()
],
"strict": [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(),
StdErrHandler(),
AliasingErrorHandler(),
DriftErrorHandler()
],
"md": [VaspErrorHandler(),
NonConvergingErrorHandler()],
"no_handler": []
}
vasp_cmd = env_chk(self["vasp_cmd"], fw_spec)
if isinstance(vasp_cmd, str):
vasp_cmd = os.path.expandvars(vasp_cmd)
vasp_cmd = shlex.split(vasp_cmd)
# initialize variables
job_type = self.get("job_type", "normal")
scratch_dir = env_chk(self.get("scratch_dir"), fw_spec)
gzip_output = self.get("gzip_output", True)
max_errors = self.get("max_errors", CUSTODIAN_MAX_ERRORS)
auto_npar = env_chk(self.get("auto_npar"),
fw_spec,
strict=False,
default=False)
gamma_vasp_cmd = env_chk(self.get("gamma_vasp_cmd"),
fw_spec,
strict=False,
default=None)
if gamma_vasp_cmd:
gamma_vasp_cmd = shlex.split(gamma_vasp_cmd)
# construct jobs
if job_type == "normal":
jobs = [
VaspJob(vasp_cmd,
auto_npar=auto_npar,
gamma_vasp_cmd=gamma_vasp_cmd)
]
elif job_type == "double_relaxation_run":
jobs = VaspJob.double_relaxation_run(
vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
half_kpts_first_relax=self.get("half_kpts_first_relax",
HALF_KPOINTS_FIRST_RELAX))
elif job_type == "metagga_opt_run":
jobs = VaspJob.metagga_opt_run(vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
half_kpts_first_relax=self.get(
"half_kpts_first_relax",
HALF_KPOINTS_FIRST_RELAX))
elif job_type == "full_opt_run":
jobs = VaspJob.full_opt_run(vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
max_steps=9,
half_kpts_first_relax=self.get(
"half_kpts_first_relax",
HALF_KPOINTS_FIRST_RELAX))
elif job_type == "neb":
# TODO: @shyuep @HanmeiTang This means that NEB can only be run (i) in reservation mode
# and (ii) when the queueadapter parameter is overridden and (iii) the queue adapter
# has a convention for nnodes (with that name). Can't the number of nodes be made a
# parameter that the user sets differently? e.g., fw_spec["neb_nnodes"] must be set
# when setting job_type=NEB? Then someone can use this feature in non-reservation
# mode and without this complication. -computron
nnodes = int(fw_spec["_queueadapter"]["nnodes"])
# TODO: @shyuep @HanmeiTang - I am not sure what the code below is doing. It looks like
# it is trying to override the number of processors. But I tried running the code
# below after setting "vasp_cmd = 'mpirun -n 16 vasp'" and the code fails.
# (i) Is this expecting an array vasp_cmd rather than String? If so, that's opposite to
# the rest of this task's convention and documentation
# (ii) can we get rid of this hacking in the first place? e.g., allowing the user to
# separately set the NEB_VASP_CMD as an env_variable and not rewriting the command
# inside this.
# -computron
# Index the tag "-n" or "-np"
index = [i for i, s in enumerate(vasp_cmd) if '-n' in s]
ppn = int(vasp_cmd[index[0] + 1])
vasp_cmd[index[0] + 1] = str(nnodes * ppn)
# Do the same for gamma_vasp_cmd
if gamma_vasp_cmd:
index = [i for i, s in enumerate(gamma_vasp_cmd) if '-n' in s]
ppn = int(gamma_vasp_cmd[index[0] + 1])
gamma_vasp_cmd[index[0] + 1] = str(nnodes * ppn)
jobs = [
VaspNEBJob(vasp_cmd,
final=False,
auto_npar=auto_npar,
gamma_vasp_cmd=gamma_vasp_cmd)
]
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handler_group = self.get("handler_group", "default")
if isinstance(handler_group, str):
handlers = handler_groups[handler_group]
else:
handlers = handler_group
if self.get("max_force_threshold"):
handlers.append(
MaxForceErrorHandler(
max_force_threshold=self["max_force_threshold"]))
if self.get("wall_time"):
handlers.append(WalltimeHandler(wall_time=self["wall_time"]))
if job_type == "neb":
validators = [
] # CINEB vasprun.xml sometimes incomplete, file structure different
else:
validators = [VasprunXMLValidator(), VaspFilesValidator()]
c = Custodian(handlers,
jobs,
validators=validators,
max_errors=max_errors,
scratch_dir=scratch_dir,
gzipped_output=gzip_output)
c.run()
if os.path.exists(zpath("custodian.json")):
stored_custodian_data = {
"custodian": loadfn(zpath("custodian.json"))
}
return FWAction(stored_data=stored_custodian_data)
def run_task(self, fw_spec):
handler_groups = {
"default": [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler()
],
"strict": [
VaspErrorHandler(),
MeshSymmetryErrorHandler(),
UnconvergedErrorHandler(),
NonConvergingErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(),
AliasingErrorHandler()
],
"md": [VaspErrorHandler(),
NonConvergingErrorHandler()],
"no_handler": []
}
vasp_cmd = env_chk(self["vasp_cmd"], fw_spec)
if isinstance(vasp_cmd, six.string_types):
vasp_cmd = os.path.expandvars(vasp_cmd)
vasp_cmd = shlex.split(vasp_cmd)
# initialize variables
job_type = self.get("job_type", "normal")
scratch_dir = env_chk(self.get("scratch_dir"), fw_spec)
gzip_output = self.get("gzip_output", True)
max_errors = self.get("max_errors", 5)
auto_npar = env_chk(self.get("auto_npar"),
fw_spec,
strict=False,
default=False)
gamma_vasp_cmd = env_chk(self.get("gamma_vasp_cmd"),
fw_spec,
strict=False,
default=None)
if gamma_vasp_cmd:
gamma_vasp_cmd = shlex.split(gamma_vasp_cmd)
# construct jobs
if job_type == "normal":
jobs = [
VaspJob(vasp_cmd,
auto_npar=auto_npar,
gamma_vasp_cmd=gamma_vasp_cmd)
]
elif job_type == "double_relaxation_run":
jobs = VaspJob.double_relaxation_run(vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
half_kpts_first_relax=False)
elif job_type == "full_opt_run":
jobs = VaspJob.full_opt_run(vasp_cmd,
auto_npar=auto_npar,
ediffg=self.get("ediffg"),
max_steps=5,
half_kpts_first_relax=False)
else:
raise ValueError("Unsupported job type: {}".format(job_type))
# construct handlers
handlers = handler_groups[self.get("handler_group", "default")]
if self.get("max_force_threshold"):
handlers.append(
MaxForceErrorHandler(
max_force_threshold=self["max_force_threshold"]))
if self.get("wall_time"):
handlers.append(WalltimeHandler(wall_time=self["wall_time"]))
validators = [VasprunXMLValidator()]
c = Custodian(handlers,
jobs,
validators=validators,
max_errors=max_errors,
scratch_dir=scratch_dir,
gzipped_output=gzip_output)
c.run()
def run_task(self, fw_spec):
# write a file containing the formula and task_type for somewhat
# easier file system browsing
self._write_formula_file(fw_spec)
fw_env = fw_spec.get("_fw_env", {})
if "mpi_cmd" in fw_env:
mpi_cmd = fw_spec["_fw_env"]["mpi_cmd"]
elif which("mpirun"):
mpi_cmd = "mpirun"
elif which("aprun"):
mpi_cmd = "aprun"
else:
raise ValueError("No MPI command found!")
# TODO: last two env vars, i.e. SGE and LoadLeveler, are untested
env_vars = ['PBS_NP', 'SLURM_NTASKS', 'NSLOTS', 'LOADL_TOTAL_TASKS']
for env_var in env_vars:
nproc = os.environ.get(env_var, None)
if nproc is not None: break
if nproc is None:
raise ValueError("None of the env vars {} found to set nproc!".format(env_vars))
v_exe = shlex.split('{} -n {} {}'.format(mpi_cmd, nproc, fw_env.get("vasp_cmd", "vasp")))
gv_exe = shlex.split('{} -n {} {}'.format(mpi_cmd, nproc, fw_env.get("gvasp_cmd", "gvasp")))
print 'host:', os.environ['HOSTNAME']
for job in self.jobs:
job.vasp_cmd = v_exe
job.gamma_vasp_cmd = gv_exe
incar_errors = check_incar(fw_spec['task_type'])
if incar_errors:
raise ValueError("Critical error: INCAR does not pass checks: {}".format(incar_errors))
logging.basicConfig(level=logging.DEBUG)
c = Custodian(self.handlers, self.jobs, max_errors=self.max_errors, gzipped_output=False, validators=[VasprunXMLValidator()]) # manual gzip
custodian_out = c.run()
if self.gzip_output:
for f in os.listdir(os.getcwd()):
if not f.lower().endswith("gz") and not f.endswith(".OU") and not f.endswith(".ER"):
with open(f, 'rb') as f_in, \
GzipFile('{}.gz'.format(f), 'wb') as f_out:
f_out.writelines(f_in)
os.remove(f)
all_errors = set()
for run in custodian_out:
for correction in run['corrections']:
all_errors.update(correction['errors'])
stored_data = {'error_list': list(all_errors)}
update_spec = {'prev_vasp_dir': os.getcwd(),
'prev_task_type': fw_spec['task_type'],
'mpsnl': fw_spec['mpsnl'],
'snlgroup_id': fw_spec['snlgroup_id'],
'run_tags': fw_spec['run_tags'],
'parameters': fw_spec.get('parameters')}
return FWAction(stored_data=stored_data, update_spec=update_spec)
def test_as_dict(self):
h = VasprunXMLValidator()
d = h.as_dict()
h2 = VasprunXMLValidator.from_dict(d)
self.assertIsInstance(h2, VasprunXMLValidator)
from pymatgen.io.vasp.inputs import Incar, Poscar, VaspInput,Potcar, Kpoints
import os,shutil
from custodian.vasp.jobs import VaspJob
from custodian.vasp.handlers import VaspErrorHandler, UnconvergedErrorHandler,MeshSymmetryErrorHandler, NonConvergingErrorHandler, PotimErrorHandler
from custodian.vasp.validators import VasprunXMLValidator
from custodian.custodian import Custodian
inc=Incar.from_file("INCAR")
pot=Potcar.from_file("POTCAR")
pos=Poscar.from_file("POSCAR")
kp=Kpoints.from_file("KPOINTS")
shutil.copy2('/users/knc6/bin/vdw_kernel.bindat','./')
vinput = VaspInput.from_directory(".")
job=VaspJob(['mpirun', '-np', '16', '/users/knc6/VASP/vasp54/src/vasp.5.4.1/bin/vasp_std'], final=False, backup=False)
handlers = [VaspErrorHandler(), MeshSymmetryErrorHandler(),UnconvergedErrorHandler(), NonConvergingErrorHandler(),PotimErrorHandler()]
validators = [VasprunXMLValidator()]
c = Custodian(handlers, [job],max_errors=5,validators=validators)
c.run()