def test_aliasing_incar(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = AliasingErrorHandler("vasp.aliasing_incar")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['aliasing_incar'])
self.assertEqual(d["actions"],
[{'action': {'_unset': {'NGY':1, 'NGZ': 1}},
'dict': 'INCAR'}, {"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}},
{"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}}])
incar = Incar.from_file('INCAR.orig')
incar["ICHARG"] = 10
incar.write_file("INCAR")
d = h.correct()
self.assertEqual(d["errors"], ['aliasing_incar'])
self.assertEqual(d["actions"],
[{'action': {'_unset': {'NGY': 1, 'NGZ': 1}},
'dict': 'INCAR'}])
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
def test_aliasing(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = AliasingErrorHandler("vasp.aliasing")
h.check()
d = h.correct()
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
self.assertEqual(d["errors"], ['aliasing'])
self.assertEqual(d["actions"], [{
'action': {
'_set': {
'NGX': 34
}
},
'dict': 'INCAR'
}, {
"file": "CHGCAR",
"action": {
"_file_delete": {
'mode': "actual"
}
}
}, {
"file": "WAVECAR",
"action": {
"_file_delete": {
'mode': "actual"
}
}
}])
def test_aliasing(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = AliasingErrorHandler("vasp.aliasing")
h.check()
d = h.correct()
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
self.assertEqual(d["errors"], ['aliasing'])
self.assertEqual(d["actions"],
[{'action': {'_set': {'NGX': 34}},
'dict': 'INCAR'}, {"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}},
{"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}}])
def test_aliasing_incar(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = AliasingErrorHandler("vasp.aliasing_incar")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ['aliasing_incar'])
self.assertEqual(d["actions"],
[{'action': {'_unset': {'NGY':1, 'NGZ': 1}},
'dict': 'INCAR'}, {"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}},
{"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}}])
incar = Incar.from_file('INCAR.orig')
incar["ICHARG"] = 10
incar.write_file("INCAR")
d = h.correct()
self.assertEqual(d["errors"], ['aliasing_incar'])
self.assertEqual(d["actions"],
[{'action': {'_unset': {'NGY': 1, 'NGZ': 1}},
'dict': 'INCAR'}])
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
def test_aliasing_incar(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = AliasingErrorHandler("vasp.aliasing_incar")
h.check()
d = h.correct()
self.assertEqual(d["errors"], ["aliasing_incar"])
self.assertEqual(
d["actions"],
[
{
"action": {
"_unset": {
"NGY": 1,
"NGZ": 1
}
},
"dict": "INCAR"
},
{
"file": "CHGCAR",
"action": {
"_file_delete": {
"mode": "actual"
}
}
},
{
"file": "WAVECAR",
"action": {
"_file_delete": {
"mode": "actual"
}
}
},
],
)
incar = Incar.from_file("INCAR.orig")
incar["ICHARG"] = 10
incar.write_file("INCAR")
d = h.correct()
self.assertEqual(d["errors"], ["aliasing_incar"])
self.assertEqual(
d["actions"],
[{
"action": {
"_unset": {
"NGY": 1,
"NGZ": 1
}
},
"dict": "INCAR"
}],
)
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
def test_aliasing(self):
os.chdir(os.path.join(test_dir, "aliasing"))
shutil.copy("INCAR", "INCAR.orig")
h = AliasingErrorHandler("vasp.aliasing")
h.check()
d = h.correct()
shutil.move("INCAR.orig", "INCAR")
clean_dir()
os.chdir(test_dir)
self.assertEqual(d["errors"], ["aliasing"])
self.assertEqual(
d["actions"],
[
{
"action": {
"_set": {
"NGX": 34
}
},
"dict": "INCAR"
},
{
"file": "CHGCAR",
"action": {
"_file_delete": {
"mode": "actual"
}
}
},
{
"file": "WAVECAR",
"action": {
"_file_delete": {
"mode": "actual"
}
}
},
],
)
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, six.string_types):
vasp_cmd = os.path.expandvars(vasp_cmd)
vasp_cmd = shlex.split(vasp_cmd)
# initialize variables
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)
jobs = [VaspJob(vasp_cmd, auto_npar=auto_npar, gamma_vasp_cmd=gamma_vasp_cmd)]
# construct handlers
handlers = handler_groups[self.get("handler_group", "default")]
validators = []
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):
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()
import sys
from custodian.custodian import Custodian
from custodian.vasp.handlers import VaspErrorHandler, \
UnconvergedErrorHandler, AliasingErrorHandler, FrozenJobErrorHandler, \
PositiveEnergyErrorHandler, MeshSymmetryErrorHandler
from custodian.vasp.jobs import VaspJob
handlers = [
VaspErrorHandler(),
UnconvergedErrorHandler(),
AliasingErrorHandler(),
FrozenJobErrorHandler(),
PositiveEnergyErrorHandler(),
MeshSymmetryErrorHandler()
]
jobs = [VaspJob(sys.argv[1:])]
c = Custodian(handlers, jobs, max_errors=10)
c.run()