def test_check_correct_ionic(self):
shutil.copy("vasprun.xml.ionic", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
os.remove("vasprun.xml")
def test_check_correct_electronic_repeat(self):
shutil.copy("vasprun.xml.electronic2", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d, {"errors": ["Unconverged"], "actions": None})
os.remove("vasprun.xml")
def test_check_correct_scan(self):
shutil.copy("vasprun.xml.scan", "vasprun.xml")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
self.assertIn({"dict": "INCAR",
"action": {"_set": {"ALGO": "All"}}},d["actions"])
os.remove("vasprun.xml")
def test_is_converged(self):
import pymatgen
print(pymatgen.__file__)
print(pymatgen.__version__)
import custodian
print(custodian.__version__)
path = os.path.join(TEST_PATH, self.path, 'unconverged', 'vasprun.xml')
handler = UnconvergedErrorHandler(path)
print(handler.check())
def test_check_correct(self):
subdir = os.path.join(test_dir, "unconverged")
os.chdir(subdir)
shutil.copy("INCAR", "INCAR.orig")
shutil.copy("KPOINTS", "KPOINTS.orig")
shutil.copy("POSCAR", "POSCAR.orig")
shutil.copy("CONTCAR", "CONTCAR.orig")
h = UnconvergedErrorHandler()
self.assertTrue(h.check())
d = h.correct()
self.assertEqual(d["errors"], ['Unconverged'])
os.remove(os.path.join(subdir, "error.1.tar.gz"))
shutil.move("INCAR.orig", "INCAR")
shutil.move("KPOINTS.orig", "KPOINTS")
shutil.move("POSCAR.orig", "POSCAR")
shutil.move("CONTCAR.orig", "CONTCAR")
def test_to_from_dict(self):
h = UnconvergedErrorHandler("random_name.xml")
h2 = UnconvergedErrorHandler.from_dict(h.as_dict())
self.assertEqual(type(h2), UnconvergedErrorHandler)
self.assertEqual(h2.output_filename, "random_name.xml")
def run_task(self, fw_spec):
ueh = UnconvergedErrorHandler()
custodian_out = ueh.correct()
return FWAction(stored_data={'error_list': custodian_out['errors']})
def run_task(self, fw_spec):
if '_fizzled_parents' in fw_spec and not 'prev_vasp_dir' in fw_spec:
prev_dir = get_loc(fw_spec['_fizzled_parents'][0]['launches'][0]['launch_dir'])
update_spec = {} # add this later when creating new FW
fizzled_parent = True
parse_dos = False
else:
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
update_spec = {'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['prev_task_type'],
'run_tags': fw_spec['run_tags'], 'parameters': fw_spec.get('parameters')}
fizzled_parent = False
parse_dos = 'Uniform' in fw_spec['prev_task_type']
if 'run_tags' in fw_spec:
self.additional_fields['run_tags'] = fw_spec['run_tags']
else:
self.additional_fields['run_tags'] = fw_spec['_fizzled_parents'][0]['spec']['run_tags']
if MOVE_TO_GARDEN_DEV:
prev_dir = move_to_garden(prev_dir, prod=False)
elif MOVE_TO_GARDEN_PROD:
prev_dir = move_to_garden(prev_dir, prod=True)
# get the directory containing the db file
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('MPVaspDrone')
logger.setLevel(logging.INFO)
sh = logging.StreamHandler(stream=sys.stdout)
sh.setLevel(getattr(logging, 'INFO'))
logger.addHandler(sh)
with open(db_path) as f:
db_creds = json.load(f)
drone = MPVaspDrone(
host=db_creds['host'], port=db_creds['port'],
database=db_creds['database'], user=db_creds['admin_user'],
password=db_creds['admin_password'],
collection=db_creds['collection'], parse_dos=parse_dos,
additional_fields=self.additional_fields,
update_duplicates=self.update_duplicates)
t_id, d = drone.assimilate(prev_dir, launches_coll=LaunchPad.auto_load().launches)
mpsnl = d['snl_final'] if 'snl_final' in d else d['snl']
snlgroup_id = d['snlgroup_id_final'] if 'snlgroup_id_final' in d else d['snlgroup_id']
update_spec.update({'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id})
print 'ENTERED task id:', t_id
stored_data = {'task_id': t_id}
if d['state'] == 'successful':
update_spec['analysis'] = d['analysis']
update_spec['output'] = d['output']
return FWAction(stored_data=stored_data, update_spec=update_spec)
# not successful - first test to see if UnconvergedHandler is needed
if not fizzled_parent:
unconverged_tag = 'unconverged_handler--{}'.format(fw_spec['prev_task_type'])
output_dir = last_relax(os.path.join(prev_dir, 'vasprun.xml'))
ueh = UnconvergedErrorHandler(output_filename=output_dir)
if ueh.check() and unconverged_tag not in fw_spec['run_tags']:
print 'Unconverged run! Creating dynamic FW...'
spec = {'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['task_type'],
'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id,
'task_type': fw_spec['prev_task_type'],
'run_tags': list(fw_spec['run_tags']),
'parameters': fw_spec.get('parameters'),
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': fw_spec['_priority']}
snl = StructureNL.from_dict(spec['mpsnl'])
spec['run_tags'].append(unconverged_tag)
spec['_queueadapter'] = QA_VASP
fws = []
connections = {}
f = Composition.from_formula(
snl.structure.composition.reduced_formula).alphabetical_formula
fws.append(FireWork(
[VaspCopyTask({'files': ['INCAR', 'KPOINTS', 'POSCAR', 'POTCAR', 'CONTCAR'],
'use_CONTCAR': False}), SetupUnconvergedHandlerTask(),
get_custodian_task(spec)], spec, name=get_slug(f + '--' + spec['task_type']),
fw_id=-2))
spec = {'task_type': 'VASP db insertion', '_allow_fizzled_parents': True,
'_priority': fw_spec['_priority'], '_queueadapter': QA_DB,
'run_tags': list(fw_spec['run_tags'])}
spec['run_tags'].append(unconverged_tag)
fws.append(
FireWork([VaspToDBTask()], spec, name=get_slug(f + '--' + spec['task_type']),
fw_id=-1))
connections[-2] = -1
wf = Workflow(fws, connections)
return FWAction(detours=wf)
# not successful and not due to convergence problem - FIZZLE
raise ValueError("DB insertion successful, but don't know how to fix this FireWork! Can't continue with workflow...")
def test_to_from_dict(self):
h = UnconvergedErrorHandler("random_name.xml")
h2 = UnconvergedErrorHandler.from_dict(h.as_dict())
self.assertEqual(type(h2), UnconvergedErrorHandler)
self.assertEqual(h2.output_filename, "random_name.xml")
from custodian.vasp.jobs import VaspJob as cvj
from custodian.vasp.validators import VaspFilesValidator, 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=True,
ediffg=-.05):
"""
cmd example:
cmd=['mpirun', '-np', '32' , '-machinefile', 'hosts','vasp_std']
"""
def run_task(self, fw_spec):
handler_groups = {
"default": [VaspErrorHandler(), MeshSymmetryErrorHandler(), UnconvergedErrorHandler(),
NonConvergingErrorHandler(),PotimErrorHandler(),
PositiveEnergyErrorHandler(), FrozenJobErrorHandler(), StdErrHandler()],
"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 launch_workflow(self,
launchpad_dir="",
k_product=50,
job=None,
user_incar_settings=None,
potcar_functional='PBE',
additional_handlers=[]):
"""
Creates a list of Fireworks. Each Firework represents calculations
that will be done on a slab system of a compound in a specific
orientation. Each Firework contains a oriented unit cell relaxation job
and a WriteSlabVaspInputs which creates os. Firework(s) depending
on whether or not Termination=True. Vasp outputs from all slab and
oriented unit cell calculations will then be inserted into a database.
Args:
launchpad_dir (str path): The path to my_launchpad.yaml. Defaults to
the current working directory containing your runs
k_product: kpts[0][0]*a. Decide k density without
kpoint0, default to 50
cwd: (str path): The curent working directory. Location of where you
want your vasp outputs to be.
job (VaspJob): The command (cmd) entered into VaspJob object. Default
is specifically set for running vasp jobs on Carver at NERSC
(use aprun for Hopper or Edison).
user_incar_settings(dict): A dict specifying additional incar
settings, default to None (ediff_per_atom=False)
potcar_functional (str): default to PBE
"""
launchpad = LaunchPad.from_file(
os.path.join(os.environ["HOME"], launchpad_dir,
"my_launchpad.yaml"))
if self.reset:
launchpad.reset('', require_password=False)
# Scratch directory reffered to by custodian.
# May be different on non-Nersc systems.
if not job:
job = VaspJob(["mpirun", "-n", "64", "vasp"],
auto_npar=False,
copy_magmom=True)
handlers = [
VaspErrorHandler(),
NonConvergingErrorHandler(),
UnconvergedErrorHandler(),
PotimErrorHandler(),
PositiveEnergyErrorHandler(),
FrozenJobErrorHandler(timeout=3600)
]
if additional_handlers:
handlers.extend(additional_handlers)
cust_params = {
"custodian_params": {
"scratch_dir":
os.path.join("/global/scratch2/sd/", os.environ["USER"])
},
"jobs": job.double_relaxation_run(job.vasp_cmd, auto_npar=False),
"handlers": handlers,
"max_errors": 100
} # will return a list of jobs
# instead of just being one job
fws = []
for key in self.miller_dict.keys():
# Enumerate through all compounds in the dictionary,
# the key is the compositional formula of the compound
print key
for miller_index in self.miller_dict[key]:
# Enumerates through all miller indices we
# want to create slabs of that compound from
print str(miller_index)
max_norm = max(
miller_index) if self.max_normal_search else None
# Whether or not we want to use the
# max_normal_search algorithm from surface.py
print 'true or false max norm is ', max_norm, self.max_normal_search
slab = SlabGenerator(self.unit_cells_dict[key][0],
miller_index,
self.ssize,
self.vsize,
max_normal_search=max_norm)
oriented_uc = slab.oriented_unit_cell
if self.fail_safe and len(oriented_uc) > 199:
break
# This method only creates the oriented unit cell, the
# slabs are created in the WriteSlabVaspInputs task.
# WriteSlabVaspInputs will create the slabs from
# the contcar of the oriented unit cell calculation
handler = []
tasks = []
folderbulk = '/%s_%s_k%s_s%sv%s_%s%s%s' % (
oriented_uc.composition.reduced_formula, 'bulk', k_product,
self.ssize, self.vsize, str(miller_index[0]),
str(miller_index[1]), str(miller_index[2]))
cwd = os.getcwd()
if self.get_bulk_e:
tasks.extend([
WriteUCVaspInputs(
oriented_ucell=oriented_uc,
folder=folderbulk,
cwd=cwd,
user_incar_settings=user_incar_settings,
potcar_functional=potcar_functional,
k_product=k_product),
RunCustodianTask(dir=folderbulk,
cwd=cwd,
**cust_params),
VaspSlabDBInsertTask(struct_type="oriented_unit_cell",
loc=folderbulk,
cwd=cwd,
miller_index=miller_index,
**self.vaspdbinsert_params)
])
# Slab will inherit average final magnetic moment
# of the bulk from outcar, will have to generalize
# this for systems with different elements later
# element = oriented_uc.species[0]
# out = Outcar(cwd+folderbulk)
# out_mag = out.magnetization
# tot_mag = [mag['tot'] for mag in out_mag]
# magmom = np.mean(tot_mag)
# user_incar_settings['MAGMOM'] = {element: magmom}
tasks.append(
WriteSlabVaspInputs(
folder=folderbulk,
cwd=cwd,
user_incar_settings=user_incar_settings,
terminations=self.terminations,
custodian_params=cust_params,
vaspdbinsert_parameters=self.vaspdbinsert_params,
potcar_functional=potcar_functional,
k_product=k_product,
miller_index=miller_index,
min_slab_size=self.ssize,
min_vacuum_size=self.vsize,
ucell=self.unit_cells_dict[key][0]))
fw = Firework(tasks, name=folderbulk)
fws.append(fw)
wf = Workflow(fws, name='Surface Calculations')
launchpad.add_wf(wf)
def run_task(self, fw_spec):
ueh = UnconvergedErrorHandler()
custodian_out = ueh.correct()
return FWAction(stored_data={'error_list': custodian_out['errors']})
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()
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()
def run_task(self, fw_spec):
if '_fizzled_parents' in fw_spec and not 'prev_vasp_dir' in fw_spec:
prev_dir = get_loc(
fw_spec['_fizzled_parents'][0]['launches'][0]['launch_dir'])
update_spec = {} # add this later when creating new FW
fizzled_parent = True
parse_dos = False
else:
prev_dir = get_loc(fw_spec['prev_vasp_dir'])
update_spec = {
'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['prev_task_type'],
'run_tags': fw_spec['run_tags'],
'parameters': fw_spec.get('parameters')
}
fizzled_parent = False
parse_dos = 'Uniform' in fw_spec['prev_task_type']
if 'run_tags' in fw_spec:
self.additional_fields['run_tags'] = fw_spec['run_tags']
else:
self.additional_fields['run_tags'] = fw_spec['_fizzled_parents'][
0]['spec']['run_tags']
if MOVE_TO_GARDEN_DEV:
prev_dir = move_to_garden(prev_dir, prod=False)
elif MOVE_TO_GARDEN_PROD:
prev_dir = move_to_garden(prev_dir, prod=True)
# get the directory containing the db file
db_dir = os.environ['DB_LOC']
db_path = os.path.join(db_dir, 'tasks_db.json')
logging.basicConfig(level=logging.INFO)
logger = logging.getLogger('MPVaspDrone')
logger.setLevel(logging.INFO)
sh = logging.StreamHandler(stream=sys.stdout)
sh.setLevel(getattr(logging, 'INFO'))
logger.addHandler(sh)
with open(db_path) as f:
db_creds = json.load(f)
drone = MPVaspDrone(host=db_creds['host'],
port=db_creds['port'],
database=db_creds['database'],
user=db_creds['admin_user'],
password=db_creds['admin_password'],
collection=db_creds['collection'],
parse_dos=parse_dos,
additional_fields=self.additional_fields,
update_duplicates=self.update_duplicates)
t_id, d = drone.assimilate(
prev_dir, launches_coll=LaunchPad.auto_load().launches)
mpsnl = d['snl_final'] if 'snl_final' in d else d['snl']
snlgroup_id = d['snlgroup_id_final'] if 'snlgroup_id_final' in d else d[
'snlgroup_id']
update_spec.update({'mpsnl': mpsnl, 'snlgroup_id': snlgroup_id})
print 'ENTERED task id:', t_id
stored_data = {'task_id': t_id}
if d['state'] == 'successful':
update_spec['analysis'] = d['analysis']
update_spec['output'] = d['output']
return FWAction(stored_data=stored_data, update_spec=update_spec)
# not successful - first test to see if UnconvergedHandler is needed
if not fizzled_parent:
unconverged_tag = 'unconverged_handler--{}'.format(
fw_spec['prev_task_type'])
output_dir = last_relax(os.path.join(prev_dir, 'vasprun.xml'))
ueh = UnconvergedErrorHandler(output_filename=output_dir)
if ueh.check() and unconverged_tag not in fw_spec['run_tags']:
print 'Unconverged run! Creating dynamic FW...'
spec = {
'prev_vasp_dir': prev_dir,
'prev_task_type': fw_spec['task_type'],
'mpsnl': mpsnl,
'snlgroup_id': snlgroup_id,
'task_type': fw_spec['prev_task_type'],
'run_tags': list(fw_spec['run_tags']),
'parameters': fw_spec.get('parameters'),
'_dupefinder': DupeFinderVasp().to_dict(),
'_priority': fw_spec['_priority']
}
snl = StructureNL.from_dict(spec['mpsnl'])
spec['run_tags'].append(unconverged_tag)
spec['_queueadapter'] = QA_VASP
fws = []
connections = {}
f = Composition.from_formula(
snl.structure.composition.reduced_formula
).alphabetical_formula
fws.append(
FireWork([
VaspCopyTask({
'files': [
'INCAR', 'KPOINTS', 'POSCAR', 'POTCAR',
'CONTCAR'
],
'use_CONTCAR':
False
}),
SetupUnconvergedHandlerTask(),
get_custodian_task(spec)
],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-2))
spec = {
'task_type': 'VASP db insertion',
'_allow_fizzled_parents': True,
'_priority': fw_spec['_priority'],
'_queueadapter': QA_DB,
'run_tags': list(fw_spec['run_tags'])
}
spec['run_tags'].append(unconverged_tag)
fws.append(
FireWork([VaspToDBTask()],
spec,
name=get_slug(f + '--' + spec['task_type']),
fw_id=-1))
connections[-2] = -1
wf = Workflow(fws, connections)
return FWAction(detours=wf)
# not successful and not due to convergence problem - FIZZLE
raise ValueError(
"DB insertion successful, but don't know how to fix this FireWork! Can't continue with workflow..."
)