def correct(self):
backup("*.nw*")
actions = []
nwi = NwInput.from_file(self.input_file)
for e in self.errors:
if e == "autoz error":
action = {
"_set": {
"geometry_options": ["units", "angstroms", "noautoz"]
}
}
actions.append(action)
elif e == "Bad convergence":
t = nwi.tasks[self.ntasks - 1]
if "cgmin" in t.theory_directives:
nwi.tasks.pop(self.ntasks - 1)
else:
t.theory_directives["cgmin"] = ""
for t in nwi.tasks:
if t.operation.startswith("freq"):
# You cannot calculate hessian with cgmin.
t.theory_directives["nocgmin"] = ""
action = {"_set": {"tasks": [t.as_dict() for t in nwi.tasks]}}
actions.append(action)
else:
# For unimplemented errors, this should just cause the job to
# die.
return {"errors": self.errors, "actions": None}
m = Modder()
for action in actions:
nwi = m.modify_object(action, nwi)
nwi.write_file(self.input_file)
return {"errors": self.errors, "actions": actions}
def correct(self):
backup("*.nw*")
actions = []
nwi = NwInput.from_file(self.input_file)
for e in self.errors:
if e == "autoz error":
action = {"_set": {"geometry_options": ["units",
"angstroms",
"noautoz"]}}
actions.append(action)
elif e == "Bad convergence":
t = nwi.tasks[self.ntasks - 1]
if "cgmin" in t.theory_directives:
nwi.tasks.pop(self.ntasks - 1)
else:
t.theory_directives["cgmin"] = ""
for t in nwi.tasks:
if t.operation.startswith("freq"):
#You cannot calculate hessian with cgmin.
t.theory_directives["nocgmin"] = ""
action = {"_set": {"tasks": [t.as_dict() for t in nwi.tasks]}}
actions.append(action)
else:
# For unimplemented errors, this should just cause the job to
# die.
return {"errors": self.errors, "actions": None}
m = Modder()
for action in actions:
nwi = m.modify_object(action, nwi)
nwi.write_file(self.input_file)
return {"errors": self.errors, "actions": actions}
def apply_corrections_to_spec(corrections, spec):
modder = Modder()
for correction in corrections:
actions = correction['actions']
for action in actions:
if action['action_type'] == 'modify_object':
if action['object']['source'] == 'fw_spec':
myobject = spec[action['object']['key']]
else:
raise NotImplementedError(
'Object source "{}" not implemented in '
'CheckTask'.format(action['object']['source']))
newobj = modder.modify_object(action['action'], myobject)
spec[action['object']['key']] = newobj
elif action['action_type'] == 'modify_dict':
if action['dict']['source'] == 'fw_spec':
mydict = spec[action['dict']['key']]
else:
raise NotImplementedError(
'Dict source "{}" not implemented in '
'CheckTask'.format(action['dict']['source']))
modder.modify(action['action'], mydict)
else:
raise NotImplementedError(
'Action type "{}" not implemented in '
'CheckTask'.format(action['action_type']))
def apply_corrections(self, fw_to_correct, corrections):
# Apply the corrections
spec = fw_to_correct.spec
modder = Modder()
for correction in corrections:
actions = correction['actions']
for action in actions:
if action['action_type'] == 'modify_object':
if action['object']['source'] == 'fw_spec':
myobject = spec[action['object']['key']]
else:
raise NotImplementedError('Object source "{}" not implemented in '
'CheckTask'.format(action['object']['source']))
newobj = modder.modify_object(action['action'], myobject)
spec[action['object']['key']] = newobj
elif action['action_type'] == 'modify_dict':
if action['dict']['source'] == 'fw_spec':
mydict = spec[action['dict']['key']]
else:
raise NotImplementedError('Dict source "{}" not implemented in '
'CheckTask'.format(action['dict']['source']))
modder.modify(action['action'], mydict)
else:
raise NotImplementedError('Action type "{}" not implemented in '
'CheckTask'.format(action['action_type']))
# Keep track of the corrections that have been applied
spec['SRC_check_corrections'] = corrections
# Update the task index
fws_task_index = int(fw_to_correct.spec['wf_task_index'].split('_')[-1])
new_index = fws_task_index + 1
# Update the Fireworks _queueadapter key
#TODO: in the future, see whether the FW queueadapter might be replaced by the qtk_queueadapter ?
# ... to be discussed with Anubhav, when the qtk queueadapter is in a qtk toolkit and not anymore
# in pymatgen/io/abinit
spec['_queueadapter'] = spec['qtk_queueadapter'].get_subs_dict()
queue_adapter_update = get_queue_adapter_update(qtk_queueadapter=spec['qtk_queueadapter'],
corrections=corrections)
# Get and update the task_input if needed
# TODO: make this more general ... right now, it is based on AbinitInput and thus is strongly tight
# to abinit due to abiinput, deps, ...
mytask = fw_to_correct.tasks[0]
task_class = mytask.__class__
decoder = MontyDecoder()
task_input = decoder.process_decoded(fw_to_correct.spec['_tasks'][0]['abiinput'])
initialization_info = fw_to_correct.spec['initialization_info']
deps = mytask.deps
# Create the new Setup/Run/Check fireworks
SRC_fws = createSRCFireworksOld(task_class=task_class, task_input=task_input, SRC_spec=spec,
initialization_info=initialization_info,
wf_task_index_prefix=spec['wf_task_index_prefix'],
current_task_index=new_index,
handlers=self.handlers, validators=self.validators,
deps=deps,
task_type=mytask.task_type, queue_adapter_update=queue_adapter_update)
wf = Workflow(fireworks=SRC_fws['fws'], links_dict=SRC_fws['links_dict'])
return FWAction(detours=[wf])
def apply_corrections_to_spec(corrections, spec):
modder = Modder()
for correction in corrections:
actions = correction['actions']
for action in actions:
if action['action_type'] == 'modify_object':
if action['object']['source'] == 'fw_spec':
myobject = spec[action['object']['key']]
else:
raise NotImplementedError('Object source "{}" not implemented in '
'CheckTask'.format(action['object']['source']))
newobj = modder.modify_object(action['action'], myobject)
spec[action['object']['key']] = newobj
elif action['action_type'] == 'modify_dict':
if action['dict']['source'] == 'fw_spec':
mydict = spec[action['dict']['key']]
else:
raise NotImplementedError('Dict source "{}" not implemented in '
'CheckTask'.format(action['dict']['source']))
modder.modify(action['action'], mydict)
else:
raise NotImplementedError('Action type "{}" not implemented in '
'CheckTask'.format(action['action_type']))
def correct(self): #pylint: disable=R0915,R0912,R0914
"""
"brmix"にてINCARにADDGRIDを追加する
"""
backup([self.output_filename, "INCAR", "KPOINTS", "POSCAR", "OUTCAR",
"vasprun.xml"])
actions = []
vi = VaspInput.from_directory(".")
if "tet" in self.errors or "dentet" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISMEAR": 0}}})
if "inv_rot_mat" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8}}})
if "brmix" in self.errors and "NELECT" in vi["INCAR"]:
#brmix error always shows up after DAV steps if NELECT is specified
self.errors.remove("brmix")
if "brmix" in self.errors or "zpotrf" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"ISYM": 0}}})
#140814 add
actions.append({"dict": "INCAR",
"action": {"_set": {"ADDGRID": True}}})
# Based on VASP forum's recommendation, you should delete the
# CHGCAR and WAVECAR when dealing with these errors.
actions.append({"file": "CHGCAR",
"action": {"_file_delete": {'mode': "actual"}}})
actions.append({"file": "WAVECAR",
"action": {"_file_delete": {'mode': "actual"}}})
if "subspacematrix" in self.errors or "rspher" in self.errors or \
"real_optlay" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"LREAL": False}}})
if "tetirr" in self.errors or "incorrect_shift" in self.errors or \
"rot_matrix" in self.errors:
actions.append({"dict": "KPOINTS",
"action": {"_set": {"generation_style": "Gamma"}}})
if "amin" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"AMIN": "0.01"}}})
if "triple_product" in self.errors:
s = vi["POSCAR"].structure
trans = SupercellTransformation(((1, 0, 0), (0, 0, 1), (0, 1, 0)))
new_s = trans.apply_transformation(s)
actions.append({"dict": "POSCAR",
"action": {"_set": {"structure": new_s.to_dict}},
"transformation": trans.to_dict})
if "pricel" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"SYMPREC": 1e-8, "ISYM": 0}}})
if "brions" in self.errors:
potim = float(vi["INCAR"].get("POTIM", 0.5)) + 0.1
actions.append({"dict": "INCAR",
"action": {"_set": {"POTIM": potim}}})
if "zbrent" in self.errors:
actions.append({"dict": "INCAR",
"action": {"_set": {"IBRION": 1}}})
if "too_few_bands" in self.errors:
if "NBANDS" in vi["INCAR"]:
nbands = int(vi["INCAR"]["NBANDS"])
else:
with open("OUTCAR") as f:
for line in f:
if "NBANDS" in line:
try:
d = line.split("=")
nbands = int(d[-1].strip())
break
except (IndexError, ValueError):
pass
actions.append({"dict": "INCAR",
"action": {"_set": {"NBANDS": int(1.1 * nbands)}}})
if "aliasing" in self.errors:
with open("OUTCAR") as f:
grid_adjusted = False
changes_dict = {}
for line in f:
if "aliasing errors" in line:
try:
grid_vector = line.split(" NG", 1)[1]
value = [int(s) for s in grid_vector.split(" ")
if s.isdigit()][0]
changes_dict["NG" + grid_vector[0]] = value
grid_adjusted = True
except (IndexError, ValueError):
pass
#Ensure that all NGX, NGY, NGZ have been checked
if grid_adjusted and 'NGZ' in line:
actions.append({"dict": "INCAR",
"action": {"_set": changes_dict}})
break
m = Modder(actions=[DictActions, FileActions])
modified = []
for a in actions:
if "dict" in a:
modified.append(a["dict"])
vi[a["dict"]] = m.modify_object(a["action"], vi[a["dict"]])
elif "file" in a:
m.modify(a["action"], a["file"])
for f in modified:
vi[f].write_file(f)
return {"errors": list(self.errors), "actions": actions}
def test_modify_object(self):
modder = Modder()
o = MyObject(1)
self.assertEqual(o.b["a"], 1)
mod_o = modder.modify_object({'_set': {'b->a': 20}}, o)
self.assertEqual(mod_o.b["a"], 20)
def test_modify_object(self):
modder = Modder()
o = MyObject(1)
self.assertEqual(o.b["a"], 1)
mod_o = modder.modify_object({'_set': {'b->a': 20}}, o)
self.assertEqual(mod_o.b["a"], 20)
def apply_corrections(self, fw_to_correct, corrections):
# Apply the corrections
spec = fw_to_correct.spec
modder = Modder()
for correction in corrections:
actions = correction['actions']
for action in actions:
if action['action_type'] == 'modify_object':
if action['object']['source'] == 'fw_spec':
myobject = spec[action['object']['key']]
else:
raise NotImplementedError(
'Object source "{}" not implemented in '
'CheckTask'.format(action['object']['source']))
newobj = modder.modify_object(action['action'], myobject)
spec[action['object']['key']] = newobj
elif action['action_type'] == 'modify_dict':
if action['dict']['source'] == 'fw_spec':
mydict = spec[action['dict']['key']]
else:
raise NotImplementedError(
'Dict source "{}" not implemented in '
'CheckTask'.format(action['dict']['source']))
modder.modify(action['action'], mydict)
else:
raise NotImplementedError(
'Action type "{}" not implemented in '
'CheckTask'.format(action['action_type']))
# Keep track of the corrections that have been applied
spec['SRC_check_corrections'] = corrections
# Update the task index
fws_task_index = int(
fw_to_correct.spec['wf_task_index'].split('_')[-1])
new_index = fws_task_index + 1
# Update the Fireworks _queueadapter key
#TODO: in the future, see whether the FW queueadapter might be replaced by the qtk_queueadapter ?
# ... to be discussed with Anubhav, when the qtk queueadapter is in a qtk toolkit and not anymore
# in pymatgen/io/abinit
spec['_queueadapter'] = spec['qtk_queueadapter'].get_subs_dict()
queue_adapter_update = get_queue_adapter_update(
qtk_queueadapter=spec['qtk_queueadapter'], corrections=corrections)
# Get and update the task_input if needed
# TODO: make this more general ... right now, it is based on AbinitInput and thus is strongly tight
# to abinit due to abiinput, deps, ...
mytask = fw_to_correct.tasks[0]
task_class = mytask.__class__
decoder = MontyDecoder()
task_input = decoder.process_decoded(
fw_to_correct.spec['_tasks'][0]['abiinput'])
initialization_info = fw_to_correct.spec['initialization_info']
deps = mytask.deps
# Create the new Setup/Run/Check fireworks
SRC_fws = createSRCFireworksOld(
task_class=task_class,
task_input=task_input,
SRC_spec=spec,
initialization_info=initialization_info,
wf_task_index_prefix=spec['wf_task_index_prefix'],
current_task_index=new_index,
handlers=self.handlers,
validators=self.validators,
deps=deps,
task_type=mytask.task_type,
queue_adapter_update=queue_adapter_update)
wf = Workflow(fireworks=SRC_fws['fws'],
links_dict=SRC_fws['links_dict'])
return FWAction(detours=[wf])