def correct(self):
content = "LSTOP = .TRUE." if not self.electronic_step_stop else \
"LABORT = .TRUE."
#Write STOPCAR
actions = [{
"file": "STOPCAR",
"action": {
"_file_create": {
'content': content
}
}
}]
if self.auto_continue:
actions.append({
"file": "STOPCAR",
"action": {
"_file_modify": {
'mode': 0o444
}
}
})
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
# Actions is being returned as None so that custodian will stop after
# STOPCAR is written. We do not want subsequent jobs to proceed.
return {"errors": ["Walltime reached"], "actions": None}
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):
content = "LSTOP = .TRUE."
chkpt_content = "Index: %d\nTime: \"%s\"" % (self.chk_counter,
datetime.datetime.now())
self.chk_counter += 1
#Write STOPCAR
actions = [{
"file": "STOPCAR",
"action": {
"_file_create": {
'content': content
}
}
}, {
"file": "chkpt.yaml",
"action": {
"_file_create": {
'content': chkpt_content
}
}
}]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
# Reset the clock.
self.start_time = datetime.datetime.now()
return {"errors": ["Checkpoint reached"], "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 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(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 correct(self):
content = "LSTOP = .TRUE." if not self.electronic_step_stop else "LABORT = .TRUE."
# Write STOPCAR
actions = [{"file": "STOPCAR", "action": {"_file_create": {"content": content}}}]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
# Actions is being returned as None so that custodian will stop after
# STOPCAR is written. We do not want subsequent jobs to proceed.
return {"errors": ["Walltime reached"], "actions": None}
def correct(self):
content = "LSTOP = .TRUE." if not self.electronic_step_stop else \
"LABORT = .TRUE."
# Write STOPCAR
actions = [{"file": "STOPCAR",
"action": {"_file_create": {'content': content}}}]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
return {"errors": ["Walltime reached"], "actions": None}
def correct(self):
d = loadfn("chkpt.yaml")
i = d["Index"]
name = shutil.make_archive(os.path.join(os.getcwd(), "vasp.chk.%d" % i), "gztar")
actions = [{"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
actions.append({"Checkpoint": name})
return {"errors": ["Stopped run."], "actions": actions}
def correct(self):
# Write ``stop`` file
actions = [{
"file": "stop",
"action": {
"_file_create": {
'content': ''
}
}
}]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
return {"errors": ["Walltime reached"], "actions": None}
def test_strict_mode(self):
modder = Modder(actions=[FileActions])
d = {"Hello": "World"}
mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
self.assertRaises(ValueError, modder.modify, mod, d)
#In non-strict mode, unknown actions are ignored.
d = {"Hello": "World"}
modder = Modder(actions=[FileActions], strict=False)
modder.modify(mod, d)
self.assertEqual(d, {"Hello": "World"})
#File actions not supported
modder = Modder()
self.assertRaises(ValueError, modder.modify,
{'_file_create': {'content': 'Test data'}},
'test_file')
def correct(self):
d = loadfn("chkpt.yaml")
i = d["Index"]
name = shutil.make_archive(
os.path.join(os.getcwd(), "vasp.chk.%d" % i), "gztar")
actions = [{"file": "CONTCAR",
"action": {"_file_copy": {"dest": "POSCAR"}}}]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
actions.append({"Checkpoint": name})
return {"errors": ["Stopped run."],
"actions": actions}
def correct(self):
content = "LSTOP = .TRUE."
chkpt_content = 'Index: %d\nTime: "%s"' % (self.chk_counter, datetime.datetime.now())
self.chk_counter += 1
# Write STOPCAR
actions = [
{"file": "STOPCAR", "action": {"_file_create": {"content": content}}},
{"file": "chkpt.yaml", "action": {"_file_create": {"content": chkpt_content}}},
]
m = Modder(actions=[FileActions])
for a in actions:
m.modify(a["action"], a["file"])
# Reset the clock.
self.start_time = datetime.datetime.now()
return {"errors": ["Checkpoint reached"], "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 test_strict_mode(self):
modder = Modder(actions=[FileActions])
d = {"Hello": "World"}
mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
self.assertRaises(ValueError, modder.modify, mod, d)
#In non-strict mode, unknown actions are ignored.
d = {"Hello": "World"}
modder = Modder(actions=[FileActions], strict=False)
modder.modify(mod, d)
self.assertEqual(d, {"Hello": "World"})
#File actions not supported
modder = Modder()
self.assertRaises(ValueError, modder.modify,
{'_file_create': {'content': 'Test data'}},
'test_file')
def test_strict_mode(self):
modder = Modder(actions=[FileActions])
d = {"Hello": "World"}
mod = {"_set": {"Hello": "Universe", "Bye": "World"}}
self.assertRaises(ValueError, modder.modify, mod, d)
# In non-strict mode, unknown actions are ignored.
d = {"Hello": "World"}
modder = Modder(actions=[FileActions], strict=False)
modder.modify(mod, d)
self.assertEqual(d, {"Hello": "World"})
# File actions not supported
modder = Modder()
self.assertRaises(
ValueError,
modder.modify,
{"_file_create": {"content": "Test data"}},
"test_file",
)
def test_dict_modify(self):
modder = Modder()
d = {"Hello": "World"}
mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'Hello': 'Universe'})
mod = {'_unset': {'Hello': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World'})
mod = {'_push': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1]})
mod = {'_push': {'List': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2]})
mod = {'_inc': {'num': 5}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 5})
mod = {'_inc': {'num': 5}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 10})
mod = {'_rename': {'num': 'number'}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
mod = {'_add_to_set': {'List': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
mod = {'_add_to_set': {'List': 3}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3], 'number': 10})
mod = {'_add_to_set': {'number': 3}}
self.assertRaises(ValueError, modder.modify, mod, d)
mod = {'_pull': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [2, 3], 'number': 10})
mod = {'_pull_all': {'List': [2, 3]}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [], 'number': 10})
mod = {'_push_all': {'List': list(range(10))}}
modder.modify(mod, d)
self.assertEqual(d, {
'Bye': 'World',
'List': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
'number': 10
})
mod = {'_pop': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {
'Bye': 'World',
'List': [0, 1, 2, 3, 4, 5, 6, 7, 8],
'number': 10
})
mod = {'_pop': {'List': -1}}
modder.modify(mod, d)
self.assertEqual(d, {
'Bye': 'World',
'List': [1, 2, 3, 4, 5, 6, 7, 8],
'number': 10
})
d = {}
mod = {'_set': {'a->b->c': 100}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}}})
mod = {'_set': {'a->b->d': 200}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 200}}})
mod = {'_set': {'a->b->d': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 300}}})
mod = {'_unset': {'a->b->d': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}}})
mod = {'_push': {'a->e->f': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}, 'e': {'f': [300]}}})
mod = {'_push_all': {'a->e->f': [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d,
{'a': {
'b': {
'c': 100
},
'e': {
'f': [300, 100, 200]
}
}})
mod = {'_inc': {'a->b->c': 2}}
modder.modify(mod, d)
self.assertEqual(d,
{'a': {
'b': {
'c': 102
},
'e': {
'f': [300, 100, 200]
}
}})
mod = {'_pull': {'a->e->f': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [100, 200]}}})
mod = {'_pull_all': {'a->e->f': [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': []}}})
mod = {'_push_all': {'a->e->f': [101, 201, 301, 401]}}
modder.modify(mod, d)
self.assertEqual(
d, {'a': {
'b': {
'c': 102
},
'e': {
'f': [101, 201, 301, 401]
}
}})
mod = {'_pop': {'a->e->f': 1}}
modder.modify(mod, d)
self.assertEqual(d,
{'a': {
'b': {
'c': 102
},
'e': {
'f': [101, 201, 301]
}
}})
mod = {'_pop': {'a->e->f': -1}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [201, 301]}}})
def test_file_modify(self):
modder = Modder(actions=[FileActions])
modder.modify({'_file_create': {'content': 'Test data'}}, 'test_file')
modder.modify({'_file_copy': {'dest': 'test_file_copy'}}, 'test_file')
modder.modify({'_file_copy': {'dest1': 'test_file_copy1',
'dest2': 'test_file_copy2'}},
'test_file')
modder.modify({'_file_move': {'dest': 'renamed_test_file'}},
'test_file')
modder.modify({'_file_delete': {'mode': "actual"}},
'renamed_test_file')
modder.modify({'_file_modify': {'mode': 0o666}}, 'test_file_copy')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy1')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy2')
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_dict_modify(self):
modder = Modder()
d = {"Hello": "World"}
mod = {'_set': {'Hello': 'Universe', 'Bye': 'World'}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'Hello': 'Universe'})
mod = {'_unset': {'Hello': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World'})
mod = {'_push': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1]})
mod = {'_push': {'List': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2]})
mod = {'_inc': {'num': 5}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 5})
mod = {'_inc': {'num': 5}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'num': 10})
mod = {'_rename': {'num': 'number'}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
mod = {'_add_to_set': {'List': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2], 'number': 10})
mod = {'_add_to_set': {'List': 3}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3], 'number': 10})
mod = {'_add_to_set': {'number': 3}}
self.assertRaises(ValueError, modder.modify, mod, d)
mod = {'_pull': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [2, 3], 'number': 10})
mod = {'_pull_all': {'List': [2, 3]}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [], 'number': 10})
mod = {'_push_all': {'List': list(range(10))}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World',
'List': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9],
'number': 10})
mod = {'_pop': {'List': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World',
'List': [0, 1, 2, 3, 4, 5, 6, 7, 8],
'number': 10})
mod = {'_pop': {'List':-1}}
modder.modify(mod, d)
self.assertEqual(d, {'Bye': 'World', 'List': [1, 2, 3, 4, 5, 6, 7, 8],
'number': 10})
d = {}
mod = {'_set': {'a->b->c': 100}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}}})
mod = {'_set': {'a->b->d': 200}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 200}}})
mod = {'_set': {'a->b->d': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100, 'd': 300}}})
mod = {'_unset': {'a->b->d': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}}})
mod = {'_push': {'a->e->f': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100}, 'e': {'f': [300]}}})
mod = {'_push_all': {'a->e->f': [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 100},
'e': {'f': [300, 100, 200]}}})
mod = {'_inc': {'a->b->c': 2}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102},
'e': {'f': [300, 100, 200]}}})
mod = {'_pull': {'a->e->f': 300}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [100, 200]}}})
mod = {'_pull_all': {'a->e->f': [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': []}}})
mod = {'_push_all': {'a->e->f': [101, 201, 301, 401]}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102},
'e': {'f': [101, 201, 301, 401]}}})
mod = {'_pop': {'a->e->f': 1}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102},
'e': {'f': [101, 201, 301]}}})
mod = {'_pop': {'a->e->f':-1}}
modder.modify(mod, d)
self.assertEqual(d, {'a': {'b': {'c': 102}, 'e': {'f': [201, 301]}}})
def test_file_modify(self):
modder = Modder(actions=[FileActions])
modder.modify({"_file_create": {"content": "Test data"}}, "test_file")
modder.modify({"_file_copy": {"dest": "test_file_copy"}}, "test_file")
modder.modify(
{"_file_copy": {"dest1": "test_file_copy1", "dest2": "test_file_copy2"}},
"test_file",
)
modder.modify({"_file_move": {"dest": "renamed_test_file"}}, "test_file")
modder.modify({"_file_delete": {"mode": "actual"}}, "renamed_test_file")
modder.modify({"_file_modify": {"mode": 0o666}}, "test_file_copy")
modder.modify({"_file_delete": {"mode": "actual"}}, "test_file_copy")
modder.modify({"_file_delete": {"mode": "actual"}}, "test_file_copy1")
modder.modify({"_file_delete": {"mode": "actual"}}, "test_file_copy2")
def test_dict_modify(self):
modder = Modder()
d = {"Hello": "World"}
mod = {"_set": {"Hello": "Universe", "Bye": "World"}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "Hello": "Universe"})
mod = {"_unset": {"Hello": 1}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World"})
mod = {"_push": {"List": 1}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1]})
mod = {"_push": {"List": 2}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2]})
mod = {"_inc": {"num": 5}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2], "num": 5})
mod = {"_inc": {"num": 5}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2], "num": 10})
mod = {"_rename": {"num": "number"}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2], "number": 10})
mod = {"_add_to_set": {"List": 2}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2], "number": 10})
mod = {"_add_to_set": {"List": 3}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2, 3], "number": 10})
mod = {"_add_to_set": {"number": 3}}
self.assertRaises(ValueError, modder.modify, mod, d)
mod = {"_pull": {"List": 1}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [2, 3], "number": 10})
mod = {"_pull_all": {"List": [2, 3]}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [], "number": 10})
mod = {"_push_all": {"List": list(range(10))}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9], "number": 10})
mod = {"_pop": {"List": 1}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [0, 1, 2, 3, 4, 5, 6, 7, 8], "number": 10})
mod = {"_pop": {"List": -1}}
modder.modify(mod, d)
self.assertEqual(d, {"Bye": "World", "List": [1, 2, 3, 4, 5, 6, 7, 8], "number": 10})
d = {}
mod = {"_set": {"a->b->c": 100}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 100}}})
mod = {"_set": {"a->b->d": 200}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 100, "d": 200}}})
mod = {"_set": {"a->b->d": 300}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 100, "d": 300}}})
mod = {"_unset": {"a->b->d": 300}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 100}}})
mod = {"_push": {"a->e->f": 300}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 100}, "e": {"f": [300]}}})
mod = {"_push_all": {"a->e->f": [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 100}, "e": {"f": [300, 100, 200]}}})
mod = {"_inc": {"a->b->c": 2}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 102}, "e": {"f": [300, 100, 200]}}})
mod = {"_pull": {"a->e->f": 300}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 102}, "e": {"f": [100, 200]}}})
mod = {"_pull_all": {"a->e->f": [100, 200]}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 102}, "e": {"f": []}}})
mod = {"_push_all": {"a->e->f": [101, 201, 301, 401]}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 102}, "e": {"f": [101, 201, 301, 401]}}})
mod = {"_pop": {"a->e->f": 1}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 102}, "e": {"f": [101, 201, 301]}}})
mod = {"_pop": {"a->e->f": -1}}
modder.modify(mod, d)
self.assertEqual(d, {"a": {"b": {"c": 102}, "e": {"f": [201, 301]}}})
def test_file_modify(self):
modder = Modder(actions=[FileActions])
modder.modify({'_file_create': {'content': 'Test data'}}, 'test_file')
modder.modify({'_file_copy': {'dest': 'test_file_copy'}}, 'test_file')
modder.modify(
{
'_file_copy': {
'dest1': 'test_file_copy1',
'dest2': 'test_file_copy2'
}
}, 'test_file')
modder.modify({'_file_move': {
'dest': 'renamed_test_file'
}}, 'test_file')
modder.modify({'_file_delete': {
'mode': "actual"
}}, 'renamed_test_file')
modder.modify({'_file_modify': {'mode': 0o666}}, 'test_file_copy')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy1')
modder.modify({'_file_delete': {'mode': "actual"}}, 'test_file_copy2')
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])
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}
