def from_dict(cls, d):
dec = MontyDecoder()
kwargs = {
k: dec.process_decoded(v)
for k, v in d.items() if k in inspect.getargspec(cls.__init__).args
}
return cls(**kwargs)
def setUp(self):
self.temps = [300, 600, 900, 1200, 1500, 1800]
self.struct = vasprun.final_structure
self.num_atoms = self.struct.composition.num_atoms
self.entries_with_temps = {
temp: GibbsComputedStructureEntry(
self.struct,
-2.436,
temp=temp,
gibbs_model="SISSO",
parameters=vasprun.incar,
entry_id="test",
)
for temp in self.temps
}
with open(
os.path.join(PymatgenTest.TEST_FILES_DIR, "Mn-O_entries.json"),
"r") as f:
data = json.load(f)
with open(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"structure_CO2.json"), "r") as f:
self.co2_struct = MontyDecoder().process_decoded(json.load(f))
self.mp_entries = [MontyDecoder().process_decoded(d) for d in data]
def from_dict(cls, d):
dec = MontyDecoder()
return cls(dec.process_decoded(d["structure"]),
d["energy"], d["correction"],
dec.process_decoded(d.get("parameters", {})),
dec.process_decoded(d.get("data", {})),
entry_id=d.get("entry_id", None))
def from_dict(cls, d):
dec = MontyDecoder()
return cls(
dec.process_decoded(d["voltage_pairs"]),
dec.process_decoded(d["working_ion_entry"]),
Composition(d["initial_comp"]),
)
def from_dict(cls, d):
"""
Args:
d (dict): Dict representation
Returns:
Class
"""
a = d["about"]
dec = MontyDecoder()
created_at = dec.process_decoded(a.get("created_at"))
data = {k: v for k, v in d["about"].items() if k.startswith("_")}
data = dec.process_decoded(data)
structure = Structure.from_dict(
d) if "lattice" in d else Molecule.from_dict(d)
return cls(
structure,
a["authors"],
projects=a.get("projects", None),
references=a.get("references", ""),
remarks=a.get("remarks", None),
data=data,
history=a.get("history", None),
created_at=created_at,
)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(d["composition"], d["energy"], d["correction"],
dec.process_decoded(d.get("parameters", {})),
dec.process_decoded(d.get("data", {})),
entry_id=d.get("entry_id", None),
attribute=d["attribute"] if "attribute" in d else None)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(dec.process_decoded(d["structure"]),
d["energy"], d["correction"],
dec.process_decoded(d.get("parameters", {})),
dec.process_decoded(d.get("data", {})),
entry_id=d.get("entry_id", None))
def from_dict(cls, d):
dec = MontyDecoder()
return cls(d["composition"], d["energy"], d["correction"],
dec.process_decoded(d.get("parameters", {})),
dec.process_decoded(d.get("data", {})),
entry_id=d.get("entry_id", None),
attribute=d["attribute"] if "attribute" in d else None)
def from_dict(cls, d):
d = d.copy()
d.pop('@module', None)
d.pop('@class', None)
dec = MontyDecoder()
d['kpts'] = dec.process_decoded(d['kpts'])
return cls(**d)
def from_dict(cls, d):
d = d.copy()
d.pop('@module', None)
d.pop('@class', None)
dec = MontyDecoder()
d['kpts'] = dec.process_decoded(d['kpts'])
return cls(**d)
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 __setstate__(self, d):
del d["@class"]
del d["@module"]
if "@version" in d:
del d["@version"]
md = MontyDecoder()
d = md.process_decoded(d)
self.__init__(**d)
def from_dict(cls, d):
d = d.copy()
d.pop("@module", None)
d.pop("@class", None)
dec = MontyDecoder()
d["spin_mode"] = dec.process_decoded(d["spin_mode"])
d["smearing"] = dec.process_decoded(d["smearing"])
d["algorithm"] = dec.process_decoded(d["algorithm"]) if d["algorithm"] else None
return cls(**d)
def from_dict(cls, d):
dec = MontyDecoder()
sub_d = {"optional_files": {}}
for k, v in d.items():
if k in ["INCAR", "POSCAR", "POTCAR", "KPOINTS"]:
sub_d[k.lower()] = dec.process_decoded(v)
elif k not in ["@module", "@class"]:
sub_d["optional_files"][k] = dec.process_decoded(v)
return cls(**sub_d)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(dec.process_decoded(d["structure"]),
d["energy"], d["correction"],
parameters={k: dec.process_decoded(v)
for k, v in d.get("parameters", {}).items()},
data={k: dec.process_decoded(v)
for k, v in d.get("data", {}).items()},
entry_id=d.get("entry_id", None))
def from_dict(cls, d):
dec = MontyDecoder()
scf_strategy = dec.process_decoded(d["scf_strategy"])
ksampling = dec.process_decoded(d["ksampling"])
nscf_nband = dec.process_decoded(d["nscf_nband"])
nscf_algorithm = dec.process_decoded(d["nscf_algorithm"])
return cls(scf_strategy=scf_strategy, ksampling=ksampling,
nscf_nband=nscf_nband, nscf_algorithm=nscf_algorithm, **d['extra_abivars'])
def from_dict(cls, d):
dec = MontyDecoder()
return cls(dec.process_decoded(d["structure"]),
d["energy"], d["correction"],
parameters={k: dec.process_decoded(v)
for k, v in d.get("parameters", {}).items()},
data={k: dec.process_decoded(v)
for k, v in d.get("data", {}).items()},
entry_id=d.get("entry_id", None))
def from_dict(cls, d):
d = d.copy()
d.pop("@module", None)
d.pop("@class", None)
dec = MontyDecoder()
d["spin_mode"] = dec.process_decoded(d["spin_mode"])
d["smearing"] = dec.process_decoded(d["smearing"])
d["algorithm"] = dec.process_decoded(d["algorithm"]) if d["algorithm"] else None
return cls(**d)
def run_task(self, fw_spec):
struct = self.get("structure") or fw_spec["structure"]
s = Structure.from_dict(struct.as_dict())
user_incar_settings = fw_spec.get("user_incar_settings", {})
vasp_input_set = MPRelaxSet(s, user_incar_settings=user_incar_settings)
dec = MontyDecoder()
vis = dec.process_decoded(vasp_input_set.as_dict())
output_dir = os.getcwd()
vis.write_input(output_dir=output_dir)
return FWAction()
def __setstate__(self, d):
"""
Double underscore method used by pickle to deserialize this object
This uses MSONable deerialization instead
"""
del d["@class"]
del d["@module"]
md = MontyDecoder()
d = md.process_decoded(d)
self.__init__(**d)
def from_dict(cls, d) -> "ComputedStructureEntry":
"""
:param d: Dict representation.
:return: ComputedStructureEntry
"""
dec = MontyDecoder()
# the first block here is for legacy ComputedEntry that were
# serialized before we had the energy_adjustments attribute.
if d["correction"] != 0 and not d.get("energy_adjustments"):
struct = dec.process_decoded(d["structure"])
return cls(
struct,
d["energy"],
correction=d["correction"],
parameters={k: dec.process_decoded(v) for k, v in d.get("parameters", {}).items()},
data={k: dec.process_decoded(v) for k, v in d.get("data", {}).items()},
entry_id=d.get("entry_id", None),
)
# this is the preferred / modern way of instantiating ComputedEntry
# we don't pass correction explicitly because it will be calculated
# on the fly from energy_adjustments
return cls(
dec.process_decoded(d["structure"]),
d["energy"],
composition=d.get("composition", None),
correction=0,
energy_adjustments=[dec.process_decoded(e) for e in d.get("energy_adjustments", {})],
parameters={k: dec.process_decoded(v) for k, v in d.get("parameters", {}).items()},
data={k: dec.process_decoded(v) for k, v in d.get("data", {}).items()},
entry_id=d.get("entry_id", None),
)
def from_dict(cls, d):
dec = MontyDecoder()
structure = dec.process_decoded(d["structure"])
pseudos = dec.process_decoded(d['pseudos'])
ksampling = dec.process_decoded(d["ksampling"])
electrons = dec.process_decoded(d["electrons"])
return cls(structure=structure, pseudos=pseudos, ksampling=ksampling, accuracy=d['accuracy'],
spin_mode=electrons.spin_mode, smearing=electrons.smearing, charge=d['charge'],
scf_algorithm=electrons.algorithm, use_symmetries=d['use_symmetries'],
**d['extra_abivars'])
def from_dict(cls, d):
dec = MontyDecoder()
if 'is_valid' in d:
return cls(controller=dec.process_decoded(d['controller']),
state=d['state'], problems=d['problems'],
actions=dec.process_decoded(d['actions']),
restart=d['restart'], is_valid=d['is_valid'])
else:
return cls(controller=dec.process_decoded(d['controller']),
state=d['state'], problems=d['problems'],
actions=dec.process_decoded(d['actions']),
restart=d['restart'])
def from_dict(cls, d):
"""
Args:
d (dict): from as_dict()
Returns:
A ComputedReaction object.
"""
dec = MontyDecoder()
reactants = [dec.process_decoded(e) for e in d["reactants"]]
products = [dec.process_decoded(e) for e in d["products"]]
return cls(reactants, products)
def featurize(self, dict_data):
"""Convert a string to a pymatgen Composition.
Args:
dict_data (dict): A MSONable dictionary. E.g. Produced from
`pymatgen.core.structure.Structure.as_dict()`.
Returns:
(object): An object with the type specified by `dict_data`.
"""
md = MontyDecoder()
return [md.process_decoded(dict_data)]
def from_dict(cls, d):
dec = MontyDecoder()
working_ion_entry = dec.process_decoded(d["working_ion_entry"])
balanced_rxn = dec.process_decoded(d["balanced_rxn"])
entries_charge = dec.process_decoded(d["entries_charge"])
entries_discharge = dec.process_decoded(d["entries_discharge"])
return ConversionVoltagePair(balanced_rxn, d["voltage"], d["mAh"],
d["vol_charge"], d["vol_discharge"],
d["mass_charge"], d["mass_discharge"],
d["frac_charge"], d["frac_discharge"],
entries_charge, entries_discharge,
working_ion_entry)
def from_dict(cls, d):
"""
Args:
d (dict): Dict representation
Returns:
InsertionElectrode
"""
from monty.json import MontyDecoder
dec = MontyDecoder()
return cls(dec.process_decoded(d["entries"]),
dec.process_decoded(d["working_ion_entry"]))
def from_dict(cls, d):
"""
Args:
d (dict): Dict representation
Returns:
ConversionElectrode
"""
dec = MontyDecoder()
return cls(dec.process_decoded(d["voltage_pairs"]),
dec.process_decoded(d["working_ion_entry"]),
Composition(d["initial_comp"]))
def from_dict(cls, d):
dec = MontyDecoder()
structure = dec.process_decoded(d["structure"])
pseudos = [Pseudo.from_file(p['filepath']) for p in d['pseudos']]
ksampling = dec.process_decoded(d["ksampling"])
spin_mode = dec.process_decoded(d["spin_mode"])
smearing = dec.process_decoded(d["smearing"])
return cls(structure=structure, pseudos=pseudos, ksampling=ksampling, accuracy=d['accuracy'],
spin_mode=spin_mode, smearing=smearing, charge=d['charge'],
scf_algorithm=d['scf_algorithm'], use_symmetries=d['use_symmetries'],
relax_algo=d['relax_algo'], **d['extra_abivars'])
def featurize(self, dict_data):
"""Convert a string to a pymatgen Composition.
Args:
dict_data (dict): A MSONable dictionary. E.g. Produced from
`pymatgen.core.structure.Structure.as_dict()`.
Returns:
(object): An object with the type specified by `dict_data`.
"""
md = MontyDecoder()
return [md.process_decoded(dict_data)]
def process_item(self, item):
mp_id = item['mp-id']
self.logger.debug("Processing {}".format(mp_id))
decoder = MontyDecoder()
ph_bs = decoder.process_decoded(item['ph_bs'])
web_doc = ph_bs.as_phononwebsite()
plotter = PhononBSPlotter(ph_bs)
ylim = (0, max(py_.flatten_deep(plotter.bs_plot_data()['frequency'])))
filelike = io.BytesIO()
plotter.save_plot(filelike, ylim=ylim, img_format="png")
image = Binary(filelike.getvalue())
filelike.close()
return dict(mp_id=mp_id, web_doc=web_doc, image=image)
def run_task(self, fw_spec):
material_id = self["material_id"]
dest_root = fw_spec["_fw_en"]["run_dest_root"]
dest = "{}/{}/bs/{}/relax".format(dest_root, os.environ["USER"],
material_id)
user_incar_settings = fw_spec.get("user_incar_settings", {})
vasp_input_set = MPStaticSet.from_prev_calc(
prev_calc_dir=dest,
standardize=1e-3,
user_incar_settings=user_incar_settings)
dec = MontyDecoder()
vis = dec.process_decoded(vasp_input_set.as_dict())
vis.write_input(".")
def from_dict(cls, d):
dec = MontyDecoder()
sub_d = {"optional_files": {}}
potcar=d.get('POTCAR',False)
if potcar:
infiles=["INCAR", "POSCAR", "POTCAR", "KPOINTS"]
else:
infiles=["INCAR", "POSCAR", "KPOINTS"]
for k, v in d.items():
if k in infiles:
sub_d[k.lower()] = dec.process_decoded(v)
elif k not in ["@module", "@class"]:
sub_d["optional_files"][k] = dec.process_decoded(v)
return cls(**sub_d)
def from_dict_legacy(cls, d):
"""
Args:
d (dict): Dict representation
Returns:
InsertionElectrode
"""
from monty.json import MontyDecoder
dec = MontyDecoder()
return InsertionElectrode( # pylint: disable=E1120
dec.process_decoded(d["entries"]),
dec.process_decoded(d["working_ion_entry"]),
)
def from_dict(cls, d):
"""
Initializes a DielTensor object from a dictionary.
Args:
d (dict): Dictionary from which the DielTensor should be initialized.
Returns:
DielTensor
"""
energies = MontyDecoder().process_decoded(d["energies"])
real_diel = MontyDecoder().process_decoded(d["real_diel"])
imag_diel = MontyDecoder().process_decoded(d["imag_diel"])
return cls(energies, real_diel + 1j * imag_diel)
def from_dict(cls, d):
a = d["about"]
dec = MontyDecoder()
created_at = dec.process_decoded(a.get("created_at"))
data = {k: v for k, v in d["about"].items()
if k.startswith("_")}
data = dec.process_decoded(data)
structure = Structure.from_dict(d) if "lattice" in d \
else Molecule.from_dict(d)
return cls(structure, a["authors"], projects=a.get("projects", None),
references=a.get("references", ""),
remarks=a.get("remarks", None), data=data,
history=a.get("history", None), created_at=created_at)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(d["composition"],
d["calculator"],
inputs={
k: dec.process_decoded(v)
for k, v in d.get("inputs", {}).items()
},
data={
k: dec.process_decoded(v)
for k, v in d.get("data", {}).items()
},
entry_id=d.get("entry_id", None),
attribute=d["attribute"] if "attribute" in d else None,
tag=d["tag"] if "tag" in d else None)
def test_entry(self):
enc = MontyEncoder()
dec = MontyDecoder()
entry = ComputedEntry("Fe2O3", 2.3)
jsonstr = enc.encode(entry)
d = dec.decode(jsonstr)
self.assertEqual(type(d), ComputedEntry)
#Check list of entries
entries = [entry, entry, entry]
jsonstr = enc.encode(entries)
d = dec.decode(jsonstr)
for i in d:
self.assertEqual(type(i), ComputedEntry)
self.assertEqual(len(d), 3)
def calc(self, item):
struct_or_mol = MontyDecoder().process_decoded(
item[self.projected_object_name])
# TODO: will combine these two functions into something more intuitive
graph = StructureMoleculeComponent._preprocess_input_to_graph(
struct_or_mol,
bonding_strategy=self.settings["bonding_strategy"],
bonding_strategy_kwargs=self.settings["bonding_strategy_kwargs"],
)
scene, legend = StructureMoleculeComponent.get_scene_and_legend(
graph,
color_scheme=self.settings["color_scheme"],
color_scale=self.settings["color_scale"],
radius_strategy=self.settings["radius_strategy"],
draw_image_atoms=self.settings["draw_image_atoms"],
bonded_sites_outside_unit_cell=self.
settings["bonded_sites_outside_unit_cell"],
hide_incomplete_bonds=self.settings["hide_incomplete_bonds"],
)
return {
"scene": scene.to_json(),
"legend": legend,
"settings": self.settings,
"source": item[self.projected_object_name],
}
def normalize(self, mode: str = "formula_unit") -> "ComputedEntry":
"""
Normalize the entry's composition and energy.
Args:
mode: "formula_unit" is the default, which normalizes to
composition.reduced_formula. The other option is "atom", which
normalizes such that the composition amounts sum to 1.
"""
factor = self._normalization_factor(mode)
new_composition = self._composition / factor
new_energy = self._energy / factor
new_entry_dict = self.as_dict()
new_entry_dict["composition"] = new_composition.as_dict()
new_entry_dict["energy"] = new_energy
# TODO: make sure EnergyAdjustments are _also_ immutable to avoid this hacking
new_energy_adjustments = MontyDecoder().process_decoded(
new_entry_dict["energy_adjustments"])
for ea in new_energy_adjustments:
ea.normalize(factor)
new_entry_dict["energy_adjustments"] = [
ea.as_dict() for ea in new_energy_adjustments
]
return self.from_dict(new_entry_dict)
def __init__(self, parameters):
self.update(parameters)
self.jobs = self['jobs']
dec = MontyDecoder()
self.handlers = map(dec.process_decoded, self['handlers'])
self.max_errors = self.get('max_errors', 1)
self.gzip_output = self.get('gzip_output', True)
def _from_dict(cls, d):
modname = d["tp_mo"]
classname = d["tp_na"]
decoded = {
k: MontyDecoder().process_decoded(v)
for k, v in d.items() if not k.startswith("@")
}
mod = __import__(modname, globals(), locals(), [classname], 0)
if hasattr(mod, classname):
cla = getattr(mod, classname)
if decoded["all_args_kwargs"] == {}:
return cla()
else:
return cla(**decoded["all_args_kwargs"])
else:
try:
return cls()
except BaseException:
raise TypeError(
"Cant find {} in {}, Please import it first.".format(
classname, modname), "NNDict = mark_classes([VoronoiNN,])"
"for i, j in NNDict.items():\n"
" locals()[i] = j")
def test_entry(self):
enc = MontyEncoder()
dec = MontyDecoder()
entry = ComputedEntry("Fe2O3", 2.3)
jsonstr = enc.encode(entry)
d = dec.decode(jsonstr)
self.assertEqual(type(d), ComputedEntry)
#Check list of entries
entries = [entry, entry, entry]
jsonstr = enc.encode(entries)
d = dec.decode(jsonstr)
for i in d:
self.assertEqual(type(i), ComputedEntry)
self.assertEqual(len(d), 3)
def from_dict(cls, d):
init = d["init_args"]
return MagOrderingTransformation(
init["mag_species_spin"],
init["order_parameter"],
energy_model=MontyDecoder().process_decoded(init["energy_model"]),
**init["enum_kwargs"])
def update_targets(self, items):
"""
Inserts the thermo docs into the thermo collection
Args:
items ([[dict]]): a list of list of thermo dictionaries to update
"""
# flatten out lists
items = list(filter(None, chain.from_iterable(items)))
# check for duplicates within this set
items = list({(v[self.thermo.key], frozenset(v["sandboxes"])): v
for v in items}.values())
# Check if already updated this run
items = [
i for i in items if i[self.thermo.key] not in self._completed_tasks
]
self._completed_tasks |= {i[self.thermo.key] for i in items}
for item in items:
if isinstance(item["last_updated"], dict):
item["last_updated"] = MontyDecoder().process_decoded(
item["last_updated"])
if len(items) > 0:
self.logger.info(f"Updating {len(items)} thermo documents")
self.thermo.update(docs=items, key=[self.thermo.key, "sandboxes"])
else:
self.logger.info("No items to update")
def from_dict(cls, dd):
dec = MontyDecoder()
return cls(mp_symbol=dd['mp_symbol'],
name=dd['name'],
alternative_names=dd['alternative_names'],
IUPAC_symbol=dd['IUPAC_symbol'],
IUCr_symbol=dd['IUCr_symbol'],
coordination=dd['coordination'],
central_site=dd['central_site'],
points=dd['points'],
solid_angles=(dd['solid_angles'] if 'solid_angles' in dd
else [4.0 * np.pi / dd['coordination']] * dd['coordination']),
deactivate=dd['deactivate'],
faces=dd['_faces'],
edges=dd['_edges'],
algorithms=[dec.process_decoded(algo_d)
for algo_d in dd['_algorithms']] if dd['_algorithms'] is not None else None,
equivalent_indices=dd['equivalent_indices'] if 'equivalent_indices' in dd else None)
def run_task(self, fw_spec):
"""
Required Parameters:
dir (str path): directory containing the vasp inputs
jobs (VaspJob): Contains the cmd needed to run vasp
Optional Parameters:
custodian_params (dict **kwargs): Contains the job and the
scratch directory for a custodian run
handlers (list of custodian handlers): Defaults to empty list
"""
dec = MontyDecoder()
dir = dec.process_decoded(self['dir'])
cwd = dec.process_decoded(self['cwd'])
# Change to the directory with the vasp inputs to run custodian
os.chdir(cwd+dir)
handlers = dec.process_decoded(self.get('handlers', []))
jobs = dec.process_decoded(self['jobs'])
max_errors = dec.process_decoded(self['max_errors'])
fw_env = fw_spec.get("_fw_env", {})
cust_params = self.get("custodian_params", {})
# Get the scratch directory
if fw_env.get('scratch_root'):
cust_params['scratch_dir'] = os.path.expandvars(
fw_env['scratch_root'])
c = Custodian(handlers=handlers, jobs=jobs, max_errors=max_errors, gzipped_output=True, **cust_params)
output = c.run()
return FWAction(stored_data=output)
def process_decoded(self, d):
"""
Recursive method to support decoding dicts and lists containing
pymatgen objects.
"""
if isinstance(d, dict) and "module" in d and "class" in d:
modname = d["module"]
classname = d["class"]
mod = __import__(modname, globals(), locals(), [classname], 0)
if hasattr(mod, classname):
cls_ = getattr(mod, classname)
data = {k: v for k, v in d.items() if k not in ["module", "class"]}
if hasattr(cls_, "from_dict"):
return cls_.from_dict(data)
return {self.process_decoded(k): self.process_decoded(v) for k, v in d.items()}
return MontyDecoder.process_decoded(self, d)
def from_dict(cls, d):
dec = MontyDecoder()
return cls([dec.process_decoded(i) for i in d['items']])
def from_dict(cls, d):
dec = MontyDecoder()
reactants = [dec.process_decoded(e) for e in d["reactants"]]
products = [dec.process_decoded(e) for e in d["products"]]
return cls(reactants, products)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(*dec.process_decoded(d['args']), **dec.process_decoded(d['kwargs']))
def from_dict(cls, d):
dec = MontyDecoder()
return cls(inverse_power=d['inverse_power'], weights_setup=dec.process_decoded(d['weights_setup']))
def from_dict(cls, m_dict):
m = MontyDecoder()
return cls(handlers=m.process_decoded(m_dict['handlers']), validators=m.process_decoded(m_dict['validators'])
, max_restarts=m_dict['max_restarts'])
def from_dict(cls, d):
dec = MontyDecoder()
entries = dec.process_decoded(d["original_entries"])
terminal_compositions = dec.process_decoded(d["terminal_compositions"])
return cls(entries, terminal_compositions,
d["normalize_terminal_compositions"])
def from_dict(cls, d):
dec = MontyDecoder()
kwargs = {k: dec.process_decoded(v) for k, v in d.items()
if k in inspect.getargspec(cls.__init__).args}
return cls(**kwargs)
def from_dict(cls, d):
from monty.json import MontyDecoder
dec = MontyDecoder()
return cls(dec.process_decoded(d["entries"]),
dec.process_decoded(d["working_ion_entry"]))
def from_dict(cls, d):
dec = MontyDecoder()
details = dec.process_decoded(d['details']) if 'details' in d else None
return cls(event_type=d['event_type'], details=details)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(handler=dec.process_decoded(d['handler']), actions=d['actions'],
event=dec.process_decoded(d['event']), reset=d['reset'])
def test_msonable(self):
compat_dict = self.aqcompat.as_dict()
decoder = MontyDecoder()
temp_compat = decoder.process_decoded(compat_dict)
self.assertIsInstance(temp_compat,MITAqueousCompatibility)
def from_dict(cls, d):
dec = MontyDecoder()
return cls(controllers=dec.process_decoded(d['controllers']))