def from_dict(cls, d):
dec = PMGJSONDecoder()
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 = PMGJSONDecoder()
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 = PMGJSONDecoder()
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):
from pymatgen.serializers.json_coders import PMGJSONDecoder
dec = PMGJSONDecoder()
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 = PMGJSONDecoder()
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(d):
dec = PMGJSONDecoder()
return ConversionElectrode(
dec.process_decoded(d["voltage_pairs"]),
dec.process_decoded(d["working_ion_entry"]),
Composition(d["initial_comp"]),
)
def from_dict(d):
dec = PMGJSONDecoder()
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 VaspInput(**sub_d)
def from_dict(cls, d):
dec = PMGJSONDecoder()
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):
a = d["about"]
dec = PMGJSONDecoder()
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 test_entry(self):
enc = PMGJSONEncoder()
dec = PMGJSONDecoder()
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 test_entry(self):
enc = PMGJSONEncoder()
dec = PMGJSONDecoder()
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=PMGJSONDecoder().process_decoded(
init["energy_model"]),
**init["enum_kwargs"])
def test_to_from_dict(self):
self.mitparamset = MITVaspInputSet()
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MaterialsProjectVaspInputSet()
self.userparamset = MaterialsProjectVaspInputSet(
{'MAGMOM': {"Fe": 10, "S": -5, "Mn3+": 100}}
)
dec = PMGJSONDecoder()
d = self.mitparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITVaspInputSet)
d = self.mitggaparam.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITGGAVaspInputSet)
d = self.mithseparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MITHSEVaspInputSet)
d = self.paramset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MaterialsProjectVaspInputSet)
d = self.userparamset.to_dict
v = dec.process_decoded(d)
self.assertEqual(type(v), MaterialsProjectVaspInputSet)
self.assertEqual(v.incar_settings["MAGMOM"],
{"Fe": 10, "S": -5, "Mn3+": 100})
def from_dict(cls, d):
dec = PMGJSONDecoder()
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):
from pymatgen.serializers.json_coders import PMGJSONDecoder
dec = PMGJSONDecoder()
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(d):
dec = PMGJSONDecoder()
return ComputedEntry(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))
def from_dict(cls, d):
dec = PMGJSONDecoder()
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):
entries = PMGJSONDecoder().process_decoded(d["all_entries"])
elements = PMGJSONDecoder().process_decoded(d["elements"])
return cls(entries, d["chempots"], elements)
def from_dict(cls, d):
from pymatgen.serializers.json_coders import PMGJSONDecoder
dec = PMGJSONDecoder()
return cls(dec.process_decoded(d["entries"]),
dec.process_decoded(d["working_ion_entry"]))
def from_dict(cls, d):
dec = PMGJSONDecoder()
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 = PMGJSONDecoder()
return cls(dec.process_decoded(d["voltage_pairs"]),
dec.process_decoded(d["working_ion_entry"]),
Composition(d["initial_comp"]))
def from_dict(cls, d):
chempots = {Element(symbol): u for symbol, u in d["chempots"].items()}
entry = PMGJSONDecoder().process_decoded(d["entry"])
return cls(entry, chempots, d["name"])
import unittest
import os
from numpy import array
from pymatgen.io.vaspio_set import MITVaspInputSet, MITHSEVaspInputSet, \
MPVaspInputSet, MITGGAVaspInputSet, MITNEBVaspInputSet,\
MPStaticVaspInputSet, MPNonSCFVaspInputSet, MITMDVaspInputSet
from pymatgen.io.vaspio.vasp_input import Poscar
from pymatgen import Specie, Lattice, Structure
from pymatgen.serializers.json_coders import PMGJSONDecoder
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
dec = PMGJSONDecoder()
class MITMPVaspInputSetTest(unittest.TestCase):
def setUp(self):
filepath = os.path.join(test_dir, 'POSCAR')
poscar = Poscar.from_file(filepath)
self.struct = poscar.structure
self.mitparamset = MITVaspInputSet()
self.mitparamset_unsorted = MITVaspInputSet(sort_structure=False)
self.mithseparamset = MITHSEVaspInputSet()
self.paramset = MPVaspInputSet()
self.userparamset = MPVaspInputSet(
user_incar_settings={'MAGMOM': {
"Fe": 10,
def from_dict(cls, d):
dec = PMGJSONDecoder()
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):
from pymatgen.serializers.json_coders import PMGJSONDecoder
dec = PMGJSONDecoder()
return cls(dec.process_decoded(d["entries"]),
dec.process_decoded(d["working_ion_entry"]))
def from_dict(cls, d):
entry = PMGJSONDecoder().process_decoded(d["entry"])
return cls(d["composition"], entry)
def __init__(self, parameters):
self.update(parameters)
self.jobs = map(VaspJob.from_dict, self['jobs'])
dec = PMGJSONDecoder()
self.handlers = map(dec.process_decoded, self['handlers'])
self.max_errors = self.get('max_errors', 1)