def process_item(self, item):
"""
Read the entries from the thermo database and group them based on the reduced composition
of the framework material (without working ion).
Args:
chemsys(string): the chemical system string to be queried
returns:
(chemsys, [group]): entry contains a list of entries the materials together by composition
"""
# sort the entries intro subgroups
# then perform PD analysis
all_entries = item['all_entries']
pd_ents = item['pd_ents']
phdi = PhaseDiagram(pd_ents)
# The working ion entries
ents_wion = list(
filter(
lambda x: x.composition.get_integer_formula_and_factor()[0] ==
self.working_ion, pd_ents))
self.working_ion_entry = min(ents_wion,
key=lambda e: e.energy_per_atom)
assert (self.working_ion_entry != None)
grouped_entries = list(self.get_sorted_subgroups(all_entries))
docs = [] # results
for group in grouped_entries:
self.logger.debug(
f"Grouped entries in all sandboxes {', '.join([en.name for en in group])}"
)
for en in group:
# skip this d_muO2 stuff if you do note have oxygen
if Element('O') in en.composition.elements:
d_muO2 = [{
'reaction': str(itr['reaction']),
'chempot': itr['chempot'],
'evolution': itr['evolution']
} for itr in phdi.get_element_profile('O', en.composition)]
else:
d_muO2 = None
en.data['muO2'] = d_muO2
en.data['decomposition_energy'] = phdi.get_e_above_hull(en)
# sort out the sandboxes
# for each sandbox core+sandbox will both contribute entries
all_sbx = [ent.data['sbxn'] for ent in group]
all_sbx = set(chain.from_iterable(all_sbx))
self.logger.debug(f"All sandboxes {', '.join(list(all_sbx))}")
for isbx in all_sbx:
group_sbx = list(
filter(
lambda ent: (isbx in ent.data['sbxn']) or (ent.data[
'sbxn'] == ['core']), group))
# Need more than one level of lithiation to define a electrode material
if len(group_sbx) == 1:
continue
self.logger.debug(
f"Grouped entries in sandbox {isbx} -- {', '.join([en.name for en in group_sbx])}"
)
try:
result = InsertionElectrode(group_sbx,
self.working_ion_entry)
assert (len(result._stable_entries) > 1)
except:
self.logger.warn(
f"Not able to generate a entries in sandbox {isbx} using the following entires-- {', '.join([en.entry_id for en in group_sbx])}"
)
continue
spacegroup = SpacegroupAnalyzer(
result.get_stable_entries(
charge_to_discharge=True)[0].structure)
d = result.as_dict_summary()
ids = [entry.entry_id for entry in result.get_all_entries()]
lowest_id = sorted(ids, key=lambda x: x.split('-')[-1])[0]
d['spacegroup'] = {
k: spacegroup._space_group_data[k]
for k in sg_fields
}
if isbx == 'core':
d['battid'] = lowest_id + '_' + self.working_ion
else:
d['battid'] = lowest_id + '_' + self.working_ion + '_' + isbx
# Only allow one sandbox value for each electrode
d['sbxn'] = [isbx]
docs.append(d)
return docs
class InsertionElectrodeTest(unittest.TestCase):
def setUp(self):
self.entry_Li = ComputedEntry("Li", -1.90753119)
with open(os.path.join(test_dir, "LiTiO2_batt.json"), "r") as f:
self.entries_LTO = json.load(f, cls=MontyDecoder)
with open(os.path.join(test_dir, "MgVO_batt.json"), "r") as file:
self.entries_MVO = json.load(file, cls=MontyDecoder)
with open(os.path.join(test_dir, "Mg_batt.json"), "r") as file:
self.entry_Mg = json.load(file, cls=MontyDecoder)
self.ie_LTO = InsertionElectrode(self.entries_LTO, self.entry_Li)
self.ie_MVO = InsertionElectrode(self.entries_MVO, self.entry_Mg)
def test_voltage(self):
#test basic voltage
self.assertAlmostEqual(self.ie_LTO.max_voltage, 2.78583901, 3)
self.assertAlmostEqual(self.ie_LTO.min_voltage, 0.89702381, 3)
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(), 1.84143141,
3)
#test voltage range selectors
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(0, 1),
0.89702381, 3)
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(2, 3),
2.78583901, 3)
#test non-existing voltage range
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(0, 0.1), 0, 3)
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(4, 5), 0, 3)
self.assertAlmostEqual(self.ie_MVO.get_average_voltage(), 2.513767, 3)
def test_capacities(self):
#test basic capacity
self.assertAlmostEqual(self.ie_LTO.get_capacity_grav(), 308.74865045,
3)
self.assertAlmostEqual(self.ie_LTO.get_capacity_vol(), 1205.99391136,
3)
#test capacity selector
self.assertAlmostEqual(self.ie_LTO.get_capacity_grav(1, 3),
154.374325225, 3)
#test alternate normalization option
self.assertAlmostEqual(self.ie_LTO.get_capacity_grav(1, 3, False),
160.803169506, 3)
self.assertIsNotNone(self.ie_LTO.as_dict_summary(True))
self.assertAlmostEqual(self.ie_MVO.get_capacity_grav(), 281.845548242,
3)
self.assertAlmostEqual(self.ie_MVO.get_capacity_vol(), 1145.80087994,
3)
def test_get_instability(self):
self.assertIsNone(self.ie_LTO.get_max_instability())
self.assertAlmostEqual(self.ie_MVO.get_max_instability(),
0.7233711650000014)
self.assertAlmostEqual(self.ie_MVO.get_min_instability(),
0.4913575099999994)
def test_get_muO2(self):
self.assertIsNone(self.ie_LTO.get_max_muO2())
self.assertAlmostEqual(self.ie_MVO.get_max_muO2(), -4.93552791875)
self.assertAlmostEqual(self.ie_MVO.get_min_muO2(), -11.06599657)
def test_entries(self):
#test that the proper number of sub-electrodes are returned
self.assertEqual(len(self.ie_LTO.get_sub_electrodes(False, True)), 3)
self.assertEqual(len(self.ie_LTO.get_sub_electrodes(True, True)), 2)
def test_get_all_entries(self):
self.ie_LTO.get_all_entries()
def test_to_from_dict(self):
d = self.ie_LTO.as_dict()
ie = InsertionElectrode.from_dict(d)
self.assertAlmostEqual(ie.max_voltage, 2.78583901, 3)
self.assertAlmostEqual(ie.min_voltage, 0.89702381, 3)
self.assertAlmostEqual(ie.get_average_voltage(), 1.84143141, 3)
#Just to make sure json string works.
json_str = json.dumps(self.ie_LTO, cls=MontyEncoder)
ie = json.loads(json_str, cls=MontyDecoder)
self.assertAlmostEqual(ie.max_voltage, 2.78583901, 3)
self.assertAlmostEqual(ie.min_voltage, 0.89702381, 3)
self.assertAlmostEqual(ie.get_average_voltage(), 1.84143141, 3)
def test_voltage_pair(self):
vpair = self.ie_LTO[0]
self.assertAlmostEqual(vpair.voltage, 2.78583901)
self.assertAlmostEqual(vpair.mAh, 13400.7411749, 2)
self.assertAlmostEqual(vpair.mass_charge, 79.8658)
self.assertAlmostEqual(vpair.mass_discharge, 83.3363)
self.assertAlmostEqual(vpair.vol_charge, 37.553684467)
self.assertAlmostEqual(vpair.vol_discharge, 37.917719932)
self.assertAlmostEqual(vpair.frac_charge, 0.0)
self.assertAlmostEqual(vpair.frac_discharge, 0.14285714285714285)
def process_item(self, item):
"""
Read the entries from the thermo database and group them based on the reduced composition
of the framework material (without working ion).
Args:
chemsys(string): the chemical system string to be queried
returns:
(chemsys, [group]): entry contains a list of entries the materials together by composition
"""
# sort the entries intro subgroups
# then perform PD analysis
all_entries = item["all_entries"]
pd_ents = item["pd_ents"]
phdi = PhaseDiagram(pd_ents)
# The working ion entries
ents_wion = list(
filter(
lambda x: x.composition.get_integer_formula_and_factor()[0]
== self.working_ion,
pd_ents,
)
)
self.working_ion_entry = min(ents_wion, key=lambda e: e.energy_per_atom)
assert self.working_ion_entry != None
grouped_entries = list(self.get_sorted_subgroups(all_entries))
docs = [] # results
for group in grouped_entries:
self.logger.debug(
f"Grouped entries in all sandboxes {', '.join([en.name for en in group])}"
)
for en in group:
# skip this d_muO2 stuff if you do note have oxygen
if Element("O") in en.composition.elements:
d_muO2 = [
{
"reaction": str(itr["reaction"]),
"chempot": itr["chempot"],
"evolution": itr["evolution"],
}
for itr in phdi.get_element_profile("O", en.composition)
]
else:
d_muO2 = None
en.data["muO2"] = d_muO2
en.data["decomposition_energy"] = phdi.get_e_above_hull(en)
# sort out the sandboxes
# for each sandbox core+sandbox will both contribute entries
all_sbx = [ent.data["_sbxn"] for ent in group]
all_sbx = set(chain.from_iterable(all_sbx))
self.logger.debug(f"All sandboxes {', '.join(list(all_sbx))}")
for isbx in all_sbx:
group_sbx = list(
filter(
lambda ent: (isbx in ent.data["_sbxn"])
or (ent.data["_sbxn"] == ["core"]),
group,
)
)
self.logger.debug(
f"Grouped entries in sandbox {', '.join([en.name for en in group_sbx])}"
)
result = InsertionElectrode(group_sbx, self.working_ion_entry)
spacegroup = SpacegroupAnalyzer(
result.get_stable_entries(charge_to_discharge=True)[0].structure
)
d = result.as_dict_summary()
# d['stable_material_ids'] = [entry.entry_id
# for entry in result.get_stable_entries()]
# d['unstable_material_ids'] = [entry.entry_id
# for entry in result.get_unstable_entries()]
# d['stability_data'] = {entry.entry_id : entry.data['decomposition_energy']
# for entry in result.get_all_entries()}
# d['muO2_data'] = {entry.entry_id : entry.data['muO2']
# for entry in result.get_all_entries()}
# sort the ids based on value
ids = [entry.entry_id for entry in result.get_all_entries()]
lowest_id = sorted(ids, key=lambda x: x.split("-")[-1])[0]
d["spacegroup"] = {
k: spacegroup._space_group_data[k] for k in sg_fields
}
if isbx == "core":
d["battid"] = lowest_id + "_" + self.working_ion
else:
d["battid"] = lowest_id + "_" + self.working_ion + "_" + isbx
# Only allow one sandbox value for each electrode
d["_sbxn"] = [isbx]
docs.append(d)
return docs
class InsertionElectrodeTest(unittest.TestCase):
def setUp(self):
self.entry_Li = ComputedEntry("Li", -1.90753119)
with open(os.path.join(test_dir, "LiTiO2_batt.json"), "r") as f:
self.entries_LTO = json.load(f, cls=MontyDecoder)
with open(os.path.join(test_dir, "MgVO_batt.json"), "r") as file:
self.entries_MVO = json.load(file, cls=MontyDecoder)
with open(os.path.join(test_dir, "Mg_batt.json"), "r") as file:
self.entry_Mg = json.load(file, cls=MontyDecoder)
self.ie_LTO = InsertionElectrode(self.entries_LTO, self.entry_Li)
self.ie_MVO = InsertionElectrode(self.entries_MVO, self.entry_Mg)
def test_voltage(self):
#test basic voltage
self.assertAlmostEqual(self.ie_LTO.max_voltage, 2.78583901, 3)
self.assertAlmostEqual(self.ie_LTO.min_voltage, 0.89702381, 3)
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(), 1.84143141,
3)
#test voltage range selectors
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(0, 1),
0.89702381, 3)
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(2, 3),
2.78583901, 3)
#test non-existing voltage range
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(0, 0.1), 0, 3)
self.assertAlmostEqual(self.ie_LTO.get_average_voltage(4, 5), 0, 3)
self.assertAlmostEqual(self.ie_MVO.get_average_voltage(), 2.513767,3)
def test_capacities(self):
#test basic capacity
self.assertAlmostEqual(self.ie_LTO.get_capacity_grav(), 308.74865045,
3)
self.assertAlmostEqual(self.ie_LTO.get_capacity_vol(), 1205.99391136,
3)
#test capacity selector
self.assertAlmostEqual(self.ie_LTO.get_capacity_grav(1, 3),
154.374325225, 3)
#test alternate normalization option
self.assertAlmostEqual(self.ie_LTO.get_capacity_grav(1, 3, False),
160.803169506, 3)
self.assertIsNotNone(self.ie_LTO.as_dict_summary(True))
self.assertAlmostEqual(self.ie_MVO.get_capacity_grav(), 281.845548242, 3)
self.assertAlmostEqual(self.ie_MVO.get_capacity_vol(), 1145.80087994, 3)
def test_get_muO2(self):
self.assertIsNone(self.ie_LTO.get_max_muO2())
def test_entries(self):
#test that the proper number of sub-electrodes are returned
self.assertEqual(len(self.ie_LTO.get_sub_electrodes(False, True)), 3)
self.assertEqual(len(self.ie_LTO.get_sub_electrodes(True, True)), 2)
def test_get_all_entries(self):
self.ie_LTO.get_all_entries()
def test_to_from_dict(self):
d = self.ie_LTO.as_dict()
ie = InsertionElectrode.from_dict(d)
self.assertAlmostEqual(ie.max_voltage, 2.78583901, 3)
self.assertAlmostEqual(ie.min_voltage, 0.89702381, 3)
self.assertAlmostEqual(ie.get_average_voltage(), 1.84143141, 3)
#Just to make sure json string works.
json_str = json.dumps(self.ie_LTO, cls=MontyEncoder)
ie = json.loads(json_str, cls=MontyDecoder)
self.assertAlmostEqual(ie.max_voltage, 2.78583901, 3)
self.assertAlmostEqual(ie.min_voltage, 0.89702381, 3)
self.assertAlmostEqual(ie.get_average_voltage(), 1.84143141, 3)
def test_voltage_pair(self):
vpair = self.ie_LTO[0]
self.assertAlmostEqual(vpair.voltage, 2.78583901)
self.assertAlmostEqual(vpair.mAh, 13400.7411749, 2)
self.assertAlmostEqual(vpair.mass_charge, 79.8658)
self.assertAlmostEqual(vpair.mass_discharge, 83.3363)
self.assertAlmostEqual(vpair.vol_charge, 37.553684467)
self.assertAlmostEqual(vpair.vol_discharge, 37.917719932)
self.assertAlmostEqual(vpair.frac_charge, 0.0)
self.assertAlmostEqual(vpair.frac_discharge, 0.14285714285714285)
)
)
self.logger.debug(
f"Grouped entries in sandbox {', '.join([en.name for en in group_sbx])}"
)
=======
group_sbx = list(filter(lambda ent : (isbx in ent.data['_sbxn']) or (ent.data['_sbxn']==['core']), group))
self.logger.debug(f"Grouped entries in sandbox {isbx} -- {', '.join([en.name for en in group_sbx])}")
>>>>>>> master
result = InsertionElectrode(group_sbx, self.working_ion_entry)
spacegroup = SpacegroupAnalyzer(
result.get_stable_entries(charge_to_discharge=True)[0].structure
)
d = result.as_dict_summary()
# d['stable_material_ids'] = [entry.entry_id
# for entry in result.get_stable_entries()]
# d['unstable_material_ids'] = [entry.entry_id
# for entry in result.get_unstable_entries()]
# d['stability_data'] = {entry.entry_id : entry.data['decomposition_energy']
# for entry in result.get_all_entries()}
# d['muO2_data'] = {entry.entry_id : entry.data['muO2']
# for entry in result.get_all_entries()}
# sort the ids based on value
ids = [entry.entry_id for entry in result.get_all_entries()]
lowest_id = sorted(ids, key=lambda x: x.split("-")[-1])[0]
d["spacegroup"] = {
k: spacegroup._space_group_data[k] for k in sg_fields
