def process_item(self, task):
"""
Process the tasks into a list of materials
Args:
task [dict] : a task doc
Returns:
list of C
"""
t_type = task_type(get(task, 'orig_inputs'))
entries = []
if not any([t in t_type for t in self.task_types]):
return []
is_hubbard = get(task, "input.is_hubbard", False)
hubbards = get(task, "input.hubbards", [])
i = 0
for calc in task.get("calcs_reversed", []):
parameters = {
"is_hubbard": is_hubbard,
"hubbards": hubbards,
"potcar_spec": get(calc, "input.potcar_spec", []),
"run_type": calc.get("run_type", "GGA")
}
for step_num, step in enumerate(get(calc, "output.ionic_steps")):
struc = Structure.from_dict(step.get("structure"))
forces = calc.get("forces", [])
if forces:
struc.add_site_property("forces", forces)
stress = calc.get("stress", None)
data = {"stress": stress} if stress else {}
data["step"] = step_num
c = ComputedStructureEntry(structure=struc,
correction=0,
energy=step.get("e_wo_entrp"),
parameters=parameters,
entry_id="{}-{}".format(
task[self.tasks.key], i),
data=data)
i += 1
d = c.as_dict()
d["chemsys"] = '-'.join(
sorted(set([e.symbol
for e in struc.composition.elements])))
d["task_type"] = task_type(get(calc, 'input'))
d["calc_name"] = get(calc, "task.name")
d["task_id"] = task[self.tasks.key]
entries.append(d)
return entries
class ComputedStructureEntryTest(unittest.TestCase):
def setUp(self):
self.entry = ComputedStructureEntry(vasprun.final_structure, vasprun.final_energy, parameters=vasprun.incar)
def test_energy(self):
self.assertAlmostEqual(self.entry.energy, -269.38319884)
self.entry.correction = 1.0
self.assertAlmostEqual(self.entry.energy, -268.38319884)
def test_composition(self):
self.assertEqual(self.entry.composition.reduced_formula, "LiFe4(PO4)4")
def test_to_from_dict(self):
d = self.entry.as_dict()
e = ComputedStructureEntry.from_dict(d)
self.assertAlmostEqual(e.energy, -269.38319884)
def test_str(self):
self.assertIsNotNone(str(self.entry))
class ComputedStructureEntryTest(unittest.TestCase):
def setUp(self):
self.entry = ComputedStructureEntry(vasprun.final_structure,
vasprun.final_energy,
parameters=vasprun.incar)
def test_energy(self):
self.assertAlmostEqual(self.entry.energy, -269.38319884)
self.entry.correction = 1.0
self.assertAlmostEqual(self.entry.energy, -268.38319884)
def test_composition(self):
self.assertEqual(self.entry.composition.reduced_formula, "LiFe4(PO4)4")
def test_to_from_dict(self):
d = self.entry.as_dict()
e = ComputedStructureEntry.from_dict(d)
self.assertAlmostEqual(e.energy, -269.38319884)
def test_str(self):
self.assertIsNotNone(str(self.entry))
class ComputedStructureEntryTest(unittest.TestCase):
def setUp(self):
self.entry = ComputedStructureEntry(vasprun.final_structure,
vasprun.final_energy,
parameters=vasprun.incar)
def test_energy(self):
self.assertAlmostEqual(self.entry.energy, -269.38319884)
self.entry.correction = 1.0
self.assertAlmostEqual(self.entry.energy, -268.38319884)
def test_composition(self):
self.assertEqual(self.entry.composition.reduced_formula, "LiFe4(PO4)4")
def test_to_from_dict(self):
d = self.entry.as_dict()
e = ComputedStructureEntry.from_dict(d)
self.assertAlmostEqual(e.energy, -269.38319884)
def test_str(self):
self.assertIsNotNone(str(self.entry))
def test_to_from_dict_structure_with_adjustment_3(self):
"""
Legacy case where the structure entry was serialized before the energy_adjustment
attribute was part of ComputedEntry
"""
# ComputedStructureEntry for Oxygen, mp-12957, as of April 2020
# with an arbitrary 1 eV correction added
d = {
"@module": "pymatgen.entries.computed_entries",
"@class": "ComputedStructureEntry",
"energy": -39.42116819,
"composition": defaultdict(float, {"O": 8.0}),
"parameters": {
"run_type": "GGA",
"is_hubbard": False,
"pseudo_potential": {
"functional": "PBE",
"labels": ["O"],
"pot_type": "paw",
},
"hubbards": {},
"potcar_symbols": ["PBE O"],
"oxide_type": "None",
},
"data": {
"oxide_type": "None"
},
"entry_id": "mp-12957",
"correction": 1,
"structure": {
"@module":
"pymatgen.core.structure",
"@class":
"Structure",
"charge":
None,
"lattice": {
"matrix": [
[-1.7795583, 0.0, 3.86158265],
[4.17564656, -3.03266995, -0.01184798],
[4.17564656, 3.03266995, -0.01184798],
],
"a":
4.251899376264673,
"b":
5.160741380296335,
"c":
5.160741380296335,
"alpha":
71.97975354157973,
"beta":
109.9211782454931,
"gamma":
109.9211782454931,
"volume":
97.67332322031668,
},
"sites": [
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.8531272, 0.15466029, 0.15466029],
"xyz": [
-0.22657617390155504,
-1.750215367360042e-17,
3.2907563697176516,
],
"label":
"O",
"properties": {
"magmom": 0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.84038763, 0.71790132, 0.21754949],
"xyz": [
2.410593174641884,
-1.5174019592685084,
3.234143088794756,
],
"label":
"O",
"properties": {
"magmom": -0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.17255465, 0.21942628, 0.21942628],
"xyz": [
1.5254221229000986,
-2.121360826524921e-18,
0.6611345262629937,
],
"label":
"O",
"properties": {
"magmom": 0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.15961237, 0.78245051, 0.28209968],
"xyz": [
4.161145821004675,
-1.5173989265985586,
0.6037435893572642,
],
"label":
"O",
"properties": {
"magmom": -0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.84038763, 0.21754949, 0.71790132],
"xyz": [
2.410593174641884,
1.5174019592685082,
3.234143088794756,
],
"label":
"O",
"properties": {
"magmom": -0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.82744535, 0.78057372, 0.78057372],
"xyz": [
5.046312697099901,
-1.3574974398403584e-16,
3.176752163737006,
],
"label":
"O",
"properties": {
"magmom": 0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.15961237, 0.28209968, 0.78245051],
"xyz": [
4.161145821004675,
1.5173989265985584,
0.6037435893572642,
],
"label":
"O",
"properties": {
"magmom": -0.002
},
},
{
"species": [{
"element": "O",
"occu": 1
}],
"abc": [0.1468728, 0.84533971, 0.84533971],
"xyz": [
6.798310993901555,
-1.7769364890338579e-16,
0.5471303202823484,
],
"label":
"O",
"properties": {
"magmom": 0.002
},
},
],
},
}
e = ComputedEntry.from_dict(d)
self.assertAlmostEqual(e.uncorrected_energy, -39.42116819)
self.assertAlmostEqual(e.energy, -38.42116819)
self.assertAlmostEqual(e.correction, 1)
assert len(e.energy_adjustments) == 1
class ComputedStructureEntryTest(unittest.TestCase):
def setUp(self):
self.entry = ComputedStructureEntry(vasprun.final_structure,
vasprun.final_energy,
parameters=vasprun.incar)
def test_energy(self):
self.assertAlmostEqual(self.entry.energy, -269.38319884)
self.entry.correction = 1.0
self.assertAlmostEqual(self.entry.energy, -268.38319884)
def test_composition(self):
self.assertEqual(self.entry.composition.reduced_formula, "LiFe4(PO4)4")
def test_to_from_dict(self):
d = self.entry.as_dict()
e = ComputedStructureEntry.from_dict(d)
self.assertAlmostEqual(e.energy, -269.38319884)
def test_str(self):
self.assertIsNotNone(str(self.entry))
def test_to_from_dict_structure_with_adjustment_3(self):
"""
Legacy case where the structure entry was serialized before the energy_adjustment
attribute was part of ComputedEntry
"""
# ComputedStructureEntry for Oxygen, mp-12957, as of April 2020
# with an arbitrary 1 eV correction added
d = {'@module': 'pymatgen.entries.computed_entries',
'@class': 'ComputedStructureEntry',
'energy': -39.42116819,
'composition': defaultdict(float, {'O': 8.0}),
'parameters': {'run_type': 'GGA',
'is_hubbard': False,
'pseudo_potential': {'functional': 'PBE',
'labels': ['O'],
'pot_type': 'paw'},
'hubbards': {},
'potcar_symbols': ['PBE O'],
'oxide_type': 'None'},
'data': {'oxide_type': 'None'},
'entry_id': 'mp-12957',
'correction': 1,
'structure': {'@module': 'pymatgen.core.structure',
'@class': 'Structure',
'charge': None,
'lattice': {'matrix': [[-1.7795583, 0.0, 3.86158265],
[4.17564656, -3.03266995, -0.01184798],
[4.17564656, 3.03266995, -0.01184798]],
'a': 4.251899376264673,
'b': 5.160741380296335,
'c': 5.160741380296335,
'alpha': 71.97975354157973,
'beta': 109.9211782454931,
'gamma': 109.9211782454931,
'volume': 97.67332322031668},
'sites': [{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.8531272, 0.15466029, 0.15466029],
'xyz': [-0.22657617390155504, -1.750215367360042e-17, 3.2907563697176516],
'label': 'O',
'properties': {'magmom': 0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.84038763, 0.71790132, 0.21754949],
'xyz': [2.410593174641884, -1.5174019592685084, 3.234143088794756],
'label': 'O',
'properties': {'magmom': -0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.17255465, 0.21942628, 0.21942628],
'xyz': [1.5254221229000986, -2.121360826524921e-18, 0.6611345262629937],
'label': 'O',
'properties': {'magmom': 0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.15961237, 0.78245051, 0.28209968],
'xyz': [4.161145821004675, -1.5173989265985586, 0.6037435893572642],
'label': 'O',
'properties': {'magmom': -0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.84038763, 0.21754949, 0.71790132],
'xyz': [2.410593174641884, 1.5174019592685082, 3.234143088794756],
'label': 'O',
'properties': {'magmom': -0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.82744535, 0.78057372, 0.78057372],
'xyz': [5.046312697099901, -1.3574974398403584e-16, 3.176752163737006],
'label': 'O',
'properties': {'magmom': 0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.15961237, 0.28209968, 0.78245051],
'xyz': [4.161145821004675, 1.5173989265985584, 0.6037435893572642],
'label': 'O',
'properties': {'magmom': -0.002}},
{'species': [{'element': 'O', 'occu': 1}],
'abc': [0.1468728, 0.84533971, 0.84533971],
'xyz': [6.798310993901555, -1.7769364890338579e-16, 0.5471303202823484],
'label': 'O',
'properties': {'magmom': 0.002}}]}}
e = ComputedEntry.from_dict(d)
self.assertAlmostEqual(e.uncorrected_energy, -39.42116819)
self.assertAlmostEqual(e.energy, -38.42116819)
self.assertAlmostEqual(e.correction, 1)
assert len(e.energy_adjustments) == 1
