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
def task_to_prop_list(self, task):
"""
Converts a task into an list of properties with associated metadata
"""
t_type = task_type(task['orig_inputs'])
t_id = task["task_id"]
# Convert the task doc into a serious of properties in the materials
# doc with the right document structure
props = []
for prop in self.__settings:
if t_type in prop["quality_score"].keys():
if has(task, prop["tasks_key"]):
props.append({
"value": get(task, prop["tasks_key"]),
"task_type": t_type,
"task_id": t_id,
"quality_score": prop["quality_score"][t_type],
"track": prop.get("track", False),
"aggregate": prop.get("aggregate", False),
"last_updated": task[self.tasks.lu_field],
"energy": get(task, "output.energy", 0.0),
"materials_key": prop["materials_key"]
})
elif not prop.get("optional", False):
self.logger.error("Failed getting {} for task: {}".format(prop["tasks_key"], t_id))
return props
def filter_and_group_tasks(self, tasks):
"""
Groups tasks by structure matching
"""
filtered_tasks = [
t for t in tasks
if task_type(t['orig_inputs']) in self.allowed_tasks
]
structures = []
for idx, t in enumerate(filtered_tasks):
s = Structure.from_dict(t["output"]['structure'])
s.index = idx
structures.append(s)
grouped_structures = group_structures(
structures,
ltol=self.ltol,
stol=self.stol,
angle_tol=self.angle_tol,
separate_mag_orderings=self.separate_mag_orderings)
for group in grouped_structures:
yield [filtered_tasks[struc.index] for struc in group]
def filter_and_group_tasks(self, tasks):
"""
Groups tasks by structure matching
"""
filtered_tasks = [
t for t in tasks
if task_type(t['orig_inputs']) in self.allowed_tasks
]
structures = []
for idx, t in enumerate(filtered_tasks):
s = Structure.from_dict(t["output"]['structure'])
s.index = idx
structures.append(s)
if self.separate_mag_orderings:
for structure in structures:
if has(structure.site_properties, "magmom"):
structure.add_spin_by_site(
structure.site_properties['magmom'])
structure.remove_site_property('magmom')
sm = StructureMatcher(ltol=self.ltol,
stol=self.stol,
angle_tol=self.angle_tol,
primitive_cell=True,
scale=True,
attempt_supercell=False,
allow_subset=False,
comparator=ElementComparator())
grouped_structures = sm.group_structures(structures)
grouped_tasks = [[filtered_tasks[struc.index] for struc in group]
for group in grouped_structures]
return grouped_tasks
def filter_and_group_tasks(self, tasks):
"""
Groups tasks by structure matching
"""
filtered_tasks = [
t for t in tasks
if task_type(t["orig_inputs"]) in self.allowed_tasks
]
structures = []
for idx, t in enumerate(filtered_tasks):
s = Structure.from_dict(t["output"]["structure"])
s.index = idx
total_mag = get(
t, "calcs_reversed.0.output.outcar.total_magnetization", 0)
s.total_magnetization = total_mag if total_mag else 0
# a fix for very old tasks that did not report site-projected magnetic moments
# so that we can group them appropriately
if (("magmom" not in s.site_properties)
and (get(t, "input.parameters.ISPIN", 1) == 2)
and has(t, "input.parameters.MAGMOM")):
# TODO: map input structure sites to output structure sites
s.add_site_property("magmom",
t["input"]["parameters"]["MAGMOM"])
structures.append(s)
grouped_structures = group_structures(
structures,
ltol=self.ltol,
stol=self.stol,
angle_tol=self.angle_tol,
separate_mag_orderings=self.separate_mag_orderings,
)
for group in grouped_structures:
yield [filtered_tasks[struc.index] for struc in group]
