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removed sandboxes
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@jmmshn
jmmshn committed Mar 2, 2021
1 parent 0704e78 commit e0f3408
Showing 1 changed file with 36 additions and 39 deletions.
75 changes: 36 additions & 39 deletions emmet-builders/emmet/builders/vasp/thermo.py
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Expand Up @@ -85,7 +85,7 @@ def get_items(self) -> Iterator[List[Dict]]:
affected_chemsys = self.get_affected_chemsys(updated_chemsys | new_chemsys)

# Remove overlapping chemical systems
to_process_chemsys = {}
to_process_chemsys = set()
for chemsys in updated_chemsys | new_chemsys | affected_chemsys:
if chemsys not in to_process_chemsys:
to_process_chemsys |= chemsys_permutations(chemsys)
Expand All @@ -99,29 +99,29 @@ def get_items(self) -> Iterator[List[Dict]]:
# Will build them in a similar manner to fast Pourbaix
for chemsys in sorted(to_process_chemsys, key=lambda x: len(x.split("-"))):
entries = self.get_entries(chemsys)

# build sandbox sets: ["a"] , ["a","b"], ["core","a","b"]
sandbox_sets = set(
[frozenset(entry.data.get("sandboxes", {})) for entry in entries]
)
sandbox_sets = maximal_spanning_non_intersecting_subsets(sandbox_sets)
self.logger.debug(f"Found {len(sandbox_sets)}: {sandbox_sets}")

for sandboxes in sandbox_sets:
# only yield maximal subsets so that we can process a equivalent sandbox combinations at a time
sandbox_entries = [
entry
for entry in entries
if all(
sandbox in entry.data.get("_sbxn", []) for sandbox in sandboxes
)
]

yield sandboxes, sandbox_entries
yield entries
# # build sandbox sets: ["a"] , ["a","b"], ["core","a","b"]
# sandbox_sets = set(
# [frozenset(entry.data.get("sandboxes", {})) for entry in entries]
# )
# sandbox_sets = maximal_spanning_non_intersecting_subsets(sandbox_sets)
# self.logger.debug(f"Found {len(sandbox_sets)}: {sandbox_sets}")
#
# for sandboxes in sandbox_sets:
# # only yield maximal subsets so that we can process a equivalent sandbox combinations at a time
# sandbox_entries = [
# entry
# for entry in entries
# if all(
# sandbox in entry.data.get("_sbxn", []) for sandbox in sandboxes
# )
# ]
#
# yield sandboxes, sandbox_entries

def process_item(self, item: Tuple[List[str], List[ComputedEntry]]):

sandboxes, entries = item
entries = item

entries = [ComputedEntry.from_dict(entry) for entry in entries]
# determine chemsys
Expand All @@ -130,26 +130,23 @@ def process_item(self, item: Tuple[List[str], List[ComputedEntry]]):
)
chemsys = "-".join(elements)

self.logger.debug(
f"Procesing {len(entries)} entries for {chemsys} - {sandboxes}"
)
self.logger.debug(f"Procesing {len(entries)} entries for {chemsys}")

material_entries = defaultdict(defaultdict(list))
material_entries = defaultdict(lambda: defaultdict(list))
pd_entries = []
for entry in entries:
material_entries[entry.entry_id][entry.data["run_type"]].append(entry)

# TODO: How to make this general and controllable via SETTINGS?
for material_id in material_entries:
if "GGA+U" in material_entries[material_id]:
pd_entries.append(material_entries[material_id]["GGA+U"])
pd_entries.extend(material_entries[material_id]["GGA+U"])
elif "GGA" in material_entries[material_id]:
pd_entries.append(material_entries[material_id]["GGA"])

pd_entries.extend(material_entries[material_id]["GGA"])
pd_entries = self.compatibility.process_entries(pd_entries)

try:
docs = ThermoDoc.from_entries(pd_entries, sandboxes=sandboxes)
docs = ThermoDoc.from_entries(pd_entries)
for doc in docs:
doc.entries = material_entries[doc.material_id]
doc.entry_types = list(material_entries[doc.material_id].keys())
Expand Down Expand Up @@ -178,9 +175,9 @@ def update_targets(self, items):
# 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()
)
# 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]

Expand All @@ -198,7 +195,7 @@ def update_targets(self, items):
else:
self.logger.info("No items to update")

def get_entries(self, chemsys: str) -> List[ComputedEntry]:
def get_entries(self, chemsys: str) -> List[Dict]:
"""
Gets a entries from the tasks collection for the corresponding chemical systems
Args:
Expand Down Expand Up @@ -230,7 +227,7 @@ def get_entries(self, chemsys: str) -> List[ComputedEntry]:
new_q["deprecated"] = False
materials_docs = list(
self.materials.query(
criteria=new_q, properties=[self.materials.key, "entries", "sandboxes"]
criteria=new_q, properties=[self.materials.key, "entries"]
)
)

Expand All @@ -240,11 +237,11 @@ def get_entries(self, chemsys: str) -> List[ComputedEntry]:

# Convert the entries into ComputedEntries and store
for doc in materials_docs:
for entry in doc.get("entries", {}):
entry["data"]["sandboxes"] = doc["sandboxes"]
elsyms = sorted(set([el for el in entry["composition"]]))
self._entries_cache["-".join(elsyms)].append(entry)
all_entries.append(entry)
for r_type, entry_dict in doc.get("entries", {}).items():
entry_dict["data"]["run_type"] = r_type
elsyms = sorted(set([el for el in entry_dict["composition"]]))
self._entries_cache["-".join(elsyms)].append(entry_dict)
all_entries.append(entry_dict)

self.logger.info(f"Total entries in {chemsys} : {len(all_entries)}")

Expand Down

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