def run_task(self, fw_spec):
mpr = MPRester(env_chk(self.get("MAPI_KEY"), fw_spec))
vasprun, outcar = get_vasprun_outcar(self.get("calc_dir", "."), parse_dos=False, parse_eigen=False)
my_entry = vasprun.get_computed_entry(inc_structure=False)
stored_data = mpr.get_stability([my_entry])[0]
if stored_data["e_above_hull"] > self.get("ehull_cutoff", 0.05):
return FWAction(stored_data=stored_data, exit=True, defuse_workflow=True)
else:
return FWAction(stored_data=stored_data)
def run_task(self, fw_spec):
mpr = MPRester(env_chk(self.get("MAPI_KEY"), fw_spec))
vasprun, outcar = get_vasprun_outcar(self.get("calc_dir", "."),
parse_dos=False,
parse_eigen=False)
my_entry = vasprun.get_computed_entry(inc_structure=False)
stored_data = mpr.get_stability([my_entry])[0]
if stored_data["e_above_hull"] > self.get("ehull_cutoff", 0.05):
logger.info("CheckStability: failed test!")
return FWAction(stored_data=stored_data, exit=True,
defuse_workflow=True)
else:
return FWAction(stored_data=stored_data)
class MaterialsEhullBuilder(AbstractBuilder):
def __init__(self, materials_write, mapi_key=None, update_all=False):
"""
Starting with an existing materials collection, adds stability information and
The Materials Project ID.
Args:
materials_write: mongodb collection for materials (write access needed)
mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set)
update_all: (bool) - if true, updates all docs. If false, only updates
docs w/o a stability key
"""
self._materials = materials_write
self.mpr = MPRester(api_key=mapi_key)
self.update_all = update_all
def run(self):
logger.info("MaterialsEhullBuilder starting...")
self._build_indexes()
q = {"thermo.energy": {"$exists": True}}
if not self.update_all:
q["stability"] = {"$exists": False}
mats = [
m for m in self._materials.find(
q, {
"calc_settings": 1,
"structure": 1,
"thermo.energy": 1,
"material_id": 1
})
]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(
m['material_id']))
try:
params = {}
for x in ["is_hubbard", "hubbards", "potcar_spec"]:
params[x] = m["calc_settings"][x]
structure = Structure.from_dict(m["structure"])
energy = m["thermo"]["energy"]
my_entry = ComputedEntry(structure.composition,
energy,
parameters=params)
# TODO: @computron This only calculates Ehull with respect to Materials Project.
# It should also account for the current database's results. -computron
self._materials.update_one({"material_id": m["material_id"]}, {
"$set": {
"stability": self.mpr.get_stability([my_entry])[0]
}
})
# TODO: @computron: also add additional properties like inverse hull energy?
# TODO: @computron it's better to use PD tool or reaction energy calculator
# Otherwise the compatibility schemes might have issues...one strategy might be
# use MP only to retrieve entries but compute the PD locally -computron
for el, elx in my_entry.composition.items():
entries = self.mpr.get_entries(el.symbol,
compatible_only=True)
min_e = min(
entries,
key=lambda x: x.energy_per_atom).energy_per_atom
energy -= elx * min_e
self._materials.update_one({"material_id": m["material_id"]}, {
"$set": {
"thermo.formation_energy_per_atom":
energy / structure.num_sites
}
})
mpids = self.mpr.find_structure(structure)
self._materials.update_one({"material_id": m["material_id"]},
{"$set": {
"mpids": mpids
}})
except:
import traceback
logger.exception("<---")
logger.exception(
"There was an error processing material_id: {}".format(m))
logger.exception(traceback.format_exc())
logger.exception("--->")
logger.info("MaterialsEhullBuilder finished processing.")
def reset(self):
logger.info("Resetting MaterialsEhullBuilder")
self._materials.update_many({}, {"$unset": {"stability": 1}})
self._build_indexes()
logger.info("Finished resetting MaterialsEhullBuilder")
def _build_indexes(self):
self._materials.create_index("stability.e_above_hull")
@classmethod
def from_file(cls, db_file, m="materials", **kwargs):
"""
Get a MaterialsEhullBuilder using only a db file
Args:
db_file: (str) path to db file
m: (str) name of "materials" collection
**kwargs: other parameters to feed into the builder, e.g. mapi_key
"""
db_write = get_database(db_file, admin=True)
return cls(db_write[m], **kwargs)
class MaterialsEhullBuilder(AbstractBuilder):
def __init__(self, materials_write, mapi_key=None, update_all=False):
"""
Starting with an existing materials collection, adds stability information and
The Materials Project ID.
Args:
materials_write: mongodb collection for materials (write access needed)
mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set)
update_all: (bool) - if true, updates all docs. If false, only updates
docs w/o a stability key
"""
self._materials = materials_write
self.mpr = MPRester(api_key=mapi_key)
self.update_all = update_all
def run(self):
print("MaterialsEhullBuilder starting...")
self._build_indexes()
q = {"thermo.energy": {"$exists": True}}
if not self.update_all:
q["stability"] = {"$exists": False}
mats = [
m for m in self._materials.find(
q, {
"calc_settings": 1,
"structure": 1,
"thermo.energy": 1,
"material_id": 1
})
]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(
m['material_id']))
try:
params = {}
for x in ["is_hubbard", "hubbards", "potcar_spec"]:
params[x] = m["calc_settings"][x]
structure = Structure.from_dict(m["structure"])
energy = m["thermo"]["energy"]
my_entry = ComputedEntry(structure.composition,
energy,
parameters=params)
self._materials.update_one({"material_id": m["material_id"]}, {
"$set": {
"stability": self.mpr.get_stability([my_entry])[0]
}
})
mpids = self.mpr.find_structure(structure)
self._materials.update_one({"material_id": m["material_id"]},
{"$set": {
"mpids": mpids
}})
except:
import traceback
print("<---")
print(
"There was an error processing material_id: {}".format(m))
traceback.print_exc()
print("--->")
print("MaterialsEhullBuilder finished processing.")
def reset(self):
self._materials.update_many({}, {"$unset": {"stability": 1}})
self._build_indexes()
def _build_indexes(self):
self._materials.create_index("stability.e_above_hull")
@classmethod
def from_file(cls, db_file, m="materials", **kwargs):
"""
Get a MaterialsEhullBuilder using only a db file
Args:
db_file: (str) path to db file
m: (str) name of "materials" collection
**kwargs: other parameters to feed into the builder, e.g. mapi_key
"""
db_write = get_database(db_file, admin=True)
return cls(db_write[m], **kwargs)
class MaterialsEhullBuilder:
def __init__(self, materials_write, mapi_key=None, update_all=False):
"""
Starting with an existing materials collection, adds stability information and
The Materials Project ID.
Args:
materials_write: mongodb collection for materials (write access needed)
mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set)
update_all: (bool) - if true, updates all docs. If false, only updates
docs w/o a stability key
"""
self._materials = materials_write
self.mpr = MPRester(api_key=mapi_key)
self.update_all = update_all
def run(self):
print("MaterialsEhullBuilder starting...")
self._build_indexes()
q = {"thermo.energy": {"$exists": True}}
if not self.update_all:
q["stability"] = {"$exists": False}
mats = [m for m in self._materials.find(q, {"calc_settings": 1, "structure": 1,
"thermo.energy": 1, "material_id": 1})]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(m['material_id']))
try:
params = {}
for x in ["is_hubbard", "hubbards", "potcar_spec"]:
params[x] = m["calc_settings"][x]
structure = Structure.from_dict(m["structure"])
energy = m["thermo"]["energy"]
my_entry = ComputedEntry(structure.composition, energy, parameters=params)
self._materials.update_one({"material_id": m["material_id"]},
{"$set": {"stability": self.mpr.get_stability([my_entry])[0]}})
mpids = self.mpr.find_structure(structure)
self._materials.update_one({"material_id": m["material_id"]}, {"$set": {"mpids": mpids}})
except:
import traceback
print("<---")
print("There was an error processing material_id: {}".format(m))
traceback.print_exc()
print("--->")
print("MaterialsEhullBuilder finished processing.")
def reset(self):
self._materials.update_many({}, {"$unset": {"stability": 1}})
self._build_indexes()
def _build_indexes(self):
self._materials.create_index("stability.e_above_hull")
@staticmethod
def from_db_file(db_file, m="materials", **kwargs):
"""
Get a MaterialsEhullBuilder using only a db file
Args:
db_file: (str) path to db file
m: (str) name of "materials" collection
**kwargs: other parameters to feed into the builder, e.g. mapi_key
"""
db_write = get_database(db_file, admin=True)
return MaterialsEhullBuilder(db_write[m], **kwargs)
class MaterialsEhullBuilder(AbstractBuilder):
def __init__(self, materials_write, mapi_key=None, update_all=False):
"""
Starting with an existing materials collection, adds stability information and
The Materials Project ID.
Args:
materials_write: mongodb collection for materials (write access needed)
mapi_key: (str) Materials API key (if MAPI_KEY env. var. not set)
update_all: (bool) - if true, updates all docs. If false, only updates
docs w/o a stability key
"""
self._materials = materials_write
self.mpr = MPRester(api_key=mapi_key)
self.update_all = update_all
def run(self):
logger.info("MaterialsEhullBuilder starting...")
self._build_indexes()
q = {"thermo.energy": {"$exists": True}}
if not self.update_all:
q["stability"] = {"$exists": False}
mats = [m for m in self._materials.find(q, {"calc_settings": 1, "structure": 1,
"thermo.energy": 1, "material_id": 1})]
pbar = tqdm(mats)
for m in pbar:
pbar.set_description("Processing materials_id: {}".format(m['material_id']))
try:
params = {}
for x in ["is_hubbard", "hubbards", "potcar_spec"]:
params[x] = m["calc_settings"][x]
structure = Structure.from_dict(m["structure"])
energy = m["thermo"]["energy"]
my_entry = ComputedEntry(structure.composition, energy, parameters=params)
# TODO: @computron This only calculates Ehull with respect to Materials Project.
# It should also account for the current database's results. -computron
self._materials.update_one({"material_id": m["material_id"]},
{"$set": {"stability": self.mpr.get_stability([my_entry])[0]}})
# TODO: @computron: also add additional properties like inverse hull energy?
# TODO: @computron it's better to use PD tool or reaction energy calculator
# Otherwise the compatibility schemes might have issues...one strategy might be
# use MP only to retrieve entries but compute the PD locally -computron
for el, elx in my_entry.composition.items():
entries = self.mpr.get_entries(el.symbol, compatible_only=True)
min_e = min(entries, key=lambda x: x.energy_per_atom).energy_per_atom
energy -= elx * min_e
self._materials.update_one({"material_id": m["material_id"]},
{"$set": {"thermo.formation_energy_per_atom": energy / structure.num_sites}})
mpids = self.mpr.find_structure(structure)
self._materials.update_one({"material_id": m["material_id"]}, {"$set": {"mpids": mpids}})
except:
import traceback
logger.exception("<---")
logger.exception("There was an error processing material_id: {}".format(m))
logger.exception(traceback.format_exc())
logger.exception("--->")
logger.info("MaterialsEhullBuilder finished processing.")
def reset(self):
logger.info("Resetting MaterialsEhullBuilder")
self._materials.update_many({}, {"$unset": {"stability": 1}})
self._build_indexes()
logger.info("Finished resetting MaterialsEhullBuilder")
def _build_indexes(self):
self._materials.create_index("stability.e_above_hull")
@classmethod
def from_file(cls, db_file, m="materials", **kwargs):
"""
Get a MaterialsEhullBuilder using only a db file
Args:
db_file: (str) path to db file
m: (str) name of "materials" collection
**kwargs: other parameters to feed into the builder, e.g. mapi_key
"""
db_write = get_database(db_file, admin=True)
return cls(db_write[m], **kwargs)
