def main():
initial_structs = []
final_structs = []
with connect(dft_db) as db:
groups = set()
for row in db.select():
groups.add(row.get('group', -1))
for g in groups:
try:
init = db.get([('group', '=', g),
('struct_type', '=', 'initial')])
final = db.get([('group', '=', g),
('struct_type', '=', 'relaxed')])
initial_structs.append(init.toatoms())
final_structs.append(final.toatoms())
except KeyError:
pass
# Sanity checks
for i, f in zip(initial_structs, final_structs):
i_formula = i.get_chemical_formula()
f_formula = f.get_chemical_formula()
assert i_formula == f_formula
print(f"Extracted {len(initial_structs)} structures")
new_struct = NewStructures(settings)
for i, f in zip(initial_structs, final_structs):
print(f"Inserting struct {i.get_chemical_formula()}")
try:
new_struct.insert_structure(i, f)
except:
pass
def initialize_db():
db_name = "data/almgsiX_clease_voldep.db"
settings = CEBulk(
Concentration(basis_elements=[['Al', 'Mg', 'Si', 'X']]),
crystalstructure='fcc',
a=4.05, size=[1, 1, 1], max_cluster_size=3,
max_cluster_dia=[5.0, 5.0],
db_name=db_name
)
settings.basis_func_type = 'binary_linear'
newStruct = NewStructures(settings)
# Insert all initial structures
counter = 0
with connect(db_local) as db:
for row in db.select():
counter += 1
print(f"Inserting structure {counter}")
name = f"group{row.group}"
atoms = row.toatoms()
newStruct.insert_structure(atoms, name=name)
data = pd.read_csv("data/bulk_mod_fit.csv")
db = connect(settings.db_name)
counter = 0
for row in data.itertuples():
print(f"Inserting final structure {counter}")
counter += 1
try:
name = f"group{row[1]}"
#print(name)
#exit()
E = row[2]
B = row[3]
V = row[4]
dBdP = row[5]
L = V**(1.0/3.0)
atoms = Atoms(cell=[L, L, L])
calc = SinglePointCalculator(atoms, energy=E)
atoms.set_calculator(calc)
print(name)
init_id = db.get([('name', '=', name)]).id
update_db(init_id, final_struct=atoms, db_name=settings.db_name,
custom_kvp_init={'bulk_mod': B, 'dBdP': dBdP})
except Exception as exc:
print(exc)
traceback.print_exc()
settings.save("data/settings_almgsiX_voldev.json")
def main():
conc = Concentration(basis_elements=[['Al', 'Mg']],
A_lb=[[10, 0]],
b_lb=[7])
settings = CEBulk(conc,
crystalstructure='fcc',
a=4.05,
size=[4, 4, 4],
max_cluster_size=4,
max_cluster_dia=[4.1, 4.1, 4.1],
db_name='almg_ce.db')
# Generate 30 structures
new_struct = NewStructures(settings, struct_per_gen=30)
new_struct.generate_random_structures()
def insert_from_db(old_db_name, setting):
db = connect(old_db_name)
names = []
for row in db.select(converged=1):
names.append(row.name)
ns = NewStructures(setting, struct_per_gen=10)
for name in names:
ignore = False
print(name)
init_struct = None
final_struct = None
energy = 0.0
num_occ = sum(1 for _ in db.select(name=name))
for row in db.select(name=name):
if row["calculator"] == "unknown":
energy = row.energy
init_struct = row.toatoms()
if num_occ != 2:
final_struct = row.toatoms()
elif row["calculator"] == 'none':
init_struct = row.toatoms()
fid = row.get('final_struct_id', -1)
if fid != -1:
final_struct = db.get(id=fid).toatoms()
energy = db.get(id=fid).get('energy', None)
if energy is None:
ignore = True
break
else:
final_struct = row.toatoms()
calc = SinglePointCalculator(final_struct, energy=energy)
final_struct.set_calculator(calc)
try:
ns.insert_structure(init_struct=init_struct,
final_struct=final_struct,
generate_template=True)
except Exception as exc:
print(str(exc))
def reconfigure_almgsi():
conc = Concentration(basis_elements=[["Al", "Mg", "Si"]])
kwargs = dict(crystalstructure="fcc", a=4.05, size=[1, 1, 1], \
db_name=db_name, max_cluster_size=4, concentration=conc, max_cluster_dia=[7.8, 5.0, 5.0])
ceBulk = CEBulk(**kwargs)
db = connect(db_name_old)
counter = 0
new_struct = NewStructures(ceBulk)
for row in db.select([('converged', '=', 1)]):
print("ROW: {}".format(counter))
counter += 1
init = row.toatoms()
final = init.copy()
energy = row.get('energy', None)
if energy is None:
final_struct_id = row.final_struct_id
energy = db.get(id=final_struct_id).energy
calc = SinglePointCalculator(final, energy=energy)
final.set_calculator(calc)
new_struct.insert_structure(init_struct=init, final_struct=final)
def main():
setting = settingFromJSON("almgsixSettings.json")
setting.db_name = 'almgsiX_dft.db'
new_struct = NewStructures(setting)
new_struct.insert_structures(traj_init="data/restricted_gs_5x1x1.traj")