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 new_db(kwargs, new_db_name):
db_name = "almgsi_newconfig.db"
kwargs["db_name"] = new_db_name
bc = BulkCrystal(**kwargs)
names = []
db = connect(db_name)
for row in db.select(converged=1):
names.append(row.name)
ns = GenerateStructures(bc, struct_per_gen=10)
for name in names:
print(name)
init_struct = None
final_struct = None
energy = 0.0
for row in db.select(name=name):
if row["calculator"] == "unknown":
energy = row.energy
init_struct = row.toatoms()
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 main(argv):
option = argv[0]
N = 4
conc = Concentration(basis_elements=[["Al", "Mg", "Si", "X"]])
kwargs = dict(crystalstructure="fcc", a=4.05, size=[N,N,N],
db_name=db_name, max_cluster_size=4, max_cluster_dia=[0.0, 0.0, 5.0, 4.1, 4.1],
concentration=conc)
ceBulk = BulkCrystal(**kwargs)
struc_generator = GenerateStructures( ceBulk, struct_per_gen=10, generation_number=100 )
if option == "reconfig_settings":
ceBulk.reconfigure_settings()
elif option == "insert":
fname = argv[1]
struc_generator.insert_structure(init_struct=fname)
elif option == "random":
atoms = get_random_structure()
struc_generator.insert_structure(init_struct=atoms)
elif option == "evaluate":
evaluate(ceBulk)
elif option == "newdb":
new_db_name = argv[1]
new_db(kwargs, new_db_name)
elif option == "reconfig_db":
corr_func = CorrFunction(ceBulk, parallel=True)
scond = [("calculator", "!=", "gpaw"),
("name", "!=", "information"),
("name", "!=", "template"),
("converged", "=", 1)]
corr_func.reconfigure_db_entries(select_cond=scond)
elif option == "gs":
get_gs_allgs(ceBulk, struc_generator)
def main(argv):
option = argv[0]
atoms = bulk("Al")
N = 4
atoms = atoms*(N, N, N)
conc = Concentration(basis_elements=[["Al","Mg","Si"]])
kwargs = dict(crystalstructure="fcc", a=4.05, size=[N, N, N], \
db_name=db_name, max_cluster_size=4, concentration=conc,
basis_function="sanchez", max_cluster_dia=[7.8, 5.0, 5.0])
ceBulk = BulkCrystal(**kwargs)
#ceBulk.reconfigure_settings()
#print (ceBulk.basis_functions)
#cf = CorrFunction( ceBulk, parallel=True)
#cf.reconfigure_db_entries(select_cond=[("converged","=","1")])
#exit()
#print(ceBulk.basis_functions)
struc_generator = GenerateStructures( ceBulk, struct_per_gen=10 )
if ( option == "generateNew" ):
struc_generator.generate_probe_structure()
elif ( option == "eval" ):
#evaluate(ceBulk)
#evaluate_l1(ceBulk)
evaluate_test(ceBulk)
#evaluate_car(ceBulk)
#evaluate_sklearn(ceBulk)
elif option == "skew":
insert_skewed_full(struc_generator, size1=int(argv[1]), size2=int(argv[2]))
elif ( option == "insert" ):
fname = argv[1]
atoms = read(fname)
struc_generator.insert_structure( init_struct=atoms )
#insert_specific_structure( ceBulk, struc_generator, atoms )
elif ( option == "formation" ):
enthalpy_of_formation(ceBulk)
elif ( option == "gsstruct" ):
if ( len(argv) != 3 ):
raise ValueError( "If option is gsstruct. The arguments has to be gsstruct mg_conc si_conc" )
mg_conc = float( argv[1] )
si_conc = float( argv[2] )
find_gs_structure( ceBulk, mg_conc, si_conc )
elif ( option == "update_conc_range" ):
update_in_conc_range()
elif ( option == "allgs" ):
find_all_gs( ceBulk, struc_generator )
elif( option == "cv_hist" ):
lambdas = np.logspace(-7,-3,8)
history = CVScoreHistory(setting=ceBulk, penalization="L1", select_cond=[("in_conc_range","=","1")] )
history.get_history( lambdas=lambdas )
history.plot()
plt.show()
elif( option == "chempot" ):
estimate_chemical_potentials(ceBulk)
elif (option == "convert2cubic"):
convert_to_cubic(ceBulk)
elif option == "new_db":
new_db_name = argv[1]
new_db(kwargs, new_db_name)
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 new_db(kwargs, new_db_name):
from ase.db import connect
from ase.calculators.singlepoint import SinglePointCalculator
old_db_name = kwargs["db_name"]
kwargs["db_name"] = new_db_name
ceBulk = BulkCrystal(**kwargs)
struc_generator = GenerateStructures( ceBulk, struct_per_gen=10 )
names = []
db = connect(old_db_name)
for row in db.select(converged=1):
names.append(row.name)
for name in names:
row = db.get(name=name, struct_type='initial')
calc = row.get("calculator", "")
energy = None
init_struct = row.toatoms()
if calc == "unknown":
energy = row.energy
if calc == "":
final_struct = db.get(id=row.final_struct_id).toatoms()
else:
try:
final_struct = db.get(name=name, struct_type='final').toatoms()
except KeyError:
final_struct = db.get(name=name, calculator='gpaw').toatoms()
if energy is not None:
sp = SinglePointCalculator(final_struct, energy=energy)
final_struct.set_calculator(sp)
assert final_struct.get_calculator() is not None
try:
struc_generator.insert_structure(init_struct=init_struct, final_struct=final_struct)
except Exception as exc:
print(str(exc))
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")