def McSim(row):
Temp=int(row[:-1])
conc_name=int(row[-1:])
print("Temperature is %s"%Temp, ",Concentration is %s"%conc_name, "\nChecking for files and directories")
db_name="FixedCell.db"
pathid="%sK"%Temp+"_Parallel"
default_path="/panfs/pfs.local/home/s376r951/Latest_Project/VASPDFT/StartingFresh/ParallelStorage" #Default path
home_path="/panfs/pfs.local/home/s376r951/Latest_Project/VASPDFT/StartingFresh"
dirname="{}".format(pathid)
dirpath=os.path.join(default_path, dirname)
os.chdir(home_path)
conc=Concentration(basis_elements=[['Au', 'Cu']])
settings=CEBulk(crystalstructure='fcc', a=3.8, size=[3,3,3],
concentration=conc, db_name=db_name,
max_cluster_size=4,
max_cluster_dia=[6.0,5.0,5.0])
os.mkdir(default_path+"%s"%pathid)
os.chdir(dirpath)
os.mkdir(dirpath+"/MeanEnergy")
os.mkdir(dirpath+"/EnergyEvol")
os.mkdir(dirpath+"/Variance")
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(argv):
conc = Concentration(basis_elements=[["Al", "Mg", "Si"]])
kwargs = dict(crystalstructure="fcc",
a=4.05,
size=[4, 4, 4],
db_name=db_name,
max_cluster_size=4,
concentration=conc,
basis_function="sanchez",
max_cluster_dia=[7.8, 5.0, 5.0])
setting = CEBulk(**kwargs)
# insert_from_db("almgsi.db", setting)
evaluate(setting)
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()
from clease import Concentration
from clease import CECrystal
basis_elements = [['Fe', 'X'], ['Fe'], ['O']]
conc = Concentration(basis_elements=basis_elements)
conc.set_conc_ranges[[(0.83333, 0.83333), (0.16667, 0.16667)], [(1, 1)],
[(1, 1)]]
print(conc.get_random_concentration())
bsg = CECrystal(basis=[(0.5, 0.5, 0.5), (0.1250, 0.1250, 0.1250),
(0.2549, 0.2549, 0.2549)],
cellpar=[5.9355, 5.9355, 5.9355, 60.0000, 60.0000, 60.0000],
supercell_factor=92,
concentration=conc,
db_name="clusterexpansion.db",
max_cluster_size=4,
max_cluster_dia=[7.6, 7.6, 4.0],
ignore_background_atoms=True)
from scipy.spatial import ConvexHull
# from atomtools.ce import ChemicalPotentialEstimator
from ase.calculators.singlepoint import SinglePointCalculator
from ase.visualize import view
from clease import Concentration
eci_fname = "data/almgsi_fcc_eci_newconfig.json"
#db_name = "almgsi_newconfig.db"
#db_name = "almgsi_multiple_templates.db"
#db_name = "almgsi_multiple_templates_dec10.db"
#db_name = "almgsi_sluiter.db"
#eci_fname = "data/almgsi_fcc_eci_sluiter.json"
# db_name_cubic = "almgsi_cubic.db"
db_name = "almgsi.db"
conc_fit = Concentration(basis_elements=[["Al", "Mg", "Si"]])
conc_fit.set_conc_ranges([[(0, 1), (0, 1), (0, 0.55)]])
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)