def test_gs_finder(self):
if (not has_CE):
self.skipTest("ASE version does not have CE")
return
no_throw = True
msg = ""
try:
db_name = "test_db_gsfinder.db"
conc_args = {
"conc_ratio_min_1": [[1, 0]],
"conc_ratio_max_1": [[0, 1]],
}
a = 4.05
ceBulk = CEBulk( crystalstructure="fcc", a=a, size=[3,3,3], basis_elements=[["Al","Mg"]], conc_args=conc_args, \
db_name=db_name, max_cluster_size=4)
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
eci = {key: 1.0 for key in cf.keys()}
gsfinder = GSFinder()
comp = {"Al": 0.5, "Mg": 0.5}
gsfinder.get_gs(ceBulk, eci, composition=comp)
except Exception as exc:
msg = str(exc)
no_throw = False
self.assertTrue(no_throw, msg=msg)
def get_eci():
bc = CEBulk(**bc_kwargs)
bc.reconfigure_settings()
cf = CorrFunction(bc)
cf = cf.get_cf(bc.atoms)
eci = {key: 0.001 for key in cf.keys()}
return eci
def insert_specific_structure(ceBulk, struct_gen, atoms):
cf = CorrFunction(ceBulk)
kvp = cf.get_cf(atoms)
conc = struct_gen.find_concentration(atoms)
print(conc)
if (struct_gen.exists_in_db(atoms, conc[0], conc[1])):
raise RuntimeError(
"The passed structure already exists in the database")
kvp = struct_gen.get_kvp(atoms, kvp, conc[0], conc[1])
struct_gen.setting.db.write(atoms, kvp)
def test_network(self):
if (not available):
self.skipTest("ASE version does not have CE!")
return
msg = ""
no_throw = True
try:
db_name = "test_db_network.db"
conc = Concentration(basis_elements=[["Al", "Mg"]])
a = 4.05
ceBulk = CEBulk(crystalstructure="fcc",
a=a,
size=[3, 3, 3],
concentration=conc,
db_name=db_name,
max_cluster_size=3,
max_cluster_dia=4.5)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
atoms = ceBulk.atoms.copy()
cf = cf.get_cf(atoms)
eci = {key: 0.001 for key in cf.keys()}
calc = CE(atoms, ceBulk, eci=eci)
trans_mat = ceBulk.trans_matrix
for name, info in ceBulk.cluster_info[0].items():
if info["size"] == 2:
net_name = name
break
obs = NetworkObserver(calc=calc,
cluster_name=[net_name],
element=["Mg"])
# Several hard coded tests
calc.update_cf((0, "Al", "Mg"))
size = 2
clusters = ceBulk.cluster_info[0][net_name]["indices"]
for sub_clust in clusters:
calc.update_cf((sub_clust[0], "Al", "Mg"))
# Call the observer
obs(None)
res = obs.fast_cluster_tracker.get_cluster_statistics_python()
self.assertEqual(res["cluster_sizes"][0], size)
size += 1
obs.get_indices_of_largest_cluster_with_neighbours()
os.remove("test_db_network.db")
except Exception as exc:
msg = "{}: {}".format(type(exc).__name__, str(exc))
no_throw = False
self.assertTrue(no_throw, msg=msg)
def get_cebulk(self):
conc = Concentration(basis_elements=[["Al","Mg"]])
ceBulk = CEBulk(crystalstructure="fcc", a=4.05, size=[3,3,3], concentration=conc, db_name=db_name,
max_cluster_size=3, max_cluster_dia=4.5)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
ecis = {key:1.0 for key in cf.keys()}
atoms = ceBulk.atoms.copy()
calc = CE( atoms, ceBulk, ecis )
return atoms
def get_cebulk(self):
conc_args = {
"conc_ratio_min_1":[[1,0]],
"conc_ratio_max_1":[[0,1]],
}
ceBulk = CEBulk( crystalstructure="fcc", a=4.05, size=[3,3,3], basis_elements=[["Al","Mg"]], conc_args=conc_args, db_name=db_name)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
ecis = {key:1.0 for key in cf.keys()}
calc = CE( ceBulk, ecis )
ceBulk.atoms.set_calculator(calc)
return ceBulk
def test_no_throw(self):
if (not has_CE):
self.skipTest("ASE version does not have ASE")
return
no_throw = True
msg = ""
try:
conc_args = {
"conc_ratio_min_1": [[1, 0]],
"conc_ratio_max_1": [[0, 1]],
}
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size": [3, 3, 3],
"basis_elements": [["Al", "Mg"]],
"conc_args": conc_args,
"db_name": "temporary_bcnucleationdb.db",
"max_cluster_size": 3
}
ceBulk = CEBulk(**kwargs)
cf = CorrFunction(ceBulk)
cf_dict = cf.get_cf(ceBulk.atoms)
ecis = {key: 1.0 for key, value in cf_dict.items()}
#calc = CE( ceBulk, ecis, size=(3,3,3) )
calc = get_ce_calc(ceBulk,
kwargs,
ecis,
size=[6, 6, 6],
db_name="sc6x6x6.db")
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
chem_pot = {"c1_0": -1.069}
T = 300
mc = SGCFreeEnergyBarrier( ceBulk.atoms, T, symbols=["Al","Mg"], \
n_windows=5, n_bins=10, min_singlet=0.5, max_singlet=1.0 )
mc.run(nsteps=100, chem_pot=chem_pot)
mc.save(fname="free_energy_barrier.json")
# Try to load the object stored
mc = SGCFreeEnergyBarrier.load(ceBulk.atoms,
"free_energy_barrier.json")
mc.run(nsteps=100, chem_pot=chem_pot)
mc.save(fname="free_energy_barrier.json")
os.remove("sc6x6x6.db")
except Exception as exc:
msg = str(exc)
no_throw = False
self.assertTrue(no_throw, msg=msg)
def get_small_BC_with_ce_calc(lat="fcc"):
db_name = "test_db_{}.db".format(lat)
a = 4.05
conc = Concentration(basis_elements=[["Al", "Mg"]])
ceBulk = CEBulk( crystalstructure=lat, a=a, size=[3,3,3], concentration=conc, \
db_name=db_name, max_cluster_size=3, max_cluster_dia=4.5)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
corrfuncs = cf.get_cf(ceBulk.atoms)
eci = {name: 1.0 for name in corrfuncs.keys()}
calc = CE(ceBulk.atoms.copy(), ceBulk, eci)
#ceBulk.atoms.set_calculator(calc)
return ceBulk, calc
def test_no_throw(self):
if (not has_ase_with_ce):
self.skipTest("The ASE version does not include the CE module!")
return
no_throw = True
msg = ""
try:
db_name = "test_db.db"
conc = Concentration(basis_elements=[["Al", "Mg"]])
ceBulk = CEBulk(crystalstructure="fcc",
a=4.05,
size=[3, 3, 3],
concentration=conc,
db_name=db_name,
max_cluster_size=3,
max_cluster_dia=4.5)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
ecis = {key: 0.001 for key in cf.keys()}
atoms = ceBulk.atoms.copy()
calc = Clease(ceBulk, cluster_name_eci=ecis) # Bug in the update
atoms.set_calculator(calc)
#ceBulk.atoms.set_calculator( calc )
mf = MeanFieldApprox(atoms, ceBulk)
chem_pot = {"c1_0": -1.05}
betas = np.linspace(1.0 / (kB * 100), 1.0 / (kB * 800), 50)
G = mf.free_energy(betas, chem_pot=chem_pot)
G = mf.free_energy(betas) # Try when chem_pot is not given
U = mf.internal_energy(betas, chem_pot=chem_pot)
U = mf.internal_energy(betas)
Cv = mf.heat_capacity(betas, chem_pot=chem_pot)
Cv = mf.heat_capacity(betas)
atoms = ceBulk.atoms.copy()
atoms[0].symbol = "Mg"
atoms[1].symbol = "Mg"
calc = CE(atoms, ceBulk, eci=ecis)
#ceBulk.atoms.set_calculator(calc)
# Test the Canonical MFA
T = [500, 400, 300, 200, 100]
canonical_mfa = CanonicalMeanField(atoms=atoms, T=T)
res = canonical_mfa.calculate()
except Exception as exc:
no_throw = False
msg = str(exc)
self.assertTrue(no_throw, msg=msg)
def get_small_BC_with_ce_calc(lat="fcc"):
db_name = "test_db_{}.db".format(lat)
conc_args = {
"conc_ratio_min_1":[[1,0]],
"conc_ratio_max_1":[[0,1]],
}
a = 4.05
ceBulk = CEBulk( crystalstructure=lat, a=a, size=[3,3,3], basis_elements=[["Al","Mg"]], conc_args=conc_args, \
db_name=db_name, max_cluster_size=3)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
corrfuncs = cf.get_cf(ceBulk.atoms)
eci = {name:1.0 for name in corrfuncs.keys()}
calc = CE( ceBulk, eci )
ceBulk.atoms.set_calculator(calc)
return ceBulk
def test_no_throw(self):
no_throw = True
if not available:
self.skipTest(reason)
return
msg = ""
# try:
conc_args = {
"conc_ratio_min_1": [[1, 0]],
"conc_ratio_max_1": [[0, 1]],
}
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size": [4, 4, 4],
"basis_elements": [["Al", "Mg"]],
"conc_args": conc_args,
"db_name": "data/temporary_bcnucleationdb.db",
"max_cluster_size": 3
}
ceBulk = CEBulk(**kwargs)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
ecis = {key: 1.0 for key in cf.keys()}
calc = CE(ceBulk, ecis)
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
T = 500
c_mg = 0.4
comp = {"Mg": c_mg, "Al": 1.0 - c_mg}
calc.set_composition(comp)
act_sampler = ActivitySampler(ceBulk.atoms,
T,
moves=[("Al", "Mg")],
mpicomm=comm)
act_sampler.runMC(mode="fixed", steps=1000)
act_sampler.get_thermodynamic()
# except Exception as exc:
# msg = str(exc)
# no_throw = False
self.assertTrue(no_throw, msg=msg)
def get_example_ecis(bc=None,bc_kwargs=None):
if ( bc is not None ):
cf = CorrFunction(bc)
else:
bc = CEBulk(**bc_kwargs)
cf = CorrFunction(bc)
cf = cf.get_cf(bc.atoms)
eci = {key: 0.001 for key in cf.keys()}
return eci
def get_example_ecis(bc=None):
cf = CorrFunction(bc)
cf = cf.get_cf(bc.atoms)
eci = {key: 0.001 for key in cf.keys()}
return eci
def get_example_cf(bc=None, atoms=None):
cf = CorrFunction(bc)
cf = cf.get_cf(atoms)
return cf
def test_no_throw(self):
if not available:
self.skipTest("ASE version does not have CE!")
return
no_throw = True
msg = ""
try:
db_name = "temp_nuc_db.db"
if os.path.exists(db_name):
os.remove(db_name)
conc = Concentration(basis_elements=[["Al", "Mg"]])
kwargs = {
"crystalstructure": "fcc", "a": 4.05,
"size": [3, 3, 3],
"concentration": conc, "db_name": db_name,
"max_cluster_size": 3,
"max_cluster_dia": 4.5
}
ceBulk = CEBulk(**kwargs)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
ecis = {key: 0.001 for key in cf.keys()}
atoms = get_atoms_with_ce_calc(ceBulk, kwargs, ecis, size=[5, 5, 5],
db_name="sc5x5x5.db")
chem_pot = {"c1_0": -1.0651526881167124}
sampler = NucleationSampler(
size_window_width=10,
chemical_potential=chem_pot, max_cluster_size=20,
merge_strategy="normalize_overlap")
nn_name = get_network_name(ceBulk.cluster_family_names_by_size)
mc = SGCNucleation(
atoms, 30000, nucleation_sampler=sampler,
network_name=[nn_name], network_element=["Mg"],
symbols=["Al", "Mg"], chem_pot=chem_pot)
mc.runMC(steps=2, equil=False)
sampler.save(fname="test_nucl.h5")
mc = CanonicalNucleationMC(
atoms, 300, nucleation_sampler=sampler,
network_name=[nn_name], network_element=["Mg"],
concentration={"Al": 0.8, "Mg": 0.2}
)
symbs = [atom.symbol for atom in atoms]
symbs[0] = "Mg"
symbs[1] = "Mg"
mc.set_symbols(symbs)
#mc.runMC(steps=2)
sampler.save(fname="test_nucl_canonical.h5")
elements = {"Mg": 6}
calc = atoms.get_calculator()
calc.set_composition({"Al": 1.0, "Mg": 0.0})
mc = FixedNucleusMC(atoms, 300,
network_name=[nn_name], network_element=["Mg"])
mc.insert_symbol_random_places("Mg", num=1, swap_symbs=["Al"])
mc.runMC(steps=2, elements=elements, init_cluster=True)
os.remove("sc5x5x5.db")
except Exception as exc:
msg = str(exc)
msg += "\n" + traceback.format_exc()
no_throw = False
self.assertTrue(no_throw, msg=msg)