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_set_singlets( self ):
if ( not has_ase_with_ce ):
self.skipTest( "ASE version does not have CE" )
return
system_types = [["Al","Mg"],["Al","Mg","Si"],["Al","Mg","Si","Cu"]]
db_name = "test_singlets.db"
n_concs = 4
no_throw = True
msg = ""
try:
for basis_elems in system_types:
conc_args = {
"conc_ratio_min_1":[[1,0]],
"conc_ratio_max_1":[[0,1]],
}
a = 4.05
mx_dia_name = get_max_cluster_dia_name()
size_arg = {mx_dia_name:a}
ceBulk = CEBulk( crystalstructure="fcc", a=a, size=[5, 5, 5], basis_elements=[basis_elems], conc_args=conc_args, \
db_name=db_name, max_cluster_size=2,**size_arg)
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 )
for _ in range(n_concs):
conc = np.random.rand(len(basis_elems))*0.97
conc /= np.sum(conc)
conc_dict = {}
for i in range(len(basis_elems)):
conc_dict[basis_elems[i]] = conc[i]
calc.set_composition(conc_dict)
ref_cf = calc.get_cf()
singlets = {}
for key,value in ref_cf.items():
if ( key.startswith("c1") ):
singlets[key] = value
comp = calc.singlet2comp(singlets)
dict_comp = "Ref {}. Computed {}".format(conc_dict,comp)
for key in comp.keys():
self.assertAlmostEqual( comp[key], conc_dict[key], msg=dict_comp, places=1 )
calc.set_singlets(singlets)
except Exception as exc:
msg = str(exc)
no_throw = False
self.assertTrue( no_throw, msg=msg )
def test_double_swaps_ternary( self ):
if ( not has_ase_with_ce ): # Disable this test
self.skipTest("ASE version has not cluster expansion")
return
db_name = "test_db_ternary.db"
conc_args = {
"conc_ratio_min_1":[[4,0,0]],
"conc_ratio_max_1":[[0,4,0]],
"conc_ratio_min_1":[[2,2,0]],
"conc_ratio_max_2":[[1,1,2]]
}
max_dia = get_max_cluster_dia_name()
size_arg = {max_dia:4.05}
ceBulk = CEBulk( crystalstructure="fcc", a=4.05, size=[4,4,4], basis_elements=[["Al","Mg","Si"]], \
conc_args=conc_args, db_name=db_name, max_cluster_size=3, **size_arg)
ceBulk.reconfigure_settings()
corr_func = CorrFunction( ceBulk )
cf = corr_func.get_cf( ceBulk.atoms )
#prefixes = [name.rpartition("_")[0] for name in cf.keys()]
#prefixes.remove("")
eci = {name:1.0 for name in cf.keys()}
calc = CE( ceBulk, eci )
n_tests = 10
# Insert 25 Mg atoms and 25 Si atoms
n = 18
for i in range(n):
calc.calculate( ceBulk.atoms, ["energy"], [(i,"Al","Mg")])
calc.calculate( ceBulk.atoms, ["energy"], [(i+n,"Al","Si")])
updated_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names( ceBulk.atoms, updated_cf.keys() )
for key in updated_cf.keys():
self.assertAlmostEqual( brute_force[key], updated_cf[key])
# Swap atoms
for i in range(n_tests):
indx1 = np.random.randint(low=0,high=len(ceBulk.atoms))
symb1 = ceBulk.atoms[indx1].symbol
indx2 = indx1
symb2 = symb1
while( symb2 == symb1 ):
indx2 = np.random.randint( low=0, high=len(ceBulk.atoms) )
symb2 = ceBulk.atoms[indx2].symbol
calc.calculate( ceBulk.atoms, ["energy"], [(indx1,symb1,symb2),(indx2,symb2,symb1)])
update_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names( ceBulk.atoms, update_cf.keys() )
for key,value in brute_force.items():
self.assertAlmostEqual( value, update_cf[key])
def init_bulk_crystal(self):
max_dia_name = get_max_cluster_dia_name()
size_arg = {max_dia_name: 4.05}
conc = Concentration(basis_elements=[["Al", "Mg", "Si"]])
ceBulk = CEBulk(crystalstructure="fcc",
a=4.05,
size=[3, 3, 3],
concentration=conc,
db_name=db_name,
max_cluster_size=3,
**size_arg)
ceBulk.reconfigure_settings()
atoms = ceBulk.atoms.copy()
calc = CE(atoms, ceBulk, ecis)
return ceBulk, atoms
def init_bulk_crystal(self):
conc_args = {
"conc_ratio_min_1": [[2, 1, 1]],
"conc_ratio_max_1": [[0, 2, 2]],
}
max_dia_name = get_max_cluster_dia_name()
size_arg = {max_dia_name: 4.05}
ceBulk = CEBulk(crystalstructure="fcc", a=4.05, size=[3, 3, 3],
basis_elements=[["Al", "Mg", "Si"]],
conc_args=conc_args, db_name=db_name,
max_cluster_size=3, **size_arg)
ceBulk.reconfigure_settings()
calc = CE(ceBulk, ecis)
ceBulk.atoms.set_calculator(calc)
return ceBulk
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_calc(self, lat):
db_name = "test_db_{}.db".format(lat)
conc = Concentration(basis_elements=[["Al", "Mg"]])
a = 4.05
ceBulk = CEBulk(crystalstructure=lat, a=a, size=[3, 3, 3],
concentration=conc, db_name=db_name,
max_cluster_size=3, max_cluster_dia=6.0)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
corrfuncs = cf.get_cf(ceBulk.atoms)
eci = {name: 1.0 for name in corrfuncs.keys()}
atoms = ceBulk.atoms.copy()
calc = CE(atoms, ceBulk, eci)
atoms.set_calculator(calc)
return atoms, ceBulk, eci
def get_calc(self, lat):
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)
return calc, ceBulk, eci
def test_ignore_atoms(self):
if not has_ase_with_ce:
self.skipTest("ASE does not have CE")
from cemc.mcmc import FixedElement
no_trow = True
msg = ""
try:
from copy import deepcopy
conc = Concentration(basis_elements=[['V', 'Li'], ['O']])
kwargs = {
"crystalstructure": "rocksalt",
"concentration": conc,
"a": 4.12,
'size': [2, 2, 2],
'cubic': True,
"max_cluster_size": 4,
"max_cluster_dia": 4.12,
"db_name": 'database.db',
'basis_function': 'sluiter',
'ignore_background_atoms': True
}
fix_elem = FixedElement(element="O")
kw_args_cpy = deepcopy(kwargs)
ceBulk = CEBulk(**kw_args_cpy)
ecis = get_example_ecis(ceBulk)
atoms = get_atoms_with_ce_calc(ceBulk,
kwargs,
eci=ecis,
size=[3, 3, 3],
db_name="ignore_test_large.db")
calc = atoms.get_calculator()
# Insert some Li atoms
num_li = 5
symbols = [atom.symbol for atom in atoms]
num_inserted = 0
for i in range(0, len(symbols)):
if symbols[i] == "V":
symbols[i] = "Li"
num_inserted += 1
if num_inserted >= num_li:
break
calc.set_symbols(symbols)
mc = Montecarlo(atoms, 800)
mc.add_constraint(fix_elem)
mc.runMC(steps=100, equil=False, mode="fixed")
# Clean up files
os.remove("ignore_test_large.db")
os.remove("database.db")
except Exception as exc:
no_trow = False
msg = str(exc)
self.assertTrue(no_trow, msg=msg)
def init_bulk_crystal(self):
conc1 = Concentration(basis_elements=[["Al","Mg"]])
conc2 = Concentration(basis_elements=[["Al","Mg"]])
ceBulk1 = CEBulk(crystalstructure="fcc", a=4.05, size=[3,3,3], concentration=conc1, db_name=db_name,
max_cluster_dia=4.5)
ceBulk1.reconfigure_settings()
ceBulk2 = CEBulk(crystalstructure="fcc", a=4.05, size=[3,3,3], concentration=conc2, db_name=db_name,
max_cluster_dia=4.5)
ceBulk2.reconfigure_settings()
atoms1 = ceBulk1.atoms.copy()
atoms2 = ceBulk2.atoms.copy()
for atom in atoms2:
atom.symbol = "Mg"
return ceBulk1, ceBulk2, atoms1, atoms2
def test_supercell( self ):
if ( not has_ase_with_ce ):
self.skipTest("ASE version does not have CE")
return
calc, ceBulk, eci = self.get_calc("fcc")
db_name = "test_db_fcc_super.db"
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": db_name,
"max_cluster_size": 3,
"max_cluster_dia": 4.05
}
kwargs_template = copy.deepcopy(kwargs)
kwargs_template["size"] = [4, 4, 4]
kwargs_template["db_name"] = "template_bc.db"
template_supercell_bc = CEBulk(**kwargs_template)
template_supercell_bc.reconfigure_settings()
ceBulk = CEBulk(**kwargs)
ceBulk.reconfigure_settings()
calc = get_ce_calc(ceBulk, kwargs, eci, size=[4, 4, 4],
db_name="sc4x4x.db")
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
corr_func = CorrFunction(template_supercell_bc)
for i in range(10):
calc.calculate(ceBulk.atoms, ["energy"], [(i, "Al", "Mg")])
updated_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names(
ceBulk.atoms, list(updated_cf.keys()))
for key, value in brute_force.items():
self.assertAlmostEqual(value, updated_cf[key])
os.remove("sc4x4x.db")
def test_self_interactions(self):
if not has_ase_with_ce:
self.skipTest("ASE does not have CE")
from cemc.ce_calculator import SelfInteractionError
a = 4.05
conc = Concentration(basis_elements=[["Au", "Cu", "Ti"]])
db_name = "test_self_interactoins.db"
kwargs = dict(crystalstructure="fcc", a=a, size=[3, 3, 3],
concentration=conc, db_name=db_name,
max_cluster_size=2, max_cluster_dia=5.0)
ceBulk = CEBulk(**kwargs)
atoms = get_atoms_with_ce_calc(ceBulk, kwargs, eci={'c0': 1.0},
size=[8, 8, 8], db_name=db_name)
with self.assertRaises(SelfInteractionError):
atoms = get_atoms_with_ce_calc(ceBulk, kwargs, eci={'c0': 1.0},
size=[1, 1, 1], db_name=db_name)
os.remove(db_name)
def init_bulk_crystal(self):
conc_args = {
"conc_ratio_min_1": [[1, 0]],
"conc_ratio_max_1": [[0, 1]],
}
ceBulk1 = CEBulk(crystalstructure="fcc",
a=4.05,
size=[3, 3, 3],
basis_elements=[["Al", "Mg"]],
conc_args=conc_args,
db_name=db_name)
ceBulk1.reconfigure_settings()
ceBulk2 = CEBulk(crystalstructure="fcc",
a=4.05,
size=[3, 3, 3],
basis_elements=[["Al", "Mg"]],
conc_args=conc_args,
db_name=db_name)
ceBulk2.reconfigure_settings()
for atom in ceBulk2.atoms:
atom.symbol = "Mg"
return ceBulk1, ceBulk2
