def test_double_swaps(self):
if not has_ase_with_ce:
self.skipTest("ASE version does not have CE")
return
for lat in self.lattices:
calc, ceBulk, eci = self.get_calc(lat)
corr_func = CorrFunction(ceBulk)
cf = corr_func.get_cf(ceBulk.atoms)
n_tests = 10
# Insert 25 Mg atoms
for i in range(25):
calc.calculate( ceBulk.atoms, ["energy"], [(i,"Al","Mg")] )
# Swap Al and Mg 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)])
updated_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names( ceBulk.atoms, updated_cf.keys() )
for key,value in brute_force.items():
self.assertAlmostEqual( value, updated_cf[key] )
def test_sequence_of_swap_moves(self):
if (not has_ase_with_ce):
self.skipTest("ASE does not have CE")
return
calc,ceBulk,eci = self.get_calc("fcc")
corr_func = CorrFunction(ceBulk)
cf = corr_func.get_cf(ceBulk.atoms)
n_tests = 10
# Insert 10 Mg atoms
for i in range(n_tests):
calc.calculate( ceBulk.atoms, ["energy"], [(i,"Al","Mg")] )
# Swap Al and Mg atoms
changes = []
for i in range(n_tests):
indx1 = i
indx2 = len(ceBulk.atoms)-i-1
symb1 = "Mg"
symb2 = "Al"
changes += [(indx1,symb1,symb2),(indx2,symb2,symb1)]
calc.calculate( ceBulk.atoms, ["energy"], changes )
updated_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names( ceBulk.atoms, updated_cf.keys() )
for key,value in brute_force.items():
self.assertAlmostEqual( value, updated_cf[key] )
def __init__(self, BC):
self.bc = BC
cf_obj = CorrFunction(self.bc)
self.init_cf = cf_obj.get_cf(self.bc.atoms)
ecis = {key: 1.0
for key in self.init_cf.keys()} # ECIs do not matter here
self.calc = CE(self.bc, ecis, initial_cf=self.init_cf)
self.bc.atoms.set_calculator(self.calc)
self.elements = self.bc.basis_elements[
0] # This should be updated to handle different site types
self.status_every_sec = 30
N = len(ecis.keys()) - 1
self.cov_matrix = np.zeros((N, N))
self.exp_value = np.zeros(N)
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 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_update(self):
if not has_ase_with_ce:
self.skipTest("ASE version does not have CE")
for lat in self.lattices:
msg = "Failed for lattice {}".format(lat)
calc, ceBulk, eci = self.get_calc(lat)
cf = CorrFunction(ceBulk)
n_tests = 10
for i in range(n_tests):
old_symb = ceBulk.atoms[i].symbol
if old_symb == "Al":
new_symb = "Mg"
else:
new_symb = "Al"
calc.update_cf((i, old_symb, new_symb))
updated_cf = calc.get_cf()
brute_force = cf.get_cf(ceBulk.atoms)
for key, value in updated_cf.items():
self.assertAlmostEqual(value, brute_force[key], msg=msg)
def test_binary_spacegroup( self ):
if ( not has_ase_with_ce ):
self.skipTest("ASE version does not have CE")
return
bs, db_name = get_bulkspacegroup_binary()
cf = CorrFunction( bs )
cf_vals = cf.get_cf( bs.atoms )
ecis = {name:1.0 for name in cf_vals.keys()}
calc = CE( bs, ecis )
bs.atoms.set_calculator( calc )
for i in range(25):
if ( bs.atoms[i].symbol == "Al" ):
new_symb = "Mg"
old_symb = "Al"
else:
new_symb = "Al"
old_symb = "Mg"
calc.calculate( bs.atoms, ["energy"], [(i,old_symb,new_symb)] )
updated_cf = calc.get_cf()
brute_force = cf.get_cf_by_cluster_names( bs.atoms, updated_cf.keys() )
for key,value in brute_force.items():
self.assertAlmostEqual( value, updated_cf[key] )
def test_random_swaps(self):
if not has_ase_with_ce:
self.skipTest("ASE version does not have CE")
return
for lat in self.lattices:
msg = "Failed for lattice {}".format(lat)
calc, ceBulk, eci = self.get_calc(lat)
n_tests = 10
corr_func = CorrFunction(ceBulk)
cf = corr_func.get_cf(ceBulk.atoms)
for i in range(n_tests):
indx = np.random.randint(low=0, high=len(ceBulk.atoms))
old_symb = ceBulk.atoms[indx].symbol
if old_symb == "Al":
new_symb = "Mg"
else:
new_symb = "Al"
calc.calculate(ceBulk.atoms, ["energy"],
[(indx, old_symb, new_symb)])
updated_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names(ceBulk.atoms, updated_cf.keys())
for key, value in updated_cf.items():
self.assertAlmostEqual(value, brute_force[key], msg=msg)