def find_gs_structure(ceBulk, mg_conc):
fname = "data/{}.json".format(db_name.split(".")[0])
with open(fname, 'r') as infile:
ecis = json.load(infile)
calc = CE(ceBulk, ecis)
ceBulk.atoms.set_calculator(calc)
conc = {"Mg": mg_conc, "Al": 1.0 - mg_conc}
calc.set_composition(conc)
print(ceBulk.basis_functions)
formula = ceBulk.atoms.get_chemical_formula()
temps = [
800, 700, 500, 300, 200, 100, 50, 20, 19, 18, 15, 14, 13, 12, 11, 10,
9, 8, 7, 6, 5, 4, 3, 2, 1
]
n_steps_per = 1000
lowest_struct = mcobs.LowestEnergyStructure(calc, None)
for T in temps:
print("Temperature {}".format(T))
mc_obj = mc.Montecarlo(ceBulk.atoms, T)
lowest_struct.mc_obj = mc_obj
mc_obj.attach(lowest_struct)
mc_obj.runMC(steps=n_steps_per, verbose=False)
thermo = mc_obj.get_thermodynamic()
print("Mean energy: {}".format(thermo["energy"]))
fname = "data/gs_structure%s.xyz" % (formula)
write(fname, lowest_struct.lowest_energy_atoms)
print("Lowest energy found: {}".format(lowest_struct.lowest_energy))
print("GS structure saved to %s" % (fname))
fname = "data/cf_functions_gs%s.csv" % (formula)
cf = calc.get_cf()
with open(fname, 'w') as outfile:
for key, value in cf.iteritems():
outfile.write("{},{}\n".format(key, value))
print("CFs saved to %s" % (fname))
return lowest_struct.lowest_energy
def test_chemical_potential(self):
if not available:
self.skipTest(avail_msg)
bc = get_ternary_BC()
ecis = {"c1_0": 0.0, "c1_1": 0.0}
atoms = bc.atoms.copy()
bf = bc.basis_functions
calc = CE(atoms, bc, eci=ecis)
groups = [{"Al": 2}, {"Mg": 1, "Si": 1}]
symbs = ["Al", "Mg", "Si"]
T = 400
chem_pots = [-0.2, -0.1, 0.0, 0.1, 0.2, 1.0]
all_al = ["Al" for _ in range(len(atoms))]
num_atom_per_fu = 2
for mu in chem_pots:
calc.set_symbols(all_al)
mc = PseudoBinarySGC(atoms,
T,
chem_pot=mu,
symbols=symbs,
groups=groups)
# At this point the chemical potentials should
# be updated
changes = [(0, "Al", "Mg"), (1, "Al", "Si")]
energy = calc.get_energy()
for change in changes:
calc.update_cf(change)
new_energy = calc.get_energy()
self.assertAlmostEqual(new_energy - energy, mu)
mc.reset_ecis()
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_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_gs(self,
BC,
ecis=None,
composition=None,
temps=None,
n_steps_per_temp=1000,
atoms=None):
"""
Computes the ground states
:param BC: Instance of *CEBulk* or *CECrystal* from ASE
:param ecis: Dictionary with the Effecitve Cluster Interactions
:param composition: Dictionary with compositions (i.e. {"Mg":0.2,"Al":0.8})
:param temps: List of cooling temperatures
:param n_steps_per_temp: Number of MC steps per temperature
"""
if atoms is None:
atoms = BC.atoms.copy()
if atoms.get_calculator() is None:
if ecis is None:
raise ValueError("When a calculator is not attached "
"the ECIs has to be given!")
calc = CE(atoms, BC, ecis)
else:
calc = atoms.get_calculator()
#print (calc.get_cf())
if (temps is None):
temps = np.linspace(1, 1500, 30)[::-1]
if (composition is not None):
calc.set_composition(composition)
minimum_energy = LowestEnergyStructure(calc, None)
for T in temps:
print("Temperature {}".format(T))
mc_obj = Montecarlo(atoms, T)
mc_obj.constraints = self.constraints
minimum_energy.mc_obj = mc_obj
mc_obj.attach(minimum_energy)
mc_obj.runMC(steps=n_steps_per_temp, verbose=False, equil=False)
thermo = mc_obj.get_thermodynamic()
result = {
"atoms": minimum_energy.atoms,
"energy": minimum_energy.lowest_energy,
"cf": minimum_energy.lowest_energy_cf
}
return result
def test_no_throw(self):
if not available:
self.skipTest(skipMsg)
no_throw = True
msg = ""
try:
bc = get_ternary_BC()
eci = get_example_ecis(bc)
atoms = bc.atoms.copy()
CE(atoms, bc, eci=eci)
mc = Montecarlo(atoms, 1000)
mc.insert_symbol_random_places("Mg", num=10, swap_symbs=["Al"])
# Note: convergence_factor should never be
# set to a negative value! Here it is done
# to make the test converged after one step
bias = AdaptiveBiasReactionPathSampler(
mc_obj=mc,
react_crd_init=DummyReacCrdInit(),
react_crd=[-1.0, 1.0],
convergence_factor=-1.0)
bias.run()
except Exception as exc:
msg = str(exc)
no_throw = False
self.assertTrue(no_throw, msg=msg)
def test_with_bias_potential(self):
if not available:
self.skipTest(avail_msg)
msg = ""
try:
os.remove("test_db_ternary.db")
except Exception:
pass
no_throw = True
try:
bc = get_ternary_BC()
ecis = get_example_ecis(bc=bc)
atoms = bc.atoms.copy()
calc = CE(atoms, bc, eci=ecis)
groups = [{"Al": 2}, {"Mg": 1, "Si": 1}]
symbs = ["Al", "Mg", "Si"]
T = 400
mc = PseudoBinarySGC(atoms,
T,
chem_pot=-0.2,
symbols=symbs,
groups=groups)
conc_init = PseudoBinaryConcInitializer(mc)
reac_crd = np.linspace(0.0, 1.0, 10)
bias_pot = reac_crd**2
bias = PseudoBinaryFreeEnergyBias(conc_init, reac_crd, bias_pot)
mc.add_bias(bias)
mc.runMC(mode="fixed", steps=100, equil=False)
os.remove("test_db_ternary.db")
except Exception as exc:
msg = "{}: {}".format(type(exc).__name__, str(exc))
no_throw = False
self.assertTrue(no_throw, msg)
def test_no_throw(self):
if not available:
self.skipTest(avail_msg)
msg = ""
try:
os.remove("test_db_ternary.db")
except Exception:
pass
no_throw = True
try:
bc = get_ternary_BC()
ecis = get_example_ecis(bc=bc)
atoms = bc.atoms.copy()
calc = CE(atoms, bc, eci=ecis)
groups = [{"Al": 2}, {"Mg": 1, "Si": 1}]
symbs = ["Al", "Mg", "Si"]
T = 400
mc = PseudoBinarySGC(atoms,
T,
chem_pot=-0.2,
symbols=symbs,
groups=groups)
mc.runMC(mode="fixed", steps=100, equil=False)
os.remove("test_db_ternary.db")
except Exception as exc:
msg = "{}: {}".format(type(exc).__name__, str(exc))
no_throw = False
self.assertTrue(no_throw, msg)
def test_pair_observer(self):
if not available:
self.skipTest(skip_msg)
no_throw = True
msg = ""
bc = get_ternary_BC()
ecis = get_example_ecis(bc=bc)
atoms = bc.atoms.copy()
calc = CE(atoms, bc, eci=ecis)
atoms.set_calculator(calc)
T = 1000
nn_names = [name for name in bc.cluster_family_names
if int(name[1]) == 2]
mc = FixedNucleusMC(
atoms, T, network_name=nn_names,
network_element=["Mg", "Si"])
mc.insert_symbol_random_places("Mg", swap_symbs=["Al"])
elements = {"Mg": 3, "Si": 3}
mc.grow_cluster(elements)
obs = PairObserver(mc.atoms, cutoff=4.1, elements=["Mg", "Si"])
mc.attach(obs)
mc.runMC(steps=200)
self.assertEqual(obs.num_pairs, obs.num_pairs_brute_force())
self.assertTrue(obs.symbols_is_synced())
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_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 __init__(self, ground_states):
self.calcs = []
self.orig_symbols = []
for ground_state in ground_states:
self.calcs.append(
CE(ground_state["atoms"],
ground_state["bc"],
ground_state["eci"],
initial_cf=ground_state["cf"]))
symbs = [atom.symbol for atom in ground_state["atoms"]]
self.orig_symbols.append(symbs)
def __init__(self, ground_states):
self.calcs = []
self.orig_symbols = []
for ground_state in ground_states:
self.calcs.append(
CE(ground_state["bc"],
ground_state["eci"],
initial_cf=ground_state["cf"]))
ground_state["bc"].atoms.set_calculator(self.calcs[-1])
symbs = [atom.symbol for atom in ground_state["bc"].atoms]
self.orig_symbols.append(symbs)
def get_atoms(self, atomID, eci):
"""
Returns an instance of the atoms object requested
"""
db = connect(self.wl_db_name)
row = db.get(id=atomID)
bcfname = row.key_value_pairs["bcfile"]
init_cf = row.data["cf"]
try:
with open(bcfname, 'rb') as infile:
bc, atoms = pck.load(infile)
calc = CE(atoms, bc, eci, initial_cf=init_cf)
return atoms
except IOError as exc:
print(str(exc))
print("Will try to recover the CEBulk object")
bc_kwargs = row.data["bc_kwargs"]
cetype = row.key_value_pairs["cetype"]
if (cetype == "CEBulk"):
small_bc = CEBulk(**bc_kwargs)
small_bc.reconfigure_settings()
else:
small_bc = CECrystal(**bc_kwargs)
small_bc.reconfigure_settings()
size = row.data["supercell_size"]
atoms = get_atoms_with_ce_calc(small_bc,
bc_kwargs,
eci=eci,
size=size)
calc = atoms.get_calculator()
# Determine the composition
count = row.count_atoms()
for key in count.keys():
count /= float(row.natoms)
calc.set_composition(count)
return atoms
except:
raise RuntimeError(
"Did not manage to return the atoms object with the proper calculator attached..."
)
def test_run(self):
if not available:
self.skipTest(reason)
bc = get_ternary_BC()
eci = get_example_ecis(bc)
atoms = bc.atoms.copy()
calc = CE(atoms, bc, eci=eci)
mc = Montecarlo(atoms, 1000000)
mc.insert_symbol_random_places("Mg", swap_symbs=["Al"], num=3)
performance_monitor = MultithreadPerformance(4)
performance_monitor.run(mc, 100)
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_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 init_bulk_crystal(self):
conc = Concentration(basis_elements=[["Al", "Mg", "Si"]])
ceBulk = CEBulk(crystalstructure="fcc",
a=4.05,
size=[4, 4, 4],
concentration=conc,
db_name=db_name,
max_cluster_size=2,
max_cluster_dia=4.0)
ceBulk.reconfigure_settings()
ecis = get_example_ecis(bc=ceBulk)
atoms = ceBulk.atoms.copy()
calc = CE(atoms, ceBulk, ecis)
return ceBulk, atoms
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 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 init_bulk_crystal(self):
conc_args = {
"conc_ratio_min_1": [[2, 1, 1]],
"conc_ratio_max_1": [[0, 2, 2]],
}
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=2,
max_cluster_dia=4.0)
ceBulk.reconfigure_settings()
ecis = get_example_ecis(bc=ceBulk)
calc = CE(ceBulk, ecis)
ceBulk.atoms.set_calculator(calc)
return ceBulk
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_raise_error_on_invalid_chem_pot(self):
if not available:
self.skipTest(avail_msg)
bc = get_ternary_BC()
ecis = get_example_ecis(bc=bc)
ecis.pop('c1_1')
atoms = bc.atoms.copy()
calc = CE(atoms, bc, eci=ecis)
atoms.set_calculator(calc)
groups = [{"Al": 2}, {"Mg": 1, "Si": 1}]
symbs = ["Al", "Mg", "Si"]
T = 400
with self.assertRaises(InvalidChemicalPotentialError):
PseudoBinarySGC(atoms,
T,
chem_pot=-0.2,
symbols=symbs,
groups=groups)
def test_save_load_calculator(self):
if not has_ase_with_ce:
self.skipTest("ASE does not have CE")
calc, ceBulk, eci = self.get_calc("fcc")
calc_fname = "calculator.json"
calc.save(calc_fname)
calc2 = CE.load(calc_fname)
os.remove(calc_fname)
self.assertEqual(calc.BC.cluster_info, calc2.BC.cluster_info)
self.assertEqual(calc.eci, calc2.eci)
self.assertEqual(calc.get_cf(), calc2.get_cf())
# Test to pickle a calculator
import pickle
pickled_string = pickle.dumps(calc)
calc2 = pickle.loads(pickled_string)
self.assertEqual(calc.BC.cluster_info, calc2.BC.cluster_info)
self.assertEqual(calc.eci, calc2.eci)
self.assertEqual(calc.get_cf(), calc2.get_cf())
def test_with_covariance_reac_crd(self):
if not available:
self.skipTest("ASE version does not have CE!")
msg = ""
no_throw = True
try:
bc = get_ternary_BC()
atoms = bc.atoms.copy()
ecis = get_example_ecis(bc=bc)
calc = CE(atoms, bc, eci=ecis)
#bc.atoms.set_calculator(calc)
T = 200
nn_names = [name for name in bc.cluster_family_names
if int(name[1]) == 2]
mc = FixedNucleusMC(
atoms, T, network_name=nn_names,
network_element=["Mg", "Si"])
elements = {"Mg": 4, "Si": 4}
mc.insert_symbol_random_places("Mg", num=1, swap_symbs=["Al"])
mc.grow_cluster(elements)
conc_init = CovarianceCrdInitializer(
fixed_nucl_mc=mc, matrix_element="Al",
cluster_elements=["Mg", "Si"])
mc.runMC(steps=100, init_cluster=False)
match, match_msg = self._spherical_nano_particle_matches(conc_init)
self.assertTrue(match, msg=match_msg)
except Exception as exc:
no_throw = False
msg = str(exc)
self.assertTrue(no_throw, msg=msg)
class PopulationVariance(object):
"""
Object that estimates the covariance and the mean of all the
correlation functions in the population
"""
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 swap_random_atoms(self):
"""
Changes the symbol of a random atom
"""
indx = np.random.randint(low=0, high=len(self.bc.atoms))
symb = self.bc.atoms[indx].symbol
new_symb = self.elements[np.random.randint(low=0,
high=len(self.elements))]
system_change = [(indx, symb, new_symb)]
self.bc.atoms._calc.calculate(self.bc.atoms, ["energy"], system_change)
def estimate(self, n_probe_structures=10000, fname=""):
"""
Estimate the covariance matrix
"""
if (fname != ""):
if (not fname.endswith(".json")):
raise ValueError(
"The program is going to write a json file so the file extension should be .json"
)
step = 0
cfs = []
cur_time = time.time()
while (step < n_probe_structures):
step += 1
if (time.time() - cur_time > self.status_every_sec):
print("Step {} of {}".format(step, n_probe_structures))
cur_time = time.time()
for i in range(len(self.bc.atoms)):
self.swap_random_atoms()
new_cfs = self.calc.get_cf()
cf_array = [
new_cfs[key] for key in self.init_cf.keys() if key != "c0"
] # Make sure that the order is the same as in init_cf
self.update_cov_matrix(cf_array)
cfs = np.array(cfs)
cov = self.cov_matrix / n_probe_structures
mu = self.exp_value / n_probe_structures
cov -= np.outer(mu, mu)
return cov, mu
def array2dict(self, cov, mu):
"""
Converts an array to a dictionary
"""
# Create dictionaries
keys = self.init_cf.keys()
del keys[keys.index("c0")]
mu_dict = {keys[i]: mu[i] for i in range(len(keys))}
cov_dict = {key: {} for key in keys}
for i in range(len(keys)):
for j in range(len(keys)):
cov_dict[keys[i]][keys[j]] = cov[i, j]
return cov_dict, mu_dict
def update_cov_matrix(self, new_cfs):
"""
Updates the covariance matrix
"""
outer = np.outer(new_cfs, new_cfs)
self.cov_matrix += outer
self.exp_value += np.array(new_cfs)
def save(self, eigval, eigvec, fname="eigenvectors.h5", fraction=0.95):
"""
Store the lowest fraction of the eigenvectors
"""
srt_indx = np.argsort(eigval)[::-1]
eigval_srt = [eigval[indx] for indx in srt_indx]
eigvec_srt = np.array([eigvec[:, indx] for indx in srt_indx]).T
cumsum_eig = np.cumsum(eigval_srt)
tot_sum = np.sum(eigval_srt)
relative_sum = cumsum_eig / tot_sum
max_indx = np.argmin(np.abs(relative_sum - fraction))
matrix = eigvec_srt[:, :max_indx]
eigen = eigval_srt[:max_indx]
with h5.File(fname, 'w') as hf:
dset_vec = hf.create_dataset("eigenvectors", data=matrix)
dset_eigen = hf.create_dataset("eigenvalues", data=eigen)
dset_eigen.attrs["fraction"] = fraction
print("Result written to {}".format(fname))
def diagonalize(self, cov, plot=False):
"""
Diagonalize the covariance matrix
"""
eigval, eigvec = np.linalg.eigh(cov)
# Sort accorting to eigenvalues
srt_indx = np.argsort(eigval)[::-1]
eigval_srt = [eigval[indx] for indx in srt_indx]
eigvec_srt = np.array([eigvec[:, indx] for indx in srt_indx]).T
cumsum_eig = np.cumsum(eigval_srt)
tot_sum = np.sum(eigval_srt)
if (plot):
x_val = np.arange(len(eigval))
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.plot(x_val, cumsum_eig / tot_sum, ls="steps")
ax.set_xlabel("Number of eigenvectors")
ax.set_ylabel("Normalized variance")
return eigval, eigvec
def plot_eigen(self, eigenvalues, eigenvectors):
"""
Creates a visualization of the eigenvectors and the eigenvalues
NOTE: Eigenvalues and eigenvectors must NOT be sorted. They have
to be given in the same order as returned by diagonalize
"""
keys = self.init_cf.keys()
del keys[keys.index("c0")]
srt_indx = np.argsort(eigenvalues)[::-1]
key_srt = [keys[indx] for indx in srt_indx]
eigval_srt = [eigenvalues[indx] for indx in srt_indx]
eigvec_srt = np.array([eigenvectors[:, indx] for indx in srt_indx]).T
grid_kw = {"hspace": 0.0, "height_ratios": [1, 4]}
fig, ax = plt.subplots(nrows=2, sharex=True, gridspec_kw=grid_kw)
x = np.arange(len(eigvec_srt))
cumsum = np.cumsum(eigval_srt)
tot_sum = np.sum(eigval_srt)
ax[0].plot(x, cumsum / tot_sum, ls="steps")
keys_srt, eigvec_srt = self.sort_eigenvectors_by_size(keys, eigvec_srt)
#ax[1].imshow( eigvec_srt, cmap="coolwarm", aspect="auto" )
print(eigvec_srt[:, 0])
# Separation lines to separate different sizes
hlines = []
size = 2
for i, name in enumerate(keys_srt):
prefix = "c{}".format(size)
if (name.startswith(prefix)):
hlines.append(i)
size += 1
for line in hlines:
ax[1].axhline(line)
return fig
def sort_eigenvectors_by_size(self, keys, eigvec):
"""
Sort the eigenvector values
"""
srt_indx = np.argsort(keys)
keys_srt = [keys[indx] for indx in srt_indx]
eigvec_srt = np.array([eigvec[indx, :] for indx in srt_indx])
return keys_srt, eigvec_srt