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 thermodynamic_integration(phase):
alat = 3.8
conc_args = {}
conc_args['conc_ratio_min_1'] = [[1, 0]]
conc_args['conc_ratio_max_1'] = [[0, 1]]
kwargs = {
"crystalstructure": 'fcc',
"a": 3.8,
"size": [10, 10, 10],
"basis_elements": [['Cu', 'Au']],
"conc_args": conc_args,
"db_name": 'temp_sgc.db',
"max_cluster_size": 3,
"max_cluster_dist": 1.5 * alat
}
bc1 = BulkCrystal(**kwargs)
bf = bc1._get_basis_functions()[0]
with open("data/eci_aucu.json", 'r') as infile:
eci = json.load(infile)
db = dataset.connect("sqlite:///{}".format(canonical_db))
tbl = db["corrfunc"]
if phase == "Au" or phase == "Cu":
atoms1 = bc1.atoms
for atom in atoms1:
atom.symbol = phase
cf1 = get_pure_cf(eci, bf[phase])
else:
atoms = read(phase)
row = tbl.find_one(runID=gs[phase])
row.pop("id")
row.pop("runID")
cf1 = row
# TODO: Fix this when running with a pure phase
symbs = [atom.symbol for atom in atoms]
cf1 = get_pure_cf(eci, bf[bc1.atoms[0].symbol])
atoms = bc1.atoms
calc = CE(bc1, eci=eci, initial_cf=cf1)
calc.set_symbols(symbs)
atoms.set_calculator(calc)
sgc_db = dataset.connect("sqlite:///{}".format(sgc_db_name))
tbl = sgc_db["results"]
tbl_cf = sgc_db["corr_func"]
mu = 0.223
nsteps = 100 * len(atoms)
equil_param = {"mode": "fixed", "maxiter": 10 * len(atoms)}
order_param = SiteOrderParameter(atoms)
T = np.linspace(100, 600, 40)
# mu = np.linspace(0.223, 0.19, 20).tolist()
mu = [0.223]
for temp in T:
for m in mu:
chemical_potential = {"c1_0": m}
# mc = SGCMonteCarlo(atoms, temp, mpicomm=comm, symbols=["Au", "Cu"])
mc = Montecarlo(atoms, temp)
mc.attach(order_param)
init_formula = atoms.get_chemical_formula()
# mc.runMC(steps=nsteps, equil_params=equil_param,
# chem_potential=chemical_potential)
mc.runMC(steps=nsteps, equil_params=equil_param)
# thermo = mc.get_thermodynamic(reset_ecis=True)
thermo = mc.get_thermodynamic()
thermo["init_formula"] = init_formula
thermo["final_formula"] = atoms.get_chemical_formula()
avg, std = order_param.get_average()
thermo["order_avg"] = avg
thermo["order_std"] = std
thermo["valid"] = True
thermo["integration_path"] = "NN"
if rank == 0:
uid = tbl.insert(thermo)
cf = calc.get_cf()
cf["runID"] = uid
tbl_cf.insert(cf)