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_covariance_observer(self):
"""Test the covariance observer."""
if not available:
self.skipTest("ASE version does not have CE!")
msg = ""
no_throw = True
from cemc.mcmc import FixEdgeLayers
from cemc.mcmc import CovarianceMatrixObserver
bc, args = get_ternary_BC(ret_args=True)
ecis = get_example_ecis(bc=bc)
atoms = get_atoms_with_ce_calc(bc, args, eci=ecis, size=[8, 8, 8], db_name="covariance_obs.db")
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"])
fixed_layers = FixEdgeLayers(atoms=mc.atoms, thickness=3.0)
mc.add_constraint(fixed_layers)
elements = {"Mg": 6, "Si": 6}
mc.insert_symbol_random_places("Mg", num=1, swap_symbs=["Al"])
mc.grow_cluster(elements)
cov_obs = CovarianceMatrixObserver(atoms=mc.atoms, cluster_elements=["Mg", "Si"])
mc.attach(cov_obs)
for _ in range(10):
mc.runMC(steps=100, elements=elements, init_cluster=False)
obs_I = cov_obs.cov_matrix
indices = []
for atom in mc.atoms:
if atom.symbol in ["Mg", "Si"]:
indices.append(atom.index)
cluster = mc.atoms[indices]
pos = cluster.get_positions()
com = np.mean(pos, axis=0)
pos -= com
cov_matrix = np.zeros((3, 3))
for i in range(pos.shape[0]):
x = pos[i, :]
cov_matrix += np.outer(x, x)
self.assertTrue(np.allclose(obs_I, cov_matrix))
os.remove("covariance_obs.db")
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)