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 free_energy_vs_layered(T, mod):
from cemc.mcmc import AdaptiveBiasReactionPathSampler
from cemc.mcmc import ReactionCrdRangeConstraint
from cemc.mcmc import DiffractionObserver
from cemc.mcmc import MinimalEnergyPath
from ase.geometry import get_layers
atoms = get_atoms(cubic=True)
atoms_cpy = atoms.copy()
layers, dist = get_layers(atoms, (0, 1, 0))
for atom in atoms_cpy:
if layers[atom.index] % 2 == 0:
atom.symbol = "Mg"
else:
atom.symbol = "Si"
symbols = [atom.symbol for atom in atoms_cpy]
atoms.get_calculator().set_symbols(symbols)
lamb = 4.05
k = 2.0 * np.pi / lamb
workdir = "data/diffraction"
# Have to perform only insert moves
mc = Montecarlo(atoms, T)
k_vec = [k, 0, 0]
observer = DiffractionObserver(atoms=atoms,
active_symbols=["Si"],
all_symbols=["Mg", "Si"],
k_vector=k_vec,
name="reflection")
if T < 250:
mc.max_attempts = 5
nsteps = 100 * len(atoms)
mep = MinimalEnergyPath(mc_obj=mc,
observer=observer,
value_name="reflection",
relax_steps=nsteps,
search_steps=nsteps,
traj_file="{}/mep_diffract{}K.traj".format(
workdir, T),
max_reac_crd=1999.0)
mep.run()
mep.save(fname="{}/mep_mep_diffract_path{}.csv".format(workdir, T))
else:
conc_cnst = ReactionCrdRangeConstraint(observer,
value_name="reflection")
conc_cnst.update_range([0, 0.5])
mc.add_constraint(conc_cnst)
reac_path = AdaptiveBiasReactionPathSampler(
mc_obj=mc,
react_crd=[0.0, 0.5],
observer=observer,
n_bins=500,
data_file="{}/layered_bias{}K.h5".format(workdir, T),
mod_factor=mod,
delete_db_if_exists=True,
mpicomm=None,
db_struct="{}/layered_bias_struct{}K.db".format(workdir, T),
react_crd_name="reflection",
ignore_equil_steps=False,
smear=2000)
reac_path.run()
reac_path.save()