def equil_and_relax(T, fname="", np_layer=0, nptype="spherical"):
bc = init_bc(50)
mc = Montecarlo(bc.atoms, T)
print ("Running at temperature {}K. Initializing from {}".format(T, fname))
layer_str = "-".join((str(item) for item in np_layers[np_layer]))
run_identifier = "{}K_layer{}".format(T, layer_str)
if fname != "":
# Initialize atoms object from file
from ase.io import read
atoms = read(fname)
symbs = [atom.symbol for atom in atoms]
mc.set_symbols(symbs)
run_identifier = "{}K_{}".format(T, atoms.get_chemical_formula())
else:
if nptype == "spherical":
# Initialize by setting a nano particle at the center
nanop = get_nanoparticle(layer=np_layer)
elif nptype == "cubic":
nanop = get_cubic_nano_particle(layer=np_layer)
run_identifier += "cubic"
else:
raise ValueError("Unknown type {}".format(nanop))
symbs = insert_nano_particle(bc.atoms.copy(), nanop)
mc.set_symbols(symbs)
print("Chemical formula: {}".format(mc.atoms.get_chemical_formula()))
nsteps = int(4E7)
camera = Snapshot(atoms=mc.atoms, trajfile=workdir+"/snapshots_equil{}.traj".format(run_identifier))
energy_evol = EnergyEvolution(mc)
mc_backup = MCBackup(mc, backup_file=workdir+"/mc_backup{}.pkl".format(run_identifier))
mc.attach(energy_evol, interval=100000)
mc.attach(camera, interval=nsteps/20)
mc.attach(mc_backup, interval=500000)
mc.runMC(steps=nsteps, equil=False)
write(workdir+"/equillibriated600K.xyz", mc.atoms)
def main():
energies = []
sizes = list(range(1, 6))
atoms = get_atoms()
two_atoms(atoms)
exit()
insert_np(6, atoms)
mc = Montecarlo(atoms, 0.1)
camera = Snapshot(atoms=mc.atoms, trajfile="/work/sophus/nuc_cluster.traj")
db = dataset.connect("sqlite:////work/sophus/mgsi_nuc_barrier_kamijo.db")
tbl = db["systems"]
mc.attach(camera, interval=100 * len(atoms))
num_mg = sum(1 for atom in atoms if atom.symbol == "Mg")
while num_mg > 2:
print(atoms.get_chemical_formula())
mc.runMC(mode="fixed", equil=False, steps=100 * len(atoms))
thermo = mc.get_thermodynamic()
tbl.insert(thermo)
# Remove one Mg atom and one Si atom
symbols = [a.symbol for a in atoms]
for i in range(20):
i = symbols.index("Si")
symbols[i] = "Al"
i = symbols.index("Mg")
symbols[i] = "Al"
mc.set_symbols(symbols)
num_mg = sum(1 for atom in atoms if atom.symbol == "Mg")
def main(size, T):
atoms = create_surface(size)
atoms = wrap_and_sort_by_position(atoms)
conc_args = {
"conc_ratio_min_1": [[64, 0, 0]],
"conc_ratio_max_1": [[24, 40, 0]],
"conc_ratio_min_2": [[64, 0, 0]],
"conc_ratio_max_2": [[22, 21, 21]]
}
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size": [4, 4, 4],
"basis_elements": [["Al", "Mg", "Si"]],
"conc_args": conc_args,
"db_name": "data/almgsi.db",
"max_cluster_size": 4
}
ceBulk = BulkCrystal(**kwargs)
eci_file = "data/almgsi_fcc_eci_newconfig.json"
with open(eci_file, 'r') as infile:
ecis = json.load(infile)
db_name = "large_cell_db{}x{}x{}.db".format(size[0], size[1], size[2])
calc = get_ce_calc(ceBulk, kwargs, ecis, size=size, db_name=db_name)
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
mc = Montecarlo(ceBulk.atoms, T)
symbs = [atom.symbol for atom in atoms]
mc.set_symbols(symbs)
# Write a copy of the current atoms object
from ase.io import write
shape_str = "-".join((str(item) for item in size))
uid_str = "{}K_{}".format(T, shape_str)
write(WORKDIR + "initial_config{}.xyz".format(uid_str), mc.atoms)
backup = MCBackup(mc,
backup_file=WORKDIR + "backup{}.xyz".format(uid_str),
db_name=WORKDIR + "mc_surface.db")
camera = Snapshot(atoms=mc.atoms,
trajfile=WORKDIR + "surface{}.traj".format(uid_str))
evol = EnergyEvolution(mc)
nsteps = int(10E6)
mc.attach(backup, interval=100000)
mc.attach(camera, interval=int(nsteps / 20))
mc.attach(evol, interval=10 * len(mc.atoms))
mc.runMC(mode="fixed", steps=nsteps, equil=False)
write(WORKDIR + "final_config{}.xyz".format(uid_str), mc.atoms)
def run(N, T):
bc = init_bc(N)
mc = Montecarlo(bc.atoms, T)
nanop = get_nanoparticle()
symbs = insert_nano_particle(bc.atoms.copy(), nanop)
mc.set_symbols(symbs)
order_param = SiteOrderParameter(mc.atoms)
nsteps = int(1E6)
equil_params = {"mode": "fixed", "window_length": int(1E5)}
mc.attach(order_param)
mc.runMC(steps=nsteps, equil=True, equil_params=equil_params)
thermo = mc.get_thermodynamic()
mean, std = order_param.get_average()
thermo["order_param_mean"] = mean
thermo["order_param_std"] = std
thermo.update(equil_params)
db = dataset.connect("sqlite:///{}".format(mc_db_name))
tbl = db["cluster_stability"]
tbl.insert(thermo)
fname = workdir + "/final_structure{}K.xyz".format(T)
write(fname, mc.atoms)
def set_symbols(self, symbs):
"""Override parents set symbols."""
Montecarlo.set_symbols(self, symbs)
self.init_cluster_info()