def pure_phase_entropy(small_bc):
from cemc.mcmc import Montecarlo
from ase.clease.tools import wrap_and_sort_by_position
from ase.io import read
from cemc.mcmc import SiteOrderParameter, Snapshot
import dataset
T = [1, 5, 10, 20, 30, 40, 50, 75, 100, 150, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310,
320, 330, 340, 350, 360, 370, 380, 390, 400, 420, 440, 460, 480, 500]
calc = get_ce_calc(small_bc, kwargs, ecis, size=[10, 10, 10], db_name="data/db10x10x10Al3Mg.db")
bc = calc.BC
bc.atoms.set_calculator(calc)
atoms = read("data/al3mg_template.xyz")
atoms = wrap_and_sort_by_position(atoms)
symbs = [atom.symbol for atom in atoms]
calc.set_symbols(symbs)
site_order = SiteOrderParameter(bc.atoms)
db = dataset.connect("sqlite:///data/pure_al3mg3.db")
syst = db["thermodynamic"]
camera = Snapshot(trajfile="data/pure_phase_entropy.traj", atoms=bc.atoms)
for temp in T:
print("Current temperature: {}K".format(temp))
site_order.reset()
mc = Montecarlo(bc.atoms, temp)
mc.attach(site_order)
mc.attach(camera, interval=50000)
equil_param = {"window_length": 100000, "mode": "fixed"}
mc.runMC(mode="fixed", steps=500000, equil=True, equil_params=equil_param)
mean, stddev = site_order.get_average()
thermo = mc.get_thermodynamic()
thermo["site_order"] = mean
thermo["site_order_std"] = stddev
syst.insert(thermo)
def sa(al_comp, kwargs, eci, db_name, size, lattice):
comp = {"Al": al_comp, "Zn": 1.0 - al_comp}
bc = BulkCrystal(**kwargs)
calc = get_ce_calc(bc, kwargs, eci, size)
bc = calc.BC
bc.atoms.set_calculator(calc)
temperatures = [800, 700, 600, 500, 400, 300, 200, 100]
N = len(bc.atoms)
if rank == 0:
print("Supercell has {} atoms".format(N))
# Define parameters for equillibration
equil_params = {"maxiter": 10 * N, "mode": "fixed"}
nsteps = 100 * N
calc.set_composition(comp)
for T in temperatures:
mc = Montecarlo(bc.atoms, T, mpicomm=comm)
mc.runMC(mode="fixed", steps=nsteps, equil_params=equil_params)
thermo = mc.get_thermodynamic()
thermo["converged"] = True
thermo["al_conc"] = al_comp
thermo["temperature"] = T
if rank == 0:
db = dataset.connect("sqlite:///{}".format(db_name))
tbl = db["results"]
tbl.insert(thermo)
if rank == 0:
fname = "data/atoms_{}_{}.xyz".format(lattice,
bc.atoms.get_chemical_formula())
write(fname, bc.atoms)
def insert_atoms( self, bc_kwargs, size=[1,1,1], composition=None, cetype="CEBulk", \
T=None, n_steps_per_temp=10000, eci=None ):
"""
Insert a new atoms object into the database
"""
if (composition is None):
raise TypeError("No composition given")
allowed_ce_types = ["CEBulk", "CECrystal"]
if (not cetype in allowed_ce_types):
raise ValueError(
"cetype has to be one of {}".format(allowed_ce_types))
self.cetype = cetype
if (eci is None):
raise ValueError(
"No ECIs given! Cannot determine required energy range!")
if (cetype == "CEBulk"):
small_bc = CEBulk(**bc_kwargs)
small_bc.reconfigure_settings()
elif (ctype == "CECrystal"):
small_bc = CECrystal(**bc_kwargs)
small_bc.reconfigure_settings()
self._check_eci(small_bc, eci)
calc = get_ce_calc(small_bc, bc_kwargs, eci=eci, size=size)
calc.set_composition(composition)
bc = calc.BC
bc.atoms.set_calculator(calc)
formula = bc.atoms.get_chemical_formula()
if (self.template_atoms_exists(formula)):
raise AtomExistsError(
"An atom object with the specified composition already exists in the database"
)
Emin, Emax = self._find_energy_range(bc.atoms, T, n_steps_per_temp)
cf = calc.get_cf()
data = {"cf": cf}
# Store this entry into the database
db = connect(self.wl_db_name)
scalc = SinglePointCalculator(bc.atoms, energy=Emin)
bc.atoms.set_calculator(scalc)
outfname = "BC_wanglandau_{}.pkl".format(
bc.atoms.get_chemical_formula())
with open(outfname, 'wb') as outfile:
pck.dump(bc, outfile)
kvp = {
"Emin": Emin,
"Emax": Emax,
"bcfile": outfname,
"cetype": self.cetype
}
data["bc_kwargs"] = bc_kwargs
data["supercell_size"] = size
db.write(calc.BC.atoms, key_value_pairs=kvp, data=data)
def sa_sgc():
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],
# "size": [2, 2, 2],
"basis_elements": [['Cu', 'Au']],
"conc_args": conc_args,
"db_name": 'temp_sgc{}.db'.format(rank),
"max_cluster_size": 3,
"max_cluster_dist": 1.5 * alat
}
with open("data/eci_aucu.json", 'r') as infile:
eci = json.load(infile)
bc = BulkCrystal(**kwargs)
bc.reconfigure_settings()
with open("data/eci_aucu.json", 'r') as infile:
eci = json.load(infile)
calc = get_ce_calc(bc, kwargs, eci=eci, size=[10, 10, 10])
bc = calc.BC
bc.atoms.set_calculator(calc)
atoms = bc.atoms
chem_pot = (np.linspace(0.19, 0.35, 50)).tolist()
T = np.linspace(100, 1000, 50)[::-1]
equil_param = {"mode": "fixed", "maxiter": 10 * len(atoms)}
nsteps = 100 * len(atoms)
sgc_db = dataset.connect("sqlite:///{}".format(sgc_db_name))
tbl = sgc_db["results"]
tbl_cf = sgc_db["corr_func"]
orig_symbs = [atom.symbol for atom in atoms]
for mu in chem_pot:
chemical_potential = {"c1_0": mu}
calc.set_symbols(orig_symbs)
for temp in T:
mc = SGCMonteCarlo(atoms, temp, mpicomm=comm, symbols=["Au", "Cu"])
init_formula = atoms.get_chemical_formula()
mc.runMC(steps=nsteps,
equil_params=equil_param,
chem_potential=chemical_potential)
thermo = mc.get_thermodynamic(reset_ecis=True)
thermo["init_formula"] = init_formula
thermo["final_formula"] = atoms.get_chemical_formula()
if rank == 0:
uid = tbl.insert(thermo)
cf = calc.get_cf()
cf["runID"] = uid
tbl_cf.insert(cf)
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 test_no_throw(self):
if (not has_CE):
self.skipTest("ASE version does not have ASE")
return
no_throw = True
msg = ""
try:
conc_args = {
"conc_ratio_min_1": [[1, 0]],
"conc_ratio_max_1": [[0, 1]],
}
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size": [3, 3, 3],
"basis_elements": [["Al", "Mg"]],
"conc_args": conc_args,
"db_name": "temporary_bcnucleationdb.db",
"max_cluster_size": 3
}
ceBulk = CEBulk(**kwargs)
cf = CorrFunction(ceBulk)
cf_dict = cf.get_cf(ceBulk.atoms)
ecis = {key: 1.0 for key, value in cf_dict.items()}
#calc = CE( ceBulk, ecis, size=(3,3,3) )
calc = get_ce_calc(ceBulk,
kwargs,
ecis,
size=[6, 6, 6],
db_name="sc6x6x6.db")
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
chem_pot = {"c1_0": -1.069}
T = 300
mc = SGCFreeEnergyBarrier( ceBulk.atoms, T, symbols=["Al","Mg"], \
n_windows=5, n_bins=10, min_singlet=0.5, max_singlet=1.0 )
mc.run(nsteps=100, chem_pot=chem_pot)
mc.save(fname="free_energy_barrier.json")
# Try to load the object stored
mc = SGCFreeEnergyBarrier.load(ceBulk.atoms,
"free_energy_barrier.json")
mc.run(nsteps=100, chem_pot=chem_pot)
mc.save(fname="free_energy_barrier.json")
os.remove("sc6x6x6.db")
except Exception as exc:
msg = str(exc)
no_throw = False
self.assertTrue(no_throw, msg=msg)
def insert_energy(conc, T):
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": [4, 4, 2],
"basis_elements": [['Cu', 'Au']],
"conc_args": conc_args,
"db_name": 'temp_sgc{}.db'.format(rank),
"max_cluster_size": 3,
"max_cluster_dist": 1.5 * alat
}
bc = BulkCrystal(**kwargs)
bc.reconfigure_settings()
with open("data/eci_aucu.json", 'r') as infile:
eci = json.load(infile)
names = bc.cluster_names
for key in eci.keys():
if key not in names:
raise ValueError("{} is not in cluster_names".format(key))
calc = get_ce_calc(bc, kwargs, eci=eci, size=[10, 10, 10])
bc = calc.BC
atoms = bc.atoms
atoms.set_calculator(calc)
comp = {"Au": conc, "Cu": 1.0 - conc}
calc.set_composition(comp)
symbs = [atom.symbol for atom in atoms]
shuffle(symbs)
calc.set_symbols(symbs)
sampler = ActivitySampler(atoms,
T,
moves=[("Au", "Cu")],
mpicomm=comm,
prob_insert_move=0.1)
equil = {"mode": "fixed", "maxiter": 10 * len(atoms)}
nsteps = 100 * len(atoms)
sampler.runMC(steps=nsteps, mode="fixed", equil_params=equil)
thermo = sampler.get_thermodynamic()
if rank == 0:
db = dataset.connect("sqlite:///{}".format(db_name))
tbl = db["results"]
tbl.insert(thermo)
def test_supercell( self ):
if ( not has_ase_with_ce ):
self.skipTest("ASE version does not have CE")
return
calc, ceBulk, eci = self.get_calc("fcc")
db_name = "test_db_fcc_super.db"
conc_args = {
"conc_ratio_min_1":[[1,0]],
"conc_ratio_max_1":[[0,1]],
}
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size":[3, 3, 3],
"basis_elements":[["Al","Mg"]],
"conc_args": conc_args,
"db_name": db_name,
"max_cluster_size": 3,
"max_cluster_dia": 4.05
}
kwargs_template = copy.deepcopy(kwargs)
kwargs_template["size"] = [4, 4, 4]
kwargs_template["db_name"] = "template_bc.db"
template_supercell_bc = CEBulk(**kwargs_template)
template_supercell_bc.reconfigure_settings()
ceBulk = CEBulk(**kwargs)
ceBulk.reconfigure_settings()
calc = get_ce_calc(ceBulk, kwargs, eci, size=[4, 4, 4],
db_name="sc4x4x.db")
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
corr_func = CorrFunction(template_supercell_bc)
for i in range(10):
calc.calculate(ceBulk.atoms, ["energy"], [(i, "Al", "Mg")])
updated_cf = calc.get_cf()
brute_force = corr_func.get_cf_by_cluster_names(
ceBulk.atoms, list(updated_cf.keys()))
for key, value in brute_force.items():
self.assertAlmostEqual(value, updated_cf[key])
os.remove("sc4x4x.db")
def run_huge():
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",
"size":[4,4,4],
"basis_elements":[["Al","Mg","Si"]],
"conc_args":conc_args,
"db_name":"some_db.db",
"max_cluster_size":4,
"a":4.05,
"ce_init_alg":"fast"
}
ceBulk = BulkCrystal( **kwargs )
with open(eci_file, 'r') as infile:
eci = json.load(infile)
calc = get_ce_calc(ceBulk, kwargs, eci=eci, size=[50,50,50])
calc.BC.atoms.set_calculator(calc)
print(calc.BC.basis_functions)
comp = {
"Al":0.9,
"Mg":0.05,
"Si":0.05
}
calc.set_composition(comp)
T = 150
T = [2000, 1500, 1200, 1000, 800, 600, 400, 293]
camera = Snapshot(trajfile=traj_file, atoms=calc.BC.atoms)
for temp in T:
print("Current temperature {}K".format(temp))
mc = Montecarlo(calc.BC.atoms, temp)
mc.attach(camera, interval=125000*20)
mc.runMC(mode="fixed", steps=125000*100, equil=False)
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 = pck.load(infile)
calc = CE(bc, eci, initial_cf=init_cf)
bc.atoms.set_calculator(calc)
return bc.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"]
calc = get_ce_calc(small_bc, bc_kwargs, eci=eci, size=size)
# Determine the composition
count = row.count_atoms()
for key in count.keys():
count /= float(row.natoms)
calc.set_composition(count)
bc = calc.BC
bc.atoms.set_calculator(calc)
return bc.atoms
except:
raise RuntimeError(
"Did not manage to return the atoms object with the proper calculator attached..."
)
def run(chem_pot, min_c1, max_c1, T):
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],
# "size": [2, 2, 2],
"basis_elements": [['Cu', 'Au']],
"conc_args": conc_args,
"db_name": 'temp_sgc_{}.db'.format(rank),
"max_cluster_size": 3,
"max_cluster_dist": 1.5 * alat
}
bc = BulkCrystal(**kwargs)
with open("data/eci_aucu.json", 'r') as infile:
eci = json.load(infile)
calc = get_ce_calc(bc, kwargs, eci=eci, size=[10, 10, 10])
bc = calc.BC
bc.atoms.set_calculator(calc)
if rank == 0:
print("Number of atoms: {}".format(len(bc.atoms)))
mc = SGCFreeEnergyBarrier(bc.atoms,
T,
n_windows=10,
n_bins=8,
min_singlet=min_c1,
max_singlet=max_c1,
mpicomm=comm,
symbols=["Au", "Cu"],
save_last_state=True)
mu = {"c1_0": chem_pot}
mc.run(nsteps=100000, chem_pot=mu)
# mc.save(fname="data/barriers/free_eng_{}_{}_{}_{}.json".format(int(min_c1*100), int(max_c1*100), int(1E6*chem_pot), T))
mc.save(fname="data/barrier_sgc_waste4.json")
def get_ce_with_calc():
conc = Concentration(basis_elements=[["Al", "Mg", "Si"]])
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size": [4, 4, 4],
"concentration": conc,
"db_name": DB_NAME,
"max_cluster_size": 4
}
ceBulk = BulkCrystal(**kwargs)
with open(ECI_FILE, 'r') as infile:
ecis = json.load(infile)
db_name = "large_cell_db10x10x10.db"
calc = get_ce_calc(ceBulk,
kwargs,
ecis,
size=[10, 10, 10],
db_name=db_name)
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
return ceBulk
def main(outfname, action):
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": 4
}
ceBulk = BulkCrystal(**kwargs)
print(ceBulk.basis_functions)
eci_file = "data/ce_hydrostatic.json"
with open(eci_file, 'r') as infile:
ecis = json.load(infile)
print(ecis)
#calc = CE( ceBulk, ecis, size=(3,3,3) )
ecis = {"c1_0": 1.0}
calc = get_ce_calc(ceBulk,
kwargs,
ecis,
size=[10, 10, 10],
free_unused_arrays_BC=True,
convert_trans_matrix=False)
exit()
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
chem_pot = {"c1_0": -1.0651526881167124}
chem_pot = {"c1_0": -1.068}
sampler = NucleationSampler( size_window_width=10, \
chemical_potential=chem_pot, max_cluster_size=150, \
merge_strategy="normalize_overlap", mpicomm=comm, max_one_cluster=True )
T = 300
mc = SGCNucleation( ceBulk.atoms, T, nucleation_sampler=sampler, \
network_name="c2_1414_1", network_element="Mg", symbols=["Al","Mg"], \
chem_pot=chem_pot, allow_solutes=True )
mg_conc = 0.04
concentration = {"Mg": mg_conc, "Al": 1.0 - mg_conc}
mc_canonical = CanonicalNucleationMC(ceBulk.atoms,
T,
nucleation_sampler=sampler,
network_name="c2_1414_1",
network_element="Mg",
concentration=concentration)
if (action == "barrier"):
mc.run(nsteps=100000)
sampler.save(fname=outfname)
elif (action == "barrier_canonical"):
mc_canonical.run(nsteps=50000)
sampler.save(fname=outfname)
elif (action == "trans_path"):
mc.find_transition_path( initial_cluster_size=90, max_size_reactant=20, min_size_product=135, \
folder="data", path_length=1000, max_attempts=10, nsteps=int(0.1*len(ceBulk.atoms)), mpicomm=comm )
#plt.show()
elif (action == "relax_path"):
relaxer = TransitionPathRelaxer(nuc_mc=mc)
relaxer.relax_path(initial_path=outfname, n_shooting_moves=50)
relaxer.path2trajectory(fname="data/relaxed_path.traj")
elif (action == "generate_paths"):
relaxer = TransitionPathRelaxer(nuc_mc=mc)
relaxer.generate_paths(initial_path=outfname,
n_paths=4,
outfile="data/tse_ensemble.json",
mpicomm=comm)
elif (action == "view_tps_indicators"):
relaxer = TransitionPathRelaxer(nuc_mc=mc)
relaxer.plot_path_statistics(path_file=outfname)
plt.show()
def surface_energy():
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 = CEBulk(**kwargs)
eci_file = "data/almgsi_fcc_eci_newconfig.json"
with open(eci_file, 'r') as infile:
ecis = json.load(infile)
size = (8, 8, 8)
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)
print(calc.get_energy() / len(calc.atoms))
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
# Get the energy of MgSi
mgsi = wrap_and_sort_by_position(get_mgsi() * (4, 4, 4))
symbs = [atom.symbol for atom in mgsi]
calc.set_symbols(symbs)
view(calc.atoms)
mgsi_energy = calc.get_energy() / len(calc.atoms)
print("Energy MgSi: {} eV/atom".format(mgsi_energy))
# Get the energy of pure al
symbs = ["Al" for _ in range(len(mgsi))]
calc.set_symbols(symbs)
view(calc.atoms)
al_energy = calc.get_energy() / len(calc.atoms)
print("Energy Al: {} eV/atom".format(al_energy))
# Get the energy of a 50% mixture
mgsi = wrap_and_sort_by_position(get_mgsi() * (4, 4, 2))
# mgsi = get_mgsi_surface100_si_si()
from scipy.spatial import cKDTree as KDTree
cell = calc.atoms.get_cell()
tree = KDTree(calc.atoms.get_positions())
symbs = [atom.symbol for atom in calc.atoms]
for atom in mgsi:
pos = np.zeros((1, 3))
pos[0, :] = atom.position
wrapped = wrap_positions(pos, cell)
if not np.allclose(wrapped, atom.position):
continue
_, indx = tree.query(atom.position)
symbs[indx] = atom.symbol
calc.set_symbols(symbs)
view(calc.atoms)
# Surface energy
mix_energy = calc.get_energy()
print("Mix energy: {} eV ({} eV/atom)".format(mix_energy, mix_energy /
len(calc.atoms)))
num_al = 0
num_mgsi = 0
for atom in calc.atoms:
if atom.symbol == "Al":
num_al += 1
elif atom.symbol == "Mg" or atom.symbol == "Si":
num_mgsi += 1
assert num_al + num_mgsi == len(calc.atoms)
dE = mix_energy - num_al * al_energy - num_mgsi * mgsi_energy
cell = calc.atoms.get_cell()
a1 = cell[0, :]
a2 = cell[1, :]
normal = np.cross(a1, a2)
area = np.sqrt(normal.dot(normal))
# Convert units
surface_tension = dE / area
mJ = J / 1000.0 # milli joules
surface_tension *= (m * m / mJ)
unit_normal = normal / area
print("Surface tension: {} mJ/m^2".format(surface_tension))
print("Direction: {}".format(unit_normal))
def test_no_throw(self):
if not available:
self.skipTest("ASE version does not have CE!")
return
no_throw = True
msg = ""
try:
conc_args = {
"conc_ratio_min_1": [[1, 0]],
"conc_ratio_max_1": [[0, 1]],
}
db_name = "temp_nuc_db.db"
if os.path.exists(db_name):
os.remove(db_name)
kwargs = {
"crystalstructure": "fcc",
"a": 4.05,
"size": [3, 3, 3],
"basis_elements": [["Al", "Mg"]],
"conc_args": conc_args,
"db_name": db_name,
"max_cluster_size": 3
}
ceBulk = CEBulk(**kwargs)
ceBulk.reconfigure_settings()
cf = CorrFunction(ceBulk)
cf = cf.get_cf(ceBulk.atoms)
ecis = {key: 0.001 for key in cf.keys()}
calc = get_ce_calc(ceBulk,
kwargs,
ecis,
size=[5, 5, 5],
db_name="sc5x5x5.db")
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
chem_pot = {"c1_0": -1.0651526881167124}
sampler = NucleationSampler(size_window_width=10,
chemical_potential=chem_pot,
max_cluster_size=20,
merge_strategy="normalize_overlap")
nn_name = get_network_name(ceBulk.cluster_family_names_by_size)
mc = SGCNucleation(ceBulk.atoms,
300,
nucleation_sampler=sampler,
network_name=[nn_name],
network_element=["Mg"],
symbols=["Al", "Mg"],
chem_pot=chem_pot)
mc.runMC(steps=2)
sampler.save(fname="test_nucl.h5")
mc = CanonicalNucleationMC(ceBulk.atoms,
300,
nucleation_sampler=sampler,
network_name=[nn_name],
network_element=["Mg"],
concentration={
"Al": 0.8,
"Mg": 0.2
})
mc.runMC(steps=2)
sampler.save(fname="test_nucl_canonical.h5")
elements = {"Mg": 6}
calc.set_composition({"Al": 1.0, "Mg": 0.0})
mc = FixedNucleusMC(ceBulk.atoms,
300,
network_name=[nn_name],
network_element=["Mg"])
mc.insert_symbol_random_places("Mg", num=1, swap_symbs=["Al"])
mc.runMC(steps=2, elements=elements)
os.remove("sc5x5x5.db")
except Exception as exc:
msg = str(exc)
no_throw = False
self.assertTrue(no_throw, msg=msg)
def main(option="relax", size=8):
from copy import deepcopy
ceBulk = BulkCrystal( **kwargs )
bc_copy = deepcopy(ceBulk)
print (ecis)
al,mg = get_pure_energies(ecis)
print ("Al energy: {} eV/atom".format(al))
print ("Mg energy: {} eV/atom".format(mg))
#exit()
#calc = CE( ceBulk, ecis, size=(3,3,3) )
calc = get_ce_calc(ceBulk, kwargs, ecis, size=[15,15,15])
ceBulk = calc.BC
ceBulk.atoms.set_calculator( calc )
#pure_energy = calc.get_energy()
#print (pure_energy)
#energy = calc.calculate( ceBulk.atoms, ["energy"],[(0,"Al","Mg")])
#print (energy)
#energy = calc.calculate( ceBulk.atoms, ["energy"], [()])
#exit()
if option == "heat":
print("Running with cluser size {}".format(size))
mc = FixedNucleusMC( ceBulk.atoms, 293, network_name=["c2_4p050_3"], network_element=["Mg"] )
cluster_entropy(mc, size=size)
return
elif option == "pure_phase":
pure_phase_entropy(bc_copy)
return
else:
sizes = range(3,51)
#sizes = np.arange(3, 51)
energies = []
cell = ceBulk.atoms.get_cell()
diag = 0.5*(cell[0, :] + cell[1, :] + cell[2, :])
pos = ceBulk.atoms.get_positions()
pos -= diag
lengths = np.sum(pos**2, axis=1)
indx = np.argmin(lengths)
symbs = [atom.symbol for atom in ceBulk.atoms]
symbs[indx] = "Mg"
print("Orig energy: {}".format(calc.get_energy()))
calc.set_symbols(symbs)
print("One atom: {}".format(calc.get_energy()))
exit()
for size in sizes:
elements = {"Mg": size}
T = np.linspace(50,1000,40)[::-1]
# Reset the symbols to only Mg
calc.set_symbols(symbs)
mc = FixedNucleusMC( ceBulk.atoms, T, network_name=["c2_4p050_3"], network_element=["Mg"] )
mc.grow_cluster(elements)
mc.current_energy = calc.get_energy()
low_en = LowestEnergyStructure( calc, mc, verbose=True )
mc.attach( low_en )
for temp in T:
print ("Temperature {}K".format(temp))
mc.T = temp
mc.runMC(steps=10000, init_cluster=False)
mc.reset()
mc.is_first = False
# atoms,clust = mc.get_atoms( atoms=low_en.atoms )
write( "{}cluster{}_all.cif".format(folder,size), low_en.atoms )
# write( "{}cluster{}_cluster.cif".format(folder,size), clust )
energies.append(low_en.lowest_energy)
print (sizes,energies)
data = np.vstack((sizes,energies)).T
np.savetxt( "{}energies_run2.txt".format(folder), data, delimiter=",")
"db_name": db_name,
"conc_args": conc_args,
"max_cluster_size": 3
}
# In this example, we just use some example ecis
eci = get_example_ecis(bc_kwargs=kwargs)
# Initialize a template CEBulk Object
ceBulk = CEBulk( **kwargs )
ceBulk.reconfigure_settings() # Nessecary for the unittests to pass
# Now we want to get a Cluster Expansion calculator for a big cell
mc_cell_size = [10,10,10]
from cemc import get_ce_calc
calc = get_ce_calc( ceBulk, kwargs, eci=eci, size=mc_cell_size, db_name="mc_obs.db")
ceBulk = calc.BC
ceBulk.atoms.set_calculator(calc)
conc = {
"Al":0.8,
"Mg":0.2
}
calc.set_composition(conc)
# Now we import the Monte Carlo class
from cemc.mcmc.montecarlo import Montecarlo
T = 400 # Run the simulation at 400K
mc_obj = Montecarlo( ceBulk.atoms, T )
# Now we define the observers
"conc_args": conc_args,
"max_cluster_size": 3
}
# Use some example ecis
eci = get_example_ecis(bc_kwargs=kwargs)
# Initialize a template CEBulk Object
ceBulk = CEBulk( **kwargs )
ceBulk.reconfigure_settings() # Nessecary for the unittest to pass
# Now we want to get a Cluster Expansion calculator for a big cell
mc_cell_size = [10, 10, 10]
from cemc import get_ce_calc
calc = get_ce_calc(ceBulk, kwargs, eci=eci, size=mc_cell_size,
db_name="sgc_large.db")
# Now er are finished with the template CEBulk
ceBulk = calc.BC
ceBulk.atoms.set_calculator( calc )
# In the SGC ensemble the simulation is run at fixed chemical potential
# The chemical potentials are subtracted from the singlet terms
# Those are ECIs starting with c1.
# In a binary system there is only one singlet term, so there is only one
# chemical potential to specify
chem_pot = {
"c1_0":-1.04
}
# Speciy the temperature