def simulate_rotate(atom="Cu", folder="all", npt_rot=90, size=1, disorder=0):
if not os.path.exists(folder):
os.makedirs(folder)
cluster = BCC(atom1=atom, atom2=atom, size=size)
angles = np.linspace(0, np.pi / 2, npt_rot)
vectors = [[np.cos(a), 0, np.sin(a)] for a in angles]
for v in vectors:
cluster.rotate_from_vectors([1, 0, 0], v).get_xyz(
file=folder + "/vector:" + str(v) + ".xyz", disorder=0.0)
def simulate_all_series(folder="all_series",
sizes=[3.0, 5.0, 7.0, 9.0, 11.0],
disorder=[0.00, 0.20, 0.40, 0.60, 0.80, 1.0],
offset=[100, 100, 20]):
"""This function is used to create a series of high symmetry
atomic positions with varying levels of disorder as well as
varying size of the cluster
"""
if not os.path.exists(folder):
os.makedirs(folder)
if not os.path.exists(folder + "/BCC6Fold"):
os.makedirs(folder + "/BCC6Fold")
if not os.path.exists(folder + "/BCC4Fold"):
os.makedirs(folder + "/BCC4Fold")
if not os.path.exists(folder + "/FCC4Fold"):
os.makedirs(folder + "/FCC4Fold")
if not os.path.exists(folder + "/FCC6Fold"):
os.makedirs(folder + "/FCC6Fold")
if not os.path.exists(folder + "/Ico2Fold"):
os.makedirs(folder + "/Ico2Fold")
if not os.path.exists(folder + "/Ico3Fold"):
os.makedirs(folder + "/Ico3Fold")
if not os.path.exists(folder + "/Ico5Fold"):
os.makedirs(folder + "/Ico5Fold")
for i_s, s in enumerate(sizes):
# BCC Simulations
b = BCC(radius=s)
print("Num BCC Atoms:", len(b))
b.get_xyz(file=folder + "/BCC4Fold" + "/size:" + str(s),
disorder=disorder,
offset=offset)
b.get_6_fold_axis(inplace=True)
b.get_xyz(file=folder + "/BCC6Fold" + "/size:" + str(s),
disorder=disorder,
offset=offset)
# FCC simulations
f = FCC(radius=s)
print("Num FCC Atoms:", len(f))
f.get_xyz(file=folder + "/FCC4Fold" + "/size:" + str(s),
disorder=disorder,
offset=offset)
f.get_6_fold_axis()
f.get_xyz(file=folder + "/FCC6Fold" + "/size:" + str(s),
disorder=disorder,
offset=offset)
# Icosahedron Simulations
i = Icosahedron(num_shells=i_s)
i.get_xyz(file=folder + "/Ico2Fold" + "/size:" + str(i_s),
disorder=disorder,
offset=offset)
i = Icosahedron(num_shells=i_s)
i.get_3_fold_axis()
i.get_xyz(file=folder + "/Ico3Fold" + "/size:" + str(i_s),
disorder=disorder,
offset=offset)
i.get_5_fold_axis()
i.get_xyz(file=folder + "/Ico5Fold" + "/size:" + str(i_s),
disorder=disorder,
offset=offset)
def simulate_series(atom="Cu",
folder="all_series",
cluster="Icosahedron",
sizes=[1, 2, 3, 4],
disorder=[0.0, 0.5, 1.0, 1.5, 2.0]):
if not os.path.exists(folder):
os.makedirs(folder)
if cluster == "Icosahedron":
for s in sizes:
i = Icosahedron(central_atom="Cu", size=s)
#5-fold
#i.rotate_from_vectors(vector1=[0, 0, 1], vector2=[0.0, -0.52573111, 0.85065081], inplace=True)
#3-fold
i.rotate_from_vectors(
vector1=[0, 0, 1],
vector2=[-0.45879397, -0.45879397, 0.45879397],
inplace=True)
for d in disorder:
i.get_xyz(file=folder + "/size:" + str(s) + "disorder:" +
str(d) + ".xyz",
disorder=d,
scale=7)
elif cluster == "FCC":
for s in sizes:
i = FCC(atom1="Cu", atom2="Cu", size=s)
#3-fold
i.rotate_from_vectors(vector1=[0, 0, 1],
vector2=[1, 1, 0],
inplace=True)
for d in disorder:
i.get_xyz(file=folder + "/size:" + str(s) + "disorder:" +
str(d) + ".xyz",
disorder=d)
elif cluster == "BCC":
for s in sizes:
i = BCC(atom1="Cu", atom2="Cu", size=s)
#3-fold
i.rotate_from_vectors(vector1=[0, 0, 1],
vector2=[1, 1, 1],
inplace=True)
for d in disorder:
i.get_xyz(file=folder + "/size:" + str(s) + "disorder:" +
str(d) + ".xyz",
disorder=d)
def simulate_all(atom="Cu",
folder="all",
cluster="Icosahedron",
npt_rot=1000,
sizes=[1, 2, 3],
disorder=[0.2, 0.4, 0.6, 0.8, 1.0]):
if not os.path.exists(folder):
os.makedirs(folder)
vectors = _get_points_on_sphere(npt=npt_rot)
if cluster == "Icosahedron":
for s in sizes:
i = Icosahedron(central_atom="Cu", size=s)
for v in vectors:
for d in disorder:
i.rotate_from_vectors([1, 0, 0], v, inplace=False).get_xyz(
file=folder + "/size:" + str(s) + "disorder:" +
str(d) + "vector:" + str(v) + ".xyz",
disorder=d)
elif cluster == "FCC":
for s in sizes:
i = FCC(atom1="Cu", atom2="Cu", size=s)
for v in vectors:
for d in disorder:
i.rotate_from_vectors([1, 0, 0], v).get_xyz(
file=folder + "/size:" + str(s) + "disorder:" +
str(d) + "vector:" + str(v) + ".xyz",
disorder=d)
elif cluster == "BCC":
for s in sizes:
i = BCC(atom1="Cu", atom2="Cu", size=s)
for v in vectors:
for d in disorder:
i.rotate_from_vectors([1, 0, 0], v).get_xyz(
file=folder + "/size:" + str(s) + "disorder:" +
str(d) + "vector:" + str(v) + ".xyz",
disorder=d)
def test_add_disorder(self):
b = BCC(atom1="Cu", atom2="Cu", lattice_parameter=3.59, radius=3)
print(len(b))
def test_4fold_axes(self):
f = BCC(atom1="Cu", atom2="Cu", lattice_parameter=2.856, radius=5)
f.get_4_fold_axis(inplace=True)
f.plot(rotate=False)
plt.show()
def test_6fold_axes(self):
b = BCC(atom1="Fe", atom2="Fe", lattice_parameter=2.856, radius=11)
print(len(b))
def test_init(self):
b = BCC(atom1="Fe", atom2="Fe", lattice_parameter=2.856, radius=3)
assert len(b) == 15
def test_to_xyz(self):
b = BCC(atom1="Zr", atom2="Cu")
b.get_xyz()