def fcc(alat, atoms, orthogonal=False):
""" Face centered cubic lattice with 1 (non-orthogonal) or 4 atoms (orthogonal)
Parameters
----------
alat : float
lattice parameter
atoms : Atom
the atom(s) in the FCC lattice
orthogonal : bool, optional
whether the lattice is orthogonal (4 atoms)
"""
if orthogonal:
sc = SuperCell(
np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], np.float64) * alat)
ah = alat / 2
g = Geometry([[0, 0, 0], [ah, ah, 0], [ah, 0, ah], [0, ah, ah]],
atoms,
sc=sc)
else:
sc = SuperCell(
np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], np.float64) * alat / 2)
g = Geometry([0, 0, 0], atoms, sc=sc)
if np.all(g.maxR(True) > 0.):
g.optimize_nsc()
return g
def bcc(alat, atom, orthogonal=False):
""" Body centered cubic lattice with 1 (non-orthogonal) or 2 atoms (orthogonal)
Parameters
----------
alat : float
lattice parameter
atom : Atom
the atom in the BCC lattice
orthogonal : bool, optional
whether the lattice is orthogonal (2 atoms)
"""
if orthogonal:
sc = SuperCell(np.array([[1, 0, 0],
[0, 1, 0],
[0, 0, 1]], np.float64) * alat)
ah = alat / 2
g = Geometry([[0, 0, 0], [ah, ah, ah]], atom, sc=sc)
else:
sc = SuperCell(np.array([[1, 1, 1],
[1, -1, 1],
[1, 1, -1]], np.float64) * alat / 2)
g = Geometry([0, 0, 0], atom, sc=sc)
g.optimize_nsc()
return g
def test_optimize_nsc1(self):
# Create a 1D chain
geom = Geometry([0] * 3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc(), [3, 3, 3]))
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc(1), [77, 3, 77]))
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc([0, 2]), [3, 77, 3]))
geom.set_nsc([77, 77, 77])
assert_true(np.allclose(geom.optimize_nsc([0, 2], R=2), [5, 77, 5]))
geom.set_nsc([1, 1, 1])
assert_true(np.allclose(geom.optimize_nsc([0, 2], R=2), [5, 1, 5]))
def sc(alat, atom):
""" Simple cubic lattice with 1 atom
Parameters
----------
alat : float
lattice parameter
atom : Atom
the atom in the SC lattice
"""
sc = SuperCell(
np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]], np.float64) * alat)
g = Geometry([0, 0, 0], atom, sc=sc)
g.optimize_nsc()
return g
def hcp(a, atoms, coa=1.63333, orthogonal=False):
""" Hexagonal closed packed lattice with 2 (non-orthogonal) or 4 atoms (orthogonal)
Parameters
----------
a : float
lattice parameter for 1st and 2nd lattice vectors
atoms : Atom
the atom(s) in the HCP lattice
coa : float, optional
c over a parameter where c is the 3rd lattice vector length
orthogonal : bool, optional
whether the lattice is orthogonal (4 atoms)
"""
# height of hcp structure
c = a * coa
a2sq = a / 2**.5
if orthogonal:
sc = SuperCell([[a + a * _c60 * 2, 0, 0], [0, a * _c30 * 2, 0],
[0, 0, c / 2]])
gt = Geometry([[0, 0, 0], [a, 0, 0], [a * _s30, a * _c30, 0],
[a * (1 + _s30), a * _c30, 0]],
atoms,
sc=sc)
# Create the rotated one on top
gr = gt.copy()
# mirror structure
gr.xyz[0, 1] += sc.cell[1, 1]
gr.xyz[1, 1] += sc.cell[1, 1]
gr = gr.translate(-np.amin(gr.xyz, axis=0))
# Now displace to get the correct offset
gr = gr.translate([0, a * _s30 / 2, 0])
g = gt.append(gr, 2)
else:
sc = SuperCell([a, a, c, 90, 90, 60])
g = Geometry([[0, 0, 0], [a2sq * _c30, a2sq * _s30, c / 2]],
atoms,
sc=sc)
if np.all(g.maxR(True) > 0.):
g.optimize_nsc()
return g
def test_optimize_nsc1(self, setup):
# Create a 1D chain
geom = Geometry([0]*3, Atom(1, R=1.), sc=1)
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc(), [3, 3, 3])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc(1), [77, 3, 77])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc([0, 2]), [3, 77, 3])
geom.set_nsc([77, 77, 77])
assert np.allclose(geom.optimize_nsc([0, 2], R=2.00000001), [5, 77, 5])
geom.set_nsc([1, 1, 1])
assert np.allclose(geom.optimize_nsc([0, 2], R=2.0000001), [5, 1, 5])
geom.set_nsc([5, 1, 5])
assert np.allclose(geom.optimize_nsc([0, 2], R=0.9999), [1, 1, 1])
