def __init__(self,
a=None,
b=None,
c=None,
alpha=None,
beta=None,
gamma=None,
a1=None,
a2=None,
a3=None,
cell_matrix=None,
orientation_matrix=None,
offset=None):
if all([
p is None
for p in (a, b, c, alpha, beta, gamma, a1, a2, a3, cell_matrix)
]):
errmsg = 'Expected lattice parameters ' + \
'`a`, `b`, `c`, `alpha`, `beta`, `gamma`\n' + \
'or lattice vectors `a1`, `a2`, `a3`\n' + \
'or a 3x3 matrix with lattice vectors for columns.'
raise ValueError(errmsg)
if cell_matrix is not None:
cell_matrix = np.asarray(cell_matrix)
a1 = np.array(cell_matrix[0, :])
a2 = np.array(cell_matrix[1, :])
a3 = np.array(cell_matrix[2, :])
if all([v is not None for v in (a1, a2, a3)]):
a1 = Vector(a1)
a2 = Vector(a2)
a3 = Vector(a3)
a = a1.length
b = a2.length
c = a3.length
alpha = np.degrees(a2.angle(a3))
beta = np.degrees(a3.angle(a1))
gamma = np.degrees(a1.angle(a2))
cell_matrix = np.matrix(
np.vstack((np.asarray(a1), np.asarray(a2), np.asarray(a3))))
self._a = a
self._b = b
self._c = c
self._alpha = alpha
self._beta = beta
self._gamma = gamma
if all([p is not None for p in (a, b, c, alpha, beta, gamma)]):
self._update_ortho_matrix()
super().__init__(nd=3,
cell_matrix=cell_matrix,
orientation_matrix=orientation_matrix,
offset=offset)
self.fmtstr = "a={a!r}, b={b!r}, c={c!r}, " + \
"alpha={alpha!r}, beta={beta!r}, gamma={gamma!r}"
def __init__(self, a=None, b=None, c=None,
alpha=None, beta=None, gamma=None,
a1=None, a2=None, a3=None, cell_matrix=None,
orientation_matrix=None, offset=None):
if all([p is None for p in (a, b, c, alpha, beta, gamma,
a1, a2, a3, cell_matrix)]):
errmsg = 'Expected lattice parameters ' + \
'`a`, `b`, `c`, `alpha`, `beta`, `gamma`\n' + \
'or lattice vectors `a1`, `a2`, `a3`\n' + \
'or a 3x3 matrix with lattice vectors for columns.'
raise ValueError(errmsg)
if cell_matrix is not None:
cell_matrix = np.asarray(cell_matrix)
a1 = np.array(cell_matrix[0, :])
a2 = np.array(cell_matrix[1, :])
a3 = np.array(cell_matrix[2, :])
if all([v is not None for v in (a1, a2, a3)]):
a1 = Vector(a1)
a2 = Vector(a2)
a3 = Vector(a3)
a = a1.length
b = a2.length
c = a3.length
alpha = np.degrees(a2.angle(a3))
beta = np.degrees(a3.angle(a1))
gamma = np.degrees(a1.angle(a2))
cell_matrix = np.matrix(np.vstack((np.asarray(a1),
np.asarray(a2),
np.asarray(a3))))
self._a = a
self._b = b
self._c = c
self._alpha = alpha
self._beta = beta
self._gamma = gamma
if all([p is not None for p in (a, b, c, alpha, beta, gamma)]):
self._update_ortho_matrix()
super().__init__(nd=3, cell_matrix=cell_matrix,
orientation_matrix=orientation_matrix,
offset=offset)
self.fmtstr = "a={a!r}, b={b!r}, c={c!r}, " + \
"alpha={alpha!r}, beta={beta!r}, gamma={gamma!r}"
def __init__(self, a=None, b=None, gamma=None,
a1=None, a2=None, cell_matrix=None,
orientation_matrix=None, offset=None):
if cell_matrix is not None:
cell_matrix = np.asarray(cell_matrix)
a1 = np.array(cell_matrix[0, :])
a2 = np.array(cell_matrix[1, :])
if a1 is not None and a2 is not None:
a1 = Vector(a1, nd=3)
a2 = Vector(a2, nd=3)
a = a1.length
b = a2.length
gamma = np.degrees(a1.angle(a2))
cell_matrix = np.matrix(np.vstack((np.asarray(a1),
np.asarray(a2),
np.asarray([0, 0, 1]))))
self._a = a
self._b = b
self._gamma = gamma
if None not in (a, b, gamma):
self._update_ortho_matrix()
super().__init__(nd=2, cell_matrix=cell_matrix,
orientation_matrix=orientation_matrix,
offset=offset)
self.fmtstr = "a={a!r}, b={b!r}, gamma={gamma!r}"
def __init__(self,
a=None,
b=None,
gamma=None,
a1=None,
a2=None,
cell_matrix=None,
orientation_matrix=None,
offset=None):
if cell_matrix is not None:
cell_matrix = np.asarray(cell_matrix)
a1 = np.array(cell_matrix[0, :])
a2 = np.array(cell_matrix[1, :])
if a1 is not None and a2 is not None:
a1 = Vector(a1, nd=3)
a2 = Vector(a2, nd=3)
a = a1.length
b = a2.length
gamma = np.degrees(a1.angle(a2))
cell_matrix = np.matrix(
np.vstack(
(np.asarray(a1), np.asarray(a2), np.asarray([0, 0, 1]))))
self._a = a
self._b = b
self._gamma = gamma
if None not in (a, b, gamma):
self._update_ortho_matrix()
super().__init__(nd=2,
cell_matrix=cell_matrix,
orientation_matrix=orientation_matrix,
offset=offset)
self.fmtstr = "a={a!r}, b={b!r}, gamma={gamma!r}"
