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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Vector Laplacian in curvilinear coordinates
The vector Laplacian is
$$
\nabla^2 \vec{u} = \nabla \cdot \nabla \vec{u}
$$
A vector identity gives the vector Laplacian as
$$
\nabla^2 \vec{u} = \nabla \nabla \cdot \vec{u} - \nabla \times \nabla \times \vec{u}
$$
We will check if this identity holds for shenfun using both cylindrical and spherical coordinates.
For reference, the vector Laplacian is given here
Cylinder coordinates are mapped to Cartesian through
$$
\begin{align}
x &= r \cos \theta \
y &= r \sin \theta \
z &= z
\end{align}
$$
and we use a domain $(r, \theta, z) \in [0, 1] \times [0, 2 \pi] \times [0, 2 \pi]$.
Spherical coordinates are mapped as
$$
\begin{align}
x &= r \sin(\theta) \cos(\phi)\
y &= r \sin(\theta) \sin(\phi)\
z &= r \cos(\theta)
\end{align}
$$
for a domain $(r, \theta, \phi) \in [0, 1] \times [0, \pi] \times [0, 2 \pi]$.
This is all we need to know for using these coordinate systems with shenfun.
Cylinder coordinates
Step1:  The vector Laplacian can now be found as
Step2:  We can look at du using the following
Step3:  Note that the basis vectors $\mathbf{b}_i$ are not unit vectors (i.e., of length 1). For this reason the equation does not look exactly like the one here. The basis vectors are
Step4:  Notice that $|\mathbf{b}{\theta}|=r$. Shenfun can use either non-normalized covariant basis vectors or normalized (physical) basis vectors of lenght 1 for describing all vectors and higher order tensors. The vector components components shown are contraviariant and as such use a superscript $u^{\theta}$ and not subscript $u{\theta}$. Note that for orthogonal coordinates the scaled unit vectors are the same for either contra- or covariant basis vectors and as such this distinction is not necessary here. The distinction is only required for non-orthogonal coordinate systems. Shenfun can handle both orthogonal and non-orthogonal coordinates, but requires that equations to be solved are separable.  
Now check the vector identity
$$
\nabla^2 \vec{u} = \nabla \nabla \cdot \vec{u} - \nabla \times \nabla \times \vec{u}
$$
Step5:  We see that the order is different, but the vector is actually identical to the previous one (du). To show that they are equal we can subtract one from the other and simplify.
Step6:  If you are not convinced we can assemble some matrices and check that du and dv behave the same way.
Step7:  A0 and A1 now contains lists of tensor product matrices, because the vector identities contain a lot of different terms (as we have seen above). To check that A0 and A1 are identical, we test the vector product of the matrices with a random vector. Since we are working with vectors we use a BlockMatrix for the combined tensor product matrices.
Step8:  Spherical coordinates
We now turn to spherical coordinates and run the same test.
Step9:  This proves that for shenfun the vector identity $\nabla^2 \vec{u} = \nabla \nabla \cdot \vec{u} - \nabla \times \nabla \times \vec{u}$ holds true also for spherical coordinates.
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Python Code:
from shenfun import *
from IPython.display import Math
import sympy as sp
config['basisvectors'] = 'normal' #'covariant' # or 
r, theta, z = psi = sp.symbols('x,y,z', real=True, positive=True)
rv = (r*sp.cos(theta), r*sp.sin(theta), z)
N = 10
F0 = FunctionSpace(N, 'F', dtype='d')
F1 = FunctionSpace(N, 'F', dtype='D')
L = FunctionSpace(N, 'L', domain=(0, 1))
T = TensorProductSpace(comm, (L, F1, F0), coordinates=(psi, rv))
V = VectorSpace(T)
u = TrialFunction(V)
du = div(u)
Math(du.tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', z: 'z'}))
du.tosympy(basis=(r*sp.cos(theta), sp.sin(theta), z), psi=psi)
Explanation: Vector Laplacian in curvilinear coordinates
The vector Laplacian is
$$
\nabla^2 \vec{u} = \nabla \cdot \nabla \vec{u}
$$
A vector identity gives the vector Laplacian as
$$
\nabla^2 \vec{u} = \nabla \nabla \cdot \vec{u} - \nabla \times \nabla \times \vec{u}
$$
We will check if this identity holds for shenfun using both cylindrical and spherical coordinates.
For reference, the vector Laplacian is given here
Cylinder coordinates are mapped to Cartesian through
$$
\begin{align}
x &= r \cos \theta \
y &= r \sin \theta \
z &= z
\end{align}
$$
and we use a domain $(r, \theta, z) \in [0, 1] \times [0, 2 \pi] \times [0, 2 \pi]$.
Spherical coordinates are mapped as
$$
\begin{align}
x &= r \sin(\theta) \cos(\phi)\
y &= r \sin(\theta) \sin(\phi)\
z &= r \cos(\theta)
\end{align}
$$
for a domain $(r, \theta, \phi) \in [0, 1] \times [0, \pi] \times [0, 2 \pi]$.
This is all we need to know for using these coordinate systems with shenfun.
Cylinder coordinates
End of explanation
du = div(grad(u))
#Math((div(grad(TrialFunction(T)))).tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', z: 'z'}))
T.coors.sg
Explanation: The vector Laplacian can now be found as
End of explanation
Math((du).tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', z: 'z'}))
Explanation: We can look at du using the following
End of explanation
Math(T.coors.latex_basis_vectors(symbol_names={r: 'r', theta: '\\theta', z: 'z'}))
Explanation: Note that the basis vectors $\mathbf{b}_i$ are not unit vectors (i.e., of length 1). For this reason the equation does not look exactly like the one here. The basis vectors are
End of explanation
dv = grad(div(u)) - curl(curl(u))
dv.simplify()
Math((dv).tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', z: 'z'}))
Explanation: Notice that $|\mathbf{b}{\theta}|=r$. Shenfun can use either non-normalized covariant basis vectors or normalized (physical) basis vectors of lenght 1 for describing all vectors and higher order tensors. The vector components components shown are contraviariant and as such use a superscript $u^{\theta}$ and not subscript $u{\theta}$. Note that for orthogonal coordinates the scaled unit vectors are the same for either contra- or covariant basis vectors and as such this distinction is not necessary here. The distinction is only required for non-orthogonal coordinate systems. Shenfun can handle both orthogonal and non-orthogonal coordinates, but requires that equations to be solved are separable.  
Now check the vector identity
$$
\nabla^2 \vec{u} = \nabla \nabla \cdot \vec{u} - \nabla \times \nabla \times \vec{u}
$$
End of explanation
dw = du-dv
dw.simplify()
Math(dw.tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', z: 'z'}))
Explanation: We see that the order is different, but the vector is actually identical to the previous one (du). To show that they are equal we can subtract one from the other and simplify.
End of explanation
v = TestFunction(V)
A0 = inner(v, du)
A1 = inner(v, dv)
Explanation: If you are not convinced we can assemble some matrices and check that du and dv behave the same way.
End of explanation
u_hat = Function(V)
u_hat[:] = np.random.random(u_hat.shape) + np.random.random(u_hat.shape)*1j
a0 = BlockMatrix(A0)
a1 = BlockMatrix(A1)
b0 = Function(V)
b1 = Function(V)
b0 = a0.matvec(u_hat, b0)
b1 = a1.matvec(u_hat, b1)
print('Error ', np.linalg.norm(b0-b1))
Explanation: A0 and A1 now contains lists of tensor product matrices, because the vector identities contain a lot of different terms (as we have seen above). To check that A0 and A1 are identical, we test the vector product of the matrices with a random vector. Since we are working with vectors we use a BlockMatrix for the combined tensor product matrices.
End of explanation
r, theta, phi = psi = sp.symbols('x,y,z', real=True, positive=True)
rv = (r*sp.sin(theta)*sp.cos(phi), r*sp.sin(theta)*sp.sin(phi), r*sp.cos(theta))
N = 6
F = FunctionSpace(N, 'F', dtype='d')
L0 = FunctionSpace(N, 'L', domain=(0, 1))
L1 = FunctionSpace(N, 'L', domain=(0, np.pi))
T = TensorProductSpace(comm, (L0, L1, F), coordinates=(psi, rv, sp.Q.positive(sp.sin(theta))))
V = VectorSpace(T)
u = TrialFunction(V)
du = div(grad(u))
dv = grad(div(u)) - curl(curl(u))
dv.simplify()
dw = du-dv
dw.simplify()
Math(dw.tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', phi: '\\phi'}))
Explanation: Spherical coordinates
We now turn to spherical coordinates and run the same test.
End of explanation
Math(du.tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', phi: '\\phi'}))
Math(T.coors.latex_basis_vectors(symbol_names={r: 'r', theta: '\\theta', phi: '\\phi'}))
Math((grad(u)).tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', phi: '\\phi'}))
Math((grad(u)[0]).tolatex(funcname='u', symbol_names={r: 'r', theta: '\\theta', phi: '\\phi'}))
Explanation: This proves that for shenfun the vector identity $\nabla^2 \vec{u} = \nabla \nabla \cdot \vec{u} - \nabla \times \nabla \times \vec{u}$ holds true also for spherical coordinates.
End of explanation
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