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# # Biharmonic equation
#
# ```{admonition} Download sources
# :class: download
# * {download}`Python script <./demo_biharmonic.py>`
# * {download}`Jupyter notebook <./demo_biharmonic.ipynb>`
# ```
# This demo illustrates how to:
#
# - Solve a linear partial differential equation
# - Use a discontinuous Galerkin method
# - Solve a fourth-order differential equation
#
# ## Equation and problem definition
#
# ### Strong formulation
#
# The biharmonic equation is a fourth-order elliptic equation.
# On the domain $\Omega \subset \mathbb{R}^{d}$, $1 \le d \le 3$, it reads
#
# $$
# \nabla^{4} u = f \quad {\rm in} \ \Omega,
# $$
#
# where $\nabla^{4} \equiv \nabla^{2} \nabla^{2}$ is the biharmonic
# operator and $f$ is a prescribed source term.
# To formulate a complete boundary value problem, the biharmonic equation
# must be complemented by suitable boundary conditions.
#
# ### Weak formulation
#
# Multiplying the biharmonic equation by a test function and integrating
# by parts twice leads to a problem of second-order derivatives, which
# would require $H^{2}$ conforming (roughly $C^{1}$ continuous) basis
# functions. To solve the biharmonic equation using Lagrange finite element
# basis functions, the biharmonic equation can be split into two second-
# order equations (see the Mixed Poisson demo for a mixed method for the
# Poisson equation), or a variational formulation can be constructed that
# imposes weak continuity of normal derivatives between finite element
# cells. This demo uses a discontinuous Galerkin approach to impose
# continuity of the normal derivative weakly.
#
# Consider a triangulation $\mathcal{T}$ of the domain $\Omega$, where
# the set of interior facets is denoted by $\mathcal{E}_h^{\rm int}$.
# Functions evaluated on opposite sides of a facet are indicated by the
# subscripts $+$ and $-$.
# Using the standard continuous Lagrange finite element space
#
# $$
# V = \left\{v \in H^{1}_{0}(\Omega)\,:\, v \in P_{k}(K) \
# \forall \ K \in \mathcal{T} \right\}
# $$
#
# and considering the boundary conditions
#
# $$
# \begin{align}
# u &= 0 \quad {\rm on} \ \partial\Omega, \\
# \nabla^{2} u &= 0 \quad {\rm on} \ \partial\Omega,
# \end{align}
# $$
#
# a weak formulation of the biharmonic problem reads: find $u \in V$ such
# that
#
# $$
# a(u,v)=L(v) \quad \forall \ v \in V,
# $$
#
# where the bilinear form is
#
# $$
# a(u, v) =
# \sum_{K \in \mathcal{T}} \int_{K} \nabla^{2} u \nabla^{2} v \, {\rm d}x \
# +\sum_{E \in \mathcal{E}_h^{\rm int}}\left(\int_{E} \frac{\alpha}{h_E}
# [\!\![ \nabla u ]\!\!] [\!\![ \nabla v ]\!\!] \, {\rm d}s
# - \int_{E} \left<\nabla^{2} u \right>[\!\![ \nabla v ]\!\!]  \, {\rm d}s
# - \int_{E} [\!\![ \nabla u ]\!\!] \left<\nabla^{2} v \right> \,
# {\rm d}s\right)
# $$
#
# and the linear form is
#
# $$
# L(v) = \int_{\Omega} fv \, {\rm d}x.
# $$
#
# Furthermore, $\left< u \right> = \frac{1}{2} (u_{+} + u_{-})$,
# $[\!\![ w ]\!\!]  = w_{+} \cdot n_{+} + w_{-} \cdot n_{-}$,
# $\alpha \ge 0$ is a penalty parameter and
# $h_E$ is a measure of the cell size.
#
# The input parameters for this demo are defined as follows:
#
# - $\Omega = [0,1] \times [0,1]$ (a unit square)
# - $\alpha = 8.0$ (penalty parameter)
# - $f = 4.0 \pi^4\sin(\pi x)\sin(\pi y)$ (source term)
#
# ## Implementation
#
# We first import the modules and functions that the program uses:


# +
from pathlib import Path

from mpi4py import MPI
from petsc4py.PETSc import ScalarType  # type: ignore

import ufl
from dolfinx import fem, io, mesh, plot
from dolfinx.fem.petsc import LinearProblem
from dolfinx.mesh import CellType, GhostMode

# -

# We begin by using {py:func}`create_rectangle
# <dolfinx.mesh.create_rectangle>` to create a rectangular
# {py:class}`Mesh <dolfinx.mesh.Mesh>` of the domain, and creating a
# finite element {py:class}`FunctionSpace <dolfinx.fem.FunctionSpace>`
# $V$ on the mesh.

msh = mesh.create_rectangle(
    comm=MPI.COMM_WORLD,
    points=((0.0, 0.0), (1.0, 1.0)),
    n=(32, 32),
    cell_type=CellType.triangle,
    ghost_mode=GhostMode.shared_facet,
)
V = fem.functionspace(msh, ("Lagrange", 2))

# The second argument to {py:func}`functionspace
# <dolfinx.fem.functionspace>` is a tuple consisting of `(family,
# degree)`, where `family` is the finite element family, and `degree`
# specifies the polynomial degree. in this case `V` consists of
# second-order, continuous Lagrange finite element functions.
# For further details of how one can specify
# finite elements as tuples, see {py:class}`ElementMetaData
# <dolfinx.fem.ElementMetaData>`.
#
# Next, we locate the mesh facets that lie on the boundary
# $\Gamma_D = \partial\Omega$.
# We do this using using {py:func}`exterior_facet_indices
# <dolfinx.mesh.exterior_facet_indices>` which returns all mesh boundary
# facets (Note: if we are only interested in a subset of those, consider
# {py:func}`locate_entities_boundary
# <dolfinx.mesh.locate_entities_boundary>`).

tdim = msh.topology.dim
msh.topology.create_connectivity(tdim - 1, tdim)
facets = mesh.exterior_facet_indices(msh.topology)

# We now find the degrees-of-freedom that are associated with the
# boundary facets using {py:func}`locate_dofs_topological
# <dolfinx.fem.locate_dofs_topological>`

dofs = fem.locate_dofs_topological(V=V, entity_dim=1, entities=facets)

# and use {py:func}`dirichletbc <dolfinx.fem.dirichletbc>` to create a
# {py:class}`DirichletBC <dolfinx.fem.DirichletBC>`
# class that represents the boundary condition. In this case, we impose
# Dirichlet boundary conditions with value $0$ on the entire boundary
# $\partial\Omega$.

bc = fem.dirichletbc(value=ScalarType(0), dofs=dofs, V=V)

# Next, we express the variational problem using UFL.
#
# First, the penalty parameter $\alpha$ is defined. In addition, we define
# a variable `h` for the cell diameter $h_E$, a variable `n`for the
# outward-facing normal vector $n$ and a variable `h_avg` for the
# average size of cells sharing a facet
# $\left< h \right> = \frac{1}{2} (h_{+} + h_{-})$. Here, the UFL syntax
# `('+')` and `('-')` restricts a function to the `('+')` and `('-')`
# sides of a facet.

alpha = ScalarType(8.0)
h = ufl.CellDiameter(msh)
n = ufl.FacetNormal(msh)
h_avg = (h("+") + h("-")) / 2.0

# After that, we can define the variational problem consisting of the
# bilinear form $a$ and the linear form $L$. The source term is prescribed
# as $f = 4.0 \pi^4\sin(\pi x)\sin(\pi y)$. Note that with `dS`,
# integration is carried out over all the interior facets
# $\mathcal{E}_h^{\rm int}$, whereas with `ds` it would be only the facets
# on the boundary of the domain, i.e. $\partial\Omega$. The jump operator
# $[\!\![ w ]\!\!] = w_{+} \cdot n_{+} + w_{-} \cdot n_{-}$ w.r.t. the
# outward-facing normal vector $n$ is in UFL available as `jump(w, n)`.

# +
# Define variational problem
u = ufl.TrialFunction(V)
v = ufl.TestFunction(V)
x = ufl.SpatialCoordinate(msh)
f = 4.0 * ufl.pi**4 * ufl.sin(ufl.pi * x[0]) * ufl.sin(ufl.pi * x[1])

a = (
    ufl.inner(ufl.div(ufl.grad(u)), ufl.div(ufl.grad(v))) * ufl.dx
    - ufl.inner(ufl.avg(ufl.div(ufl.grad(u))), ufl.jump(ufl.grad(v), n)) * ufl.dS
    - ufl.inner(ufl.jump(ufl.grad(u), n), ufl.avg(ufl.div(ufl.grad(v)))) * ufl.dS
    + alpha / h_avg * ufl.inner(ufl.jump(ufl.grad(u), n), ufl.jump(ufl.grad(v), n)) * ufl.dS
)
L = ufl.inner(f, v) * ufl.dx
# -

# We create a {py:class}`LinearProblem <dolfinx.fem.petsc.LinearProblem>`
# object that brings together the variational problem, the Dirichlet
# boundary condition, and which specifies the linear solver. In this
# case we use a direct (LU) solver. The {py:func}`solve
# <dolfinx.fem.petsc.LinearProblem.solve>` will compute a solution.

problem = LinearProblem(
    a,
    L,
    bcs=[bc],
    petsc_options_prefix="demo_biharmonic_",
    petsc_options={"ksp_type": "preonly", "pc_type": "lu"},
)
uh = problem.solve()
assert isinstance(uh, fem.Function)
assert problem.solver.getConvergedReason() > 0

# The solution can be written to a  {py:class}`XDMFFile
# <dolfinx.io.XDMFFile>` file visualization with ParaView or VisIt

out_folder = Path("out_biharmonic")
out_folder.mkdir(parents=True, exist_ok=True)
with io.XDMFFile(msh.comm, out_folder / "biharmonic.xdmf", "w") as file:
    V1 = fem.functionspace(msh, ("Lagrange", 1))
    u1 = fem.Function(V1)
    u1.interpolate(uh)
    file.write_mesh(msh)
    file.write_function(u1)

# and displayed using [pyvista](https://docs.pyvista.org/).

# +
try:
    import pyvista

    cells, types, x = plot.vtk_mesh(V)
    grid = pyvista.UnstructuredGrid(cells, types, x)
    grid.point_data["u"] = uh.x.array.real
    grid.set_active_scalars("u")
    plotter = pyvista.Plotter()
    plotter.add_mesh(grid, show_edges=True)
    warped = grid.warp_by_scalar()
    plotter.add_mesh(warped)
    if pyvista.OFF_SCREEN:
        plotter.screenshot(out_folder / "uh_biharmonic.png")
    else:
        plotter.show()
except ModuleNotFoundError:
    print("'pyvista' is required to visualise the solution")
    print("Install 'pyvista' with pip: 'python3 -m pip install pyvista'")