Rayleigh-Benard demo using Irksome and patch smoothing

.github/ISSUE_TEMPLATE/bug_report.md

@@ -27,7 +27,7 @@ Please do not add screenshots unless the bug is purely graphical.
 **Environment:**
  - OS: [eg: Linux, MacOS, WSL (Windows Subsystem for Linux)] add this as a label too!
  - Python version: [eg: 3.9.7]
- - Output of `firedrake-status`
+ - Output of `pip list`
  - Any relevant environment variables or modifications [eg: PYOP2_DEBUG=1]
 
 **Additional Info**

.github/workflows/core.yml

@@ -179,6 +179,7 @@ jobs:
           pip cache remove slepc4py
 
           if [ ${{ inputs.target_branch }} = 'release' ]; then
+            EXTRA_BUILD_ARGS=''
             EXTRA_PIP_FLAGS=''
           else
             : # Install build dependencies
@@ -192,12 +193,13 @@ jobs:
             pip install --no-deps ngsPETSc netgen-mesher netgen-occt
 
             : # We have to pass '--no-build-isolation' to use a custom petsc4py
+            EXTRA_BUILD_ARGS='--no-isolation'
             EXTRA_PIP_FLAGS='--no-build-isolation'
           fi
 
           : # Install from an sdist so we can make sure that it is not ill-formed
           pip install build
-          python -m build ./firedrake-repo --sdist
+          python -m build ./firedrake-repo --sdist "$EXTRA_BUILD_ARGS"
 
           pip install --verbose $EXTRA_PIP_FLAGS \
             --no-binary h5py \

demos/boussinesq/boussinesq.py.rst

@@ -0,0 +1,269 @@
+Steady Boussinesq problem with integral constraints
+===================================================
+
+.. rst-class:: emphasis
+
+    This demo demonstrates how integral constraints can be imposed on a field
+    that appears nonlinearly in the governing equations.
+
+    The demo was contributed by `Aaron Baier-Reinio
+    <mailto:[email protected]>`__ and `Kars Knook
+    <mailto:[email protected]>`__.
+
+We consider a nondimensionalised steady Boussinesq problem.
+The domain is :math:`\Omega \subset \mathbb{R}^2`
+with boundary :math:`\Gamma`. The boundary value problem is:
+
+.. math::
+
+    -\nabla \cdot (\mu(T) \epsilon (u)) + \nabla p - f T &= 0 \quad \textrm{in}\ \Omega,
+
+    \nabla \cdot u &= 0 \quad \textrm{in}\ \Omega,
+
+    u \cdot \nabla T - \nabla^2 T &= 0 \quad \textrm{in}\ \Omega,
+
+    u &= 0 \quad \textrm{on}\ \Gamma,
+
+    \nabla T \cdot n &= g \quad \textrm{on}\ \Gamma.
+
+The unknowns are the :math:`\mathbb{R}^2`-valued velocity :math:`u`,
+scalar pressure :math:`p` and temperature :math:`T`.
+The viscosity :math:`\mu(T)` is assumed to be a known function of :math:`T`.
+Moreover :math:`\epsilon (u)` denotes the symmetric gradient of :math:`u`
+and :math:`f = (0, -1)^T` the acceleration due to gravity.
+Inhomogeneous Neumann boundary conditions are imposed on :math:`\nabla T \cdot n` through 
+given data :math:`g` which must satisfy a compatibility condition
+
+.. math::
+
+    \int_{\Gamma} g \ {\rm d} s = 0.
+
+Evidently the pressure :math:`p` is only determined up to a constant, since it only appears in
+the problem through its gradient. This choice of constant is arbitrary and does not affect the model.
+The situation regarding the temperature :math:`T` is, however, more subtle.
+For the sake of discussion let us first assume that :math:`\mu(T) = \mu_0` is a constant that does
+not depend on :math:`T`. It is then clear that, just like the pressure, the temperature :math:`T`
+is undetermined up to a constant. We shall pin this down by enforcing that the mean of :math:`T`
+is a user-supplied constant :math:`T_0`,
+
+.. math::
+
+    \int_{\Omega} (T - T_0) \ {\rm d} x = 0.
+
+The Boussinesq approximation assumes that density varies linearly with temperature.
+Hence, this constraint can be viewed as an indirect imposition on the total mass of fluid in :math:`\Omega`.
+
+Now suppose that :math:`\mu(T)` does depend on :math:`T`.
+For simplicity we use a basic power law :math:`\mu(T) = 10^{-4} \cdot T^{1/2}`
+but emphasise that the precise functional form of :math:`\mu(T)` is unimportant to this demo.
+We must still impose the integral constraint on :math:`T` to obtain a unique solution,
+but the value of :math:`T_0` now affects the model in a non-trivial way since :math:`\mu(T)` and 
+:math:`T` are coupled (c.f. the figures at the bottom of the demo).
+**In particular, this is not a "trivial" situation like the incompressible
+Stokes problem where the discretized Jacobians have a nullspace corresponding to the constant pressures.
+Instead, we have an integral constraint on** :math:`T` **even though
+the discretized Jacobians do not have a nullspace corresponding to the constant temperatures.**
+
+We build the mesh using :doc:`netgen <netgen_mesh.py>`, choosing a trapezoidal geometry
+to prevent hydrostatic equilibrium and allow for a non-trivial velocity solution.::
+
+    from firedrake import *
+    import netgen.occ as ngocc
+
+    wp = ngocc.WorkPlane()
+    wp.MoveTo(0, 0)
+    wp.LineTo(2, 0)
+    wp.LineTo(2, 1)
+    wp.LineTo(0, 2)
+    wp.LineTo(0, 0)
+
+    shape = wp.Face()
+    shape.edges.Min(ngocc.X).name = "left"
+    shape.edges.Max(ngocc.X).name = "right"
+
+    ngmesh = ngocc.OCCGeometry(shape, dim=2).GenerateMesh(maxh=0.1)
+
+    left_id = [i+1 for i, name in enumerate(ngmesh.GetRegionNames(dim=1)) if name == "left"]
+    right_id = [i+1 for i, name in enumerate(ngmesh.GetRegionNames(dim=1)) if name == "right"]
+
+    mesh = Mesh(ngmesh)
+    x, y = SpatialCoordinate(mesh)
+
+Next we set up the discrete function spaces.
+We use lowest-order Taylor--Hood elements for the velocity and pressure,
+and continuous piecewise-linear elements for the temperature.
+We introduce a Lagrange multiplier to enforce the integral constraint on :math:`T`::
+
+    U = VectorFunctionSpace(mesh, "CG", degree=2)
+    V = FunctionSpace(mesh, "CG", degree=1)
+    W = FunctionSpace(mesh, "CG", degree=1)
+    R = FunctionSpace(mesh, "R", 0)
+
+    Z = U * V * W * R
+
+The trial and test functions are:::
+
+    z = Function(Z)
+    (u, p, T_aux, l) = split(z)
+    (v, q, w, s) = split(TestFunction(Z))
+
+    T = T_aux + l
+
+The test Lagrange multiplier :code:`s` will allow us to impose the integral constraint on the temperature.
+We use the trial Lagrange multiplier :code:`l` by decomposing the discretized temperature field :code:`T`
+as :code:`T = T_aux + l` where :code:`T_aux` is the trial function from :code:`W`.
+The value of :code:`l` will then be determined by the integral constraint on :code:`T`.
+
+The remaining problem data to be specified is the Neumann data,
+viscosity, acceleration due to gravity and :math:`T_0`.
+For the Neumann data we choose a parabolic profile on the left and right edges,
+and zero data on the top and bottom.::
+
+    g_left = y*(y-2)                # Neumann data on the left
+    g_right = -8*y*(y-1)            # Neumann data on the right
+    mu = (1e-4) * T ** (1/2)        # Viscosity
+    f = as_vector([0, -1])          # Acceleration due to gravity
+    T0 = Constant(1)                # Mean of the temperature
+
+The nonlinear form for the problem is:::
+
+    F = (mu * inner(sym(grad(u)), sym(grad(v))) * dx    # Viscous terms
+     - inner(p, div(v)) * dx                            # Pressure gradient
+     - inner(f, T*v) * dx                               # Buoyancy term
+     - inner(div(u), q) * dx                            # Incompressibility constraint
+     + inner(dot(u, grad(T)), w) * dx                   # Temperature advection term
+     + inner(grad(T), grad(w)) * dx                     # Temperature diffusion term
+     - inner(g_left, w) * ds(tuple(left_id))            # Weakly imposed Neumann BC terms
+     - inner(g_right, w) * ds(tuple(right_id))          # Weakly imposed Neumann BC terms
+     + inner(T - T0, s) * dx                            # Integral constraint on T
+     )
+
+and the (strongly enforced) Dirichlet boundary conditions on :math:`u` are enforced by::
+
+    bc_u = DirichletBC(Z.sub(0), 0, "on_boundary")
+
+At this point we could form and solve a :class:`~.NonlinearVariationalProblem`
+using :code:`F` and :code:`bc_u`. However, the resultant problem has a nullspace of
+dimension 2, corresponding to (i) shifting :math:`p` by a constant :math:`C_1`
+and (ii) shifting :math:`l` by a constant :math:`C_2` while simultaneuosly shifting
+:math:`T_{\textrm{aux}}` by :math:`-C_2`.
+
+One way of dealing with nullspaces in Firedrake is to pass a :code:`nullspace` and
+:code:`transpose_nullspace` to :class:`~.NonlinearVariationalSolver`. However, sometimes 
+this approach may not be practical. First, for nonlinear problems with Jacobians that 
+are not symmetric, it may not obvious what the :code:`transpose_nullspace` is. A second 
+reason is that, when using customised PETSc linear solvers, it may be desirable
+to directly eliminate the nullspace from the assembled Jacobian matrix, since one
+cannot always be sure that the linear solver at hand is correctly utilising the provided
+:code:`nullspace` and :code:`transpose_nullspace`.
+
+To directly eliminate the nullspace we introduce a class :code:`FixAtPointBC` which
+implements a boundary condition that fixes a field at a single point.::
+
+    import firedrake.utils as firedrake_utils
+
+    class FixAtPointBC(firedrake.DirichletBC):
+        r'''A special BC object for pinning a function at a point.
+
+        :arg V: the :class:`.FunctionSpace` on which the boundary condition should be applied.
+        :arg g: the boundary condition value.
+        :arg bc_point: the point at which to pin the function.
+            The location of the finite element DOF nearest to bc_point is actually used.
+        '''
+        def __init__(self, V, g, bc_point):
+            super(FixAtPointBC, self).__init__(V, g, bc_point)
+            if isinstance(bc_point, tuple):
+                bc_point = as_vector(bc_point)
+            self.bc_point = bc_point
+
+        @firedrake_utils.cached_property
+        def nodes(self):
+            V = self.function_space()
+            x = firedrake.SpatialCoordinate(V.mesh())
+            xdist = x - self.bc_point
+
+            test = firedrake.TestFunction(V)
+            trial = firedrake.TrialFunction(V)
+            xphi = firedrake.assemble(ufl.inner(xdist * test, xdist * trial) * ufl.dx, diagonal=True)
+            phi = firedrake.assemble(ufl.inner(test, trial) * ufl.dx, diagonal=True)
+            with xphi.dat.vec as xu, phi.dat.vec as u:
+                xu.pointwiseDivide(xu, u)
+                min_index, min_value = xu.min()     # Find the index of the DOF closest to bc_point
+
+            nodes = V.dof_dset.lgmap.applyInverse([min_index])
+            nodes = nodes[nodes >= 0]
+            return nodes
+
+We use this to fix the pressure and auxiliary temperature at the origin:::
+
+    aux_bcs = [FixAtPointBC(Z.sub(1), 0, as_vector([0, 0])), 
+               FixAtPointBC(Z.sub(2), 0, as_vector([0, 0]))]
+
+:code:`FixAtPointBC` takes three arguments: the function space to fix, the value with which it
+will be fixed, and the location at which to fix. Generally :code:`FixAtPointBC` will not fix
+the function at exactly the supplied point; it will fix it at the finite element DOF closest
+to that point. By default CG elements have DOFs on all mesh vertices, so if the supplied
+point if a mesh vertex then CG fields will be fixed at exactly the supplied point.
+
+.. warning::
+
+    A :code:`FixAtPointBC` does more than just fix the corresponding trial function
+    at the chosen DOF. It also ensures that the corresponding test function
+    (which is equal to one at that DOF and zero at all others)
+    will no longer be used in the discretized variational problem.
+    One must be sure that it is mathematically acceptable to do this.
+
+    In the present setting this is acceptable owing to the homogeneous Dirichlet
+    boundary conditions on :math:`u` and compatibility condition :math:`\int_{\Gamma} g \ {\rm d} s = 0`
+    on the Neumann data. The former ensures that the rows in the discretized Jacobian
+    corresponding to the incompressibility constraint are linearly dependent
+    (if there are :math:`M` rows, only :math:`M-1` of them are linearly independent, since
+    the boundary conditions on :math:`u` ensure that 
+    :math:`\int_{\Omega} \nabla \cdot u {\rm d} x = 0` automatically).
+    Similarily the rows in the Jacobian corresponding to the temperature advection-diffusion
+    equation are linearly independent (again, if there are :math:`M` rows, 
+    only :math:`M-1` of them are linearly independent).
+    The effect of :code:`FixAtPointBC` will be to remove one of the rows corresponding
+    to the incompressibility constraint and one corresponding to the temperature advection-diffusion
+    equation. Which row ends up getting removed is determined by the location of :code:`bc_point`,
+    but in the present setting removing a given row is mathematically equivalent to removing any one of the others.
+
+    One could envisage a more complicated scenario than the one in this demo, wherein the Neumann data
+    depends nonlinearly on some other problem unknowns, and it only satisfies the compatibility condition
+    approximately (e.g. up to some discretization error).
+    In this case one would have to be very careful when using :code:`FixAtPointBC` --
+    although similar cautionary behaviour would also have to be taken if using 
+    :code:`nullspace` and :code:`transpose_nullspace` instead.
+
+Finally, we form and solve the nonlinear variational problem for :math:`T_0 \in \{1, 10, 100, 1000, 10000 \}`::
+
+    NLVP = NonlinearVariationalProblem(F, z, bcs=[bc_u]+aux_bcs)
+    NLVS = NonlinearVariationalSolver(NLVP)
+
+    (u, p, T_aux, l) = z.subfunctions
+    File = VTKFile(f"output/boussinesq.pvd")
+
+    for i in range(0, 5):
+        T0.assign(10**(i))
+        l.assign(Constant(T0))
+        NLVS.solve()
+
+        u_out = assemble(project(u, Z.sub(0)))
+        p_out = assemble(project(p, Z.sub(1)))
+        T_out = assemble(project(T, Z.sub(2)))
+
+        u_out.rename("u")
+        p_out.rename("p")
+        T_out.rename("T")
+
+        File.write(u_out, p_out, T_out, time=i)
+
+The temperature and stream lines for :math:`T_0=1` and :math:`T_0=10000` are displayed below on the left and right respectively.
+
++-------------------------+-------------------------+
+| .. image:: T0_1.png     | .. image:: T0_10000.png |
+|    :width: 100%         |    :width: 100%         |
++-------------------------+-------------------------+
+
+A Python script version of this demo can be found :demo:`here
+<boussinesq.py>`.