#206: Bubble shear demo (unfinished)

demos/bubble_shear.py

@@ -0,0 +1,285 @@
+# Goal-oriented mesh adaptation for a 2D time-dependent problem
+# =============================================================
+
+# In a `previous demo <./bubble_shear.py.html>`__, we considered the advection of a
+# scalar concentration field in a non-uniform background velocity field. The demo
+# concluded with labelling the problem as a good candidate for a goal-oriented mesh
+# adaptation approach. This is what we set out to do in this demo.
+#
+# We will use the same setup as in the original demo, but a small modifiction to the
+# :meth:`get_form` function is necessary in order to take into account a prescribed
+# time-dependent background velocity field which is not passed to
+# :class:`GoalOrientedMeshSeq`. ::
+
+from animate.adapt import adapt
+from animate.metric import RiemannianMetric
+from firedrake import *
+
+from goalie_adjoint import *
+
+T = 6.0
+
+
+def velocity_expression(mesh, t):
+    x, y = SpatialCoordinate(mesh)
+    u_expr = as_vector(
+        [
+            2 * sin(pi * x) ** 2 * sin(2 * pi * y) * cos(2 * pi * t / T),
+            -sin(2 * pi * x) * sin(pi * y) ** 2 * cos(2 * pi * t / T),
+        ]
+    )
+    return u_expr
+
+
+fields = ["c"]
+
+
+def get_function_spaces(mesh):
+    return {"c": FunctionSpace(mesh, "CG", 1)}
+
+
+def ball_initial_condition(x, y):
+    ball_r0, ball_x0, ball_y0 = 0.15, 0.5, 0.65
+    r = sqrt(pow(x - ball_x0, 2) + pow(y - ball_y0, 2))
+    return conditional(r < ball_r0, 1.0, 0.0)
+
+
+def get_initial_condition(mesh_seq):
+    fs = mesh_seq.function_spaces["c"][0]
+    x, y = SpatialCoordinate(mesh_seq[0])
+    ball = ball_initial_condition(x, y)
+    c0 = assemble(interpolate(ball, fs))
+    return {"c": c0}
+
+
+def get_solver(mesh_seq):
+    def solver(index):
+        Q = mesh_seq.function_spaces["c"][index]
+        V = VectorFunctionSpace(mesh_seq[index], "CG", 1)
+        R = FunctionSpace(mesh_seq[index], "R", 0)
+
+        c, c_ = mesh_seq.fields["c"]
+
+        tp = mesh_seq.time_partition
+        t_start, t_end = tp.subintervals[index]
+        t = Function(R).assign(t_start)
+        dt = Function(R).assign(tp.timesteps[index])
+        theta = Function(R).assign(0.5)  # Crank-Nicolson implicitness
+
+        # Compute the velocity field at t_start
+        u = Function(V)
+        u_ = Function(V)
+        u_expression = velocity_expression(mesh_seq[index], t)
+        u_.interpolate(u_expression)
+
+        # SUPG stabilisation parameter
+        D = Function(R).assign(0.1)  # diffusivity coefficient
+        h = CellSize(mesh_seq[index])  # mesh cell size
+        U = sqrt(dot(u, u))  # velocity magnitude
+        tau = 0.5 * h / U
+        tau = min_value(tau, U * h / (6 * D))
+
+        phi = TestFunction(Q)
+        phi += tau * dot(u, grad(phi))
+
+        a = c * phi * dx + dt * theta * dot(u, grad(c)) * phi * dx
+        L = c_ * phi * dx - dt * (1 - theta) * dot(u_, grad(c_)) * phi * dx
+        F = a - L
+        mesh_seq.read_forms({"c": F})
+
+        bcs = DirichletBC(mesh_seq.function_spaces["c"][index], 0.0, "on_boundary")
+        nlvp = NonlinearVariationalProblem(F, c, bcs=bcs)
+        nlvs = NonlinearVariationalSolver(nlvp, ad_block_tag="c")
+
+        # Time integrate from t_start to t_end
+        while float(t) < t_end + 0.5 * float(dt):
+            # Update the background velocity field at the current timestep
+            u.interpolate(u_expression)
+
+            # Solve the advection equation
+            nlvs.solve()
+            yield
+
+            # Update the 'lagged' concentration and velocity field
+            c_.assign(c)
+            u_.assign(u)
+            t.assign(t + dt)
+
+        return {"c": c}
+
+    return solver
+
+
+# In the `first demo <bubble_shear.py>`__ where we considered this problem, the
+# :meth:`get_form` method was only called from within the :meth:`get_solver`, so we were
+# able to pass the velocity field as an argument when calling :meth:`get_form`. However,
+# in the context of goal-oriented mesh adaptation,  the :meth:`get_form` method is
+# called from within :class:`GoalOrientedMeshSeq` while computing error indicators.
+# There, only those fields that are passed to :class:`GoalOrientedMeshSeq` are passed to
+# :meth:`get_form`. Currently, Goalie does not consider passing non-prognostic fields
+# to this method during the error-estimation step, so the velocity would not be updated
+# in time. To account for this, we need to add some code for updating the velocity
+# field when it is not present in the dictionary of fields passed. ::
+
+
+# To compute the adjoint, we must also define the goal functional. As motivated in
+# the previous demo, we will use the L2 norm of the difference between the
+# concentration field at :math:`t=0` and :math:`t=T/2`, i.e. the simulation end time.
+#
+# .. math::
+#   J(c) := \int_{\Omega} (c(x, y, T/2) - c_0(x, y))^2 \, dx \, dy. ::
+
+
+def get_qoi(mesh_seq, index):
+    def qoi():
+        c0 = mesh_seq.get_initial_condition()["c"]
+        c0_proj = project(c0, mesh_seq.function_spaces["c"][index])
+        c = mesh_seq.fields["c"][0]
+
+        J = (c - c0_proj) * (c - c0_proj) * dx
+        return J
+
+    return qoi
+
+
+# We must also define the adaptor function to drive the mesh adaptation process. Here
+# we compute the anisotropic DWR metric which requires us to compute the hessian of the
+# tracer concentration field. We combine each metric in a subinterval by intersection.
+# We will only run two iterations of the fixed point iteration algorithm so we do not
+# ramp up the complexity. ::
+
+
+def adaptor(mesh_seq, solutions, indicators):
+    iteration = mesh_seq.fp_iteration
+    mp = {
+        "dm_plex_metric": {
+            "target_complexity": 1000,
+            "p": 1.0,
+            "h_min": 1e-04,
+            "h_max": 1.0,
+        }
+    }
+
+    metrics = []
+    for i, mesh in enumerate(mesh_seq):
+        c_solutions = solutions["c"]["forward"][i]
+
+        P1_ten = TensorFunctionSpace(mesh, "CG", 1)
+        subinterval_metric = RiemannianMetric(P1_ten)
+
+        for j, c_sol in enumerate(c_solutions):
+            # Recover the Hessian of the forward solution
+            hessian = RiemannianMetric(P1_ten)
+            hessian.compute_hessian(c_sol)
+
+            metric = RiemannianMetric(P1_ten)
+            metric.set_parameters(mp)
+
+            # Compute an anisotropic metric from the error indicator field and Hessian
+            metric.compute_anisotropic_dwr_metric(indicators["c"][i][j], hessian)
+
+            # Combine the metrics from each exported timestep in the subinterval
+            subinterval_metric.intersect(metric)
+        metrics.append(metric)
+
+    # Normalise the metrics in space and time
+    space_time_normalise(metrics, mesh_seq.time_partition, mp)
+
+    # Apply mesh adaptation
+    # mesh_seq.set_meshes(map(adapt, mesh_seq, metrics))
+    for i, metric in enumerate(metrics):
+        mesh_seq[i] = adapt(mesh_seq[i], metric)
+    num_dofs = mesh_seq.count_vertices()
+    num_elem = mesh_seq.count_elements()
+    pyrint(f"Fixed point iteration {iteration}:")
+    pyrint(f"  qoi: {mesh_seq.qoi_values[-1]:.2e}")
+    for i, (ndofs, nelem, metric) in enumerate(zip(num_dofs, num_elem, metrics)):
+        pyrint(
+            f"  subinterval {i}, complexity: {metric.complexity():4.0f}"
+            f", dofs: {ndofs:4d}, elements: {nelem:4d}"
+        )
+
+    return True
+
+
+# Finally, we can define the :class:`GoalOrientedMeshSeq` and run the fixed point
+# iteration. For the purposes of this demo, we divide the time interval into 6
+# subintervals and only run two iterations of the fixed point iteration, which is not
+# enough to reach convergence. ::
+
+n = 50
+dt = 0.01
+maxiter = 2  # maximum number of fixed point iterations
+
+num_subintervals = 6
+meshes = [UnitSquareMesh(n, n) for _ in range(num_subintervals)]
+end_time = T / 2
+time_partition = TimePartition(
+    end_time,
+    num_subintervals,
+    dt,
+    fields,
+    num_timesteps_per_export=5,
+)
+
+msq = GoalOrientedMeshSeq(
+    time_partition,
+    meshes,
+    get_function_spaces=get_function_spaces,
+    get_initial_condition=get_initial_condition,
+    get_solver=get_solver,
+    get_qoi=get_qoi,
+    qoi_type="end_time",
+)
+parameters = GoalOrientedAdaptParameters({"maxiter": maxiter})
+solutions, indicators = msq.fixed_point_iteration(adaptor, parameters=parameters)
+
+# Let us plot the intermediate and final solutions, as well as the final adapted meshes. ::
+
+import matplotlib.pyplot as plt
+from firedrake.pyplot import tripcolor, triplot
+
+fig, axes = plt.subplots(2, 3, figsize=(7.5, 5), sharex=True, sharey=True)
+
+for i, ax in enumerate(axes.flatten()):
+    ax.set_aspect("equal")
+    ax.set_xlim(0, 1)
+    ax.set_ylim(0, 1)
+    # ax.tick_params(axis='both', which='major', labelsize=6)
+
+    # Plot the solution at the final subinterval timestep
+    time = time_partition.subintervals[i][-1]
+    tripcolor(solutions["c"]["forward"][i][-1], axes=ax, cmap="coolwarm")
+    triplot(msq[i], axes=ax, interior_kw={"linewidth": 0.08})
+    ax.annotate(f"t={time:.2f}", (0.05, 0.05), color="white")
+
+fig.tight_layout(pad=0.3)
+fig.savefig("bubble_shear-goal_oriented.jpg", dpi=300, bbox_inches="tight")
+
+fig, axes, tcs = plot_indicator_snapshots(
+    indicators,
+    time_partition,
+    "c",
+)
+fig.savefig("bubble_shear-goal_oriented-indicators.jpg", dpi=300, bbox_inches="tight")
+
+# .. figure:: bubble_shear-goal_oriented.jpg
+#    :figwidth: 80%
+#    :align: center
+#
+# Compared to the solution obtained on a fixed uniform mesh in the previous demo, we
+# observe that the final solution at :math:`t=T/2` better matches the initial tracer
+# bubble :math:`c_0` and is less diffused. Despite employing only two fixed
+# point iterations, the goal-oriented mesh adaptation process was still able to
+# significantly improve the accuracy of the solution while reducing the number of
+# degrees of freedom by half.
+#
+# As shown in the above figure, the bubble experiences extreme deformation and requires
+# frequent adaptation to be resolved accurately (surely more than 5, as in this demo!).
+# We encourage users to experiment with different numbers of subintervals, number of
+# exports per subinterval, adaptor functions, and other parameters to explore the
+# convergence of the fixed point iteration. Another interesting experiment would be to
+# compare the impact of switching to an explicit time integration and using a smaller
+# timestep to maintain numerical stability (look at CFL condition).
+#
+# This tutorial can be dowloaded as a `Python script <bubble_shear-goal_oriented.py>`__.