First working version of AMR on a 2D cubed sphere

examples/p4est_2d_dgsem/elixir_euler_cubed_sphere_shell_amr.jl

@@ -0,0 +1,127 @@
+
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# semidiscretization of the linear advection equation
+
+equations = CompressibleEulerEquations3D(1.4)
+
+# Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux
+polydeg = 3
+solver = DGSEM(polydeg = polydeg, surface_flux = flux_lax_friedrichs)
+
+# Initial condition for a Gaussian density profile with constant pressure
+# and the velocity of a rotating solid body
+function initial_condition_advection_sphere(x, t, equations::CompressibleEulerEquations3D)
+    # Gaussian density
+    rho = 1.0 + exp(-20 * (x[1]^2 + x[3]^2))
+    # Constant pressure
+    p = 1.0
+
+    # Spherical coordinates for the point x
+    if sign(x[2]) == 0.0
+        signy = 1.0
+    else
+        signy = sign(x[2])
+    end
+    # Co-latitude
+    colat = acos(x[3] / sqrt(x[1]^2 + x[2]^2 + x[3]^2))
+    # Latitude (auxiliary variable)
+    lat = -colat + 0.5 * pi
+    # Longitude
+    r_xy = sqrt(x[1]^2 + x[2]^2)
+    if r_xy == 0.0
+        phi = pi / 2
+    else
+        phi = signy * acos(x[1] / r_xy)
+    end
+
+    # Compute the velocity of a rotating solid body
+    # (alpha is the angle between the rotation axis and the polar axis of the spherical coordinate system)
+    v0 = 1.0 # Velocity at the "equator"
+    alpha = 0.0 #pi / 4
+    v_long = v0 * (cos(lat) * cos(alpha) + sin(lat) * cos(phi) * sin(alpha))
+    v_lat = -v0 * sin(phi) * sin(alpha)
+
+    # Transform to Cartesian coordinate system
+    v1 = -cos(colat) * cos(phi) * v_lat - sin(phi) * v_long
+    v2 = -cos(colat) * sin(phi) * v_lat + cos(phi) * v_long
+    v3 = sin(colat) * v_lat
+
+    return prim2cons(SVector(rho, v1, v2, v3, p), equations)
+end
+
+# Source term function to transform the Euler equations into the linear advection equations with variable advection velocity
+function source_terms_convert_to_linear_advection(u, du, x, t,
+                                                  equations::CompressibleEulerEquations3D)
+    v1 = u[2] / u[1]
+    v2 = u[3] / u[1]
+    v3 = u[4] / u[1]
+
+    s2 = du[1] * v1 - du[2]
+    s3 = du[1] * v2 - du[3]
+    s4 = du[1] * v3 - du[4]
+    s5 = 0.5 * (s2 * v1 + s3 * v2 + s4 * v3) - du[5]
+
+    return SVector(0.0, s2, s3, s4, s5)
+end
+
+initial_condition = initial_condition_advection_sphere
+
+mesh = Trixi.P4estMeshCubedSphere2D(5, 1.0, polydeg = polydeg, initial_refinement_level = 0)
+
+# A semidiscretization collects data structures and functions for the spatial discretization
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
+                                    source_terms = source_terms_convert_to_linear_advection)
+
+###############################################################################
+# ODE solvers, callbacks etc.
+
+# Create ODE problem with time span from 0.0 to π
+tspan = (0.0, pi)
+ode = semidiscretize(semi, tspan)
+
+# At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
+# and resets the timers
+summary_callback = SummaryCallback()
+
+# The AnalysisCallback allows to analyse the solution in regular intervals and prints the results
+analysis_callback = AnalysisCallback(semi, interval = 10,
+                                     save_analysis = true,
+                                     extra_analysis_integrals = (Trixi.density,))
+
+# The SaveSolutionCallback allows to save the solution to a file in regular intervals
+save_solution = SaveSolutionCallback(interval = 10,
+                                     solution_variables = cons2prim)
+
+# The StepsizeCallback handles the re-calculation of the maximum Δt after each time step
+stepsize_callback = StepsizeCallback(cfl = 0.7)
+
+# AMR callback
+amr_indicator = IndicatorLöhner(semi, variable = Trixi.density)
+
+amr_controller = ControllerThreeLevel(semi, amr_indicator,
+                                      base_level = 0,
+                                      med_level = 1, med_threshold = 0.02,
+                                      max_level = 2, max_threshold = 0.03)
+
+amr_callback = AMRCallback(semi, amr_controller,
+                           interval = 1,
+                           adapt_initial_condition = true,
+                           adapt_initial_condition_only_refine = true)
+
+# Create a CallbackSet to collect all callbacks such that they can be passed to the ODE solver
+callbacks = CallbackSet(summary_callback, analysis_callback,
+                        stepsize_callback, amr_callback, save_solution)
+
+###############################################################################
+# run the simulation
+
+# OrdinaryDiffEq's `solve` method evolves the solution in time and executes the passed callbacks
+sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false),
+            dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
+            save_everystep = false, callback = callbacks);
+
+# Print the timer summary
+summary_callback()

src/solvers/dgsem_p4est/containers.jl

@@ -49,22 +49,24 @@ function Base.resize!(elements::P4estElementContainer, capacity)
     _inverse_jacobian, _surface_flux_values = elements
 
     n_dims = ndims(elements)
+    ndims_spa = size(elements.node_coordinates, 1)
     n_nodes = size(elements.node_coordinates, 2)
     n_variables = size(elements.surface_flux_values, 1)
 
-    resize!(_node_coordinates, n_dims * n_nodes^n_dims * capacity)
+    resize!(_node_coordinates, ndims_spa * n_nodes^n_dims * capacity)
     elements.node_coordinates = unsafe_wrap(Array, pointer(_node_coordinates),
-                                            (n_dims, ntuple(_ -> n_nodes, n_dims)...,
+                                            (ndims_spa, ntuple(_ -> n_nodes, n_dims)...,
                                              capacity))
 
-    resize!(_jacobian_matrix, n_dims^2 * n_nodes^n_dims * capacity)
+    resize!(_jacobian_matrix, ndims_spa * n_dims * n_nodes^n_dims * capacity)
     elements.jacobian_matrix = unsafe_wrap(Array, pointer(_jacobian_matrix),
-                                           (n_dims, n_dims,
+                                           (ndims_spa, n_dims,
                                             ntuple(_ -> n_nodes, n_dims)..., capacity))
 
-    resize!(_contravariant_vectors, length(_jacobian_matrix))
+    resize!(_contravariant_vectors, ndims_spa^2 * n_nodes^n_dims * capacity)
     elements.contravariant_vectors = unsafe_wrap(Array, pointer(_contravariant_vectors),
-                                                 size(elements.jacobian_matrix))
+                                           (ndims_spa, ndims_spa,
+                                            ntuple(_ -> n_nodes, n_dims)..., capacity))
 
     resize!(_inverse_jacobian, n_nodes^n_dims * capacity)
     elements.inverse_jacobian = unsafe_wrap(Array, pointer(_inverse_jacobian),

src/solvers/dgsem_tree/indicators_2d.jl

@@ -260,6 +260,19 @@ function create_cache(typ::Type{IndicatorLöhner}, mesh, equations::AbstractEqua
     create_cache(typ, equations, dg.basis)
 end
 
+# this method is used when the indicator is constructed as for AMR
+function create_cache(typ::Type{IndicatorLöhner}, mesh::AbstractMesh{2}, equations::AbstractEquations{3},
+                      dg::DGSEM, cache)
+    @unpack basis = dg
+    alpha = Vector{real(basis)}()
+
+    A = Array{real(basis), ndims(mesh)}
+    indicator_threaded = [A(undef, nnodes(basis), nnodes(basis))
+                          for _ in 1:Threads.nthreads()]
+
+    return (; alpha, indicator_threaded)
+end
+
 function (löhner::IndicatorLöhner)(u::AbstractArray{<:Any, 4},
                                    mesh, equations, dg::DGSEM, cache;
                                    kwargs...)