WIP: Implement mimetic metrics

Project.toml

@@ -19,7 +19,9 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
 MuladdMacro = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
 Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 P4est = "7d669430-f675-4ae7-b43e-fab78ec5a902"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
@@ -59,8 +61,8 @@ HDF5 = "0.14, 0.15, 0.16"
 IfElse = "0.1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
-Makie = "0.19"
 MPI = "0.20"
+Makie = "0.19"
 MuladdMacro = "0.2.2"
 Octavian = "0.3.5"
 OffsetArrays = "1.3"

examples/p4est_3d_dgsem/elixir_test_mimetic_metrics.jl

@@ -0,0 +1,158 @@
+using LinearAlgebra
+using OrdinaryDiffEq
+using Trixi
+using StaticArrays
+using Plots
+
+###############################################################################
+# semidiscretization of the linear advection equation
+
+advection_velocity = (0.2, -0.7, 0.5)
+equations = LinearScalarAdvectionEquation3D(advection_velocity)
+
+# Mapping as described in https://arxiv.org/abs/2012.12040
+function mapping(xi, eta, zeta)
+  # Transform input variables between -1 and 1 onto our crazy domain
+
+  y = eta + 0.1 * (cos(pi * xi) *
+                   cos(pi * eta) *
+                   cos(pi * zeta))
+
+  x = xi + 0.1 * (cos(pi * xi) *
+                   cos(pi * eta) *
+                   cos(pi * zeta))
+
+  z = zeta + 0.1 * (cos(pi * xi) *
+                   cos(pi * eta) *
+                   cos(pi * zeta))
+
+  #= x = xi
+  y = eta
+  z = zeta =#
+  return SVector(x, y, z)
+end
+
+cells_per_dimension = (1, 1, 1) # The p4est implementation works with one tree per direction only
+
+
+exact_jacobian = false
+mimetic = false
+final_time = 1e-3
+
+initial_condition = initial_condition_constant
+
+#= polydeg_geo = 15
+polydeg = 10 =#
+
+max_polydeg = 20
+n_polydeg_geo = 4
+errors_sol_inf = zeros(max_polydeg,n_polydeg_geo)
+errors_sol_L2 = zeros(max_polydeg,n_polydeg_geo)
+polydeg_geos = [2, 3, 5, 10]
+#polydeg_geos = [30]
+for i in 1:n_polydeg_geo
+  polydeg_geo = polydeg_geos[i]
+  for polydeg in 1:max_polydeg
+
+    solver = DGSEM(polydeg, flux_lax_friedrichs)
+
+    # Create curved mesh with 8 x 8 x 8 elements
+    boundary_condition = BoundaryConditionDirichlet(initial_condition)
+    boundary_conditions = Dict(
+      :x_neg => boundary_condition,
+      :x_pos => boundary_condition,
+      :y_neg => boundary_condition,
+      :y_pos => boundary_condition,
+      :z_neg => boundary_condition,
+      :z_pos => boundary_condition
+    )
+    println("polydeg_geo: ", polydeg_geo)
+    #mesh = P4estMesh(cells_per_dimension; polydeg = polydeg_geo, mapping = mapping, mimetic = mimetic, exact_jacobian = exact_jacobian, initial_refinement_level = 0, periodicity = true)
+    mesh = P4estMesh(cells_per_dimension; polydeg = polydeg_geo, mapping = mapping, mimetic = mimetic, exact_jacobian = exact_jacobian, initial_refinement_level = 0, periodicity = false)
+
+    # Refine bottom left quadrant of each tree to level 3
+    function refine_fn(p8est, which_tree, quadrant)
+        quadrant_obj = unsafe_load(quadrant)
+        if quadrant_obj.x == 0 && quadrant_obj.y == 0 && quadrant_obj.z == 0 && quadrant_obj.level < 2
+          # return true (refine)
+          return Cint(1)
+        else
+          # return false (don't refine)
+          return Cint(0)
+        end
+      end
+
+      # Refine recursively until each bottom left quadrant of a tree has level 3
+      # The mesh will be rebalanced before the simulation starts
+      refine_fn_c = @cfunction(refine_fn, Cint, (Ptr{Trixi.p8est_t}, Ptr{Trixi.p4est_topidx_t}, Ptr{Trixi.p8est_quadrant_t}))
+      Trixi.refine_p4est!(mesh.p4est, true, refine_fn_c, C_NULL)
+
+    # A semidiscre  tization collects data structures and functions for the spatial discretization
+    #semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
+    semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, boundary_conditions = boundary_conditions)
+
+    # Create ODE problem with time span from 0.0 to 1.0
+    ode = semidiscretize(semi, (0.0, final_time));
+
+    summary_callback = SummaryCallback()
+
+    # The AnalysisCallback allows to analyse the solution in regular intervals and prints the results
+    analysis_callback = AnalysisCallback(semi, interval=100)
+
+    # The StepsizeCallback handles the re-calculation of the maximum Δt after each time step
+    stepsize_callback = StepsizeCallback(cfl=0.1)
+
+    # The SaveSolutionCallback allows to save the solution to a file in regular intervals
+    save_solution = SaveSolutionCallback(interval=100,
+                                        solution_variables=cons2prim)
+
+    #= amr_indicator = IndicatorHennemannGassner(semi,
+                                              alpha_max=1.0,
+                                              alpha_min=0.0001,
+                                              alpha_smooth=false,
+                                              variable=Trixi.energy_total)
+
+    amr_controller = ControllerThreeLevel(semi, amr_indicator,
+                                          base_level=4,
+                                          max_level=6, max_threshold=0.01)
+
+    #= amr_controller = ControllerThreeLevel(semi, IndicatorMax(semi, variable=first),
+                                          base_level=4,
+                                          med_level=5, med_threshold=0.1,
+                                          max_level=6, max_threshold=0.6) =#
+    amr_callback = AMRCallback(semi, amr_controller,
+                              interval=5,
+                              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, save_solution)
+
+
+    ###############################################################################
+    # run the simulation
+
+    # OrdinaryDiffEq's `solve` method evolves the solution in time and executes the passed callbacks
+    sol = solve(ode, Euler(), #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);
+
+
+    summary_callback()
+    errors = analysis_callback(sol)
+
+    errors_sol_L2[polydeg, i] = errors.l2[1]
+    errors_sol_inf[polydeg, i] = errors.linf[1]
+
+  end
+end
+
+for i in 1:n_polydeg_geo
+  plot!(errors_sol_inf[:,i], xaxis=:log, yaxis=:log, label = "polydeg_geo="*string(polydeg_geos[i]), linewidth=2, thickness_scaling = 1)
+end
+plot!(title = "mimetic="*string(mimetic)*", exact_jacobian="*string(exact_jacobian))
+plot!(xlabel = "polydeg", ylabel = "|u_ex - u_disc|_inf")
+
+plot!(ylims=(1e-15,1e-1))
+
+plot!(xticks=([2, 4, 8, 16], ["2", "4", "8", "16"]))

examples/p4est_3d_dgsem/elixir_test_mimetic_metrics_parent.jl

@@ -0,0 +1,158 @@
+#using LinearAlgebra
+using OrdinaryDiffEq
+using Trixi
+#using StaticArrays
+#using Plots
+
+###############################################################################
+# semidiscretization of the linear advection equation
+
+advection_velocity = (0.2, -0.7, 0.5)
+equations = LinearScalarAdvectionEquation3D(advection_velocity)
+
+# Mapping as described in https://arxiv.org/abs/2012.12040
+function mapping(xi, eta, zeta)
+  # Transform input variables between -1 and 1 onto our crazy domain
+
+  y = eta + 0.1 * (cos(pi * xi) *
+                   cos(pi * eta) *
+                   cos(pi * zeta))
+
+  x = xi + 0.1 * (cos(pi * xi) *
+                   cos(pi * y) *
+                   cos(pi * zeta))
+
+  z = zeta + 0.1 * (cos(pi * x) *
+                   cos(pi * y) *
+                   cos(pi * zeta))
+
+  #= x = xi
+  y = eta
+  z = zeta =#
+  return SVector(x, y, z)
+end
+
+cells_per_dimension = (1, 1, 1) # The p4est implementation works with one tree per direction only
+
+
+exact_jacobian = false
+mimetic = false
+final_time = 1e-3
+
+initial_condition = initial_condition_constant
+
+max_polydeg = 1
+n_polydeg_geo = 4
+errors_sol_inf = zeros(max_polydeg,n_polydeg_geo)
+errors_sol_L2 = zeros(max_polydeg,n_polydeg_geo)
+polydeg_geos = [2, 3, 5, 10]
+#polydeg_geos = [5]
+
+polydeg = 5
+
+# Refine bottom left quadrant of each tree to level 3
+function refine_fn(p8est, which_tree, quadrant)
+    quadrant_obj = unsafe_load(quadrant)
+    if quadrant_obj.x == 0 && quadrant_obj.y == 0 && quadrant_obj.z == 0 && quadrant_obj.level < 2
+        # return true (refine)
+        return Cint(1)
+    else
+        # return false (don't refine)
+        return Cint(0)
+    end
+end
+
+for i in 1:n_polydeg_geo
+    for polydeg in 1:max_polydeg
+        polydeg_geo = polydeg_geos[i]
+
+        solver = DGSEM(polydeg, flux_lax_friedrichs)
+
+        # Create curved mesh with 8 x 8 x 8 elements
+        boundary_condition = BoundaryConditionDirichlet(initial_condition)
+        boundary_conditions = Dict(
+            :x_neg => boundary_condition,
+            :x_pos => boundary_condition,
+            :y_neg => boundary_condition,
+            :y_pos => boundary_condition,
+            :z_neg => boundary_condition,
+            :z_pos => boundary_condition
+        )
+        println("polydeg_geo: ", polydeg_geo)
+        #mesh = P4estMesh(cells_per_dimension; polydeg = polydeg_geo, mapping = mapping, mimetic = mimetic, exact_jacobian = exact_jacobian, initial_refinement_level = 0, periodicity = true)
+        mesh = P4estMesh(cells_per_dimension; polydeg = polydeg_geo, mapping = mapping, mimetic = mimetic, exact_jacobian = exact_jacobian, initial_refinement_level = 0, periodicity = false, polydeg_parent_metrics = polydeg_geo)
+
+        # Refine recursively until each bottom left quadrant of a tree has level 3
+        # The mesh will be rebalanced before the simulation starts
+        refine_fn_c = @cfunction(refine_fn, Cint, (Ptr{Trixi.p8est_t}, Ptr{Trixi.p4est_topidx_t}, Ptr{Trixi.p8est_quadrant_t}))
+        Trixi.refine_p4est!(mesh.p4est, true, refine_fn_c, C_NULL)
+
+        # A semidiscre  tization collects data structures and functions for the spatial discretization
+        #semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
+        semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, boundary_conditions = boundary_conditions)
+
+        # Create ODE problem with time span from 0.0 to 1.0
+        ode = semidiscretize(semi, (0.0, final_time));
+
+        summary_callback = SummaryCallback()
+
+        # The AnalysisCallback allows to analyse the solution in regular intervals and prints the results
+        analysis_callback = AnalysisCallback(semi, interval=100)
+
+        # The StepsizeCallback handles the re-calculation of the maximum Δt after each time step
+        stepsize_callback = StepsizeCallback(cfl=0.1)
+
+        # The SaveSolutionCallback allows to save the solution to a file in regular intervals
+        save_solution = SaveSolutionCallback(interval=100,
+                                            solution_variables=cons2prim)
+
+        #= amr_indicator = IndicatorHennemannGassner(semi,
+                                                    alpha_max=1.0,
+                                                    alpha_min=0.0001,
+                                                    alpha_smooth=false,
+                                                    variable=Trixi.energy_total)
+
+        amr_controller = ControllerThreeLevel(semi, amr_indicator,
+                                                base_level=4,
+                                                max_level=6, max_threshold=0.01)
+
+        #= amr_controller = ControllerThreeLevel(semi, IndicatorMax(semi, variable=first),
+                                                base_level=4,
+                                                med_level=5, med_threshold=0.1,
+                                                max_level=6, max_threshold=0.6) =#
+        amr_callback = AMRCallback(semi, amr_controller,
+                                    interval=5,
+                                    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, save_solution)
+
+
+        ###############################################################################
+        # run the simulation
+
+        # OrdinaryDiffEq's `solve` method evolves the solution in time and executes the passed callbacks
+        sol = solve(ode, Euler(), #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);
+
+
+        summary_callback()
+        errors = analysis_callback(sol)
+
+        errors_sol_L2[polydeg, i] = errors.l2[1]
+        errors_sol_inf[polydeg, i] = errors.linf[1]
+    end
+end
+#=end
+
+for i in 1:n_polydeg_geo
+  plot!(errors_sol_inf[:,i], xaxis=:log, yaxis=:log, label = "polydeg_geo="*string(polydeg_geos[i]), linewidth=2, thickness_scaling = 1)
+end
+plot!(title = "mimetic="*string(mimetic)*", exact_jacobian="*string(exact_jacobian))
+plot!(xlabel = "polydeg", ylabel = "|u_ex - u_disc|_inf")
+
+plot!(ylims=(1e-15,1e-1))
+
+plot!(xticks=([2, 4, 8, 16], ["2", "4", "8", "16"])) =#