Add positivity-limiter to the AMRCallback

examples/p4est_2d_dgsem/elixir_euler_double_mach_amr.jl

@@ -131,28 +131,32 @@ save_solution = SaveSolutionCallback(interval = 100,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+# positivity limiter necessary for this example with strong shocks
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
+                                                         variables = (Trixi.density,
+                                                                      pressure))
+
 amr_indicator = IndicatorLöhner(semi, variable = Trixi.density)
 
 amr_controller = ControllerThreeLevel(semi, amr_indicator,
                                       base_level = 0,
                                       med_level = 3, med_threshold = 0.05,
                                       max_level = 6, max_threshold = 0.1)
 
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 1,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         save_solution,
                         amr_callback)
 
-# positivity limiter necessary for this example with strong shocks
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
-                                                     variables = (Trixi.density, pressure))
-
 ###############################################################################
 # run the simulation
-sol = solve(ode, SSPRK43(stage_limiter!);
+sol = solve(ode, SSPRK43(stage_limiter! = positivity_limiter);
             ode_default_options()..., callback = callbacks);

examples/p4est_2d_dgsem/elixir_euler_forward_step_amr.jl

@@ -136,29 +136,33 @@ save_solution = SaveSolutionCallback(interval = 2000,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+# positivity limiter necessary for this example with strong shocks
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
+                                                         variables = (Trixi.density,
+                                                                      pressure))
+
 amr_indicator = IndicatorLöhner(semi, variable = Trixi.density)
 
 amr_controller = ControllerThreeLevel(semi, amr_indicator,
                                       base_level = 0,
                                       med_level = 2, med_threshold = 0.05,
                                       max_level = 5, max_threshold = 0.1)
 
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 5,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         save_solution,
                         amr_callback)
 
-# positivity limiter necessary for this example with strong shocks
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
-                                                     variables = (Trixi.density, pressure))
-
 ###############################################################################
 # run the simulation
-sol = solve(ode, SSPRK43(stage_limiter!);
+sol = solve(ode, SSPRK43(stage_limiter! = positivity_limiter);
             maxiters = 999999, ode_default_options()...,
             callback = callbacks);

examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder.jl

@@ -116,29 +116,33 @@ save_solution = SaveSolutionCallback(interval = 1000,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+# positivity limiter necessary for this example with strong shocks. Very sensitive
+# to the order of the limiter variables, pressure must come first.
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-7, 1.0e-6),
+                                                         variables = (pressure,
+                                                                      Trixi.density))
+
 amr_indicator = IndicatorLöhner(semi, variable = Trixi.density)
 
 amr_controller = ControllerThreeLevel(semi, amr_indicator,
                                       base_level = 0,
                                       med_level = 3, med_threshold = 0.05,
                                       max_level = 5, max_threshold = 0.1)
 
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 1,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         save_solution,
                         amr_callback)
 
-# positivity limiter necessary for this example with strong shocks. Very sensitive
-# to the order of the limiter variables, pressure must come first.
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-7, 1.0e-6),
-                                                     variables = (pressure, Trixi.density))
-
 ###############################################################################
 # run the simulation
-sol = solve(ode, SSPRK43(stage_limiter!);
+sol = solve(ode, SSPRK43(stage_limiter! = positivity_limiter);
             ode_default_options()..., callback = callbacks);

examples/t8code_2d_dgsem/elixir_euler_weak_blast_wave_amr.jl

@@ -36,7 +36,7 @@ initial_condition = initial_condition_weak_blast_wave
 # In the `StepsizeCallback`, though, the less diffusive `max_abs_speeds` is employed which is consistent with `max_abs_speed`.
 # Thus, we exchanged in PR#2458 the default wave speed used in the LLF flux to `max_abs_speed`.
 # To ensure that every example still runs we specify explicitly `FluxLaxFriedrichs(max_abs_speed_naive)`.
-# We remark, however, that the now default `max_abs_speed` is in general recommended due to compliance with the 
+# We remark, however, that the now default `max_abs_speed` is in general recommended due to compliance with the
 # `StepsizeCallback` (CFL-Condition) and less diffusion.
 surface_flux = FluxLaxFriedrichs(max_abs_speed_naive)
 volume_flux = flux_ranocha
@@ -97,7 +97,11 @@ amr_controller = ControllerThreeLevel(semi, amr_indicator,
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 5,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6,
+                                                                                        5.0e-6),
+                                                                          variables = (Trixi.density,
+                                                                                       pressure)))
 
 stepsize_callback = StepsizeCallback(cfl = 0.5)
 

examples/t8code_3d_dgsem/elixir_euler_weak_blast_wave_amr.jl

@@ -37,7 +37,7 @@ initial_condition = initial_condition_weak_blast_wave
 # In the `StepsizeCallback`, though, the less diffusive `max_abs_speeds` is employed which is consistent with `max_abs_speed`.
 # Thus, we exchanged in PR#2458 the default wave speed used in the LLF flux to `max_abs_speed`.
 # To ensure that every example still runs we specify explicitly `FluxLaxFriedrichs(max_abs_speed_naive)`.
-# We remark, however, that the now default `max_abs_speed` is in general recommended due to compliance with the 
+# We remark, however, that the now default `max_abs_speed` is in general recommended due to compliance with the
 # `StepsizeCallback` (CFL-Condition) and less diffusion.
 surface_flux = FluxLaxFriedrichs(max_abs_speed_naive)
 volume_flux = flux_ranocha
@@ -99,7 +99,11 @@ amr_controller = ControllerThreeLevel(semi, amr_indicator,
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 1,
                            adapt_initial_condition = false,
-                           adapt_initial_condition_only_refine = false)
+                           adapt_initial_condition_only_refine = false,
+                           limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6,
+                                                                                        5.0e-6),
+                                                                          variables = (Trixi.density,
+                                                                                       pressure)))
 
 stepsize_callback = StepsizeCallback(cfl = 0.5)
 

examples/tree_1d_dgsem/elixir_euler_positivity.jl

@@ -82,16 +82,25 @@ save_solution = SaveSolutionCallback(interval = 100,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
+                                                         variables = (Trixi.density,
+                                                                      pressure))
+
 amr_indicator = IndicatorLöhner(semi,
                                 variable = density_pressure)
+
 amr_controller = ControllerThreeLevel(semi, amr_indicator,
                                       base_level = 4,
                                       med_level = 0, med_threshold = 0.1, # med_level = current level
                                       max_level = 6, max_threshold = 0.3)
+
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 2,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 stepsize_callback = StepsizeCallback(cfl = 0.5)
 
@@ -100,12 +109,11 @@ callbacks = CallbackSet(summary_callback,
                         save_solution,
                         amr_callback, stepsize_callback)
 
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
-                                                     variables = (Trixi.density, pressure))
-
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(stage_limiter!, williamson_condition = false);
+sol = solve(ode,
+            CarpenterKennedy2N54(stage_limiter! = positivity_limiter,
+                                 williamson_condition = false);
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             ode_default_options()..., callback = callbacks);

examples/tree_2d_dgsem/elixir_euler_astro_jet_amr.jl

@@ -87,6 +87,11 @@ save_solution = SaveSolutionCallback(interval = 5000,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+# positivity limiter necessary for this tough example
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
+                                                         variables = (Trixi.density,
+                                                                      pressure))
+
 amr_indicator = IndicatorHennemannGassner(semi,
                                           alpha_max = 1.0,
                                           alpha_min = 0.0001,
@@ -99,21 +104,20 @@ amr_controller = ControllerThreeLevelCombined(semi, amr_indicator, indicator_sc,
                                               max_level = 8, max_threshold = 0.003,
                                               max_threshold_secondary = indicator_sc.alpha_max)
 
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 1,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         amr_callback, save_solution)
 
-# positivity limiter necessary for this tough example
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
-                                                     variables = (Trixi.density, pressure))
-
 ###############################################################################
 # run the simulation
 # use adaptive time stepping based on error estimates, time step roughly dt = 1e-7
-sol = solve(ode, SSPRK43(stage_limiter!);
+sol = solve(ode, SSPRK43(stage_limiter! = positivity_limiter);
             ode_default_options()..., callback = callbacks);

examples/tree_2d_dgsem/elixir_euler_colliding_flow_amr.jl

@@ -89,6 +89,11 @@ save_solution = SaveSolutionCallback(interval = 1000,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+# positivity limiter necessary for this tough example
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
+                                                         variables = (Trixi.density,
+                                                                      pressure))
+
 # Simulation also feasible without AMR: AMR reduces CPU time by a factor of about 2
 amr_indicator = IndicatorHennemannGassner(semi,
                                           alpha_max = 1.0,
@@ -102,21 +107,20 @@ amr_controller = ControllerThreeLevelCombined(semi, amr_indicator, indicator_sc,
                                               max_level = 8, max_threshold = 0.003,
                                               max_threshold_secondary = indicator_sc.alpha_max)
 
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 1,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 callbacks = CallbackSet(summary_callback,
                         analysis_callback, alive_callback,
                         amr_callback, save_solution)
 
-# positivity limiter necessary for this tough example
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
-                                                     variables = (Trixi.density, pressure))
-
 ###############################################################################
 # run the simulation
 # use adaptive time stepping based on error estimates, time step roughly dt = 5e-3
-sol = solve(ode, SSPRK43(stage_limiter!);
+sol = solve(ode, SSPRK43(stage_limiter! = positivity_limiter);
             ode_default_options()..., callback = callbacks);

examples/tree_2d_dgsem/elixir_euler_positivity.jl

@@ -84,16 +84,25 @@ save_solution = SaveSolutionCallback(interval = 100,
                                      save_final_solution = true,
                                      solution_variables = cons2prim)
 
+positivity_limiter = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
+                                                         variables = (Trixi.density,
+                                                                      pressure))
+
 amr_indicator = IndicatorLöhner(semi,
                                 variable = density_pressure)
+
 amr_controller = ControllerThreeLevel(semi, amr_indicator,
                                       base_level = 4,
                                       med_level = 0, med_threshold = 0.1, # med_level = current level
                                       max_level = 6, max_threshold = 0.3)
+
+# Set `limiter! = positivity_limiter` to apply the positivity-preserving limiter after 
+# coarsening and refinement steps.
 amr_callback = AMRCallback(semi, amr_controller,
                            interval = 2,
                            adapt_initial_condition = true,
-                           adapt_initial_condition_only_refine = true)
+                           adapt_initial_condition_only_refine = true,
+                           limiter! = positivity_limiter)
 
 stepsize_callback = StepsizeCallback(cfl = 0.8)
 
@@ -102,12 +111,11 @@ callbacks = CallbackSet(summary_callback,
                         save_solution,
                         amr_callback, stepsize_callback)
 
-stage_limiter! = PositivityPreservingLimiterZhangShu(thresholds = (5.0e-6, 5.0e-6),
-                                                     variables = (Trixi.density, pressure))
-
 ###############################################################################
 # run the simulation
 
-sol = solve(ode, CarpenterKennedy2N54(stage_limiter!, williamson_condition = false);
+sol = solve(ode,
+            CarpenterKennedy2N54(stage_limiter! = positivity_limiter,
+                                 williamson_condition = false);
             dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
             ode_default_options()..., callback = callbacks);