Merge branch 'main' into docs-custom-mpi-hdf5

trixi-framework · Nov 19, 2023 · f857f59 · f857f59
2 parents d60fc7a + 1635d31
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diff --git a/NEWS.md b/NEWS.md
@@ -38,7 +38,8 @@ for human readability.
 - Wetting and drying feature and examples for 1D and 2D shallow water equations
 - Implementation of the polytropic Euler equations in 2D
 - Implementation of the quasi-1D shallow water equations
-- Subcell positivity limiting support for conservative variables in 2D for `TreeMesh`
+- Subcell (positivity and local min/max) limiting support for conservative variables
+  in 2D for `TreeMesh`
 - AMR for hyperbolic-parabolic equations on 2D/3D `TreeMesh`
 - Added `GradientVariables` type parameter to `AbstractEquationsParabolic`
 

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
-version = "0.6.1-pre"
+version = "0.6.2-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"

diff --git a/benchmark/Project.toml b/benchmark/Project.toml
@@ -8,4 +8,4 @@ Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 BenchmarkTools = "0.5, 0.7, 1.0"
 OrdinaryDiffEq = "5.65, 6"
 PkgBenchmark = "0.2.10"
-Trixi = "0.4, 0.5"
+Trixi = "0.4, 0.5, 0.6"
diff --git a/examples/p4est_2d_dgsem/elixir_advection_restart.jl b/examples/p4est_2d_dgsem/elixir_advection_restart.jl
@@ -31,7 +31,7 @@ save_solution.condition.save_initial_solution = false
 
 integrator = init(ode, CarpenterKennedy2N54(williamson_condition = false),
                   dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
-                  save_everystep = false, callback = callbacks);
+                  save_everystep = false, callback = callbacks, maxiters = 100_000);
 
 # Get the last time index and work with that.
 load_timestep!(integrator, restart_filename)

diff --git a/examples/p4est_3d_dgsem/elixir_advection_restart.jl b/examples/p4est_3d_dgsem/elixir_advection_restart.jl
@@ -29,7 +29,7 @@ save_solution.condition.save_initial_solution = false
 
 integrator = init(ode, CarpenterKennedy2N54(williamson_condition = false),
                   dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
-                  save_everystep = false, callback = callbacks);
+                  save_everystep = false, callback = callbacks, maxiters = 100_000);
 
 # Get the last time index and work with that.
 load_timestep!(integrator, restart_filename)

diff --git a/examples/structured_2d_dgsem/elixir_advection_restart.jl b/examples/structured_2d_dgsem/elixir_advection_restart.jl
@@ -30,7 +30,7 @@ save_solution.condition.save_initial_solution = false
 
 integrator = init(ode, CarpenterKennedy2N54(williamson_condition = false),
                   dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
-                  save_everystep = false, callback = callbacks);
+                  save_everystep = false, callback = callbacks, maxiters = 100_000);
 
 # Get the last time index and work with that.
 load_timestep!(integrator, restart_filename)

diff --git a/examples/structured_3d_dgsem/elixir_advection_restart.jl b/examples/structured_3d_dgsem/elixir_advection_restart.jl
@@ -29,7 +29,7 @@ save_solution.condition.save_initial_solution = false
 
 integrator = init(ode, CarpenterKennedy2N54(williamson_condition = false),
                   dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
-                  save_everystep = false, callback = callbacks);
+                  save_everystep = false, callback = callbacks, maxiters = 100_000);
 
 # Get the last time index and work with that.
 load_timestep!(integrator, restart_filename)

diff --git a/examples/tree_2d_dgsem/elixir_advection_restart.jl b/examples/tree_2d_dgsem/elixir_advection_restart.jl
@@ -29,7 +29,7 @@ save_solution.condition.save_initial_solution = false
 
 integrator = init(ode, alg,
                   dt = dt, # solve needs some value here but it will be overwritten by the stepsize_callback
-                  save_everystep = false, callback = callbacks; ode_default_options()...)
+                  callback = callbacks, maxiters = 100_000; ode_default_options()...)
 
 # Load saved context for adaptive time integrator
 if integrator.opts.adaptive

diff --git a/examples/tree_2d_dgsem/elixir_euler_blast_wave_sc_subcell_nonperiodic.jl b/examples/tree_2d_dgsem/elixir_euler_blast_wave_sc_subcell_nonperiodic.jl
@@ -0,0 +1,93 @@
+
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# semidiscretization of the compressible Euler equations
+
+equations = CompressibleEulerEquations2D(1.4)
+
+"""
+    initial_condition_blast_wave(x, t, equations::CompressibleEulerEquations2D)
+
+A medium blast wave taken from
+- Sebastian Hennemann, Gregor J. Gassner (2020)
+  A provably entropy stable subcell shock capturing approach for high order split form DG
+  [arXiv: 2008.12044](https://arxiv.org/abs/2008.12044)
+"""
+function initial_condition_blast_wave(x, t, equations::CompressibleEulerEquations2D)
+    # Modified From Hennemann & Gassner JCP paper 2020 (Sec. 6.3) -> "medium blast wave"
+    # Set up polar coordinates
+    inicenter = SVector(0.0, 0.0)
+    x_norm = x[1] - inicenter[1]
+    y_norm = x[2] - inicenter[2]
+    r = sqrt(x_norm^2 + y_norm^2)
+    phi = atan(y_norm, x_norm)
+    sin_phi, cos_phi = sincos(phi)
+
+    # Calculate primitive variables
+    rho = r > 0.5 ? 1.0 : 1.1691
+    v1 = r > 0.5 ? 0.0 : 0.1882 * cos_phi
+    v2 = r > 0.5 ? 0.0 : 0.1882 * sin_phi
+    p = r > 0.5 ? 1.0E-3 : 1.245
+
+    return prim2cons(SVector(rho, v1, v2, p), equations)
+end
+initial_condition = initial_condition_blast_wave
+
+boundary_condition = BoundaryConditionDirichlet(initial_condition)
+
+surface_flux = flux_lax_friedrichs
+volume_flux = flux_ranocha
+basis = LobattoLegendreBasis(3)
+limiter_idp = SubcellLimiterIDP(equations, basis;
+                                local_minmax_variables_cons = ["rho"])
+volume_integral = VolumeIntegralSubcellLimiting(limiter_idp;
+                                                volume_flux_dg = volume_flux,
+                                                volume_flux_fv = surface_flux)
+solver = DGSEM(basis, surface_flux, volume_integral)
+
+coordinates_min = (-2.0, -2.0)
+coordinates_max = (2.0, 2.0)
+mesh = TreeMesh(coordinates_min, coordinates_max,
+                initial_refinement_level = 6,
+                n_cells_max = 10_000,
+                periodicity = false)
+
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
+                                    boundary_conditions = boundary_condition)
+
+###############################################################################
+# ODE solvers, callbacks etc.
+
+tspan = (0.0, 2.0)
+ode = semidiscretize(semi, tspan)
+
+summary_callback = SummaryCallback()
+
+analysis_interval = 100
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
+
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
+
+save_solution = SaveSolutionCallback(interval = 100,
+                                     save_initial_solution = true,
+                                     save_final_solution = true,
+                                     solution_variables = cons2prim)
+
+stepsize_callback = StepsizeCallback(cfl = 0.3)
+
+callbacks = CallbackSet(summary_callback,
+                        analysis_callback, alive_callback,
+                        save_solution,
+                        stepsize_callback)
+
+###############################################################################
+# run the simulation
+
+stage_callbacks = (SubcellLimiterIDPCorrection(), BoundsCheckCallback(save_errors = false))
+
+sol = Trixi.solve(ode, Trixi.SimpleSSPRK33(stage_callbacks = stage_callbacks);
+                  dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
+                  save_everystep = false, callback = callbacks);
+summary_callback() # print the timer summary
diff --git a/examples/tree_2d_dgsem/elixir_euler_sedov_blast_wave_sc_subcell.jl b/examples/tree_2d_dgsem/elixir_euler_sedov_blast_wave_sc_subcell.jl
@@ -0,0 +1,91 @@
+
+using OrdinaryDiffEq
+using Trixi
+
+###############################################################################
+# semidiscretization of the compressible Euler equations
+gamma = 1.4
+equations = CompressibleEulerEquations2D(gamma)
+
+"""
+    initial_condition_sedov_blast_wave(x, t, equations::CompressibleEulerEquations2D)
+
+The Sedov blast wave setup based on Flash
+- https://flash.rochester.edu/site/flashcode/user_support/flash_ug_devel/node187.html#SECTION010114000000000000000
+"""
+function initial_condition_sedov_blast_wave(x, t, equations::CompressibleEulerEquations2D)
+    # Set up polar coordinates
+    inicenter = SVector(0.0, 0.0)
+    x_norm = x[1] - inicenter[1]
+    y_norm = x[2] - inicenter[2]
+    r = sqrt(x_norm^2 + y_norm^2)
+
+    # Setup based on https://flash.rochester.edu/site/flashcode/user_support/flash_ug_devel/node187.html#SECTION010114000000000000000
+    r0 = 0.21875 # = 3.5 * smallest dx (for domain length=4 and max-ref=6)
+    # r0 = 0.5 # = more reasonable setup
+    E = 1.0
+    p0_inner = 3 * (equations.gamma - 1) * E / (3 * pi * r0^2)
+    p0_outer = 1.0e-5 # = true Sedov setup
+    # p0_outer = 1.0e-3 # = more reasonable setup
+
+    # Calculate primitive variables
+    rho = 1.0
+    v1 = 0.0
+    v2 = 0.0
+    p = r > r0 ? p0_outer : p0_inner
+
+    return prim2cons(SVector(rho, v1, v2, p), equations)
+end
+initial_condition = initial_condition_sedov_blast_wave
+
+surface_flux = flux_lax_friedrichs
+volume_flux = flux_chandrashekar
+basis = LobattoLegendreBasis(3)
+limiter_idp = SubcellLimiterIDP(equations, basis;
+                                local_minmax_variables_cons = ["rho"])
+volume_integral = VolumeIntegralSubcellLimiting(limiter_idp;
+                                                volume_flux_dg = volume_flux,
+                                                volume_flux_fv = surface_flux)
+solver = DGSEM(basis, surface_flux, volume_integral)
+
+coordinates_min = (-2.0, -2.0)
+coordinates_max = (2.0, 2.0)
+mesh = TreeMesh(coordinates_min, coordinates_max,
+                initial_refinement_level = 3,
+                n_cells_max = 100_000)
+
+semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
+
+###############################################################################
+# ODE solvers, callbacks etc.
+
+tspan = (0.0, 3.0)
+ode = semidiscretize(semi, tspan)
+
+summary_callback = SummaryCallback()
+
+analysis_interval = 1000
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval)
+
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
+
+save_solution = SaveSolutionCallback(interval = 1000,
+                                     save_initial_solution = true,
+                                     save_final_solution = true,
+                                     solution_variables = cons2prim)
+
+stepsize_callback = StepsizeCallback(cfl = 0.6)
+
+callbacks = CallbackSet(summary_callback,
+                        analysis_callback, alive_callback,
+                        stepsize_callback,
+                        save_solution)
+###############################################################################
+# run the simulation
+
+stage_callbacks = (SubcellLimiterIDPCorrection(), BoundsCheckCallback(save_errors = false))
+
+sol = Trixi.solve(ode, Trixi.SimpleSSPRK33(stage_callbacks = stage_callbacks);
+                  dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback
+                  save_everystep = false, callback = callbacks);
+summary_callback() # print the timer summary
diff --git a/examples/tree_2d_dgsem/elixir_euler_shockcapturing_subcell.jl b/examples/tree_2d_dgsem/elixir_euler_shockcapturing_subcell.jl
@@ -39,7 +39,7 @@ surface_flux = flux_lax_friedrichs
 volume_flux = flux_ranocha
 basis = LobattoLegendreBasis(3)
 limiter_idp = SubcellLimiterIDP(equations, basis;
-                                positivity_variables_cons = [1],
+                                positivity_variables_cons = ["rho"],
                                 positivity_correction_factor = 0.5)
 volume_integral = VolumeIntegralSubcellLimiting(limiter_idp;
                                                 volume_flux_dg = volume_flux,