Merge branch 'main' into visualize_mpi_rank

trixi-framework · Nov 14, 2024 · a01c682 · a01c682
2 parents d1f6d44 + 07f960f
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diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml
@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.25.0
+        uses: crate-ci/typos@v1.27.0
diff --git a/NEWS.md b/NEWS.md
@@ -4,6 +4,14 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju
 used in the Julia ecosystem. Notable changes will be documented in this file
 for human readability.
 
+## Changes in the v0.9 lifecycle
+
+#### Added
+
+- New time integrator `PairedExplicitRK3`, implementing the third-order paired explicit Runge-Kutta
+  method with [Convex.jl](https://github.com/jump-dev/Convex.jl), [ECOS.jl](https://github.com/jump-dev/ECOS.jl),
+  and [NLsolve.jl](https://github.com/JuliaNLSolvers/NLsolve.jl) ([#2008])
+
 ## Changes when updating to v0.9 from v0.8.x
 
 #### Added

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 = "0.9.3-DEV"
+version = "0.9.6-DEV"
 
 [deps]
 Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
@@ -36,6 +36,7 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StartUpDG = "472ebc20-7c99-4d4b-9470-8fde4e9faa0f"
 Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 StaticArrayInterface = "0d7ed370-da01-4f52-bd93-41d350b8b718"
@@ -55,10 +56,12 @@ UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 
 [extensions]
 TrixiConvexECOSExt = ["Convex", "ECOS"]
 TrixiMakieExt = "Makie"
+TrixiNLsolveExt = "NLsolve"
 
 [compat]
 Accessors = "0.1.12"
@@ -79,9 +82,10 @@ IfElse = "0.1"
 LinearAlgebra = "1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.151"
-MPI = "0.20"
+MPI = "0.20.6"
 Makie = "0.19, 0.20"
 MuladdMacro = "0.2.2"
+NLsolve = "4.5.1"
 Octavian = "0.3.21"
 OffsetArrays = "1.12"
 P4est = "0.4.9"
@@ -96,14 +100,15 @@ Requires = "1.1"
 SciMLBase = "1.90, 2"
 SimpleUnPack = "1.1"
 SparseArrays = "1"
+StableRNGs = "1.0.2"
 StartUpDG = "0.17.7, 1.1.5"
 Static = "0.8.7"
 StaticArrayInterface = "1.4"
 StaticArrays = "1.5"
 StrideArrays = "0.1.26"
 StructArrays = "0.6.11"
 SummationByPartsOperators = "0.5.41"
-T8code = "0.5"
+T8code = "0.7"
 TimerOutputs = "0.5.7"
 Triangulate = "2.2"
 TriplotBase = "0.1"
@@ -116,3 +121,4 @@ julia = "1.8"
 Convex = "f65535da-76fb-5f13-bab9-19810c17039a"
 ECOS = "e2685f51-7e38-5353-a97d-a921fd2c8199"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
diff --git a/docs/literate/src/files/subcell_shock_capturing.jl b/docs/literate/src/files/subcell_shock_capturing.jl
@@ -229,8 +229,6 @@ plot(sol)
 # approach using the [`SaveSolutionCallback`](@ref), [`Trixi2Vtk`](https://github.com/trixi-framework/Trixi2Vtk.jl)
 # and [ParaView](https://www.paraview.org/download/). More details about this procedure
 # can be found in the [visualization documentation](@ref visualization).
-# Unfortunately, the support for subcell limiting data is not yet merged into the main branch
-# of Trixi2Vtk but lies in the branch [`bennibolm/node-variables`](https://github.com/bennibolm/Trixi2Vtk.jl/tree/node-variables).
 #-
 # With that implementation and the standard procedure used for Trixi2Vtk you get the following
 # dropdown menu in ParaView.

diff --git a/examples/dgmulti_2d/elixir_advection_diffusion.jl b/examples/dgmulti_2d/elixir_advection_diffusion.jl
@@ -51,7 +51,7 @@ summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
 analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
-callbacks = CallbackSet(summary_callback, alive_callback)
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation

diff --git a/examples/dgmulti_2d/elixir_advection_diffusion_nonperiodic.jl b/examples/dgmulti_2d/elixir_advection_diffusion_nonperiodic.jl
@@ -67,7 +67,7 @@ summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
 analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
-callbacks = CallbackSet(summary_callback, alive_callback)
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation

diff --git a/examples/dgmulti_2d/elixir_navierstokes_convergence.jl b/examples/dgmulti_2d/elixir_navierstokes_convergence.jl
@@ -208,7 +208,7 @@ summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
 analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
-callbacks = CallbackSet(summary_callback, alive_callback)
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation

diff --git a/examples/dgmulti_2d/elixir_navierstokes_convergence_curved.jl b/examples/dgmulti_2d/elixir_navierstokes_convergence_curved.jl
@@ -216,7 +216,7 @@ summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
 analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
-callbacks = CallbackSet(summary_callback, alive_callback)
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation

diff --git a/examples/dgmulti_2d/elixir_navierstokes_lid_driven_cavity.jl b/examples/dgmulti_2d/elixir_navierstokes_lid_driven_cavity.jl
@@ -57,13 +57,13 @@ semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabol
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 10.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
 analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg))
-callbacks = CallbackSet(summary_callback, alive_callback)
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation

diff --git a/examples/dgmulti_3d/elixir_navierstokes_taylor_green_vortex.jl b/examples/dgmulti_3d/elixir_navierstokes_taylor_green_vortex.jl
@@ -62,9 +62,8 @@ alive_callback = AliveCallback(alive_interval = 10)
 analysis_interval = 100
 analysis_callback = AnalysisCallback(semi, interval = analysis_interval, uEltype = real(dg),
                                      extra_analysis_integrals = (energy_kinetic,
-                                                                 energy_internal,
-                                                                 enstrophy))
-callbacks = CallbackSet(summary_callback, alive_callback)
+                                                                 energy_internal))
+callbacks = CallbackSet(summary_callback, alive_callback, analysis_callback)
 
 ###############################################################################
 # run the simulation

diff --git a/examples/p4est_2d_dgsem/elixir_advection_basic.jl b/examples/p4est_2d_dgsem/elixir_advection_basic.jl
@@ -31,7 +31,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergen
 # ODE solvers, callbacks etc.
 
 # Create ODE problem with time span from 0.0 to 1.0
-ode = semidiscretize(semi, (0.0, 1.0));
+ode = semidiscretize(semi, (0.0, 1.0))
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_diffusion_nonperiodic_curved.jl b/examples/p4est_2d_dgsem/elixir_advection_diffusion_nonperiodic_curved.jl
@@ -68,7 +68,7 @@ semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabol
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 1.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_diffusion_periodic.jl b/examples/p4est_2d_dgsem/elixir_advection_diffusion_periodic.jl
@@ -55,7 +55,7 @@ semi = SemidiscretizationHyperbolicParabolic(mesh,
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 1.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_diffusion_periodic_amr.jl b/examples/p4est_2d_dgsem/elixir_advection_diffusion_periodic_amr.jl
@@ -47,7 +47,7 @@ semi = SemidiscretizationHyperbolicParabolic(mesh,
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 0.5)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_diffusion_periodic_curved.jl b/examples/p4est_2d_dgsem/elixir_advection_diffusion_periodic_curved.jl
@@ -60,7 +60,7 @@ semi = SemidiscretizationHyperbolicParabolic(mesh,
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 1.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_extended.jl b/examples/p4est_2d_dgsem/elixir_advection_extended.jl
@@ -40,7 +40,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
 
 # Create ODE problem with time span from 0.0 to 1.0
 tspan = (0.0, 1.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_nonconforming_flag.jl b/examples/p4est_2d_dgsem/elixir_advection_nonconforming_flag.jl
@@ -52,7 +52,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergen
 # ODE solvers, callbacks etc.
 
 # Create ODE problem with time span from 0.0 to 0.2
-ode = semidiscretize(semi, (0.0, 0.2));
+ode = semidiscretize(semi, (0.0, 0.2))
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/p4est_2d_dgsem/elixir_advection_restart.jl b/examples/p4est_2d_dgsem/elixir_advection_restart.jl
@@ -24,7 +24,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
 
 tspan = (load_time(restart_filename), 2.0)
 dt = load_dt(restart_filename)
-ode = semidiscretize(semi, tspan, restart_filename);
+ode = semidiscretize(semi, tspan, restart_filename)
 
 # Do not overwrite the initial snapshot written by elixir_advection_extended.jl.
 save_solution.condition.save_initial_solution = false

diff --git a/examples/p4est_2d_dgsem/elixir_advection_restart_amr.jl b/examples/p4est_2d_dgsem/elixir_advection_restart_amr.jl
@@ -24,7 +24,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
 
 tspan = (load_time(restart_filename), 2.0)
 dt = load_dt(restart_filename)
-ode = semidiscretize(semi, tspan, restart_filename);
+ode = semidiscretize(semi, tspan, restart_filename)
 
 # Do not overwrite the initial snapshot written by elixir_advection_extended.jl.
 save_solution.condition.save_initial_solution = false

diff --git a/examples/p4est_2d_dgsem/elixir_eulergravity_convergence.jl b/examples/p4est_2d_dgsem/elixir_eulergravity_convergence.jl
@@ -50,7 +50,7 @@ semi = SemidiscretizationEulerGravity(semi_euler, semi_gravity, parameters)
 ###############################################################################
 # ODE solvers, callbacks etc.
 tspan = (0.0, 0.5)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 

diff --git a/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity.jl b/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity.jl
@@ -61,7 +61,7 @@ semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabol
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 25.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 100)

diff --git a/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity_amr.jl b/examples/p4est_2d_dgsem/elixir_navierstokes_lid_driven_cavity_amr.jl
@@ -61,7 +61,7 @@ semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabol
 
 # Create ODE problem with time span `tspan`
 tspan = (0.0, 25.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 alive_callback = AliveCallback(alive_interval = 2000)

diff --git a/examples/p4est_3d_dgsem/elixir_advection_restart.jl b/examples/p4est_3d_dgsem/elixir_advection_restart.jl
@@ -22,7 +22,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergen
 
 tspan = (load_time(restart_filename), 2.0)
 dt = load_dt(restart_filename)
-ode = semidiscretize(semi, tspan, restart_filename);
+ode = semidiscretize(semi, tspan, restart_filename)
 
 # Do not overwrite the initial snapshot written by elixir_advection_extended.jl.
 save_solution.condition.save_initial_solution = false

diff --git a/examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl b/examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl
@@ -60,7 +60,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
 # ODE solvers, callbacks etc.
 
 # Create ODE problem with time span from 0.0 to 0.1
-ode = semidiscretize(semi, (0.0, 0.1));
+ode = semidiscretize(semi, (0.0, 0.1))
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers

diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl
@@ -48,7 +48,7 @@ semi = SemidiscretizationEulerGravity(semi_euler, semi_gravity, parameters)
 ###############################################################################
 # ODE solvers, callbacks etc.
 tspan = (0.0, 0.5)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 

diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl
@@ -101,7 +101,7 @@ semi = SemidiscretizationEulerGravity(semi_euler, semi_gravity, parameters)
 ###############################################################################
 # ODE solvers, callbacks etc.
 tspan = (0.0, 5.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 

diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl
@@ -99,8 +99,8 @@ volume_integral = VolumeIntegralShockCapturingHG(indicator_sc;
                                                  volume_flux_fv = surface_flux)
 solver_euler = DGSEM(basis, surface_flux, volume_integral)
 
-coordinates_min = (-4, -4)
-coordinates_max = (4, 4)
+coordinates_min = (-4.0, -4.0)
+coordinates_max = (4.0, 4.0)
 mesh = TreeMesh(coordinates_min, coordinates_max,
                 initial_refinement_level = 2,
                 n_cells_max = 100_000,
@@ -183,7 +183,7 @@ semi = SemidiscretizationEulerGravity(semi_euler, semi_gravity, parameters)
 ###############################################################################
 # ODE solvers, callbacks etc.
 tspan = (0.0, 1.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 

diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_hypdiff_convergence.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_hypdiff_convergence.jl
@@ -33,7 +33,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
 # ODE solvers, callbacks etc.
 
 tspan = (0.0, 5.0)
-ode = semidiscretize(semi, tspan);
+ode = semidiscretize(semi, tspan)
 
 summary_callback = SummaryCallback()
 

diff --git a/examples/structured_1d_dgsem/elixir_advection_basic.jl b/examples/structured_1d_dgsem/elixir_advection_basic.jl
@@ -28,7 +28,7 @@ semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergen
 # ODE solvers, callbacks etc.
 
 # Create ODE problem with time span from 0.0 to 1.0
-ode = semidiscretize(semi, (0.0, 1.0));
+ode = semidiscretize(semi, (0.0, 1.0))
 
 # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
 # and resets the timers