Merge branch 'main' into more-trixitest

Author: JoshuaLampert

CITATION.bib

@@ -0,0 +1,7 @@
+@misc{winters2025trixi,
+  title={{TrixiShallowWater.jl}: {S}hallow water simulations with {T}rixi.jl},
+  author={Winters, Andrew R and Ersing, Patrick and Ranocha, Hendrik and Schlottke-Lakemper, Michael},
+  year={2025},
+  howpublished={\url{https://github.com/trixi-framework/TrixiShallowWater.jl}},
+  doi={10.5281/zenodo.15206520}
+}

Project.toml

@@ -19,5 +19,5 @@ Printf = "1"
 Roots = "2.1.6"
 Static = "1.1.1"
 StaticArrays = "1.9"
-Trixi = "0.12"
-julia = "1.10"
+Trixi = "0.13"
+julia = "1.10"

README.md

@@ -85,6 +85,19 @@ clone Trixi.jl, can be found in the
 [Development section](https://trixi-framework.github.io/TrixiShallowWater.jl/stable/development/)
 of the documentation.
 
+## Referencing
+You can directly refer to TrixiShallowWater.jl as
+
+```bibtex
+@misc{winters2025trixi,
+  title={{TrixiShallowWater.jl}: {S}hallow water simulations with {T}rixi.jl},
+  author={Winters, Andrew R and Ersing, Patrick and Ranocha, Hendrik and Schlottke-Lakemper, Michael},
+  year={2025},
+  howpublished={\url{https://github.com/trixi-framework/TrixiShallowWater.jl}},
+  doi={10.5281/zenodo.15206520}
+}
+```
+
 ## Authors
 TrixiShallowWater.jl is maintained by the
 [Trixi authors](https://github.com/trixi-framework/Trixi.jl/blob/main/AUTHORS.md).
@@ -110,4 +123,4 @@ or [create an issue](https://github.com/trixi-framework/TrixiShallowWater.jl/iss
 This project has benefited from funding from [Vetenskapsrådet](https://www.vr.se)
 (VR, Swedish Research Council), Sweden
 through the VR Starting Grant "Shallow water flows including sediment transport and morphodynamics",
-VR grant agreement 2020-03642 VR.
+VR grant agreement 2020-03642 VR.

docs/Project.toml

@@ -25,6 +25,6 @@ HOHQMesh = "0.2"
 Literate = "2.20"
 OrdinaryDiffEqLowStorageRK = "1.3"
 OrdinaryDiffEqSSPRK = "1.2"
-Trixi = "0.12"
+Trixi = "0.13"
 Trixi2Vtk = "0.3.16"
 TrixiBottomTopography = "0.1"

docs/src/index.md

@@ -53,6 +53,19 @@ julia> using Pkg
 julia> Pkg.add(["Trixi", "Trixi2Vtk", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqSSPRK", "Plots"])
 ```
 
+## Referencing
+You can directly refer to TrixiShallowWater.jl as
+
+```bibtex
+@misc{winters2025trixi,
+  title={{TrixiShallowWater.jl}: {S}hallow water simulations with {T}rixi.jl},
+  author={Winters, Andrew R and Ersing, Patrick and Ranocha, Hendrik and Schlottke-Lakemper, Michael},
+  year={2025},
+  howpublished={\url{https://github.com/trixi-framework/TrixiShallowWater.jl}},
+  doi={10.5281/zenodo.15206520}
+}
+```
+
 ## Authors
 TrixiShallowWater.jl is maintained by the
 [Trixi authors](https://github.com/trixi-framework/Trixi.jl/blob/main/AUTHORS.md).
@@ -80,4 +93,4 @@ or [create an issue](https://github.com/trixi-framework/TrixiShallowWater.jl/iss
 This project has benefited from funding from [Vetenskapsrådet](https://www.vr.se)
 (VR, Swedish Research Council), Sweden
 through the VR Starting Grant "Shallow water flows including sediment transport and morphodynamics",
-VR grant agreement 2020-03642 VR.
+VR grant agreement 2020-03642 VR.

examples/dgmulti_1d/elixir_shallow_water_quasi_1d.jl

@@ -11,7 +11,15 @@ equations = ShallowWaterEquationsQuasi1D(gravity = 9.81)
 initial_condition = initial_condition_convergence_test
 
 volume_flux = (flux_chan_etal, flux_nonconservative_chan_etal)
-surface_flux = (FluxPlusDissipation(flux_chan_etal, DissipationLocalLaxFriedrichs()),
+# Up to Trixi.jl version 0.13.0, `max_abs_speed_naive` was used as the default wave speed estimate of
+# `DissipationLocalLaxFriedrichs(), i.e., `DissipationLocalLaxFriedrichs(max_abs_speed = max_abs_speed_naive)`.
+# 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 of Trixi.jl the default wave speed used in the LLF flux and dissipation operator to `max_abs_speed`.
+# To ensure that every example still runs we specify explicitly `DissipationLocalLaxFriedrichs(max_abs_speed_naive)`.
+# 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 = (FluxPlusDissipation(flux_chan_etal,
+                                    DissipationLocalLaxFriedrichs(max_abs_speed_naive)),
                 flux_nonconservative_chan_etal)
 
 dg = DGMulti(polydeg = 4, element_type = Line(), approximation_type = SBP(),

examples/dgmulti_2d/elixir_shallowwater_source_terms.jl

@@ -10,7 +10,14 @@ equations = ShallowWaterEquations2D(gravity = 9.81)
 initial_condition = initial_condition_convergence_test
 
 volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal)
-surface_flux = (flux_lax_friedrichs, flux_nonconservative_fjordholm_etal)
+# Up to Trixi.jl version 0.13.0, `max_abs_speed_naive` was used as the default wave speed estimate of
+# `const flux_lax_friedrichs = FluxLaxFriedrichs(), i.e., `FluxLaxFriedrichs(max_abs_speed = max_abs_speed_naive)`.
+# 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 of Trixi.jl 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 
+# `StepsizeCallback` (CFL-Condition) and less diffusion.
+surface_flux = (FluxLaxFriedrichs(max_abs_speed_naive), flux_nonconservative_fjordholm_etal)
 dg = DGMulti(polydeg = 3, element_type = Quad(), approximation_type = SBP(),
              surface_integral = SurfaceIntegralWeakForm(surface_flux),
              volume_integral = VolumeIntegralFluxDifferencing(volume_flux))

examples/p4est_2d_dgsem/elixir_shallowwater_multilayer_monai_flood_amr.jl

@@ -142,8 +142,15 @@ end
 
 volume_flux = (flux_ersing_etal, flux_nonconservative_ersing_etal)
 
+# Up to Trixi.jl version 0.13.0, `max_abs_speed_naive` was used as the default wave speed estimate of
+# `DissipationLocalLaxFriedrichs(), i.e., `DissipationLocalLaxFriedrichs(max_abs_speed = max_abs_speed_naive)`.
+# 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 of Trixi.jl the default wave speed used in the LLF flux and dissipation operator to `max_abs_speed`.
+# To ensure that every example still runs we specify explicitly `DissipationLocalLaxFriedrichs(max_abs_speed_naive)`.
+# 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 = (FluxHydrostaticReconstruction(FluxPlusDissipation(flux_ersing_etal,
-                                                                  DissipationLocalLaxFriedrichs()),
+                                                                  DissipationLocalLaxFriedrichs(max_abs_speed_naive)),
                                               hydrostatic_reconstruction_ersing_etal),
                 FluxHydrostaticReconstruction(flux_nonconservative_ersing_etal,
                                               hydrostatic_reconstruction_ersing_etal))

examples/p4est_2d_dgsem/elixir_shallowwater_multilayer_perturbation_wet_dry_amr.jl

@@ -55,8 +55,15 @@ boundary_condition = Dict(:all => boundary_condition_slip_wall)
 
 volume_flux = (flux_ersing_etal, flux_nonconservative_ersing_etal)
 
+# Up to Trixi.jl version 0.13.0, `max_abs_speed_naive` was used as the default wave speed estimate of
+# `DissipationLocalLaxFriedrichs(), i.e., `DissipationLocalLaxFriedrichs(max_abs_speed = max_abs_speed_naive)`.
+# 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 of Trixi.jl the default wave speed used in the LLF flux and dissipation operator to `max_abs_speed`.
+# To ensure that every example still runs we specify explicitly `DissipationLocalLaxFriedrichs(max_abs_speed_naive)`.
+# 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 = (FluxHydrostaticReconstruction(FluxPlusDissipation(flux_ersing_etal,
-                                                                  DissipationLocalLaxFriedrichs()),
+                                                                  DissipationLocalLaxFriedrichs(max_abs_speed_naive)),
                                               hydrostatic_reconstruction_ersing_etal),
                 FluxHydrostaticReconstruction(flux_nonconservative_ersing_etal,
                                               hydrostatic_reconstruction_ersing_etal))

examples/p4est_2d_dgsem/elixir_shallowwater_multilayer_three_mound_dam_break_amr.jl

@@ -90,8 +90,15 @@ boundary_conditions = Dict(:Bottom => boundary_condition_slip_wall,
 
 volume_flux = (flux_ersing_etal, flux_nonconservative_ersing_etal)
 
+# Up to Trixi.jl version 0.13.0, `max_abs_speed_naive` was used as the default wave speed estimate of
+# `DissipationLocalLaxFriedrichs(), i.e., `DissipationLocalLaxFriedrichs(max_abs_speed = max_abs_speed_naive)`.
+# 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 of Trixi.jl the default wave speed used in the LLF flux and dissipation operator to `max_abs_speed`.
+# To ensure that every example still runs we specify explicitly `DissipationLocalLaxFriedrichs(max_abs_speed_naive)`.
+# 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 = (FluxHydrostaticReconstruction(FluxPlusDissipation(flux_ersing_etal,
-                                                                  DissipationLocalLaxFriedrichs()),
+                                                                  DissipationLocalLaxFriedrichs(max_abs_speed_naive)),
                                               hydrostatic_reconstruction_ersing_etal),
                 FluxHydrostaticReconstruction(flux_nonconservative_ersing_etal,
                                               hydrostatic_reconstruction_ersing_etal))