add TODOs for code pieces that should move to TrixiShallowWater package

examples/structured_2d_dgsem/elixir_shallowwater_conical_island.jl

@@ -4,6 +4,8 @@ using Trixi
 
  ###############################################################################
  # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations2D(gravity_constant=9.81, H0=1.4)
 

examples/structured_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl

@@ -4,6 +4,8 @@ using Trixi
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations2D(gravity_constant=9.81)
 

examples/structured_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl

@@ -5,6 +5,8 @@ using Printf: @printf, @sprintf
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 
 equations = ShallowWaterEquations2D(gravity_constant=9.812)

examples/tree_1d_dgsem/elixir_shallowwater_beach.jl

@@ -4,6 +4,8 @@ using Trixi
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations1D(gravity_constant=9.812)
 

examples/tree_1d_dgsem/elixir_shallowwater_parabolic_bowl.jl

@@ -4,6 +4,8 @@ using Trixi
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations1D(gravity_constant=9.81)
 

examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl

@@ -5,6 +5,8 @@ using Printf: @printf, @sprintf
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations1D(gravity_constant=9.812)
 

examples/tree_2d_dgsem/elixir_shallowwater_conical_island.jl

@@ -4,6 +4,8 @@ using Trixi
 
 ###############################################################################
 # semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations2D(gravity_constant=9.81, H0=1.4)
 

examples/tree_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl

@@ -4,6 +4,8 @@ using Trixi
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations2D(gravity_constant=9.81)
 

examples/tree_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl

@@ -5,6 +5,8 @@ using Printf: @printf, @sprintf
 
 ###############################################################################
 # Semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
 
 equations = ShallowWaterEquations2D(gravity_constant=9.812)
 

examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl

@@ -5,6 +5,9 @@ using Trixi
 
 ###############################################################################
 # semidiscretization of the shallow water equations
+#
+# TODO: TrixiShallowWater: wet/dry example elixir
+
 
 equations = ShallowWaterEquations2D(gravity_constant=9.81, H0=1.875,
                                     threshold_limiter=1e-12, threshold_wet=1e-14)

src/Trixi.jl

@@ -162,6 +162,7 @@ export flux, flux_central, flux_lax_friedrichs, flux_hll, flux_hllc, flux_hlle,
        flux_fjordholm_etal, flux_nonconservative_fjordholm_etal, flux_es_fjordholm_etal,
        flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal,
        hydrostatic_reconstruction_audusse_etal, flux_nonconservative_audusse_etal,
+       # TODO: TrixiShallowWater: move anything with "chen_noelle" to new file
        hydrostatic_reconstruction_chen_noelle, flux_nonconservative_chen_noelle,
        flux_hll_chen_noelle,
        FluxPlusDissipation, DissipationGlobalLaxFriedrichs, DissipationLocalLaxFriedrichs,
@@ -217,6 +218,7 @@ export DG,
        VolumeIntegralFluxDifferencing,
        VolumeIntegralPureLGLFiniteVolume,
        VolumeIntegralShockCapturingHG, IndicatorHennemannGassner,
+       # TODO: TrixiShallowWater: move new indicator
        IndicatorHennemannGassnerShallowWater,
        VolumeIntegralUpwind,
        SurfaceIntegralWeakForm, SurfaceIntegralStrongForm,

src/callbacks_stage/callbacks_stage.jl

@@ -6,5 +6,6 @@
 #! format: noindent
 
 include("positivity_zhang_shu.jl")
+# TODO: TrixiShallowWater: move specific limiter file
 include("positivity_shallow_water.jl")
 end # @muladd

src/callbacks_stage/positivity_shallow_water.jl

@@ -5,6 +5,8 @@
 @muladd begin
 #! format: noindent
 
+# TODO: TrixiShallowWater: generic wet/dry limiter
+
 """
     PositivityPreservingLimiterShallowWater(; variables)
 

src/callbacks_stage/positivity_shallow_water_dg1d.jl

@@ -5,6 +5,8 @@
 @muladd begin
 #! format: noindent
 
+# TODO: TrixiShallowWater: 1D wet/dry limiter should move
+
 function limiter_shallow_water!(u, threshold::Real, variable,
                                 mesh::AbstractMesh{1},
                                 equations::ShallowWaterEquations1D,

src/callbacks_stage/positivity_shallow_water_dg2d.jl

@@ -5,6 +5,8 @@
 @muladd begin
 #! format: noindent
 
+# TODO: TrixiShallowWater: 2D wet/dry limiter should move
+
 function limiter_shallow_water!(u, threshold::Real, variable,
                                 mesh::AbstractMesh{2},
                                 equations::ShallowWaterEquations2D, dg::DGSEM, cache)

src/equations/numerical_fluxes.jl

@@ -263,6 +263,8 @@ See [`FluxHLL`](@ref).
 """
 const flux_hll = FluxHLL()
 
+# TODO: TrixiShallowWater: move the chen_noelle flux structure to the new package
+
 # An empty version of the `min_max_speed_chen_noelle` function is declared here
 # in order to create a dimension agnostic version of `flux_hll_chen_noelle`.
 # The full description of this wave speed estimate can be found in the docstrings

src/equations/shallow_water_1d.jl

@@ -50,6 +50,8 @@ References for the SWE are many but a good introduction is available in Chapter
   Finite Volume Methods for Hyperbolic Problems
   [DOI: 10.1017/CBO9780511791253](https://doi.org/10.1017/CBO9780511791253)
 """
+# TODO: TrixiShallowWater: where should the `threshold_limiter` and `threshold_wet` live?
+# how to "properly" export these constants across the two packages?
 struct ShallowWaterEquations1D{RealT <: Real} <: AbstractShallowWaterEquations{1, 3}
     gravity::RealT # gravitational constant
     H0::RealT      # constant "lake-at-rest" total water height
@@ -347,6 +349,7 @@ Further details on the hydrostatic reconstruction and its motivation can be foun
   A new hydrostatic reconstruction scheme based on subcell reconstructions
   [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074)
 """
+# TODO: TrixiShallowWater: move wet/dry specific routine
 @inline function flux_nonconservative_chen_noelle(u_ll, u_rr,
                                                   orientation::Integer,
                                                   equations::ShallowWaterEquations1D)
@@ -495,6 +498,7 @@ Further details on this hydrostatic reconstruction and its motivation can be fou
   A new hydrostatic reconstruction scheme based on subcell reconstructions
   [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074)
 """
+# TODO: TrixiShallowWater: move wet/dry specific routine
 @inline function hydrostatic_reconstruction_chen_noelle(u_ll, u_rr,
                                                         equations::ShallowWaterEquations1D)
     # Unpack left and right water heights and bottom topographies
@@ -617,6 +621,7 @@ Further details on this hydrostatic reconstruction and its motivation can be fou
   A new hydrostatic reconstruction scheme based on subcell reconstructions
   [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074)
 """
+# TODO: TrixiShallowWater: move wet/dry specific routine
 @inline function min_max_speed_chen_noelle(u_ll, u_rr, orientation::Integer,
                                            equations::ShallowWaterEquations1D)
     # Get the velocity quantities
@@ -736,6 +741,9 @@ end
 # Calculate the error for the "lake-at-rest" test case where H = h+b should
 # be a constant value over time. Note, assumes there is a single reference
 # water height `H0` with which to compare.
+#
+# TODO: TrixiShallowWater: where should `threshold_limiter` live? May need
+# to modify or have different versions of the `lake_at_rest_error` function
 @inline function lake_at_rest_error(u, equations::ShallowWaterEquations1D)
     h, _, b = u
 

src/equations/shallow_water_2d.jl

@@ -53,6 +53,8 @@ References for the SWE are many but a good introduction is available in Chapter
   Finite Volume Methods for Hyperbolic Problems
   [DOI: 10.1017/CBO9780511791253](https://doi.org/10.1017/CBO9780511791253)
 """
+# TODO: TrixiShallowWater: where should the `threshold_limiter` and `threshold_wet` live?
+# how to "properly" export these constants across the two packages?
 struct ShallowWaterEquations2D{RealT <: Real} <: AbstractShallowWaterEquations{2, 4}
     gravity::RealT # gravitational constant
     H0::RealT      # constant "lake-at-rest" total water height
@@ -469,6 +471,7 @@ Further details on this hydrostatic reconstruction and its motivation can be fou
   A new hydrostatic reconstruction scheme based on subcell reconstructions
   [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074)
 """
+# TODO: TrixiShallowWater: move wet/dry specific routine
 @inline function hydrostatic_reconstruction_chen_noelle(u_ll, u_rr,
                                                         equations::ShallowWaterEquations2D)
     # Unpack left and right water heights and bottom topographies
@@ -622,6 +625,7 @@ Further details on the hydrostatic reconstruction and its motivation can be foun
   A new hydrostatic reconstruction scheme based on subcell reconstructions
   [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074)
 """
+# TODO: TrixiShallowWater: move wet/dry specific routine
 @inline function flux_nonconservative_chen_noelle(u_ll, u_rr, orientation::Integer,
                                                   equations::ShallowWaterEquations2D)
     # Pull the water height and bottom topography on the left
@@ -962,6 +966,7 @@ the reference below. The definition of the wave speeds are given in Equation (2.
   A new hydrostatic reconstruction scheme based on subcell reconstructions
   [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074)
 """
+# TODO: TrixiShallowWater: move wet/dry specific routine
 @inline function min_max_speed_chen_noelle(u_ll, u_rr, orientation::Integer,
                                            equations::ShallowWaterEquations2D)
     h_ll = waterheight(u_ll, equations)
@@ -1106,6 +1111,9 @@ end
 # Calculate the error for the "lake-at-rest" test case where H = h+b should
 # be a constant value over time. Note, assumes there is a single reference
 # water height `H0` with which to compare.
+#
+# TODO: TrixiShallowWater: where should `threshold_limiter` live? May need
+# to modify or have different versions of the `lake_at_rest_error` function
 @inline function lake_at_rest_error(u, equations::ShallowWaterEquations2D)
     h, _, _, b = u
 

src/equations/shallow_water_two_layer_1d.jl

@@ -5,6 +5,8 @@
 @muladd begin
 #! format: noindent
 
+# TODO: TrixiShallowWater: 1D two layer equations should move to new package
+
 @doc raw"""
     ShallowWaterTwoLayerEquations1D(gravity, H0, rho_upper, rho_lower)