update to Trixi.jl v0.13

Project.toml

@@ -20,7 +20,7 @@ StrideArrays = "d1fa6d79-ef01-42a6-86c9-f7c551f8593b"
 Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 
 [compat]
-ForwardDiff = "0.10.36"
+ForwardDiff = "0.10.36, 1"
 HDF5 = "0.16.10, 0.17"
 LinearAlgebra = "1"
 LoopVectorization = "0.12.118"
@@ -33,5 +33,5 @@ Static = "0.8, 1"
 StaticArrayInterface = "1.5.1"
 StaticArrays = "1"
 StrideArrays = "0.1.28"
-Trixi = "0.9.9, 0.10, 0.11, 0.12"
+Trixi = "0.13"
 julia = "1.9"

docs/make.jl

@@ -12,6 +12,9 @@ end
 links = InterLinks("Trixi" => ("https://trixi-framework.github.io/TrixiDocumentation/stable/",
                                "https://trixi-framework.github.io/TrixiDocumentation/stable/objects.inv"))
 
+# Search for any unresolvable `@ref` reference in external sources
+fallbacks = ExternalFallbacks(; automatic = true)
+
 # Define module-wide setups such that the respective modules are available in doctests
 DocMeta.setdocmeta!(TrixiAtmo, :DocTestSetup, :(using TrixiAtmo);
                     recursive = true)
@@ -95,7 +98,7 @@ makedocs(;
              "Contributing" => "contributing.md",
              "Code of Conduct" => "code_of_conduct.md",
              "License" => "license.md"],
-         plugins = [links],)
+         plugins = [links, fallbacks],)
 
 deploydocs(;
            repo = "github.com/trixi-framework/TrixiAtmo.jl",

src/equations/covariant_advection.jl

@@ -110,9 +110,9 @@ end
 end
 
 # Maximum contravariant wave speed with respect to specific basis vector
-@inline function Trixi.max_abs_speed_naive(u_ll, u_rr, aux_vars_ll, aux_vars_rr,
-                                           orientation::Integer,
-                                           equations::CovariantLinearAdvectionEquation2D)
+@inline function Trixi.max_abs_speed(u_ll, u_rr, aux_vars_ll, aux_vars_rr,
+                                     orientation::Integer,
+                                     equations::CovariantLinearAdvectionEquation2D)
     vcon_ll = velocity_contravariant(u_ll, equations)  # Contravariant components on left side
     vcon_rr = velocity_contravariant(u_rr, equations)  # Contravariant components on right side
     return max(abs(vcon_ll[orientation]), abs(vcon_rr[orientation]))

src/equations/covariant_shallow_water.jl

@@ -217,9 +217,9 @@ end
 end
 
 # Maximum wave speed along the normal direction in reference space
-@inline function Trixi.max_abs_speed_naive(u_ll, u_rr, aux_vars_ll, aux_vars_rr,
-                                           orientation,
-                                           equations::AbstractCovariantShallowWaterEquations2D)
+@inline function Trixi.max_abs_speed(u_ll, u_rr, aux_vars_ll, aux_vars_rr,
+                                     orientation,
+                                     equations::AbstractCovariantShallowWaterEquations2D)
     # Geometric variables
     Gcon_ll = metric_contravariant(aux_vars_ll, equations)
     Gcon_rr = metric_contravariant(aux_vars_rr, equations)

src/equations/shallow_water_3d.jl

@@ -407,6 +407,28 @@ end
     return max(abs(v_ll), abs(v_rr)) + max(c_ll, c_rr) * norm(normal_direction)
 end
 
+@inline function Trixi.max_abs_speed(u_ll, u_rr, normal_direction::AbstractVector,
+                                     equations::ShallowWaterEquations3D)
+    # Extract and compute the velocities in the normal direction
+    v1_ll, v2_ll, v3_ll = velocity(u_ll, equations)
+    v1_rr, v2_rr, v3_rr = velocity(u_rr, equations)
+    v_ll = v1_ll * normal_direction[1] + v2_ll * normal_direction[2] +
+           v3_ll * normal_direction[3]
+    v_rr = v1_rr * normal_direction[1] + v2_rr * normal_direction[2] +
+           v3_rr * normal_direction[3]
+
+    # Compute the wave celerity on the left and right
+    h_ll = waterheight(u_ll, equations)
+    h_rr = waterheight(u_rr, equations)
+
+    c_ll = sqrt(max(equations.gravity * h_ll, 0.0f0))
+    c_rr = sqrt(max(equations.gravity * h_rr, 0.0f0))
+
+    # The normal velocities are already scaled by the norm
+    norm_ = norm(normal_direction)
+    return max(abs(v_ll) + c_ll * norm_, abs(v_rr) + c_rr * norm_)
+end
+
 # Specialized `DissipationLocalLaxFriedrichs` to avoid spurious dissipation in the bottom topography
 @inline function (dissipation::DissipationLocalLaxFriedrichs)(u_ll, u_rr,
                                                               orientation_or_normal_direction,

src/semidiscretization/semidiscretization_hyperbolic_2d_manifold_in_3d.jl

@@ -16,24 +16,28 @@ function Trixi.SemidiscretizationHyperbolic(mesh::P4estMesh{2},
                                             # `RealT` is used as real type for node locations etc.
                                             # while `uEltype` is used as element type of solutions etc.
                                             RealT = real(solver), uEltype = RealT,
-                                            initial_cache = NamedTuple(),
                                             metric_terms = MetricTermsCrossProduct(),
                                             auxiliary_field = nothing)
     cache = (;
              Trixi.create_cache(mesh, equations, solver, RealT, metric_terms,
-                                auxiliary_field, uEltype)..., initial_cache...)
+                                auxiliary_field, uEltype)...)
     _boundary_conditions = Trixi.digest_boundary_conditions(boundary_conditions, mesh,
                                                             solver,
                                                             cache)
 
+    Trixi.check_periodicity_mesh_boundary_conditions(mesh, _boundary_conditions)
+
+    performance_counter = Trixi.PerformanceCounter()
+
     SemidiscretizationHyperbolic{typeof(mesh), typeof(equations),
                                  typeof(initial_condition),
                                  typeof(_boundary_conditions), typeof(source_terms),
                                  typeof(solver), typeof(cache)}(mesh, equations,
                                                                 initial_condition,
                                                                 _boundary_conditions,
                                                                 source_terms, solver,
-                                                                cache)
+                                                                cache,
+                                                                performance_counter)
 end
 
 # Constructor for SemidiscretizationHyperbolic for the covariant form. Requires 
@@ -49,23 +53,27 @@ function Trixi.SemidiscretizationHyperbolic(mesh::P4estMesh{NDIMS, NDIMS_AMBIENT
                                             # `RealT` is used as real type for node locations etc.
                                             # while `uEltype` is used as element type of solutions etc.
                                             RealT = real(solver), uEltype = RealT,
-                                            initial_cache = NamedTuple(),
                                             metric_terms = MetricTermsCovariantSphere(),
                                             auxiliary_field = nothing) where {NDIMS,
                                                                               NDIMS_AMBIENT}
     cache = (;
              Trixi.create_cache(mesh, equations, solver, RealT, metric_terms,
-                                auxiliary_field, uEltype)..., initial_cache...)
+                                auxiliary_field, uEltype)...)
     _boundary_conditions = Trixi.digest_boundary_conditions(boundary_conditions, mesh,
                                                             solver,
                                                             cache)
 
+    Trixi.check_periodicity_mesh_boundary_conditions(mesh, _boundary_conditions)
+
+    performance_counter = Trixi.PerformanceCounter()
+
     SemidiscretizationHyperbolic{typeof(mesh), typeof(equations),
                                  typeof(initial_condition),
                                  typeof(_boundary_conditions), typeof(source_terms),
                                  typeof(solver), typeof(cache)}(mesh, equations,
                                                                 initial_condition,
                                                                 _boundary_conditions,
                                                                 source_terms, solver,
-                                                                cache)
+                                                                cache,
+                                                                performance_counter)
 end

src/solvers/dgsem_p4est/dg_2d_manifold_in_3d_covariant.jl

@@ -66,7 +66,7 @@ function Trixi.rhs!(du, u, t,
 end
 
 # Compute coefficients for an initial condition that uses auxiliary variables
-function Trixi.compute_coefficients!(u, func, t, mesh::P4estMesh{2},
+function Trixi.compute_coefficients!(backend::Nothing, u, func, t, mesh::P4estMesh{2},
                                      equations::AbstractCovariantEquations{2}, dg::DG,
                                      cache)
     (; aux_node_vars) = cache.auxiliary_variables

test/Project.toml

@@ -15,5 +15,5 @@ OrdinaryDiffEq = "6.91"
 OrdinaryDiffEqLowStorageRK = "1.2"
 OrdinaryDiffEqSSPRK = "1.2"
 Test = "1"
-Trixi = "0.9.9, 0.10, 0.11, 0.12"
+Trixi = "0.13"
 TrixiTest = "0.1"