Feature t8code: Extending to 3D (#1535)

* Initial commit for the new feature using t8code as meshing backend. * Delete t8code_2d_dgsem * Added new examples and tests. Testing updates for T8code.jl. * Worked in the comments. * Fixed spelling. * Update src/auxiliary/auxiliary.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Added whitespace in Unions. * Adapted commented out code block reporting the no. of elements per level. * Added dummy save mesh support for . * Added test . * Added to method signature. * Deleted unnecessary comments. * Removed commented out tests. * Fixed Morton ordering bug in 2D at mortar interfaces. * Disabled `save_solution` callbacks and added more tests. * Added more tests. * Updated code according to the review. * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/solvers/dgsem_t8code/containers_2d.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Code cleanup. * Updated to [email protected] * Fixing minor issues. * Fixed typo. * Code cleanup. * Enabled `set_ghost` in examples. * Generalized type info in function signature. * Added namespace qualifier. * Updated comments. * Refactored code and deleted lots of it. * Removed a copy operation. * Initial commit. * Fxinig minor bugs. * Fixed minor typo. * Added first 3d example and fixed segfault. * Added many 3D examples and tests. * Backup. * Fixed merging issues. * Adding more tests. * Fixed some merging issues and formatting. * Fixed spelling. * Fixed spelling and changed assert macro. * Applied automatic formatting. * Applied automatic formatting. * Backup. * Removed superfluous outer constructor for T8codeMesh. * Added return statement for consistency. * Fixed wrong indentation by autoformatter. * Added comments. * Made sure an exception is thrown. * Changed flags for sc_init for t8code initialization. * Updated formatting. * Workaround for error about calling MPI routines after MPI has been finalized. * Upped to T8code v0.4.1. * Added mpi_finailize_hook for proper memory cleanup. * Added t8code to test_threaded.jl * Added a `save_mesh_file` call in order to satisfy code coverage. * Improved finalizer logic for T8coeMesh. * Refined code. * Restructured to do blocks. * Moved save_mesh_file call to test file. * Fixed spelling error. * Made sc_finalize optional. * Fixed spelling. * Cleaned up examples. * Updated and cleaned t8code solver codes. * Updated tests for t8code 3D code. * Fixed spelling. * Update elixir_euler_source_terms_nonconforming_unstructured_curved.jl * Update elixir_euler_source_terms_nonconforming_unstructured_curved.jl * Fixed indentation. * Update src/solvers/dgsem_structured/dg_3d.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/solvers/dgsem_t8code/containers_3d.jl Co-authored-by: Andrew Winters <[email protected]> * Update src/callbacks_step/amr_dg3d.jl Co-authored-by: Andrew Winters <[email protected]> * Update examples/t8code_3d_dgsem/elixir_euler_ec.jl Co-authored-by: Andrew Winters <[email protected]> * Update examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl Co-authored-by: Andrew Winters <[email protected]> * Update examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl Co-authored-by: Andrew Winters <[email protected]> * Update src/solvers/dgsem_structured/dg_3d.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/callbacks_step/analysis_dg3d.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update examples/t8code_3d_dgsem/elixir_euler_free_stream.jl Co-authored-by: Andrew Winters <[email protected]> * Removed NDIMS from T8codeMesh construction in case of p4est/p8est connectivity input. * Aligned T8codeMesh constructur with other mesh constructors. * Update examples/t8code_3d_dgsem/elixir_euler_sedov.jl Co-authored-by: Andrew Winters <[email protected]> * Update examples/t8code_3d_dgsem/elixir_euler_sedov.jl Co-authored-by: Andrew Winters <[email protected]> * Cleanup up. * Added @allocated test. * Fixed formatting. * Applied formatter. * Code cleanup. * Removed unused member variable. * Apply suggestions from code review Co-authored-by: Daniel Doehring <[email protected]> * suggestions from review * fix format (strange?) * Added comments to help interpreting the source code. * Update src/callbacks_step/amr_dg3d.jl Co-authored-by: Benedict <[email protected]> * Adhered to unified mesh constructor calling scheme. * Applied formatter. * Switched to Float64 instead of Cdouble. * Update src/meshes/t8code_mesh.jl Co-authored-by: Daniel Doehring <[email protected]> * Refactored negative volume check. * Applied formatter. * Fixed typo resp. bug. * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * add missing allocation checks * Some refactoring. * Deleted msh file. * Fixed a bug. * Code cleanup. * Ignore gmsh files. * Removed adapt! from global namespace. * Added documentation. * Added @test_warn to test. * Applied formatter. * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Joshua Lampert <[email protected]> * Turned @warn to @info. * Code cleanup and added @deprecated routines in order to avoid breaking release. * Applied formatter. * Added formatter pragmas to avoid ugly formatting. --------- Co-authored-by: Johannes Markert <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Andrew Winters <[email protected]> Co-authored-by: Benedict <[email protected]> Co-authored-by: Daniel Doehring <[email protected]> Co-authored-by: Benedict Geihe <[email protected]> Co-authored-by: Joshua Lampert <[email protected]>
trixi-framework · Jan 19, 2024 · 1946f9d · 1946f9d
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -70,6 +70,7 @@ jobs:
           - p4est_part1
           - p4est_part2
           - t8code_part1
+          - t8code_part2
           - unstructured_dgmulti
           - parabolic
           - paper_self_gravitating_gas_dynamics

diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,7 @@
 *.mesh
 *.bson
 *.inp
+*.msh
 **/Manifest.toml
 out*/
 docs/build

diff --git a/examples/t8code_2d_dgsem/elixir_advection_amr_solution_independent.jl b/examples/t8code_2d_dgsem/elixir_advection_amr_solution_independent.jl
@@ -93,12 +93,10 @@ solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 coordinates_min = (-5.0, -5.0)
 coordinates_max = (5.0, 5.0)
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 trees_per_dimension = (1, 1)
 
 mesh = T8codeMesh(trees_per_dimension, polydeg = 3,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 1)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

diff --git a/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl
@@ -41,9 +41,9 @@ isfile(mesh_file) ||
 # we can create a t8code mesh.
 conn = Trixi.read_inp_p4est(mesh_file, Val(2))
 
-mesh = T8codeMesh{2}(conn, polydeg = 3,
-                     mapping = mapping_flag,
-                     initial_refinement_level = 1)
+mesh = T8codeMesh(conn, polydeg = 3,
+                  mapping = mapping_flag,
+                  initial_refinement_level = 1)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
                                     boundary_conditions = boundary_conditions)

diff --git a/examples/t8code_2d_dgsem/elixir_advection_basic.jl b/examples/t8code_2d_dgsem/elixir_advection_basic.jl
@@ -16,12 +16,10 @@ solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 coordinates_min = (-1.0, -1.0) # minimum coordinates (min(x), min(y))
 coordinates_max = (1.0, 1.0) # maximum coordinates (max(x), max(y))
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 trees_per_dimension = (8, 8)
 
 mesh = T8codeMesh(trees_per_dimension, polydeg = 3,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 1)
 
 # A semidiscretization collects data structures and functions for the spatial discretization

diff --git a/examples/t8code_2d_dgsem/elixir_advection_nonconforming_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_nonconforming_flag.jl
@@ -20,31 +20,28 @@ f4(s) = SVector(s, 1.0 + sin(0.5 * pi * s))
 faces = (f1, f2, f3, f4)
 mapping = Trixi.transfinite_mapping(faces)
 
-# Create P4estMesh with 3 x 2 trees and 6 x 4 elements,
+# Create T8codeMesh with 3 x 2 trees and 6 x 4 elements,
 # approximate the geometry with a smaller polydeg for testing.
 trees_per_dimension = (3, 2)
 mesh = T8codeMesh(trees_per_dimension, polydeg = 3,
                   mapping = mapping,
                   initial_refinement_level = 1)
 
-function adapt_callback(forest,
-                        forest_from,
-                        which_tree,
-                        lelement_id,
-                        ts,
-                        is_family,
-                        num_elements,
-                        elements_ptr)::Cint
-    vertex = Vector{Cdouble}(undef, 3)
-
-    elements = unsafe_wrap(Array, elements_ptr, num_elements)
-
-    Trixi.t8_element_vertex_reference_coords(ts, elements[1], 0, pointer(vertex))
+# Note: This is actually a `p4est_quadrant_t` which is much bigger than the
+# following struct. But we only need the first three fields for our purpose.
+struct t8_dquad_t
+    x::Int32
+    y::Int32
+    level::Int8
+    # [...] # See `p4est.h` in `p4est` for more info.
+end
 
-    level = Trixi.t8_element_level(ts, elements[1])
+# Refine quadrants of each tree at lower left edge to level 4.
+function adapt_callback(forest, ltreeid, eclass_scheme, lelemntid, elements, is_family,
+                        user_data)
+    el = unsafe_load(Ptr{t8_dquad_t}(elements[1]))
 
-    # TODO: Make this condition more general.
-    if vertex[1] < 1e-8 && vertex[2] < 1e-8 && level < 4
+    if el.x == 0 && el.y == 0 && el.level < 4
         # return true (refine)
         return 1
     else
@@ -53,26 +50,7 @@ function adapt_callback(forest,
     end
 end
 
-Trixi.@T8_ASSERT(Trixi.t8_forest_is_committed(mesh.forest)!=0);
-
-# Init new forest.
-new_forest_ref = Ref{Trixi.t8_forest_t}()
-Trixi.t8_forest_init(new_forest_ref);
-new_forest = new_forest_ref[]
-
-# Check out `examples/t8_step4_partition_balance_ghost.jl` in
-# https://github.com/DLR-AMR/T8code.jl for detailed explanations.
-let set_from = C_NULL, recursive = 1, set_for_coarsening = 0, no_repartition = 0
-    Trixi.t8_forest_set_user_data(new_forest, C_NULL)
-    Trixi.t8_forest_set_adapt(new_forest, mesh.forest,
-                              Trixi.@t8_adapt_callback(adapt_callback), recursive)
-    Trixi.t8_forest_set_balance(new_forest, set_from, no_repartition)
-    Trixi.t8_forest_set_partition(new_forest, set_from, set_for_coarsening)
-    Trixi.t8_forest_set_ghost(new_forest, 1, Trixi.T8_GHOST_FACES)
-    Trixi.t8_forest_commit(new_forest)
-end
-
-mesh.forest = new_forest
+Trixi.adapt!(mesh, adapt_callback)
 
 # A semidiscretization collects data structures and functions for the spatial discretization
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergence_test,

diff --git a/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl
@@ -38,9 +38,9 @@ isfile(mesh_file) ||
 # we can create a t8code mesh.
 conn = Trixi.read_inp_p4est(mesh_file, Val(2))
 
-mesh = T8codeMesh{2}(conn, polydeg = 3,
-                     mapping = mapping_flag,
-                     initial_refinement_level = 2)
+mesh = T8codeMesh(conn, polydeg = 3,
+                  mapping = mapping_flag,
+                  initial_refinement_level = 2)
 
 # A semidiscretization collects data structures and functions for the spatial discretization.
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,

diff --git a/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl b/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl
@@ -40,25 +40,17 @@ isfile(mesh_file) ||
 # we can create a t8code mesh.
 conn = Trixi.read_inp_p4est(mesh_file, Val(2))
 
-mesh = T8codeMesh{2}(conn, polydeg = 3,
-                     mapping = mapping,
-                     initial_refinement_level = 1)
-
-function adapt_callback(forest,
-                        forest_from,
-                        which_tree,
-                        lelement_id,
-                        ts,
-                        is_family,
-                        num_elements,
-                        elements_ptr)::Cint
-    vertex = Vector{Cdouble}(undef, 3)
+mesh = T8codeMesh(conn, polydeg = 3,
+                  mapping = mapping,
+                  initial_refinement_level = 1)
 
-    elements = unsafe_wrap(Array, elements_ptr, num_elements)
+function adapt_callback(forest, ltreeid, eclass_scheme, lelemntid, elements, is_family,
+                        user_data)
+    vertex = Vector{Cdouble}(undef, 3)
 
-    Trixi.t8_element_vertex_reference_coords(ts, elements[1], 0, pointer(vertex))
+    Trixi.t8_element_vertex_reference_coords(eclass_scheme, elements[1], 0, vertex)
 
-    level = Trixi.t8_element_level(ts, elements[1])
+    level = Trixi.t8_element_level(eclass_scheme, elements[1])
 
     # TODO: Make this condition more general.
     if vertex[1] < 1e-8 && vertex[2] < 1e-8 && level < 3
@@ -70,26 +62,7 @@ function adapt_callback(forest,
     end
 end
 
-Trixi.@T8_ASSERT(Trixi.t8_forest_is_committed(mesh.forest)!=0);
-
-# Init new forest.
-new_forest_ref = Ref{Trixi.t8_forest_t}()
-Trixi.t8_forest_init(new_forest_ref);
-new_forest = new_forest_ref[]
-
-# Check out `examples/t8_step4_partition_balance_ghost.jl` in
-# https://github.com/DLR-AMR/T8code.jl for detailed explanations.
-let set_from = C_NULL, recursive = 1, set_for_coarsening = 0, no_repartition = 0
-    Trixi.t8_forest_set_user_data(new_forest, C_NULL)
-    Trixi.t8_forest_set_adapt(new_forest, mesh.forest,
-                              Trixi.@t8_adapt_callback(adapt_callback), recursive)
-    Trixi.t8_forest_set_balance(new_forest, set_from, no_repartition)
-    Trixi.t8_forest_set_partition(new_forest, set_from, set_for_coarsening)
-    Trixi.t8_forest_set_ghost(new_forest, 1, Trixi.T8_GHOST_FACES)
-    Trixi.t8_forest_commit(new_forest)
-end
-
-mesh.forest = new_forest
+Trixi.adapt!(mesh, adapt_callback)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
                                     boundary_conditions = Dict(:all => BoundaryConditionDirichlet(initial_condition)))

diff --git a/examples/t8code_2d_dgsem/elixir_euler_sedov.jl b/examples/t8code_2d_dgsem/elixir_euler_sedov.jl
@@ -58,12 +58,10 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux,
 coordinates_min = (-1.0, -1.0)
 coordinates_max = (1.0, 1.0)
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 trees_per_dimension = (4, 4)
 
 mesh = T8codeMesh(trees_per_dimension, polydeg = 4,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 2, periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

diff --git a/examples/t8code_2d_dgsem/elixir_euler_shockcapturing_ec.jl b/examples/t8code_2d_dgsem/elixir_euler_shockcapturing_ec.jl
@@ -29,12 +29,10 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux,
 coordinates_min = (-1.0, -1.0)
 coordinates_max = (1.0, 1.0)
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 trees_per_dimension = (4, 4)
 
 mesh = T8codeMesh(trees_per_dimension, polydeg = 4,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 2, periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

diff --git a/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl
@@ -40,25 +40,17 @@ isfile(mesh_file) ||
 # we can create a t8code mesh.
 conn = Trixi.read_inp_p4est(mesh_file, Val(2))
 
-mesh = T8codeMesh{2}(conn, polydeg = 3,
-                     mapping = mapping_flag,
-                     initial_refinement_level = 1)
-
-function adapt_callback(forest,
-                        forest_from,
-                        which_tree,
-                        lelement_id,
-                        ts,
-                        is_family,
-                        num_elements,
-                        elements_ptr)::Cint
-    vertex = Vector{Cdouble}(undef, 3)
+mesh = T8codeMesh(conn, polydeg = 3,
+                  mapping = mapping_flag,
+                  initial_refinement_level = 1)
 
-    elements = unsafe_wrap(Array, elements_ptr, num_elements)
+function adapt_callback(forest, ltreeid, eclass_scheme, lelemntid, elements, is_family,
+                        user_data)
+    vertex = Vector{Cdouble}(undef, 3)
 
-    Trixi.t8_element_vertex_reference_coords(ts, elements[1], 0, pointer(vertex))
+    Trixi.t8_element_vertex_reference_coords(eclass_scheme, elements[1], 0, pointer(vertex))
 
-    level = Trixi.t8_element_level(ts, elements[1])
+    level = Trixi.t8_element_level(eclass_scheme, elements[1])
 
     # TODO: Make this condition more general.
     if vertex[1] < 1e-8 && vertex[2] < 1e-8 && level < 2
@@ -70,26 +62,7 @@ function adapt_callback(forest,
     end
 end
 
-@assert(Trixi.t8_forest_is_committed(mesh.forest)!=0);
-
-# Init new forest.
-new_forest_ref = Ref{Trixi.t8_forest_t}()
-Trixi.t8_forest_init(new_forest_ref);
-new_forest = new_forest_ref[]
-
-# Check out `examples/t8_step4_partition_balance_ghost.jl` in
-# https://github.com/DLR-AMR/T8code.jl for detailed explanations.
-let set_from = C_NULL, recursive = 1, set_for_coarsening = 0, no_repartition = 0
-    Trixi.t8_forest_set_user_data(new_forest, C_NULL)
-    Trixi.t8_forest_set_adapt(new_forest, mesh.forest,
-                              Trixi.@t8_adapt_callback(adapt_callback), recursive)
-    Trixi.t8_forest_set_balance(new_forest, set_from, no_repartition)
-    Trixi.t8_forest_set_partition(new_forest, set_from, set_for_coarsening)
-    Trixi.t8_forest_set_ghost(new_forest, 1, Trixi.T8_GHOST_FACES)
-    Trixi.t8_forest_commit(new_forest)
-end
-
-mesh.forest = new_forest
+Trixi.adapt!(mesh, adapt_callback)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
                                     source_terms = source_terms,

diff --git a/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl b/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl
@@ -16,10 +16,8 @@ coordinates_max = (2.0, 2.0)
 
 trees_per_dimension = (1, 1)
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 mesh = T8codeMesh(trees_per_dimension, polydeg = 1,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 2)
 
 semi_euler = SemidiscretizationHyperbolic(mesh, equations_euler, initial_condition,

diff --git a/examples/t8code_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/t8code_2d_dgsem/elixir_mhd_alfven_wave.jl
@@ -11,18 +11,17 @@ initial_condition = initial_condition_convergence_test
 
 # Get the DG approximation space
 volume_flux = (flux_central, flux_nonconservative_powell)
+
 solver = DGSEM(polydeg = 4, surface_flux = (flux_hlle, flux_nonconservative_powell),
                volume_integral = VolumeIntegralFluxDifferencing(volume_flux))
 
 coordinates_min = (0.0, 0.0)
 coordinates_max = (sqrt(2.0), sqrt(2.0))
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 trees_per_dimension = (8, 8)
 
 mesh = T8codeMesh(trees_per_dimension, polydeg = 3,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 0, periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

diff --git a/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl b/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl
@@ -78,9 +78,9 @@ isfile(mesh_file) ||
 # we can create a t8code mesh.
 conn = Trixi.read_inp_p4est(mesh_file, Val(2))
 
-mesh = T8codeMesh{2}(conn, polydeg = 4,
-                     mapping = mapping_twist,
-                     initial_refinement_level = 1)
+mesh = T8codeMesh(conn, polydeg = 4,
+                  mapping = mapping_twist,
+                  initial_refinement_level = 1)
 
 boundary_condition = BoundaryConditionDirichlet(initial_condition)
 boundary_conditions = Dict(:all => boundary_condition)

diff --git a/examples/t8code_2d_dgsem/elixir_shallowwater_source_terms.jl b/examples/t8code_2d_dgsem/elixir_shallowwater_source_terms.jl
@@ -22,12 +22,10 @@ solver = DGSEM(polydeg = 3,
 coordinates_min = (0.0, 0.0) # minimum coordinates (min(x), min(y))
 coordinates_max = (sqrt(2.0), sqrt(2.0))  # maximum coordinates (max(x), max(y))
 
-mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
-
 trees_per_dimension = (8, 8)
 
 mesh = T8codeMesh(trees_per_dimension, polydeg = 3,
-                  mapping = mapping,
+                  coordinates_min = coordinates_min, coordinates_max = coordinates_max,
                   initial_refinement_level = 1)
 
 # A semidiscretization collects data structures and functions for the spatial discretization
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,7 @@ @@
     *.mesh
     *.bson
     *.inp
+    *.msh
     **/Manifest.toml
     out*/
     docs/build
@@ Expand Down @@