reorganize elixirs (#672)

* rename paper examples * move example elixirs * update benchmarks * adapt more hard-coded elixir paths * make docstring of examples_dir a Documenter example * some additions to the docstrings of functions related to examples * adapt more elixir path * more detailed README of the examples [skip ci] Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * use suffic _eoc for convergence test elixirs * unify names elixir_euler_nonperiodic -> elixir_euler_source_terms_nonperiodic * _eoc -> _convergence in elixirs Co-authored-by: Michael Schlottke-Lakemper <[email protected]>
trixi-framework · Jun 28, 2021 · 5b89962 · 5b89962
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -62,7 +62,7 @@ jobs:
           - 2d_threaded
           - 3d_part1
           - 3d_part2
-          - paper-self-gravitating-gas-dynamics
+          - paper_self_gravitating_gas_dynamics
           - misc
         include:
           - version: '1.6'

diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl
@@ -4,49 +4,39 @@ using Trixi
 
 const SUITE = BenchmarkGroup()
 
-let dimension = "2d"
-  SUITE[dimension] = BenchmarkGroup()
-  EXAMPLES_DIR = joinpath(examples_dir(), dimension)
-  for elixir in [joinpath(EXAMPLES_DIR, "elixir_advection_extended.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_advection_extended_curved.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_advection_amr_nonperiodic.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_advection_nonperiodic_curved.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_euler_ec.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_euler_ec_curved.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_euler_nonperiodic_curved.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_euler_unstructured_quad_wall_bc.jl"), # this is the only elixir working for polydeg=3
-                 joinpath(EXAMPLES_DIR, "elixir_euler_vortex_mortar.jl"),
-                 joinpath(EXAMPLES_DIR, "elixir_euler_vortex_mortar_shockcapturing.jl"),
-                 joinpath(@__DIR__, "elixir_2d_euler_vortex_tree.jl"),
-                 joinpath(@__DIR__, "elixir_2d_euler_vortex_structured.jl"),
-                 joinpath(@__DIR__, "elixir_2d_euler_vortex_unstructured.jl")]
-    SUITE[dimension][basename(elixir)] = BenchmarkGroup()
-    for polydeg in [3, 7]
-      trixi_include(elixir, tspan=(0.0, 1.0e-10); polydeg)
-      SUITE[dimension][basename(elixir)]["p$(polydeg)_rhs!"] = @benchmarkable Trixi.rhs!(
-        $(similar(sol.u[end])), $(copy(sol.u[end])), $(semi), $(first(tspan)))
-      SUITE[dimension][basename(elixir)]["p$(polydeg)_analysis"] = @benchmarkable ($analysis_callback)($sol)
-    end
-  end
-end
-
-let dimension = "3d"
-  SUITE[dimension] = BenchmarkGroup()
-  EXAMPLES_DIR = joinpath(examples_dir(), dimension)
-  for elixir in ["elixir_advection_extended.jl",
-                 "elixir_advection_nonperiodic_curved.jl",
-                 "elixir_euler_ec.jl",
-                 "elixir_euler_ec_curved.jl",
-                 "elixir_euler_nonperiodic_curved.jl",
-                 "elixir_euler_mortar.jl",
-                 "elixir_euler_shockcapturing.jl"]
-    SUITE[dimension][basename(elixir)] = BenchmarkGroup()
-    for polydeg in [3, 7]
-      trixi_include(joinpath(EXAMPLES_DIR, elixir), tspan=(0.0, 1.0e-10); polydeg)
-      SUITE[dimension][basename(elixir)]["p$(polydeg)_rhs!"] = @benchmarkable Trixi.rhs!(
-        $(similar(sol.u[end])), $(copy(sol.u[end])), $(semi), $(first(tspan)))
-      SUITE[dimension][basename(elixir)]["p$(polydeg)_analysis"] = @benchmarkable ($analysis_callback)($sol)
-    end
+for elixir in [joinpath(examples_dir(), "tree_2d_dgsem", "elixir_advection_extended.jl"),
+               joinpath(examples_dir(), "tree_2d_dgsem", "elixir_advection_amr_nonperiodic.jl"),
+               joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_ec.jl"),
+               joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_vortex_mortar.jl"),
+               joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_vortex_mortar_shockcapturing.jl"),
+               joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_ec.jl"),
+               joinpath(examples_dir(), "structured_2d_dgsem", "elixir_advection_extended.jl"),
+               joinpath(examples_dir(), "structured_2d_dgsem", "elixir_advection_nonperiodic.jl"),
+               joinpath(examples_dir(), "structured_2d_dgsem", "elixir_euler_ec.jl"),
+               joinpath(examples_dir(), "strcutured_2d_dgsem", "elixir_euler_source_terms_nonperiodic.jl"),
+               joinpath(examples_dir(), "structured_2d_dgsem", "elixir_mhd_ec.jl"),
+               joinpath(examples_dir(), "unstrcutured_2d_dgsem", "elixir_euler_wall_bc.jl"), # this is the only elixir working for polydeg=3
+               joinpath(examples_dir(), "p4est_2d_dgsem", "elixir_advection_extended.jl"),
+               joinpath(@__DIR__, "elixir_2d_euler_vortex_tree.jl"),
+               joinpath(@__DIR__, "elixir_2d_euler_vortex_structured.jl"),
+               joinpath(@__DIR__, "elixir_2d_euler_vortex_unstructured.jl"),
+               joinpath(examples_dir(), "tree_3d_dgsem", "elixir_advection_extended.jl"),
+               joinpath(examples_dir(), "tree_3d_dgsem", "elixir_euler_ec.jl"),
+               joinpath(examples_dir(), "tree_3d_dgsem", "elixir_euler_mortar.jl"),
+               joinpath(examples_dir(), "tree_3d_dgsem", "elixir_euler_shockcapturing.jl"),
+               joinpath(examples_dir(), "tree_3d_dgsem", "elixir_mhd_ec.jl"),
+               joinpath(examples_dir(), "structured_3d_dgsem", "elixir_advection_nonperiodic.jl"),
+               joinpath(examples_dir(), "structured_3d_dgsem", "elixir_euler_ec.jl"),
+               joinpath(examples_dir(), "structured_3d_dgsem", "elixir_euler_source_terms_nonperiodic.jl"),
+               joinpath(examples_dir(), "structured_3d_dgsem", "elixir_mhd_ec.jl"),
+               joinpath(examples_dir(), "p4est_3d_dgsem", "elixir_advection_extended.jl"),]
+  benchname = basename(dirname(elixir)) * "/" * basename(elixir)
+  SUITE[benchname] = BenchmarkGroup()
+  for polydeg in [3, 7]
+    trixi_include(elixir, tspan=(0.0, 1.0e-10); polydeg)
+    SUITE[benchname]["p$(polydeg)_rhs!"] = @benchmarkable Trixi.rhs!(
+      $(similar(sol.u[end])), $(copy(sol.u[end])), $(semi), $(first(tspan)))
+    SUITE[benchname]["p$(polydeg)_analysis"] = @benchmarkable ($analysis_callback)($sol)
   end
 end
 
@@ -55,7 +45,7 @@ let
   SUITE["latency"]["default_example"] = @benchmarkable run(
     `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(default_example())'`) seconds=60
   for polydeg in [3, 7]
-    command = "using Trixi; trixi_include(joinpath(examples_dir(), \"2d\", \"elixir_advection_extended.jl\"), tspan=(0.0, 1.0e-10), polydeg=$(polydeg), save_restart=TrivialCallback(), save_solution=TrivialCallback())"
+    command = "using Trixi; trixi_include(joinpath(examples_dir(), \"tree_2d_dgsem\", \"elixir_advection_extended.jl\"), tspan=(0.0, 1.0e-10), polydeg=$(polydeg), save_restart=TrivialCallback(), save_solution=TrivialCallback())"
     SUITE["latency"]["polydeg_$polydeg"] = @benchmarkable run($`$(Base.julia_cmd()) -e $command`) seconds=60
   end
 end
diff --git a/examples/README.md b/examples/README.md
@@ -1,28 +1,38 @@
 # Example elixirs for Trixi
 
-This folder contains example files ("elixirs") that can be used to just try out Trixi and
-that also serve as a starting point to create new simulation setups.
+This folder contains example files ("elixirs") that can be used to just try out
+Trixi and that also serve as a starting point to create new simulation setups.
 Furthermore, these files are also the basis for our automated Trixi tests and
-**each new file put in here** should be added to the test sets in
-`../test/test_examples_Xd_equation.jl`.
+**each new file put in here** should be added to the test sets.
+
+In general, the elixirs are sorted by
+
+- the mesh type,
+- the spatial dimension,
+- and the discretization type
+
+at the top level. Inside each folder, the elixirs are sorted by the equations,
+then the setup, and then, optionally, configuration details. For example,
+`elixir_euler_kelvin_helmholtz_instability_amr.jl` indicates an *elixir* for the
+compressible *Euler* equations, running the *Kelvin-Helmholtz instability* setup
+with adaptive mesh refinement (*AMR*) enabled.
 
 There are also a few files that were configured such that they lend themselves
 to doing convergence tests with `convergence_test`, i.e., to determine the
 experimental order of convergence (EOC):
 
-* [`2d/elixir_advection_basic.jl`](2d/elixir_advection_basic.jl):
+* [`tree_2d_dgsem/elixir_advection_basic.jl`](tree_2d_dgsem/elixir_advection_basic.jl):
   EOC tests for linear scalar advection with `polydeg = 3`.
-* [`2d/elixir_euler_source_terms.jl`](2d/elixir_euler_source_terms.jl):
+* [`tree_2d_dgsem/elixir_euler_source_terms.jl`](tree_2d_dgsem/elixir_euler_source_terms.jl):
   EOC tests for Euler equations with `polydeg = 3`.
-* [`2d/elixir_mhd_alfven_wave.jl`](2d/elixir_mhd_alfven_wave.jl):
+* [`tree_2d_dgsem/elixir_mhd_alfven_wave.jl`](tree_2d_dgsem/elixir_mhd_alfven_wave.jl):
   EOC tests for MHD equations with `polydeg = 3`.
-* [`2d/elixir_hypdiff_lax_friedrichs.jl`](2d/elixir_hypdiff_lax_friedrichs.jl):
+* [`tree_2d_dgsem/elixir_hypdiff_lax_friedrichs.jl`](tree_2d_dgsem/elixir_hypdiff_lax_friedrichs.jl):
   EOC tests for hyperbolic diffusion equations with `polydeg = 4`.
 
-Similar setups are available for other spatial dimensions in the directories
-`1d` and `3d`.
+Similar setups are available for other spatial dimensions and for other mesh types.
 
 In general, a good first elixir to try out as a new user is
-[`2d/elixir_advection_basic.jl`](2d/elixir_advection_basic.jl),
+[`tree_2d_dgsem/elixir_advection_basic.jl`](tree_2d_dgsem/elixir_advection_basic.jl),
 as it is short, takes less than a second to run, and uses only the basic features
 of Trixi.
diff --git a/...vection_amr_solution_independent_p4est.jl → ...xir_advection_amr_solution_independent.jl b/...vection_amr_solution_independent_p4est.jl → ...xir_advection_amr_solution_independent.jl
diff --git a/..._advection_amr_p4est_unstructured_flag.jl → ...elixir_advection_amr_unstructured_flag.jl b/..._advection_amr_p4est_unstructured_flag.jl → ...elixir_advection_amr_unstructured_flag.jl
diff --git a/examples/2d/elixir_advection_basic_p4est.jl → .../p4est_2d_dgsem/elixir_advection_basic.jl b/examples/2d/elixir_advection_basic_p4est.jl → .../p4est_2d_dgsem/elixir_advection_basic.jl
diff --git a/...les/2d/elixir_advection_extended_p4est.jl → ...est_2d_dgsem/elixir_advection_extended.jl b/...les/2d/elixir_advection_extended_p4est.jl → ...est_2d_dgsem/elixir_advection_extended.jl
diff --git a/...ir_advection_p4est_non_conforming_flag.jl → ...d_dgsem/elixir_advection_nonconforming.jl b/...ir_advection_p4est_non_conforming_flag.jl → ...d_dgsem/elixir_advection_nonconforming.jl
diff --git a/...p4est_non_conforming_flag_unstructured.jl → ...r_advection_nonconforming_unstructured.jl b/...p4est_non_conforming_flag_unstructured.jl → ...r_advection_nonconforming_unstructured.jl
diff --git a/...ples/2d/elixir_advection_restart_p4est.jl → ...4est_2d_dgsem/elixir_advection_restart.jl b/...ples/2d/elixir_advection_restart_p4est.jl → ...4est_2d_dgsem/elixir_advection_restart.jl
@@ -5,7 +5,7 @@ using Trixi
 ###############################################################################
 # create a restart file
 
-elixir_file = "elixir_advection_extended_p4est.jl"
+elixir_file = "elixir_advection_extended.jl"
 restart_file = "restart_000047.h5"
 
 trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))

diff --git a/...ples/2d/elixir_euler_free_stream_p4est.jl → ...4est_2d_dgsem/elixir_euler_free_stream.jl b/...ples/2d/elixir_euler_free_stream_p4est.jl → ...4est_2d_dgsem/elixir_euler_free_stream.jl
diff --git a/...ples/2d/elixir_euler_nonperiodic_p4est.jl → .../elixir_euler_source_terms_nonperiodic.jl b/...ples/2d/elixir_euler_nonperiodic_p4est.jl → .../elixir_euler_source_terms_nonperiodic.jl
diff --git a/...r_euler_nonperiodic_p4est_unstructured.jl → ..._source_terms_nonperiodic_unstructured.jl b/...r_euler_nonperiodic_p4est_unstructured.jl → ..._source_terms_nonperiodic_unstructured.jl
diff --git a/.../2d/elixir_eulergravity_eoc_test_p4est.jl → ..._dgsem/elixir_eulergravity_convergence.jl b/.../2d/elixir_eulergravity_eoc_test_p4est.jl → ..._dgsem/elixir_eulergravity_convergence.jl
diff --git a/examples/3d/elixir_advection_amr_p4est.jl → ...es/p4est_3d_dgsem/elixir_advection_amr.jl b/examples/3d/elixir_advection_amr_p4est.jl → ...es/p4est_3d_dgsem/elixir_advection_amr.jl
diff --git a/...dvection_amr_p4est_unstructured_curved.jl → ...ixir_advection_amr_unstructured_curved.jl b/...dvection_amr_p4est_unstructured_curved.jl → ...ixir_advection_amr_unstructured_curved.jl
diff --git a/examples/3d/elixir_advection_basic_p4est.jl → .../p4est_3d_dgsem/elixir_advection_basic.jl b/examples/3d/elixir_advection_basic_p4est.jl → .../p4est_3d_dgsem/elixir_advection_basic.jl
diff --git a/.../elixir_advection_p4est_non_conforming.jl → ...d_dgsem/elixir_advection_nonconforming.jl b/.../elixir_advection_p4est_non_conforming.jl → ...d_dgsem/elixir_advection_nonconforming.jl
diff --git a/...ples/3d/elixir_advection_restart_p4est.jl → ...4est_3d_dgsem/elixir_advection_restart.jl b/...ples/3d/elixir_advection_restart_p4est.jl → ...4est_3d_dgsem/elixir_advection_restart.jl
@@ -5,7 +5,7 @@ using Trixi
 ###############################################################################
 # create a restart file
 
-trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_basic_p4est.jl"),
+trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_basic.jl"),
               trees_per_dimension=(2, 2, 2))
 
 

diff --git a/...ir_advection_p4est_unstructured_curved.jl → ...m/elixir_advection_unstructured_curved.jl b/...ir_advection_p4est_unstructured_curved.jl → ...m/elixir_advection_unstructured_curved.jl
diff --git a/examples/3d/elixir_euler_ec_p4est.jl → examples/p4est_3d_dgsem/elixir_euler_ec.jl b/examples/3d/elixir_euler_ec_p4est.jl → examples/p4est_3d_dgsem/elixir_euler_ec.jl
diff --git a/...ples/3d/elixir_euler_free_stream_p4est.jl → ...4est_3d_dgsem/elixir_euler_free_stream.jl b/...ples/3d/elixir_euler_free_stream_p4est.jl → ...4est_3d_dgsem/elixir_euler_free_stream.jl
diff --git a/...lixir_euler_free_stream_p4est_extruded.jl → ...gsem/elixir_euler_free_stream_extruded.jl b/...lixir_euler_free_stream_p4est_extruded.jl → ...gsem/elixir_euler_free_stream_extruded.jl
diff --git a/...ples/3d/elixir_euler_nonperiodic_p4est.jl → .../elixir_euler_source_terms_nonperiodic.jl b/...ples/3d/elixir_euler_nonperiodic_p4est.jl → .../elixir_euler_source_terms_nonperiodic.jl
diff --git a/...r-self-gravitating-gas-dynamics/README.md → ...r_self_gravitating_gas_dynamics/README.md b/...r-self-gravitating-gas-dynamics/README.md → ...r_self_gravitating_gas_dynamics/README.md
@@ -13,44 +13,44 @@ https://doi.org/10.5281/zenodo.3996575.
 ```julia
 julia> using Trixi
 
-julia> convergence_test("examples/paper-self-gravitating-gas-dynamics/elixir_euler_eoc_test.jl", 4)
+julia> convergence_test("examples/paper_self_gravitating_gas_dynamics/elixir_euler_convergence.jl", 4)
 ```
 
 **polydeg = 4**:
 ```julia
 julia> using Trixi
 
-julia> convergence_test("examples/paper-self-gravitating-gas-dynamics/elixir_euler_eoc_test.jl", 4, polydeg=4)
+julia> convergence_test("examples/paper_self_gravitating_gas_dynamics/elixir_euler_convergence.jl", 4, polydeg=4)
 ```
 
 ## Sec. 4.1.2, Table 3, EOC tests hyperbolic diffusion
 **polydeg = 3**:
 ```julia
 julia> using Trixi
 
-julia> convergence_test("examples/paper-self-gravitating-gas-dynamics/elixir_hypdiff_eoc_test.jl", 4)
+julia> convergence_test("examples/paper_self_gravitating_gas_dynamics/elixir_hypdiff_convergence.jl", 4)
 ```
 
 **polydeg = 4**:
 ```julia
 julia> using Trixi
 
-julia> convergence_test("examples/paper-self-gravitating-gas-dynamics/elixir_hypdiff_eoc_test.jl", 4, polydeg=4)
+julia> convergence_test("examples/paper_self_gravitating_gas_dynamics/elixir_hypdiff_convergence.jl", 4, polydeg=4)
 ```
 
 ## Sec. 4.1.3, Table 4, EOC tests coupled Euler-gravity
 **polydeg = 3**:
 ```julia
 julia> using Trixi
 
-julia> convergence_test("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_eoc_test.jl", 4)
+julia> convergence_test("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl", 4)
 ```
 
 **polydeg = 4**:
 ```julia
 julia> using Trixi
 
-julia> convergence_test("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_eoc_test.jl", 4, polydeg=4)
+julia> convergence_test("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl", 4, polydeg=4)
 ```
 
 ## Sec. 4.1.3, Table 5, EOC tests coupled Euler-gravity (update gravity once per step)
@@ -60,7 +60,7 @@ This is only available in Trixi `v0.2`.
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_jeans_instability.jl")
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl")
 ```
 
 ## Sec. 4.2.1, Figure 4, Jeans energies with Euler/CK45 and gravity/CK45 (update gravity once per step)
@@ -70,7 +70,7 @@ This is only available in Trixi `v0.2`.
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_jeans_instability.jl",
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl",
                       parameters=ParametersEulerGravity(background_density=1.5e7,
                                                         gravitational_constant=6.674e-8,
                                                         cfl=2.4,
@@ -84,7 +84,7 @@ One must also shrink the analysis interval in the above command, e.g.,
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_jeans_instability.jl",
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl",
                      analysis_interval=1)
 ```
 to generate necessary data for the plots to look nice. Then run the python
@@ -99,29 +99,29 @@ to generate the figure.
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl", tspan=(0.0, 0.5))
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl", tspan=(0.0, 0.5))
 ```
 
 **T = 1.0:**
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl")
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl")
 ```
 
 ## Sec. 4.2.2, Figure 7a, T=0.5, Sedov + gravity with Euler/CK45 and gravity/RK3S*
 **AMR mesh:**
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl", tspan=(0.0, 0.5))
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl", tspan=(0.0, 0.5))
 ```
 
 **Uniform mesh:**
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl",
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl",
                      amr_callback=TrivialCallback(), initial_refinement_level=8, t_end=0.5)
 ```
 
@@ -130,14 +130,14 @@ julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulerg
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl")
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl")
 ```
 
 **Uniform mesh:**
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl",
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl",
                      amr_callback=TrivialCallback(), initial_refinement_level=8)
 ```
 
@@ -146,14 +146,14 @@ julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulerg
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl")
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl")
 ```
 
 **Uniform mesh:**
 ```julia
 julia> using Trixi
 
-julia> trixi_include("examples/paper-self-gravitating-gas-dynamics/elixir_eulergravity_sedov_blast_wave.jl",
+julia> trixi_include("examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl",
                      amr_callback=TrivialCallback(), initial_refinement_level=8)
 ```
 

diff --git a/...ing-gas-dynamics/elixir_euler_eoc_test.jl → ..._gas_dynamics/elixir_euler_convergence.jl b/...ing-gas-dynamics/elixir_euler_eoc_test.jl → ..._gas_dynamics/elixir_euler_convergence.jl
diff --git a/...-dynamics/elixir_eulergravity_eoc_test.jl → ...namics/elixir_eulergravity_convergence.jl b/...-dynamics/elixir_eulergravity_eoc_test.jl → ...namics/elixir_eulergravity_convergence.jl
diff --git a/.../elixir_eulergravity_jeans_instability.jl → .../elixir_eulergravity_jeans_instability.jl b/.../elixir_eulergravity_jeans_instability.jl → .../elixir_eulergravity_jeans_instability.jl
diff --git a/...s/elixir_eulergravity_sedov_blast_wave.jl → ...s/elixir_eulergravity_sedov_blast_wave.jl b/...s/elixir_eulergravity_sedov_blast_wave.jl → ...s/elixir_eulergravity_sedov_blast_wave.jl
diff --git a/...g-gas-dynamics/elixir_hypdiff_eoc_test.jl → ...as_dynamics/elixir_hypdiff_convergence.jl b/...g-gas-dynamics/elixir_hypdiff_eoc_test.jl → ...as_dynamics/elixir_hypdiff_convergence.jl
diff --git a/examples/1d/elixir_advection_basic_curved.jl → ...ctured_1d_dgsem/elixir_advection_basic.jl b/examples/1d/elixir_advection_basic_curved.jl → ...ctured_1d_dgsem/elixir_advection_basic.jl
diff --git a/...1d/elixir_advection_nonperiodic_curved.jl → ..._1d_dgsem/elixir_advection_nonperiodic.jl b/...1d/elixir_advection_nonperiodic_curved.jl → ..._1d_dgsem/elixir_advection_nonperiodic.jl
diff --git a/...es/1d/elixir_euler_source_terms_curved.jl → ...red_1d_dgsem/elixir_euler_source_terms.jl b/...es/1d/elixir_euler_source_terms_curved.jl → ...red_1d_dgsem/elixir_euler_source_terms.jl
diff --git a/...les/1d/elixir_euler_nonperiodic_curved.jl → .../elixir_euler_source_terms_nonperiodic.jl b/...les/1d/elixir_euler_nonperiodic_curved.jl → .../elixir_euler_source_terms_nonperiodic.jl
diff --git a/examples/2d/elixir_advection_basic_curved.jl → ...ctured_2d_dgsem/elixir_advection_basic.jl b/examples/2d/elixir_advection_basic_curved.jl → ...ctured_2d_dgsem/elixir_advection_basic.jl
diff --git a/...es/2d/elixir_advection_extended_curved.jl → ...red_2d_dgsem/elixir_advection_extended.jl b/...es/2d/elixir_advection_extended_curved.jl → ...red_2d_dgsem/elixir_advection_extended.jl
diff --git a/...2d/elixir_advection_free_stream_curved.jl → ..._2d_dgsem/elixir_advection_free_stream.jl b/...2d/elixir_advection_free_stream_curved.jl → ..._2d_dgsem/elixir_advection_free_stream.jl
diff --git a/...2d/elixir_advection_nonperiodic_curved.jl → ..._2d_dgsem/elixir_advection_nonperiodic.jl b/...2d/elixir_advection_nonperiodic_curved.jl → ..._2d_dgsem/elixir_advection_nonperiodic.jl
diff --git a/...ples/2d/elixir_advection_parallelogram.jl → ...d_dgsem/elixir_advection_parallelogram.jl b/...ples/2d/elixir_advection_parallelogram.jl → ...d_dgsem/elixir_advection_parallelogram.jl
diff --git a/...les/2d/elixir_advection_restart_curved.jl → ...ured_2d_dgsem/elixir_advection_restart.jl b/...les/2d/elixir_advection_restart_curved.jl → ...ured_2d_dgsem/elixir_advection_restart.jl
@@ -5,7 +5,7 @@ using Trixi
 ###############################################################################
 # create a restart file
 
-elixir_file = "elixir_advection_extended_curved.jl"
+elixir_file = "elixir_advection_extended.jl"
 restart_file = "restart_000047.h5"
 
 trixi_include(@__MODULE__, joinpath(@__DIR__, elixir_file))

diff --git a/examples/2d/elixir_advection_rotated.jl → ...ured_2d_dgsem/elixir_advection_rotated.jl b/examples/2d/elixir_advection_rotated.jl → ...ured_2d_dgsem/elixir_advection_rotated.jl
diff --git a/examples/2d/elixir_advection_waving_flag.jl → ..._2d_dgsem/elixir_advection_waving_flag.jl b/examples/2d/elixir_advection_waving_flag.jl → ..._2d_dgsem/elixir_advection_waving_flag.jl
diff --git a/examples/2d/elixir_euler_ec_curved.jl → ...es/structured_2d_dgsem/elixir_euler_ec.jl b/examples/2d/elixir_euler_ec_curved.jl → ...es/structured_2d_dgsem/elixir_euler_ec.jl
diff --git a/...les/2d/elixir_euler_free_stream_curved.jl → ...ured_2d_dgsem/elixir_euler_free_stream.jl b/...les/2d/elixir_euler_free_stream_curved.jl → ...ured_2d_dgsem/elixir_euler_free_stream.jl
diff --git a/...es/2d/elixir_euler_source_terms_curved.jl → ...red_2d_dgsem/elixir_euler_source_terms.jl b/...es/2d/elixir_euler_source_terms_curved.jl → ...red_2d_dgsem/elixir_euler_source_terms.jl
diff --git a/...les/2d/elixir_euler_nonperiodic_curved.jl → .../elixir_euler_source_terms_nonperiodic.jl b/...les/2d/elixir_euler_nonperiodic_curved.jl → .../elixir_euler_source_terms_nonperiodic.jl
@@ -9,8 +9,6 @@ equations = CompressibleEulerEquations2D(1.4)
 
 initial_condition = initial_condition_convergence_test
 
-source_terms = source_terms_convergence_test
-
 # you can either use a single function to impose the BCs weakly in all
 # 2*ndims == 4 directions or you can pass a tuple containing BCs for each direction
 boundary_condition = BoundaryConditionDirichlet(initial_condition)
@@ -26,7 +24,7 @@ coordinates_max = (2.0, 2.0)
 mesh = CurvedMesh((16, 16), coordinates_min, coordinates_max, periodicity=false)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
-                                    source_terms=source_terms,
+                                    source_terms=source_terms_convergence_test,
                                     boundary_conditions=boundary_conditions)
 
 

diff --git a/...lixir_euler_source_terms_parallelogram.jl → ...lixir_euler_source_terms_parallelogram.jl b/...lixir_euler_source_terms_parallelogram.jl → ...lixir_euler_source_terms_parallelogram.jl
diff --git a/...s/2d/elixir_euler_source_terms_rotated.jl → ...gsem/elixir_euler_source_terms_rotated.jl b/...s/2d/elixir_euler_source_terms_rotated.jl → ...gsem/elixir_euler_source_terms_rotated.jl
diff --git a/.../elixir_euler_source_terms_waving_flag.jl → .../elixir_euler_source_terms_waving_flag.jl b/.../elixir_euler_source_terms_waving_flag.jl → .../elixir_euler_source_terms_waving_flag.jl
diff --git a/...s/2d/elixir_hypdiff_nonperiodic_curved.jl → ...ed_2d_dgsem/elixir_hypdiff_nonperiodic.jl b/...s/2d/elixir_hypdiff_nonperiodic_curved.jl → ...ed_2d_dgsem/elixir_hypdiff_nonperiodic.jl
diff --git a/examples/2d/elixir_mhd_alfven_wave_curved.jl → ...ctured_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/2d/elixir_mhd_alfven_wave_curved.jl → ...ctured_2d_dgsem/elixir_mhd_alfven_wave.jl
diff --git a/examples/2d/elixir_mhd_ec_curved.jl → ...ples/structured_2d_dgsem/elixir_mhd_ec.jl b/examples/2d/elixir_mhd_ec_curved.jl → ...ples/structured_2d_dgsem/elixir_mhd_ec.jl
diff --git a/examples/3d/elixir_advection_basic_curved.jl → ...ctured_3d_dgsem/elixir_advection_basic.jl b/examples/3d/elixir_advection_basic_curved.jl → ...ctured_3d_dgsem/elixir_advection_basic.jl
diff --git a/...3d/elixir_advection_free_stream_curved.jl → ..._3d_dgsem/elixir_advection_free_stream.jl b/...3d/elixir_advection_free_stream_curved.jl → ..._3d_dgsem/elixir_advection_free_stream.jl
diff --git a/...3d/elixir_advection_nonperiodic_curved.jl → ..._3d_dgsem/elixir_advection_nonperiodic.jl b/...3d/elixir_advection_nonperiodic_curved.jl → ..._3d_dgsem/elixir_advection_nonperiodic.jl
diff --git a/...les/3d/elixir_advection_restart_curved.jl → ...ured_3d_dgsem/elixir_advection_restart.jl b/...les/3d/elixir_advection_restart_curved.jl → ...ured_3d_dgsem/elixir_advection_restart.jl
@@ -5,7 +5,7 @@ using Trixi
 ###############################################################################
 # create a restart file
 
-trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_basic_curved.jl"), 
+trixi_include(@__MODULE__, joinpath(@__DIR__, "elixir_advection_basic.jl"),
               cells_per_dimension=(4, 4, 4))
 
 

diff --git a/examples/3d/elixir_euler_ec_curved.jl → ...es/structured_3d_dgsem/elixir_euler_ec.jl b/examples/3d/elixir_euler_ec_curved.jl → ...es/structured_3d_dgsem/elixir_euler_ec.jl
diff --git a/...les/3d/elixir_euler_free_stream_curved.jl → ...ured_3d_dgsem/elixir_euler_free_stream.jl b/...les/3d/elixir_euler_free_stream_curved.jl → ...ured_3d_dgsem/elixir_euler_free_stream.jl
diff --git a/...es/3d/elixir_euler_source_terms_curved.jl → ...red_3d_dgsem/elixir_euler_source_terms.jl b/...es/3d/elixir_euler_source_terms_curved.jl → ...red_3d_dgsem/elixir_euler_source_terms.jl
diff --git a/...les/3d/elixir_euler_nonperiodic_curved.jl → .../elixir_euler_source_terms_nonperiodic.jl b/...les/3d/elixir_euler_nonperiodic_curved.jl → .../elixir_euler_source_terms_nonperiodic.jl
diff --git a/examples/3d/elixir_mhd_alfven_wave_curved.jl → ...ctured_3d_dgsem/elixir_mhd_alfven_wave.jl b/examples/3d/elixir_mhd_alfven_wave_curved.jl → ...ctured_3d_dgsem/elixir_mhd_alfven_wave.jl
diff --git a/examples/3d/elixir_mhd_ec_curved.jl → ...ples/structured_3d_dgsem/elixir_mhd_ec.jl b/examples/3d/elixir_mhd_ec_curved.jl → ...ples/structured_3d_dgsem/elixir_mhd_ec.jl
diff --git a/examples/1d/elixir_advection_amr.jl → ...les/tree_1d_dgsem/elixir_advection_amr.jl b/examples/1d/elixir_advection_amr.jl → ...les/tree_1d_dgsem/elixir_advection_amr.jl
diff --git a/...es/1d/elixir_advection_amr_nonperiodic.jl → ...dgsem/elixir_advection_amr_nonperiodic.jl b/...es/1d/elixir_advection_amr_nonperiodic.jl → ...dgsem/elixir_advection_amr_nonperiodic.jl
diff --git a/examples/1d/elixir_advection_basic.jl → ...s/tree_1d_dgsem/elixir_advection_basic.jl b/examples/1d/elixir_advection_basic.jl → ...s/tree_1d_dgsem/elixir_advection_basic.jl
diff --git a/examples/1d/elixir_advection_extended.jl → ...ree_1d_dgsem/elixir_advection_extended.jl b/examples/1d/elixir_advection_extended.jl → ...ree_1d_dgsem/elixir_advection_extended.jl
diff --git a/examples/1d/elixir_burgers_basic.jl → ...les/tree_1d_dgsem/elixir_burgers_basic.jl b/examples/1d/elixir_burgers_basic.jl → ...les/tree_1d_dgsem/elixir_burgers_basic.jl
diff --git a/...les/1d/elixir_burgers_linear_stability.jl → ..._dgsem/elixir_burgers_linear_stability.jl b/...les/1d/elixir_burgers_linear_stability.jl → ..._dgsem/elixir_burgers_linear_stability.jl
diff --git a/examples/1d/elixir_euler_blast_wave.jl → .../tree_1d_dgsem/elixir_euler_blast_wave.jl b/examples/1d/elixir_euler_blast_wave.jl → .../tree_1d_dgsem/elixir_euler_blast_wave.jl
diff --git a/.../elixir_euler_convergence_test_pure_fv.jl → ...dgsem/elixir_euler_convergence_pure_fv.jl b/.../elixir_euler_convergence_test_pure_fv.jl → ...dgsem/elixir_euler_convergence_pure_fv.jl
diff --git a/examples/1d/elixir_euler_density_wave.jl → ...ree_1d_dgsem/elixir_euler_density_wave.jl b/examples/1d/elixir_euler_density_wave.jl → ...ree_1d_dgsem/elixir_euler_density_wave.jl
diff --git a/examples/1d/elixir_euler_ec.jl → examples/tree_1d_dgsem/elixir_euler_ec.jl b/examples/1d/elixir_euler_ec.jl → examples/tree_1d_dgsem/elixir_euler_ec.jl
diff --git a/examples/1d/elixir_euler_positivity.jl → .../tree_1d_dgsem/elixir_euler_positivity.jl b/examples/1d/elixir_euler_positivity.jl → .../tree_1d_dgsem/elixir_euler_positivity.jl
diff --git a/examples/1d/elixir_euler_sedov_blast_wave.jl → ...1d_dgsem/elixir_euler_sedov_blast_wave.jl b/examples/1d/elixir_euler_sedov_blast_wave.jl → ...1d_dgsem/elixir_euler_sedov_blast_wave.jl
diff --git a/.../elixir_euler_sedov_blast_wave_pure_fv.jl → .../elixir_euler_sedov_blast_wave_pure_fv.jl b/.../elixir_euler_sedov_blast_wave_pure_fv.jl → .../elixir_euler_sedov_blast_wave_pure_fv.jl
diff --git a/examples/1d/elixir_euler_shockcapturing.jl → ...e_1d_dgsem/elixir_euler_shockcapturing.jl b/examples/1d/elixir_euler_shockcapturing.jl → ...e_1d_dgsem/elixir_euler_shockcapturing.jl
diff --git a/examples/1d/elixir_euler_source_terms.jl → ...ree_1d_dgsem/elixir_euler_source_terms.jl b/examples/1d/elixir_euler_source_terms.jl → ...ree_1d_dgsem/elixir_euler_source_terms.jl
diff --git a/examples/1d/elixir_euler_nonperiodic.jl → .../elixir_euler_source_terms_nonperiodic.jl b/examples/1d/elixir_euler_nonperiodic.jl → .../elixir_euler_source_terms_nonperiodic.jl
@@ -9,8 +9,6 @@ equations = CompressibleEulerEquations1D(1.4)
 
 initial_condition = initial_condition_convergence_test
 
-source_terms = source_terms_convergence_test
-
 # you can either use a single function to impose the BCs weakly in all
 # 1*ndims == 2 directions or you can pass a tuple containing BCs for
 # each direction
@@ -29,7 +27,7 @@ mesh = TreeMesh(coordinates_min, coordinates_max,
 
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
-                                    source_terms=source_terms,
+                                    source_terms=source_terms_convergence_test,
                                     boundary_conditions=boundary_conditions)
 
 

diff --git a/examples/1d/elixir_eulergravity_eoc_test.jl → ..._dgsem/elixir_eulergravity_convergence.jl b/examples/1d/elixir_eulergravity_eoc_test.jl → ..._dgsem/elixir_eulergravity_convergence.jl
diff --git a/examples/1d/elixir_eulermulti_eoc_ec.jl → ...dgsem/elixir_eulermulti_convergence_ec.jl b/examples/1d/elixir_eulermulti_eoc_ec.jl → ...dgsem/elixir_eulermulti_convergence_ec.jl
diff --git a/examples/1d/elixir_eulermulti_eoc_es.jl → ...dgsem/elixir_eulermulti_convergence_es.jl b/examples/1d/elixir_eulermulti_eoc_es.jl → ...dgsem/elixir_eulermulti_convergence_es.jl
diff --git a/examples/1d/elixir_eulermulti_ec.jl → ...les/tree_1d_dgsem/elixir_eulermulti_ec.jl b/examples/1d/elixir_eulermulti_ec.jl → ...les/tree_1d_dgsem/elixir_eulermulti_ec.jl
diff --git a/examples/1d/elixir_eulermulti_es.jl → ...les/tree_1d_dgsem/elixir_eulermulti_es.jl b/examples/1d/elixir_eulermulti_es.jl → ...les/tree_1d_dgsem/elixir_eulermulti_es.jl
diff --git a/...eulermulti_two_interacting_blast_waves.jl → ...eulermulti_two_interacting_blast_waves.jl b/...eulermulti_two_interacting_blast_waves.jl → ...eulermulti_two_interacting_blast_waves.jl
diff --git a/...1d/elixir_hypdiff_harmonic_nonperiodic.jl → ...em/elixir_hypdiff_harmonic_nonperiodic.jl b/...1d/elixir_hypdiff_harmonic_nonperiodic.jl → ...em/elixir_hypdiff_harmonic_nonperiodic.jl
diff --git a/examples/1d/elixir_hypdiff_nonperiodic.jl → ...ee_1d_dgsem/elixir_hypdiff_nonperiodic.jl b/examples/1d/elixir_hypdiff_nonperiodic.jl → ...ee_1d_dgsem/elixir_hypdiff_nonperiodic.jl
diff --git a/examples/1d/elixir_mhd_alfven_wave.jl → ...s/tree_1d_dgsem/elixir_mhd_alfven_wave.jl b/examples/1d/elixir_mhd_alfven_wave.jl → ...s/tree_1d_dgsem/elixir_mhd_alfven_wave.jl
diff --git a/examples/1d/elixir_mhd_briowu_shock_tube.jl → ..._1d_dgsem/elixir_mhd_briowu_shock_tube.jl b/examples/1d/elixir_mhd_briowu_shock_tube.jl → ..._1d_dgsem/elixir_mhd_briowu_shock_tube.jl
diff --git a/examples/1d/elixir_mhd_ec.jl → examples/tree_1d_dgsem/elixir_mhd_ec.jl b/examples/1d/elixir_mhd_ec.jl → examples/tree_1d_dgsem/elixir_mhd_ec.jl
diff --git a/...ples/1d/elixir_mhd_ryujones_shock_tube.jl → ...d_dgsem/elixir_mhd_ryujones_shock_tube.jl b/...ples/1d/elixir_mhd_ryujones_shock_tube.jl → ...d_dgsem/elixir_mhd_ryujones_shock_tube.jl
diff --git a/...les/1d/elixir_mhd_shu_osher_shock_tube.jl → ..._dgsem/elixir_mhd_shu_osher_shock_tube.jl b/...les/1d/elixir_mhd_shu_osher_shock_tube.jl → ..._dgsem/elixir_mhd_shu_osher_shock_tube.jl
diff --git a/...les/1d/elixir_mhd_torrilhon_shock_tube.jl → ..._dgsem/elixir_mhd_torrilhon_shock_tube.jl b/...les/1d/elixir_mhd_torrilhon_shock_tube.jl → ..._dgsem/elixir_mhd_torrilhon_shock_tube.jl
diff --git a/...s/1d/elixir_mhdmulti_briowu_shock_tube.jl → ...gsem/elixir_mhdmulti_briowu_shock_tube.jl b/...s/1d/elixir_mhdmulti_briowu_shock_tube.jl → ...gsem/elixir_mhdmulti_briowu_shock_tube.jl
diff --git a/examples/1d/elixir_mhdmulti_eoc.jl → ...e_1d_dgsem/elixir_mhdmulti_convergence.jl b/examples/1d/elixir_mhdmulti_eoc.jl → ...e_1d_dgsem/elixir_mhdmulti_convergence.jl
diff --git a/examples/1d/elixir_mhdmulti_ec.jl → examples/tree_1d_dgsem/elixir_mhdmulti_ec.jl b/examples/1d/elixir_mhdmulti_ec.jl → examples/tree_1d_dgsem/elixir_mhdmulti_ec.jl
diff --git a/examples/1d/elixir_mhdmulti_es.jl → examples/tree_1d_dgsem/elixir_mhdmulti_es.jl b/examples/1d/elixir_mhdmulti_es.jl → examples/tree_1d_dgsem/elixir_mhdmulti_es.jl
diff --git a/examples/2d/elixir_advection_amr.jl → ...les/tree_2d_dgsem/elixir_advection_amr.jl b/examples/2d/elixir_advection_amr.jl → ...les/tree_2d_dgsem/elixir_advection_amr.jl
diff --git a/.../2d/elixir_advection_amr_coarsen_twice.jl → ...sem/elixir_advection_amr_coarsen_twice.jl b/.../2d/elixir_advection_amr_coarsen_twice.jl → ...sem/elixir_advection_amr_coarsen_twice.jl
diff --git a/...es/2d/elixir_advection_amr_nonperiodic.jl → ...dgsem/elixir_advection_amr_nonperiodic.jl b/...es/2d/elixir_advection_amr_nonperiodic.jl → ...dgsem/elixir_advection_amr_nonperiodic.jl
diff --git a/...s/2d/elixir_advection_amr_refine_twice.jl → ...gsem/elixir_advection_amr_refine_twice.jl b/...s/2d/elixir_advection_amr_refine_twice.jl → ...gsem/elixir_advection_amr_refine_twice.jl
diff --git a/...xir_advection_amr_solution_independent.jl → ...xir_advection_amr_solution_independent.jl b/...xir_advection_amr_solution_independent.jl → ...xir_advection_amr_solution_independent.jl
diff --git a/.../2d/elixir_advection_amr_visualization.jl → ...sem/elixir_advection_amr_visualization.jl b/.../2d/elixir_advection_amr_visualization.jl → ...sem/elixir_advection_amr_visualization.jl
diff --git a/examples/2d/elixir_advection_basic.jl → ...s/tree_2d_dgsem/elixir_advection_basic.jl b/examples/2d/elixir_advection_basic.jl → ...s/tree_2d_dgsem/elixir_advection_basic.jl
diff --git a/examples/2d/elixir_advection_callbacks.jl → ...ee_2d_dgsem/elixir_advection_callbacks.jl b/examples/2d/elixir_advection_callbacks.jl → ...ee_2d_dgsem/elixir_advection_callbacks.jl
diff --git a/examples/2d/elixir_advection_extended.jl → ...ree_2d_dgsem/elixir_advection_extended.jl b/examples/2d/elixir_advection_extended.jl → ...ree_2d_dgsem/elixir_advection_extended.jl
diff --git a/examples/2d/elixir_advection_mortar.jl → .../tree_2d_dgsem/elixir_advection_mortar.jl b/examples/2d/elixir_advection_mortar.jl → .../tree_2d_dgsem/elixir_advection_mortar.jl
diff --git a/examples/2d/elixir_advection_restart.jl → ...tree_2d_dgsem/elixir_advection_restart.jl b/examples/2d/elixir_advection_restart.jl → ...tree_2d_dgsem/elixir_advection_restart.jl
diff --git a/...es/2d/elixir_advection_timeintegration.jl → ...dgsem/elixir_advection_timeintegration.jl b/...es/2d/elixir_advection_timeintegration.jl → ...dgsem/elixir_advection_timeintegration.jl
diff --git a/examples/2d/elixir_ape_convergence_test.jl → ...s/tree_2d_dgsem/elixir_ape_convergence.jl b/examples/2d/elixir_ape_convergence_test.jl → ...s/tree_2d_dgsem/elixir_ape_convergence.jl
diff --git a/examples/2d/elixir_ape_gauss.jl → examples/tree_2d_dgsem/elixir_ape_gauss.jl b/examples/2d/elixir_ape_gauss.jl → examples/tree_2d_dgsem/elixir_ape_gauss.jl
diff --git a/examples/2d/elixir_ape_gauss_wall.jl → ...es/tree_2d_dgsem/elixir_ape_gauss_wall.jl b/examples/2d/elixir_ape_gauss_wall.jl → ...es/tree_2d_dgsem/elixir_ape_gauss_wall.jl
diff --git a/examples/2d/elixir_ape_gaussian_source.jl → ...ee_2d_dgsem/elixir_ape_gaussian_source.jl b/examples/2d/elixir_ape_gaussian_source.jl → ...ee_2d_dgsem/elixir_ape_gaussian_source.jl
diff --git a/examples/2d/elixir_ape_monopole.jl → ...ples/tree_2d_dgsem/elixir_ape_monopole.jl b/examples/2d/elixir_ape_monopole.jl → ...ples/tree_2d_dgsem/elixir_ape_monopole.jl
diff --git a/examples/2d/elixir_euler_blast_wave.jl → .../tree_2d_dgsem/elixir_euler_blast_wave.jl b/examples/2d/elixir_euler_blast_wave.jl → .../tree_2d_dgsem/elixir_euler_blast_wave.jl
diff --git a/examples/2d/elixir_euler_blast_wave_amr.jl → ...e_2d_dgsem/elixir_euler_blast_wave_amr.jl b/examples/2d/elixir_euler_blast_wave_amr.jl → ...e_2d_dgsem/elixir_euler_blast_wave_amr.jl
diff --git a/...les/2d/elixir_euler_blast_wave_pure_fv.jl → ..._dgsem/elixir_euler_blast_wave_pure_fv.jl b/...les/2d/elixir_euler_blast_wave_pure_fv.jl → ..._dgsem/elixir_euler_blast_wave_pure_fv.jl
diff --git a/examples/2d/elixir_euler_blob_amr.jl → ...es/tree_2d_dgsem/elixir_euler_blob_amr.jl b/examples/2d/elixir_euler_blob_amr.jl → ...es/tree_2d_dgsem/elixir_euler_blob_amr.jl
diff --git a/examples/2d/elixir_euler_blob_mortar.jl → ...tree_2d_dgsem/elixir_euler_blob_mortar.jl b/examples/2d/elixir_euler_blob_mortar.jl → ...tree_2d_dgsem/elixir_euler_blob_mortar.jl
diff --git a/.../elixir_euler_convergence_test_pure_fv.jl → ...dgsem/elixir_euler_convergence_pure_fv.jl b/.../elixir_euler_convergence_test_pure_fv.jl → ...dgsem/elixir_euler_convergence_pure_fv.jl
diff --git a/examples/2d/elixir_euler_density_wave.jl → ...ree_2d_dgsem/elixir_euler_density_wave.jl b/examples/2d/elixir_euler_density_wave.jl → ...ree_2d_dgsem/elixir_euler_density_wave.jl
diff --git a/examples/2d/elixir_euler_ec.jl → examples/tree_2d_dgsem/elixir_euler_ec.jl b/examples/2d/elixir_euler_ec.jl → examples/tree_2d_dgsem/elixir_euler_ec.jl
diff --git a/...xir_euler_kelvin_helmholtz_instability.jl → ...xir_euler_kelvin_helmholtz_instability.jl b/...xir_euler_kelvin_helmholtz_instability.jl → ...xir_euler_kelvin_helmholtz_instability.jl
diff --git a/...euler_kelvin_helmholtz_instability_amr.jl → ...euler_kelvin_helmholtz_instability_amr.jl b/...euler_kelvin_helmholtz_instability_amr.jl → ...euler_kelvin_helmholtz_instability_amr.jl
diff --git a/examples/2d/elixir_euler_positivity.jl → .../tree_2d_dgsem/elixir_euler_positivity.jl b/examples/2d/elixir_euler_positivity.jl → .../tree_2d_dgsem/elixir_euler_positivity.jl
diff --git a/examples/2d/elixir_euler_sedov_blast_wave.jl → ...2d_dgsem/elixir_euler_sedov_blast_wave.jl b/examples/2d/elixir_euler_sedov_blast_wave.jl → ...2d_dgsem/elixir_euler_sedov_blast_wave.jl
diff --git a/examples/2d/elixir_euler_shockcapturing.jl → ...e_2d_dgsem/elixir_euler_shockcapturing.jl b/examples/2d/elixir_euler_shockcapturing.jl → ...e_2d_dgsem/elixir_euler_shockcapturing.jl
diff --git a/examples/2d/elixir_euler_source_terms.jl → ...ree_2d_dgsem/elixir_euler_source_terms.jl b/examples/2d/elixir_euler_source_terms.jl → ...ree_2d_dgsem/elixir_euler_source_terms.jl
diff --git a/..._euler_source_terms_amr_refine_coarsen.jl → ..._euler_source_terms_amr_refine_coarsen.jl b/..._euler_source_terms_amr_refine_coarsen.jl → ..._euler_source_terms_amr_refine_coarsen.jl
diff --git a/examples/2d/elixir_euler_nonperiodic.jl → .../elixir_euler_source_terms_nonperiodic.jl b/examples/2d/elixir_euler_nonperiodic.jl → .../elixir_euler_source_terms_nonperiodic.jl
@@ -9,17 +9,17 @@ equations = CompressibleEulerEquations2D(1.4)
 
 initial_condition = initial_condition_convergence_test
 
-source_terms = source_terms_convergence_test
-
 # you can either use a single function to impose the BCs weakly in all
 # 2*ndims == 4 directions or you can pass a tuple containing BCs for each direction
 boundary_condition = BoundaryConditionDirichlet(initial_condition)
 boundary_conditions = (x_neg=boundary_condition,
                        x_pos=boundary_condition,
                        y_neg=boundary_condition,
                        y_pos=boundary_condition,)
+
 solver = DGSEM(polydeg=3, surface_flux=flux_lax_friedrichs)
 
+
 coordinates_min = (0, 0)
 coordinates_max = (2, 2)
 mesh = TreeMesh(coordinates_min, coordinates_max,
@@ -29,7 +29,7 @@ mesh = TreeMesh(coordinates_min, coordinates_max,
 
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver,
-                                    source_terms=source_terms,
+                                    source_terms=source_terms_convergence_test,
                                     boundary_conditions=boundary_conditions)
 
 

diff --git a/examples/2d/elixir_euler_vortex.jl → ...ples/tree_2d_dgsem/elixir_euler_vortex.jl b/examples/2d/elixir_euler_vortex.jl → ...ples/tree_2d_dgsem/elixir_euler_vortex.jl
diff --git a/examples/2d/elixir_euler_vortex_amr.jl → .../tree_2d_dgsem/elixir_euler_vortex_amr.jl b/examples/2d/elixir_euler_vortex_amr.jl → .../tree_2d_dgsem/elixir_euler_vortex_amr.jl
diff --git a/examples/2d/elixir_euler_vortex_mortar.jl → ...ee_2d_dgsem/elixir_euler_vortex_mortar.jl b/examples/2d/elixir_euler_vortex_mortar.jl → ...ee_2d_dgsem/elixir_euler_vortex_mortar.jl
diff --git a/...xir_euler_vortex_mortar_shockcapturing.jl → ...xir_euler_vortex_mortar_shockcapturing.jl b/...xir_euler_vortex_mortar_shockcapturing.jl → ...xir_euler_vortex_mortar_shockcapturing.jl
diff --git a/...es/2d/elixir_euler_vortex_mortar_split.jl → ...dgsem/elixir_euler_vortex_mortar_split.jl b/...es/2d/elixir_euler_vortex_mortar_split.jl → ...dgsem/elixir_euler_vortex_mortar_split.jl
diff --git a/.../2d/elixir_euler_vortex_shockcapturing.jl → ...sem/elixir_euler_vortex_shockcapturing.jl b/.../2d/elixir_euler_vortex_shockcapturing.jl → ...sem/elixir_euler_vortex_shockcapturing.jl
diff --git a/examples/2d/elixir_eulermulti_eoc_ec.jl → ...dgsem/elixir_eulermulti_convergence_ec.jl b/examples/2d/elixir_eulermulti_eoc_ec.jl → ...dgsem/elixir_eulermulti_convergence_ec.jl
diff --git a/examples/2d/elixir_eulermulti_eoc_es.jl → ...dgsem/elixir_eulermulti_convergence_es.jl b/examples/2d/elixir_eulermulti_eoc_es.jl → ...dgsem/elixir_eulermulti_convergence_es.jl
diff --git a/examples/2d/elixir_eulermulti_ec.jl → ...les/tree_2d_dgsem/elixir_eulermulti_ec.jl b/examples/2d/elixir_eulermulti_ec.jl → ...les/tree_2d_dgsem/elixir_eulermulti_ec.jl
diff --git a/examples/2d/elixir_eulermulti_es.jl → ...les/tree_2d_dgsem/elixir_eulermulti_es.jl b/examples/2d/elixir_eulermulti_es.jl → ...les/tree_2d_dgsem/elixir_eulermulti_es.jl
diff --git a/...ples/2d/elixir_eulermulti_shock_bubble.jl → ...d_dgsem/elixir_eulermulti_shock_bubble.jl b/...ples/2d/elixir_eulermulti_shock_bubble.jl → ...d_dgsem/elixir_eulermulti_shock_bubble.jl
diff --git a/...ir_eulermulti_shock_bubble_3components.jl → ...ir_eulermulti_shock_bubble_3components.jl b/...ir_eulermulti_shock_bubble_3components.jl → ...ir_eulermulti_shock_bubble_3components.jl
diff --git a/...ir_eulermulti_shock_bubble_7components.jl → ...ir_eulermulti_shock_bubble_7components.jl b/...ir_eulermulti_shock_bubble_7components.jl → ...ir_eulermulti_shock_bubble_7components.jl
diff --git a/.../2d/elixir_eulermulti_shock_bubble_amr.jl → ...sem/elixir_eulermulti_shock_bubble_amr.jl b/.../2d/elixir_eulermulti_shock_bubble_amr.jl → ...sem/elixir_eulermulti_shock_bubble_amr.jl
diff --git a/examples/2d/elixir_hypdiff_godunov.jl → ...s/tree_2d_dgsem/elixir_hypdiff_godunov.jl b/examples/2d/elixir_hypdiff_godunov.jl → ...s/tree_2d_dgsem/elixir_hypdiff_godunov.jl
diff --git a/...2d/elixir_hypdiff_harmonic_nonperiodic.jl → ...em/elixir_hypdiff_harmonic_nonperiodic.jl b/...2d/elixir_hypdiff_harmonic_nonperiodic.jl → ...em/elixir_hypdiff_harmonic_nonperiodic.jl
diff --git a/examples/2d/elixir_hypdiff_lax_friedrichs.jl → ...2d_dgsem/elixir_hypdiff_lax_friedrichs.jl b/examples/2d/elixir_hypdiff_lax_friedrichs.jl → ...2d_dgsem/elixir_hypdiff_lax_friedrichs.jl
diff --git a/examples/2d/elixir_hypdiff_nonperiodic.jl → ...ee_2d_dgsem/elixir_hypdiff_nonperiodic.jl b/examples/2d/elixir_hypdiff_nonperiodic.jl → ...ee_2d_dgsem/elixir_hypdiff_nonperiodic.jl
diff --git a/examples/2d/elixir_lbm_constant.jl → ...ples/tree_2d_dgsem/elixir_lbm_constant.jl b/examples/2d/elixir_lbm_constant.jl → ...ples/tree_2d_dgsem/elixir_lbm_constant.jl
diff --git a/examples/2d/elixir_lbm_couette.jl → examples/tree_2d_dgsem/elixir_lbm_couette.jl b/examples/2d/elixir_lbm_couette.jl → examples/tree_2d_dgsem/elixir_lbm_couette.jl
diff --git a/examples/2d/elixir_lbm_lid_driven_cavity.jl → ..._2d_dgsem/elixir_lbm_lid_driven_cavity.jl b/examples/2d/elixir_lbm_lid_driven_cavity.jl → ..._2d_dgsem/elixir_lbm_lid_driven_cavity.jl
diff --git a/examples/2d/elixir_mhd_alfven_wave.jl → ...s/tree_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/2d/elixir_mhd_alfven_wave.jl → ...s/tree_2d_dgsem/elixir_mhd_alfven_wave.jl
diff --git a/examples/2d/elixir_mhd_alfven_wave_mortar.jl → ...2d_dgsem/elixir_mhd_alfven_wave_mortar.jl b/examples/2d/elixir_mhd_alfven_wave_mortar.jl → ...2d_dgsem/elixir_mhd_alfven_wave_mortar.jl
diff --git a/examples/2d/elixir_mhd_blast_wave.jl → ...es/tree_2d_dgsem/elixir_mhd_blast_wave.jl b/examples/2d/elixir_mhd_blast_wave.jl → ...es/tree_2d_dgsem/elixir_mhd_blast_wave.jl
diff --git a/examples/2d/elixir_mhd_ec.jl → examples/tree_2d_dgsem/elixir_mhd_ec.jl b/examples/2d/elixir_mhd_ec.jl → examples/tree_2d_dgsem/elixir_mhd_ec.jl
diff --git a/examples/2d/elixir_mhd_orszag_tang.jl → ...s/tree_2d_dgsem/elixir_mhd_orszag_tang.jl b/examples/2d/elixir_mhd_orszag_tang.jl → ...s/tree_2d_dgsem/elixir_mhd_orszag_tang.jl
diff --git a/examples/2d/elixir_mhd_rotor.jl → examples/tree_2d_dgsem/elixir_mhd_rotor.jl b/examples/2d/elixir_mhd_rotor.jl → examples/tree_2d_dgsem/elixir_mhd_rotor.jl
diff --git a/examples/2d/elixir_mhdmulti_eoc.jl → ...e_2d_dgsem/elixir_mhdmulti_convergence.jl b/examples/2d/elixir_mhdmulti_eoc.jl → ...e_2d_dgsem/elixir_mhdmulti_convergence.jl
diff --git a/examples/2d/elixir_mhdmulti_ec.jl → examples/tree_2d_dgsem/elixir_mhdmulti_ec.jl b/examples/2d/elixir_mhdmulti_ec.jl → examples/tree_2d_dgsem/elixir_mhdmulti_ec.jl
diff --git a/examples/2d/elixir_mhdmulti_es.jl → examples/tree_2d_dgsem/elixir_mhdmulti_es.jl b/examples/2d/elixir_mhdmulti_es.jl → examples/tree_2d_dgsem/elixir_mhdmulti_es.jl
diff --git a/examples/2d/elixir_mhdmulti_rotor.jl → ...es/tree_2d_dgsem/elixir_mhdmulti_rotor.jl b/examples/2d/elixir_mhdmulti_rotor.jl → ...es/tree_2d_dgsem/elixir_mhdmulti_rotor.jl
diff --git a/examples/3d/elixir_advection_amr.jl → ...les/tree_3d_dgsem/elixir_advection_amr.jl b/examples/3d/elixir_advection_amr.jl → ...les/tree_3d_dgsem/elixir_advection_amr.jl
diff --git a/examples/3d/elixir_advection_basic.jl → ...s/tree_3d_dgsem/elixir_advection_basic.jl b/examples/3d/elixir_advection_basic.jl → ...s/tree_3d_dgsem/elixir_advection_basic.jl
diff --git a/examples/3d/elixir_advection_extended.jl → ...ree_3d_dgsem/elixir_advection_extended.jl b/examples/3d/elixir_advection_extended.jl → ...ree_3d_dgsem/elixir_advection_extended.jl
diff --git a/examples/3d/elixir_advection_mortar.jl → .../tree_3d_dgsem/elixir_advection_mortar.jl b/examples/3d/elixir_advection_mortar.jl → .../tree_3d_dgsem/elixir_advection_mortar.jl
diff --git a/examples/3d/elixir_advection_restart.jl → ...tree_3d_dgsem/elixir_advection_restart.jl b/examples/3d/elixir_advection_restart.jl → ...tree_3d_dgsem/elixir_advection_restart.jl
diff --git a/examples/3d/elixir_euler_amr.jl → examples/tree_3d_dgsem/elixir_euler_amr.jl b/examples/3d/elixir_euler_amr.jl → examples/tree_3d_dgsem/elixir_euler_amr.jl
diff --git a/examples/3d/elixir_euler_blob_amr.jl → ...es/tree_3d_dgsem/elixir_euler_blob_amr.jl b/examples/3d/elixir_euler_blob_amr.jl → ...es/tree_3d_dgsem/elixir_euler_blob_amr.jl
diff --git a/examples/3d/elixir_euler_eoc_test.jl → ...tree_3d_dgsem/elixir_euler_convergence.jl b/examples/3d/elixir_euler_eoc_test.jl → ...tree_3d_dgsem/elixir_euler_convergence.jl
diff --git a/.../elixir_euler_convergence_test_pure_fv.jl → ...dgsem/elixir_euler_convergence_pure_fv.jl b/.../elixir_euler_convergence_test_pure_fv.jl → ...dgsem/elixir_euler_convergence_pure_fv.jl
diff --git a/examples/3d/elixir_euler_density_pulse.jl → ...ee_3d_dgsem/elixir_euler_density_pulse.jl b/examples/3d/elixir_euler_density_pulse.jl → ...ee_3d_dgsem/elixir_euler_density_pulse.jl
diff --git a/examples/3d/elixir_euler_ec.jl → examples/tree_3d_dgsem/elixir_euler_ec.jl b/examples/3d/elixir_euler_ec.jl → examples/tree_3d_dgsem/elixir_euler_ec.jl
diff --git a/examples/3d/elixir_euler_mortar.jl → ...ples/tree_3d_dgsem/elixir_euler_mortar.jl b/examples/3d/elixir_euler_mortar.jl → ...ples/tree_3d_dgsem/elixir_euler_mortar.jl
diff --git a/examples/3d/elixir_euler_sedov_blast_wave.jl → ...3d_dgsem/elixir_euler_sedov_blast_wave.jl b/examples/3d/elixir_euler_sedov_blast_wave.jl → ...3d_dgsem/elixir_euler_sedov_blast_wave.jl
diff --git a/examples/3d/elixir_euler_shockcapturing.jl → ...e_3d_dgsem/elixir_euler_shockcapturing.jl b/examples/3d/elixir_euler_shockcapturing.jl → ...e_3d_dgsem/elixir_euler_shockcapturing.jl
diff --git a/...les/3d/elixir_euler_shockcapturing_amr.jl → ..._dgsem/elixir_euler_shockcapturing_amr.jl b/...les/3d/elixir_euler_shockcapturing_amr.jl → ..._dgsem/elixir_euler_shockcapturing_amr.jl
diff --git a/examples/3d/elixir_euler_source_terms.jl → ...ree_3d_dgsem/elixir_euler_source_terms.jl b/examples/3d/elixir_euler_source_terms.jl → ...ree_3d_dgsem/elixir_euler_source_terms.jl
diff --git a/...es/3d/elixir_euler_taylor_green_vortex.jl → ...dgsem/elixir_euler_taylor_green_vortex.jl b/...es/3d/elixir_euler_taylor_green_vortex.jl → ...dgsem/elixir_euler_taylor_green_vortex.jl
diff --git a/examples/3d/elixir_eulergravity_eoc_test.jl → ..._dgsem/elixir_eulergravity_convergence.jl b/examples/3d/elixir_eulergravity_eoc_test.jl → ..._dgsem/elixir_eulergravity_convergence.jl
diff --git a/examples/3d/elixir_hypdiff_lax_friedrichs.jl → ...3d_dgsem/elixir_hypdiff_lax_friedrichs.jl b/examples/3d/elixir_hypdiff_lax_friedrichs.jl → ...3d_dgsem/elixir_hypdiff_lax_friedrichs.jl
diff --git a/examples/3d/elixir_hypdiff_nonperiodic.jl → ...ee_3d_dgsem/elixir_hypdiff_nonperiodic.jl b/examples/3d/elixir_hypdiff_nonperiodic.jl → ...ee_3d_dgsem/elixir_hypdiff_nonperiodic.jl
diff --git a/examples/3d/elixir_lbm_constant.jl → ...ples/tree_3d_dgsem/elixir_lbm_constant.jl b/examples/3d/elixir_lbm_constant.jl → ...ples/tree_3d_dgsem/elixir_lbm_constant.jl
diff --git a/...ples/3d/elixir_lbm_taylor_green_vortex.jl → ...d_dgsem/elixir_lbm_taylor_green_vortex.jl b/...ples/3d/elixir_lbm_taylor_green_vortex.jl → ...d_dgsem/elixir_lbm_taylor_green_vortex.jl
diff --git a/examples/3d/elixir_mhd_alfven_wave.jl → ...s/tree_3d_dgsem/elixir_mhd_alfven_wave.jl b/examples/3d/elixir_mhd_alfven_wave.jl → ...s/tree_3d_dgsem/elixir_mhd_alfven_wave.jl
diff --git a/examples/3d/elixir_mhd_alfven_wave_mortar.jl → ...3d_dgsem/elixir_mhd_alfven_wave_mortar.jl b/examples/3d/elixir_mhd_alfven_wave_mortar.jl → ...3d_dgsem/elixir_mhd_alfven_wave_mortar.jl
diff --git a/examples/3d/elixir_mhd_ec.jl → examples/tree_3d_dgsem/elixir_mhd_ec.jl b/examples/3d/elixir_mhd_ec.jl → examples/tree_3d_dgsem/elixir_mhd_ec.jl
diff --git a/...ixir_advection_unstructured_quad_basic.jl → ...ctured_2d_dgsem/elixir_advection_basic.jl b/...ixir_advection_unstructured_quad_basic.jl → ...ctured_2d_dgsem/elixir_advection_basic.jl
diff --git a/...lixir_ape_unstructured_quad_gauss_wall.jl → ...uctured_2d_dgsem/elixir_ape_gauss_wall.jl b/...lixir_ape_unstructured_quad_gauss_wall.jl → ...uctured_2d_dgsem/elixir_ape_gauss_wall.jl
diff --git a/...d/elixir_euler_unstructured_quad_basic.jl → ...structured_2d_dgsem/elixir_euler_basic.jl b/...d/elixir_euler_unstructured_quad_basic.jl → ...structured_2d_dgsem/elixir_euler_basic.jl
diff --git a/...s/2d/elixir_euler_unstructured_quad_ec.jl → .../unstructured_2d_dgsem/elixir_euler_ec.jl b/...s/2d/elixir_euler_unstructured_quad_ec.jl → .../unstructured_2d_dgsem/elixir_euler_ec.jl
diff --git a/...ir_euler_unstructured_quad_free_stream.jl → ...ured_2d_dgsem/elixir_euler_free_stream.jl b/...ir_euler_unstructured_quad_free_stream.jl → ...ured_2d_dgsem/elixir_euler_free_stream.jl
diff --git a/...lixir_euler_unstructured_quad_periodic.jl → ...uctured_2d_dgsem/elixir_euler_periodic.jl b/...lixir_euler_unstructured_quad_periodic.jl → ...uctured_2d_dgsem/elixir_euler_periodic.jl