trixi-framework · sloede · Oct 11, 2020 · Oct 9, 2020 · Oct 9, 2020 · Oct 9, 2020
diff --git a/docs/src/development.md b/docs/src/development.md
@@ -47,7 +47,7 @@ julia> using Revise; using Trixi
 ```
 You can run a simulation by executing
 ```julia
-julia> Trixi.run("examples/2d/parameters.toml")
+julia> Trixi.run("examples/2d/parameters_advection_basic.toml")
 ```
 Together, all of these commands can take some time, roughly half a minute on a
 modern workstation. Most of the time is spent on compilation of Julia code etc.

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -153,9 +153,9 @@ seconds, while subsequent runs require less than 50 *milli*seconds.
 To automatically determine the experimental order of convergence (EOC) for a
 given setup, execute
 ```julia
-Trixi.convtest("examples/2d/parameters.toml", 4)
+Trixi.convtest("examples/2d/parameters_advection_basic.toml", 4)
 ```
-This will run a convergence test with the parameters file `examples/2d/parameters.toml`,
+This will run a convergence test with the parameters file `examples/2d/parameters_advection_basic.toml`,
 using four iterations with different initial refinement levels. The initial
 iteration will use the parameters file unchanged, while for each subsequent
 iteration the `initial_refinement_level` parameter is incremented by one.
@@ -187,7 +187,7 @@ mean      3.99
 
 An example with multiple variables looks like this:
 ```julia
-julia> Trixi.convtest("examples/2d/parameters_source_terms.toml", 3)
+julia> Trixi.convtest("examples/2d/parameters_euler_source_terms.toml", 3)
 ```
 ```
 [...]

diff --git a/examples/1d/parameters_amr.jl → examples/1d/elixir_advection_amr.jl b/examples/1d/parameters_amr.jl → examples/1d/elixir_advection_amr.jl
@@ -1,7 +1,3 @@
-# TODO: Taal refactor, rename to
-# - linear_advection_amr.jl
-# - advection_amr.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/1d/parameters.jl → examples/1d/elixir_advection_basic.jl b/examples/1d/parameters.jl → examples/1d/elixir_advection_basic.jl
@@ -1,7 +1,3 @@
-# TODO: Taal refactor, rename to
-# - linear_advection.jl
-# - advection_basic.jl
-# or something similar? parameters.jl isn't really helpful...
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/...d/parameters_blast_wave_shockcapturing.jl → ...elixir_euler_blast_wave_shockcapturing.jl b/...d/parameters_blast_wave_shockcapturing.jl → ...elixir_euler_blast_wave_shockcapturing.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_blast_wave_shockcapturing.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/1d/parameters_ec.jl → examples/1d/elixir_euler_ec.jl b/examples/1d/parameters_ec.jl → examples/1d/elixir_euler_ec.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_ec.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/1d/parameters_nonperiodic.jl → examples/1d/elixir_euler_nonperiodic.jl b/examples/1d/parameters_nonperiodic.jl → examples/1d/elixir_euler_nonperiodic.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_nonperiodic.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/1d/parameters_source_terms.jl → examples/1d/elixir_euler_source_terms.jl b/examples/1d/parameters_source_terms.jl → examples/1d/elixir_euler_source_terms.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_source_terms.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/1d/parameters_amr.toml → examples/1d/parameters_advection_amr.toml b/examples/1d/parameters_amr.toml → examples/1d/parameters_advection_amr.toml
diff --git a/examples/1d/parameters_amr_nonperiodic.toml → ...parameters_advection_amr_nonperiodic.toml b/examples/1d/parameters_amr_nonperiodic.toml → ...parameters_advection_amr_nonperiodic.toml
diff --git a/examples/1d/parameters.toml → examples/1d/parameters_advection_basic.toml b/examples/1d/parameters.toml → examples/1d/parameters_advection_basic.toml
diff --git a/...parameters_blast_wave_shockcapturing.toml → ...ters_euler_blast_wave_shockcapturing.toml b/...parameters_blast_wave_shockcapturing.toml → ...ters_euler_blast_wave_shockcapturing.toml
diff --git a/examples/1d/parameters_density_wave.toml → ...les/1d/parameters_euler_density_wave.toml b/examples/1d/parameters_density_wave.toml → ...les/1d/parameters_euler_density_wave.toml
diff --git a/examples/1d/parameters_ec.toml → examples/1d/parameters_euler_ec.toml b/examples/1d/parameters_ec.toml → examples/1d/parameters_euler_ec.toml
diff --git a/examples/1d/parameters_nonperiodic.toml → ...ples/1d/parameters_euler_nonperiodic.toml b/examples/1d/parameters_nonperiodic.toml → ...ples/1d/parameters_euler_nonperiodic.toml
diff --git a/...ters_sedov_blast_wave_shockcapturing.toml → ...uler_sedov_blast_wave_shockcapturing.toml b/...ters_sedov_blast_wave_shockcapturing.toml → ...uler_sedov_blast_wave_shockcapturing.toml
diff --git a/examples/1d/parameters_source_terms.toml → ...les/1d/parameters_euler_source_terms.toml b/examples/1d/parameters_source_terms.toml → ...les/1d/parameters_euler_source_terms.toml
diff --git a/...eters_weak_blast_wave_shockcapturing.toml → ...euler_weak_blast_wave_shockcapturing.toml b/...eters_weak_blast_wave_shockcapturing.toml → ...euler_weak_blast_wave_shockcapturing.toml
diff --git a/examples/2d/parameters_amr.jl → examples/2d/elixir_advection_amr.jl b/examples/2d/parameters_amr.jl → examples/2d/elixir_advection_amr.jl
@@ -1,7 +1,3 @@
-# TODO: Taal refactor, rename to
-# - linear_advection_amr.jl
-# - advection_amr.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/parameters.jl → examples/2d/elixir_advection_basic.jl b/examples/2d/parameters.jl → examples/2d/elixir_advection_basic.jl
@@ -1,7 +1,3 @@
-# TODO: Taal refactor, rename to
-# - linear_advection.jl
-# - advection_basic.jl
-# or something similar? parameters.jl isn't really helpful...
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/parameters_mortar.jl → examples/2d/elixir_advection_mortar.jl b/examples/2d/parameters_mortar.jl → examples/2d/elixir_advection_mortar.jl
@@ -1,7 +1,3 @@
-# TODO: Taal refactor, rename to
-# - linear_advection_mortar.jl
-# - advection_mortar.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/...d/parameters_blast_wave_shockcapturing.jl → ...elixir_euler_blast_wave_shockcapturing.jl b/...d/parameters_blast_wave_shockcapturing.jl → ...elixir_euler_blast_wave_shockcapturing.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_blast_wave_shockcapturing.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/...rameters_blast_wave_shockcapturing_amr.jl → ...ir_euler_blast_wave_shockcapturing_amr.jl b/...rameters_blast_wave_shockcapturing_amr.jl → ...ir_euler_blast_wave_shockcapturing_amr.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_blast_wave_shockcapturing_amr.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/parameters_ec.jl → examples/2d/elixir_euler_ec.jl b/examples/2d/parameters_ec.jl → examples/2d/elixir_euler_ec.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_ec.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/jeans_instability.jl → ...elixir_euler_gravity_jeans_instability.jl b/examples/2d/jeans_instability.jl → ...elixir_euler_gravity_jeans_instability.jl
diff --git a/examples/2d/sedov_self_gravity.jl → .../elixir_euler_gravity_sedov_blast_wave.jl b/examples/2d/sedov_self_gravity.jl → .../elixir_euler_gravity_sedov_blast_wave.jl
diff --git a/examples/2d/parameters_nonperiodic.jl → examples/2d/elixir_euler_nonperiodic.jl b/examples/2d/parameters_nonperiodic.jl → examples/2d/elixir_euler_nonperiodic.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_nonperiodic.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/parameters_source_terms.jl → examples/2d/elixir_euler_source_terms.jl b/examples/2d/parameters_source_terms.jl → examples/2d/elixir_euler_source_terms.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - euler_source_terms.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/parameters_ec_mhd.jl → examples/2d/elixir_mhd_ec.jl b/examples/2d/parameters_ec_mhd.jl → examples/2d/elixir_mhd_ec.jl
@@ -1,6 +1,3 @@
-# TODO: Taal refactor, rename to
-# - mhd_ec.jl
-# or something similar?
 
 using OrdinaryDiffEq
 using Trixi

diff --git a/examples/2d/parameters_amr.toml → examples/2d/parameters_advection_amr.toml b/examples/2d/parameters_amr.toml → examples/2d/parameters_advection_amr.toml
diff --git a/examples/2d/parameters_amr_nonperiodic.toml → ...parameters_advection_amr_nonperiodic.toml b/examples/2d/parameters_amr_nonperiodic.toml → ...parameters_advection_amr_nonperiodic.toml
diff --git a/examples/2d/parameters.toml → examples/2d/parameters_advection_basic.toml b/examples/2d/parameters.toml → examples/2d/parameters_advection_basic.toml
diff --git a/examples/2d/parameters_mortar.toml → examples/2d/parameters_advection_mortar.toml b/examples/2d/parameters_mortar.toml → examples/2d/parameters_advection_mortar.toml
diff --git a/examples/2d/parameters_ec_performance_test.toml b/examples/2d/parameters_ec_performance_test.toml
diff --git a/...parameters_blast_wave_shockcapturing.toml → ...ters_euler_blast_wave_shockcapturing.toml b/...parameters_blast_wave_shockcapturing.toml → ...ters_euler_blast_wave_shockcapturing.toml
diff --git a/...meters_blast_wave_shockcapturing_amr.toml → ..._euler_blast_wave_shockcapturing_amr.toml b/...meters_blast_wave_shockcapturing_amr.toml → ..._euler_blast_wave_shockcapturing_amr.toml
diff --git a/examples/2d/parameters_blob.toml → examples/2d/parameters_euler_blob.toml b/examples/2d/parameters_blob.toml → examples/2d/parameters_euler_blob.toml
diff --git a/examples/2d/parameters_blob_amr.toml → examples/2d/parameters_euler_blob_amr.toml b/examples/2d/parameters_blob_amr.toml → examples/2d/parameters_euler_blob_amr.toml
diff --git a/examples/2d/parameters_density_wave.toml → ...les/2d/parameters_euler_density_wave.toml b/examples/2d/parameters_density_wave.toml → ...les/2d/parameters_euler_density_wave.toml
diff --git a/examples/2d/parameters_ec.toml → examples/2d/parameters_euler_ec.toml b/examples/2d/parameters_ec.toml → examples/2d/parameters_euler_ec.toml
diff --git a/examples/2d/parameters_ec_mortar.toml → examples/2d/parameters_euler_ec_mortar.toml b/examples/2d/parameters_ec_mortar.toml → examples/2d/parameters_euler_ec_mortar.toml
diff --git a/examples/2d/parameters_khi.toml → examples/2d/parameters_euler_khi.toml b/examples/2d/parameters_khi.toml → examples/2d/parameters_euler_khi.toml
diff --git a/examples/2d/parameters_khi_amr.toml → examples/2d/parameters_euler_khi_amr.toml b/examples/2d/parameters_khi_amr.toml → examples/2d/parameters_euler_khi_amr.toml
diff --git a/examples/2d/parameters_nonperiodic.toml → ...ples/2d/parameters_euler_nonperiodic.toml b/examples/2d/parameters_nonperiodic.toml → ...ples/2d/parameters_euler_nonperiodic.toml
diff --git a/..._sedov_blast_wave_shockcapturing_amr.toml → ..._sedov_blast_wave_shockcapturing_amr.toml b/..._sedov_blast_wave_shockcapturing_amr.toml → ..._sedov_blast_wave_shockcapturing_amr.toml
diff --git a/examples/2d/parameters_source_terms.toml → ...les/2d/parameters_euler_source_terms.toml b/examples/2d/parameters_source_terms.toml → ...les/2d/parameters_euler_source_terms.toml
diff --git a/examples/2d/parameters_vortex.toml → examples/2d/parameters_euler_vortex.toml b/examples/2d/parameters_vortex.toml → examples/2d/parameters_euler_vortex.toml
diff --git a/examples/2d/parameters_amr_vortex.toml → examples/2d/parameters_euler_vortex_amr.toml b/examples/2d/parameters_amr_vortex.toml → examples/2d/parameters_euler_vortex_amr.toml
diff --git a/examples/2d/parameters_mortar_vortex.toml → ...es/2d/parameters_euler_vortex_mortar.toml b/examples/2d/parameters_mortar_vortex.toml → ...es/2d/parameters_euler_vortex_mortar.toml
diff --git a/...es/2d/parameters_mortar_vortex_split.toml → ...parameters_euler_vortex_mortar_split.toml b/...es/2d/parameters_mortar_vortex_split.toml → ...parameters_euler_vortex_mortar_split.toml
diff --git a/...s_mortar_vortex_split_shockcapturing.toml → ...r_vortex_mortar_split_shockcapturing.toml b/...s_mortar_vortex_split_shockcapturing.toml → ...r_vortex_mortar_split_shockcapturing.toml
diff --git a/...rameters_vortex_split_shockcapturing.toml → ...rs_euler_vortex_split_shockcapturing.toml b/...rameters_vortex_split_shockcapturing.toml → ...rs_euler_vortex_split_shockcapturing.toml
diff --git a/...eters_weak_blast_wave_shockcapturing.toml → ...euler_weak_blast_wave_shockcapturing.toml b/...eters_weak_blast_wave_shockcapturing.toml → ...euler_weak_blast_wave_shockcapturing.toml
diff --git a/examples/2d/parameters_alfven_wave.toml → examples/2d/parameters_mhd_alfven_wave.toml b/examples/2d/parameters_alfven_wave.toml → examples/2d/parameters_mhd_alfven_wave.toml
diff --git a/...les/2d/parameters_mortar_alfven_wave.toml → ...2d/parameters_mhd_alfven_wave_mortar.toml b/...les/2d/parameters_mortar_alfven_wave.toml → ...2d/parameters_mhd_alfven_wave_mortar.toml
diff --git a/examples/2d/parameters_ec_mhd.toml → examples/2d/parameters_mhd_ec.toml b/examples/2d/parameters_ec_mhd.toml → examples/2d/parameters_mhd_ec.toml
diff --git a/examples/2d/parameters_orszag_tang.toml → examples/2d/parameters_mhd_orszag_tang.toml b/examples/2d/parameters_orszag_tang.toml → examples/2d/parameters_mhd_orszag_tang.toml
diff --git a/examples/2d/parameters_rotor.toml → examples/2d/parameters_mhd_rotor.toml b/examples/2d/parameters_rotor.toml → examples/2d/parameters_mhd_rotor.toml
diff --git a/examples/3d/parameters_amr.toml → examples/3d/parameters_advection_amr.toml b/examples/3d/parameters_amr.toml → examples/3d/parameters_advection_amr.toml
diff --git a/examples/3d/parameters.toml → examples/3d/parameters_advection_basic.toml b/examples/3d/parameters.toml → examples/3d/parameters_advection_basic.toml
diff --git a/examples/3d/parameters_mortar.toml → examples/3d/parameters_advection_mortar.toml b/examples/3d/parameters_mortar.toml → examples/3d/parameters_advection_mortar.toml
diff --git a/examples/3d/parameters_amr_euler.toml → examples/3d/parameters_euler_amr.toml b/examples/3d/parameters_amr_euler.toml → examples/3d/parameters_euler_amr.toml
diff --git a/examples/3d/parameters_amr_blob.toml → examples/3d/parameters_euler_blob_amr.toml b/examples/3d/parameters_amr_blob.toml → examples/3d/parameters_euler_blob_amr.toml
diff --git a/examples/3d/parameters_density_pulse.toml → ...es/3d/parameters_euler_density_pulse.toml b/examples/3d/parameters_density_pulse.toml → ...es/3d/parameters_euler_density_pulse.toml
diff --git a/examples/3d/parameters_ec.toml → examples/3d/parameters_euler_ec.toml b/examples/3d/parameters_ec.toml → examples/3d/parameters_euler_ec.toml
diff --git a/examples/3d/parameters_eoc_test_euler.toml → examples/3d/parameters_euler_eoc_test.toml b/examples/3d/parameters_eoc_test_euler.toml → examples/3d/parameters_euler_eoc_test.toml
diff --git a/...eters_eoc_test_coupled_euler_gravity.toml → ...3d/parameters_euler_gravity_eoc_test.toml b/...eters_eoc_test_coupled_euler_gravity.toml → ...3d/parameters_euler_gravity_eoc_test.toml
diff --git a/examples/3d/parameters_mortar_euler.toml → examples/3d/parameters_euler_mortar.toml b/examples/3d/parameters_mortar_euler.toml → examples/3d/parameters_euler_mortar.toml
diff --git a/.../3d/parameters_sedov_shock_capturing.toml → ...uler_sedov_blast_wave_shockcapturing.toml b/.../3d/parameters_sedov_shock_capturing.toml → ...uler_sedov_blast_wave_shockcapturing.toml
diff --git a/examples/3d/parameters_shock_capturing.toml → ...s/3d/parameters_euler_shockcapturing.toml b/examples/3d/parameters_shock_capturing.toml → ...s/3d/parameters_euler_shockcapturing.toml
diff --git a/examples/3d/parameters_source_terms.toml → ...les/3d/parameters_euler_source_terms.toml b/examples/3d/parameters_source_terms.toml → ...les/3d/parameters_euler_source_terms.toml
diff --git a/...es/3d/parameters_taylor_green_vortex.toml → ...parameters_euler_taylor_green_vortex.toml b/...es/3d/parameters_taylor_green_vortex.toml → ...parameters_euler_taylor_green_vortex.toml
diff --git a/examples/3d/parameters_alfven_wave.toml → examples/3d/parameters_mhd_alfven_wave.toml b/examples/3d/parameters_alfven_wave.toml → examples/3d/parameters_mhd_alfven_wave.toml
diff --git a/...les/3d/parameters_mortar_alfven_wave.toml → ...3d/parameters_mhd_alfven_wave_mortar.toml b/...les/3d/parameters_mortar_alfven_wave.toml → ...3d/parameters_mhd_alfven_wave_mortar.toml
diff --git a/examples/3d/parameters_ec_mhd.toml → examples/3d/parameters_mhd_ec.toml b/examples/3d/parameters_ec_mhd.toml → examples/3d/parameters_mhd_ec.toml
diff --git a/examples/3d/parameters_orszag_tang.toml → examples/3d/parameters_mhd_orszag_tang.toml b/examples/3d/parameters_orszag_tang.toml → examples/3d/parameters_mhd_orszag_tang.toml
diff --git a/examples/README.md b/examples/README.md
@@ -9,15 +9,15 @@ There are also a few files that were configured such that they lend themselves
 to doing convergence tests with `convtest`, i.e., to determine the experimental order
 of convergence (EOC):
 
-* [`parameters.toml`](parameters.toml):
+* [`parameters_advection_basic.toml`](parameters_advection_basic.toml):
   EOC tests for linear scalar advection with `polydeg = 3`.
-* [`parameters_source_terms.toml`](parameters_source_terms.toml):
+* [`parameters_euler_source_terms.toml`](parameters_euler_source_terms.toml):
   EOC tests for Euler equations with `polydeg = 3`.
-* [`parameters_alfven_wave.toml`](parameters_alfven_wave.toml):
+* [`parameters_mhd_alfven_wave.toml`](parameters_mhd_alfven_wave.toml):
   EOC tests for MHD equations with `polydeg = 3`.
 * [`parameters_hyp_diff_llf.toml`](parameters_hyp_diff_llf.toml):
   EOC tests for hyperbolic diffusion equations with `polydeg = 4`.
 
 In general, a good first parameter file to try out as a new user is
-[`parameters.toml`](parameters.toml), as it is short, takes less than a second
+[`parameters_advection_basic.toml`](parameters_advection_basic.toml), as it is short, takes less than a second
 to run, and uses only the basic features of Trixi.
diff --git a/examples/paper-self-gravitating-gas-dynamics/README.md b/examples/paper-self-gravitating-gas-dynamics/README.md
@@ -3,63 +3,63 @@
 ## Sec. 4.1.1, Table 2, EOC tests compressible Euler
 **polydeg = 3**:
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_euler.toml", 4)
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_euler_eoc_test.toml", 4)
 ```
 
 **polydeg = 4**:
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_euler.toml", 4, polydeg=4)
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_euler_eoc_test.toml", 4, polydeg=4)
 ```
 
 ## Sec. 4.1.2, Table 3, EOC tests hyperbolic diffusion
 **polydeg = 3**:
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_hyperbolic_diffusion.toml", 4)
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_hyp_diff_eoc_test.toml", 4)
 ```
 
 **polydeg = 4**:
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_hyperbolic_diffusion.toml", 4, polydeg=4)
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_hyp_diff_eoc_test.toml", 4, polydeg=4)
 ```
 
 ## Sec. 4.1.3, Table 4, EOC tests coupled Euler-gravity
 **polydeg = 3**:
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_coupled_euler_gravity.toml", 4)
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_eoc_test.toml", 4)
 ```
 
 **polydeg = 4**:
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_coupled_euler_gravity.toml", 4, polydeg=4)
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_eoc_test.toml", 4, polydeg=4)
 ```
 
 ## Sec. 4.1.3, Table 5, EOC tests coupled Euler-gravity (update gravity once per step)
 ```julia
-Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_eoc_test_coupled_euler_gravity.toml", 4,
+Trixi.convtest("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_eoc_test.toml", 4,
                update_gravity_once_per_stage=false)
 ```
 
 ## Sec. 4.2.1, Figures 3 + 5a, Jeans energies with Euler/CK45 and gravity/CK45
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_jeans_instability.toml")
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_jeans_instability.toml")
 ```
 
 ## Sec. 4.2.1, Figure 4, Jeans energies with Euler/CK45 and gravity/CK45 (update gravity once per step)
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_jeans_instability.toml",
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_jeans_instability.toml",
           update_gravity_once_per_stage=false)
 ```
 
 ## Sec. 4.2.1, Figure 5b, Jeans energies with Euler/CK45 and gravity/RK3S*
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_jeans_instability.toml",
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_jeans_instability.toml",
           time_integration_scheme_gravity="timestep_gravity_erk52_3Sstar!", cfl_gravity=1.2)
 ```
 
 ## Sec. 4.2.1, Creating Jeans energies figures 3 and 4
 One must also shrink the analysis interval in the above command, e.g.,
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_jeans_instability.toml",
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_jeans_instability.toml",
           analysis_interval=1)
 ```
 to generate necessary data for the plots to look nice. Then run the python
@@ -72,47 +72,47 @@ to generate the figure.
 ## Sec. 4.2.2, Figure 6, T=0.5, AMR meshes for Sedov + gravity
 **T = 0.0 and T = 0.5:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml", t_end=0.5)
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml", t_end=0.5)
 ```
 
 **T = 1.0:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml")
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml")
 ```
 
 ## Sec. 4.2.2, Figure 7a, T=0.5, Sedov + gravity with Euler/CK45 and gravity/RK3S*
 **AMR mesh:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml", t_end=0.5)
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml", t_end=0.5)
 ```
 
 **Uniform mesh:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml",
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml",
           amr_interval=0, initial_refinement_level=8, t_end=0.5)
 ```
 
 ## Sec. 4.2.2, Figure 7b, T=1.0, Sedov + gravity with Euler/CK45 and gravity/RK3S*
 **AMR mesh:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml")
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml")
 ```
 
 **Uniform mesh:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml",
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml",
           amr_interval=0, initial_refinement_level=8)
 ```
 
 ## Sec. 4.2.2, Table 6, Sedov + gravity, performance uniform vs. AMR
 **AMR mesh:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml")
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml")
 ```
 
 **Uniform mesh:**
 ```julia
-Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_sedov_self_gravity.toml",
+Trixi.run("examples/paper-self-gravitating-gas-dynamics/parameters_euler_gravity_sedov_blast_wave.toml",
           amr_interval=0, initial_refinement_level=8)
 ```
 

diff --git a/...s-dynamics/parameters_eoc_test_euler.toml → ...s-dynamics/parameters_euler_eoc_test.toml b/...s-dynamics/parameters_eoc_test_euler.toml → ...s-dynamics/parameters_euler_eoc_test.toml
diff --git a/...eters_eoc_test_coupled_euler_gravity.toml → ...cs/parameters_euler_gravity_eoc_test.toml b/...eters_eoc_test_coupled_euler_gravity.toml → ...cs/parameters_euler_gravity_eoc_test.toml
diff --git a/...ynamics/parameters_jeans_instability.toml → ...ters_euler_gravity_jeans_instability.toml b/...ynamics/parameters_jeans_instability.toml → ...ters_euler_gravity_jeans_instability.toml
diff --git a/...namics/parameters_sedov_self_gravity.toml → ...eters_euler_gravity_sedov_blast_wave.toml b/...namics/parameters_sedov_self_gravity.toml → ...eters_euler_gravity_sedov_blast_wave.toml
diff --git a/...meters_eoc_test_hyperbolic_diffusion.toml → ...ynamics/parameters_hyp_diff_eoc_test.toml b/...meters_eoc_test_hyperbolic_diffusion.toml → ...ynamics/parameters_hyp_diff_eoc_test.toml
diff --git a/src/auxiliary/auxiliary.jl b/src/auxiliary/auxiliary.jl
@@ -127,7 +127,7 @@ end
 
 Return the path to an example parameter file that can be used to quickly see Trixi in action.
 """
-default_example() = joinpath(examples_dir(), "2d", "parameters.jl")
+default_example() = joinpath(examples_dir(), "2d", "elixir_advection_basic.jl")
 
 
 """

diff --git a/src/callbacks/amr_dg1d.jl b/src/callbacks/amr_dg1d.jl
@@ -48,7 +48,12 @@ function refine!(u_ode::AbstractVector, adaptor, mesh::TreeMesh{1},
         element_id += 1
       end
     end
-    @assert element_id == nelements(dg, cache) + 1 || element_id == nelements(dg, cache) + 2^ndims(mesh) "element_id = $element_id, nelements(dg, cache) = $(nelements(dg, cache))"
+    @boundscheck begin
+      # If everything is correct, we should have processed all elements.
+      # Depending on whether the last element processed above had to be refined or not,
+      # the counter `element_id` can have two different values at the end.
+      @assert element_id == nelements(dg, cache) + 1 || element_id == nelements(dg, cache) + 2^ndims(mesh) "element_id = $element_id, nelements(dg, cache) = $(nelements(dg, cache))"
+    end
   end # GC.@preserve old_u_ode
 
   # TODO: Taal performance, allow initializing the stuff in place, making use of resize!
@@ -177,7 +182,10 @@ function coarsen!(u_ode::AbstractVector, adaptor, mesh::TreeMesh{1},
         element_id += 1
       end
     end
-    @assert element_id == nelements(dg, cache) + 1 "element_id = $element_id, nelements(dg, cache) = $(nelements(dg, cache))"
+    @boundscheck begin
+      # If everything is correct, we should have processed all elements.
+      @assert element_id == nelements(dg, cache) + 1 "element_id = $element_id, nelements(dg, cache) = $(nelements(dg, cache))"
+    end
   end # GC.@preserve old_u_ode
 
   # TODO: Taal performance, allow initializing the stuff in place, making use of resize!