Merge remote-tracking branch 'origin/main' into TrixiSW-separation

NEWS.md

@@ -11,6 +11,7 @@ for human readability.
 - `flux_hllc` on non-cartesian meshes for `CompressibleEulerEquations{2,3}D`
 - Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, 
   can now be digested by Trixi in 2D and 3D.
+- Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh`
 
 ## Changes when updating to v0.6 from v0.5.x
 

Project.toml

@@ -9,6 +9,7 @@ ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -57,6 +58,7 @@ ConstructionBase = "1.3"
 DataStructures = "0.18.15"
 DiffEqBase = "6 - 6.143"
 DiffEqCallbacks = "2.25"
+Downloads = "1.6"
 EllipsisNotation = "1.0"
 FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"

benchmark/elixir_2d_euler_vortex_unstructured.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -49,11 +48,9 @@ end
 initial_condition = initial_condition_isentropic_vortex
 solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 
-default_mesh_file = joinpath(@__DIR__, "mesh_uniform_cartesian.mesh")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/ranocha/f4ea19ba3b62348968c971db43d7798b/raw/a506abb9479c020920cf6068c142670fc1a9aadc/mesh_uniform_cartesian.mesh",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/ranocha/f4ea19ba3b62348968c971db43d7798b/raw/a506abb9479c020920cf6068c142670fc1a9aadc/mesh_uniform_cartesian.mesh",
+                           joinpath(@__DIR__, "mesh_uniform_cartesian.mesh"))
+
 mesh = UnstructuredMesh2D(mesh_file, periodicity = true)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)

docs/make.jl

@@ -108,6 +108,7 @@ makedocs(
             ],
             "Time integration" => "time_integration.md",
             "Callbacks" => "callbacks.md",
+            "Coupling" => "multi-physics_coupling.md"
         ],
         "Advanced topics & developers" => [
             "Conventions" =>"conventions.md",

docs/src/multi-physics_coupling.md

@@ -0,0 +1,46 @@
+# [Multi-physics coupling](@id multi-physics-coupling)
+A complex simulation can consist of different spatial domains in which
+different equations are being solved, different numerical methods being used
+or the grid structure is different.
+One example would be a fluid in a tank and an extended hot plate attached to it.
+We would then like to solve the Navier-Stokes equations in the fluid domain
+and the heat conduction equations in the plate.
+The coupling would happen at the interface through the exchange of thermal energy.
+
+
+## Converter coupling
+It may happen that the two systems to be coupled do not share any variables, but
+share some of the physics.
+In such a situation, the same physics is just represented in a different form and with
+a different set of variables.
+This is the case, for instance assuming two domains, if there is a fluid system in one domain
+and a Vlasov system in the other domain.
+In that case we would have variables representing distribution functions of
+the Vlasov system on one side and variables representing the mechanical quantities, like density,
+of the fluid system.
+To translate the fields from one description to the other one needs to use
+converter functions.
+These functions need to be hand tailored by the user in the elixir file where each
+pair of coupled systems requires two coupling functions, one for each direction.
+
+In the general case, we have a system $A$ with $m$ variables
+$u_{A,i}, \: i = 1, \dots, m$ and another
+system $B$ with $n$ variables $u_{B,j}, \: j = 1, \dots, n$.
+We then define two coupling functions, one that transforms $u_A$ into $u_B$
+and one that goes the other way.
+
+In their minimal form they take the position vector $x$, state vector $u$
+and the equations of the two coupled systems
+and return the transformed variables.
+By passing the equations we can make use of their parameters, if they are required.
+Examples can be seen in `examples/structured_2d_dgsem/elixir_advection_coupled.jl`.
+
+
+## Warning about binary compatibility
+Currently the coordinate values on the nodes can differ by machine precision when
+simulating the mesh and when splitting the mesh in multiple domains.
+This is an issue coming from the coordinate interpolation on the nodes.
+As a result, running a simulation in a single system and in two coupled domains
+may result in a difference of the order of the machine precision.
+While this is not an issue for most practical problems, it is best to keep this in mind when comparing test runs.
+

examples/dgmulti_2d/elixir_euler_hohqmesh.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -30,12 +29,8 @@ dg = DGMulti(polydeg = 8, element_type = Quad(), approximation_type = SBP(),
 
 ###############################################################################
 # Get the curved quad mesh from a file (downloads the file if not available locally)
-
-default_mesh_file = joinpath(@__DIR__, "mesh_trixi_unstructured_mesh_docs.mesh")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/andrewwinters5000/52056f1487853fab63b7f4ed7f171c80/raw/9d573387dfdbb8bce2a55db7246f4207663ac07f/mesh_trixi_unstructured_mesh_docs.mesh",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/52056f1487853fab63b7f4ed7f171c80/raw/9d573387dfdbb8bce2a55db7246f4207663ac07f/mesh_trixi_unstructured_mesh_docs.mesh",
+                           joinpath(@__DIR__, "mesh_trixi_unstructured_mesh_docs.mesh"))
 
 mesh = DGMultiMesh(dg, mesh_file)
 

examples/p4est_2d_dgsem/elixir_advection_amr_unstructured_flag.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -31,10 +30,8 @@ Trixi.validate_faces(faces)
 mapping_flag = Trixi.transfinite_mapping(faces)
 
 # Unstructured mesh with 24 cells of the square domain [-1, 1]^n
-mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
+                           joinpath(@__DIR__, "square_unstructured_2.inp"))
 
 mesh = P4estMesh{2}(mesh_file, polydeg = 3,
                     mapping = mapping_flag,

examples/p4est_2d_dgsem/elixir_advection_unstructured_flag.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -29,10 +28,8 @@ Trixi.validate_faces(faces)
 mapping_flag = Trixi.transfinite_mapping(faces)
 
 # Unstructured mesh with 24 cells of the square domain [-1, 1]^n
-mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
+                           joinpath(@__DIR__, "square_unstructured_2.inp"))
 
 mesh = P4estMesh{2}(mesh_file, polydeg = 3,
                     mapping = mapping_flag,

examples/p4est_2d_dgsem/elixir_euler_blast_wave_amr.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -50,10 +49,8 @@ volume_integral = VolumeIntegralShockCapturingHG(indicator_sc;
 solver = DGSEM(basis, surface_flux, volume_integral)
 
 # Unstructured mesh with 48 cells of the square domain [-1, 1]^n
-mesh_file = joinpath(@__DIR__, "square_unstructured_1.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp",
+                           joinpath(@__DIR__, "square_unstructured_1.inp"))
 
 mesh = P4estMesh{2}(mesh_file, polydeg = 3, initial_refinement_level = 1)
 

examples/p4est_2d_dgsem/elixir_euler_double_mach_amr.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -99,11 +98,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux,
                volume_integral = volume_integral)
 
 # Get the unstructured quad mesh from a file (downloads the file if not available locally)
-default_mesh_file = joinpath(@__DIR__, "abaqus_double_mach.inp")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/andrewwinters5000/a0806ef0d03cf5ea221af523167b6e32/raw/61ed0eb017eb432d996ed119a52fb041fe363e8c/abaqus_double_mach.inp",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/a0806ef0d03cf5ea221af523167b6e32/raw/61ed0eb017eb432d996ed119a52fb041fe363e8c/abaqus_double_mach.inp",
+                           joinpath(@__DIR__, "abaqus_double_mach.inp"))
 
 mesh = P4estMesh{2}(mesh_file)
 

examples/p4est_2d_dgsem/elixir_euler_forward_step_amr.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -104,11 +103,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux,
                volume_integral = volume_integral)
 
 # Get the unstructured quad mesh from a file (downloads the file if not available locally)
-default_mesh_file = joinpath(@__DIR__, "abaqus_forward_step.inp")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/andrewwinters5000/b346ee6aa5446687f128eab8b37d52a7/raw/cd1e1d43bebd8d2631a07caec45585ec8456ca4c/abaqus_forward_step.inp",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/b346ee6aa5446687f128eab8b37d52a7/raw/cd1e1d43bebd8d2631a07caec45585ec8456ca4c/abaqus_forward_step.inp",
+                           joinpath(@__DIR__, "abaqus_forward_step.inp"))
 
 mesh = P4estMesh{2}(mesh_file)
 

examples/p4est_2d_dgsem/elixir_euler_free_stream.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -31,10 +30,8 @@ end
 # Get the uncurved mesh from a file (downloads the file if not available locally)
 
 # Unstructured mesh with 48 cells of the square domain [-1, 1]^n
-mesh_file = joinpath(@__DIR__, "square_unstructured_1.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp",
+                           joinpath(@__DIR__, "square_unstructured_1.inp"))
 
 # Map the unstructured mesh with the mapping above
 mesh = P4estMesh{2}(mesh_file, polydeg = 3, mapping = mapping, initial_refinement_level = 1)

examples/p4est_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -31,10 +30,8 @@ mapping_flag = Trixi.transfinite_mapping(faces)
 
 # Get the uncurved mesh from a file (downloads the file if not available locally)
 # Unstructured mesh with 24 cells of the square domain [-1, 1]^n
-mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
+                           joinpath(@__DIR__, "square_unstructured_2.inp"))
 
 mesh = P4estMesh{2}(mesh_file, polydeg = 3,
                     mapping = mapping_flag,

examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder.jl

@@ -13,7 +13,6 @@
 #
 # Keywords: supersonic flow, shock capturing, AMR, unstructured curved mesh, positivity preservation, compressible Euler, 2D
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -82,11 +81,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux,
                volume_integral = volume_integral)
 
 # Get the unstructured quad mesh from a file (downloads the file if not available locally)
-default_mesh_file = joinpath(@__DIR__, "abaqus_cylinder_in_channel.inp")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/andrewwinters5000/a08f78f6b185b63c3baeff911a63f628/raw/addac716ea0541f588b9d2bd3f92f643eb27b88f/abaqus_cylinder_in_channel.inp",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/a08f78f6b185b63c3baeff911a63f628/raw/addac716ea0541f588b9d2bd3f92f643eb27b88f/abaqus_cylinder_in_channel.inp",
+                           joinpath(@__DIR__, "abaqus_cylinder_in_channel.inp"))
 
 mesh = P4estMesh{2}(mesh_file)
 

examples/p4est_2d_dgsem/elixir_euler_wall_bc_amr.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -39,11 +38,8 @@ solver = DGSEM(polydeg = 5, surface_flux = flux_lax_friedrichs,
                volume_integral = VolumeIntegralFluxDifferencing(volume_flux))
 
 # Get the unstructured quad mesh from a file (downloads the file if not available locally)
-default_mesh_file = joinpath(@__DIR__, "abaqus_gingerbread_man.inp")
-isfile(default_mesh_file) ||
-    download("https://gist.githubusercontent.com/andrewwinters5000/0e9e990a04b5105d1d2e3096a6e41272/raw/0d924b1d7e7d3cc1070a6cc22fe1d501687aa6dd/abaqus_gingerbread_man.inp",
-             default_mesh_file)
-mesh_file = default_mesh_file
+mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/0e9e990a04b5105d1d2e3096a6e41272/raw/0d924b1d7e7d3cc1070a6cc22fe1d501687aa6dd/abaqus_gingerbread_man.inp",
+                           joinpath(@__DIR__, "abaqus_gingerbread_man.inp"))
 
 mesh = P4estMesh{2}(mesh_file)
 

examples/p4est_2d_dgsem/elixir_mhd_rotor.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -69,10 +68,8 @@ function mapping_twist(xi, eta)
     return SVector(x, y)
 end
 
-mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp",
+                           joinpath(@__DIR__, "square_unstructured_2.inp"))
 
 mesh = P4estMesh{2}(mesh_file,
                     polydeg = 4,

examples/p4est_3d_dgsem/elixir_advection_amr_unstructured_curved.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -49,10 +48,8 @@ function mapping(xi, eta, zeta)
 end
 
 # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3
-mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp",
+                           joinpath(@__DIR__, "cube_unstructured_2.inp"))
 
 # Mesh polydeg of 2 (half the solver polydeg) to ensure FSP (see above).
 mesh = P4estMesh{3}(mesh_file, polydeg = 2,

examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -46,10 +45,8 @@ function mapping(xi, eta, zeta)
 end
 
 # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3
-mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp",
+                           joinpath(@__DIR__, "cube_unstructured_1.inp"))
 
 mesh = P4estMesh{3}(mesh_file, polydeg = 3,
                     mapping = mapping,

examples/p4est_3d_dgsem/elixir_euler_ec.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -46,10 +45,8 @@ function mapping(xi_, eta_, zeta_)
 end
 
 # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3
-mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp",
+                           joinpath(@__DIR__, "cube_unstructured_2.inp"))
 
 mesh = P4estMesh{3}(mesh_file, polydeg = 5,
                     mapping = mapping,

examples/p4est_3d_dgsem/elixir_euler_free_stream.jl

@@ -1,5 +1,4 @@
 
-using Downloads: download
 using OrdinaryDiffEq
 using Trixi
 
@@ -47,10 +46,8 @@ function mapping(xi_, eta_, zeta_)
 end
 
 # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3
-mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp")
-isfile(mesh_file) ||
-    download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp",
-             mesh_file)
+mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp",
+                           joinpath(@__DIR__, "cube_unstructured_1.inp"))
 
 # Mesh polydeg of 2 (half the solver polydeg) to ensure FSP (see above).
 mesh = P4estMesh{3}(mesh_file, polydeg = 2,