Feature/1717 nodal api by ShahuK283 · Pull Request #2854 · trixi-framework/Trixi.jl

ShahuK283 · 2026-03-09T19:22:04Z

Thanks for the great discussion on #1717! I've opened this Draft PR with a prototype that returns StructArrays of SVectors. It uses ntuple and views over Trixi's internal wrap_array to collapse the n_vars dimension with zero allocations, yielding purely spatial arrays.

@jlchan - Does this StructArray format align well with your usual workflows?

For now, I have just added the foundational extraction API (get_u and get_coordinates). If this approach looks right to everyone, Michael's wishlist for spatial interpolation can be done next in a separate PR!

Let me know what you think

github-actions · 2026-03-09T19:22:15Z

jlchan

Hi @ShahuK283! Thanks for the PR; I just replied to the discussion in #1717, and lean towards plain Vector{<:StructArray} return types. I'm happy to do StructArrays if @ranocha or @sloede prefer though.

…rixi-framework#1717)

…/Trixi.jl into feature/1717-nodal-api

codecov · 2026-03-13T12:06:10Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 97.11%. Comparing base (f380eb1) to head (88f3dc0).
⚠️ Report is 13 commits behind head on main.

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@@            Coverage Diff             @@
##             main    #2854      +/-   ##
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+ Coverage   97.04%   97.11%   +0.06%     
==========================================
  Files         605      608       +3     
  Lines       47303    47308       +5     
==========================================
+ Hits        45905    45940      +35     
+ Misses       1398     1368      -30

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ShahuK283 · 2026-03-13T17:48:09Z

Hi! All CI checks have passed except for format-suggestion and Codecov. I believe this is because the new get_u and get_coordinates functions aren't being called anywhere in the test suite yet.

I have a quick test ready to verify them:

Test nodal API

sol = solve(ode, dt=1.0, maxiters=1)
@test size(Trixi.get_u(sol)) == (1, 4, 4, 256)
@test size(Trixi.get_coordinates(sol)) == (2, 4, 4, 256)

Before I add this, I wanted to ask what the preferred approach is:
Should I append these lines to an existing file (like test/test_tree_2d_advection.jl) to reuse an existing sol object, or would you prefer I create a new dedicated test file for the API?

jlchan · 2026-03-13T18:09:12Z

I think you can call an existing elixir to get a valid `sol` object. I believe some other tests for visualization do so?

…

On Fri, Mar 13, 2026 at 12:48 PM ShahuK283 ***@***.***> wrote: *ShahuK283* left a comment (trixi-framework/Trixi.jl#2854) <#2854 (comment)> Hi! All CI checks have passed except for format-suggestion and Codecov. I believe this is because the new get_u and get_coordinates functions aren't being called anywhere in the test suite yet. I have a quick test ready to verify them: Test nodal API sol = solve(ode, dt=1.0, maxiters=1) @test <https://github.com/test> size(Trixi.get_u(sol)) == (1, 4, 4, 256) @test <https://github.com/test> size(Trixi.get_coordinates(sol)) == (2, 4, 4, 256) Before I add this, I wanted to ask what the preferred approach is: Should I append these lines to an existing file (like test/test_tree_2d_advection.jl) to reuse an existing sol object, or would you prefer I create a new dedicated test file for the API? — Reply to this email directly, view it on GitHub <#2854 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI2HUCX237US62ICHGN4VD4QRCW5AVCNFSM6AAAAACWMHUVJKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DANJWHA4TKMZTGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

ShahuK283 · 2026-03-14T04:30:21Z

Hi @jlchan, I have updated the dimensions to correctly match with the variables in SVector. I also added the Nodal API tests in test_tree_2d_advection.jl using the existing elixir as you suggested, and checked for formatting errors.
Can you review this?

jlchan

Looks good, just had a few questions. Also, I'm partial to just using plain Vector{<:SVector} instead of StructArrays if that's simpler.

jlchan · 2026-03-14T17:36:40Z

src/auxiliary/solution_interface.jl

+end
+
+function get_coordinates(semi::AbstractSemidiscretization)
+    x_raw = semi.cache.elements.node_coordinates


I don't think this works for all Semidiscretization types; it might be good to dispatch using mesh_equations_solver_cache and then specialize on the solver or mesh type. For example, it doesn't work with DGMulti

added multiple dispatch in get_coordinates via mesh_equations_solver_cache(semi) to route coordinate extraction.
It returns cache.elements.node_coordinates for standard meshes and mesh.md.xyz for DGMultiMesh.

jlchan · 2026-03-14T17:37:05Z

test/test_tree_2d_advection.jl

+    @test size(Trixi.get_u(sol)) == (4, 4, 256)
+    @test size(Trixi.get_coordinates(sol)) == (4, 4, 256)


Might be good to also add a test that the retrieved values are correct.

We should also add more tests for other mesh types.

I added the Nodal API test suites to cover TreeMesh, StructuredMesh, UnstructuredMesh, and DGMulti. The tests now verify exact value correctness (e.g., @test coords == semi.cache.elements.node_coordinates) rather than just checking dimensions.

src/auxiliary/solution_interface.jl

jlchan · 2026-03-14T17:38:04Z

src/auxiliary/solution_interface.jl

+function get_u(u_ode, semi::AbstractSemidiscretization)
+    u_raw = wrap_array(u_ode, semi)
+    n_vars = nvariables(semi)
+    @assert ndims(u_raw)>=3 "Unexpected wrap_array shape: $(size(u_raw))"


What is this guarding against?

ranocha

Thanks for working on this!

ranocha · 2026-03-15T09:12:21Z

src/auxiliary/solution_interface.jl

+function get_u(sol)
+    semi = sol.prob.p
+    u_ode = sol.u[end]
+    return get_u(u_ode, semi)
+end
+
+function get_u(u_ode, semi::AbstractSemidiscretization)
+    u_raw = wrap_array(u_ode, semi)


These are the two methods that should be documented (get a docstring). We should also mention them briefly in the documentation, e.g., introduce a new subsection "Custom visualization" in https://trixi-framework.github.io/TrixiDocumentation/stable/visualization/ and mention these methods there together with an example.

ranocha · 2026-03-15T09:13:54Z

src/Trixi.jl

 using SparseArrays: AbstractSparseMatrix, AbstractSparseMatrixCSC, sparse, droptol!,
                    rowvals, nzrange, nonzeros
-
+using StructArrays


We already load the package below: @reexport using StructArrays: StructArrays, StructArray.

Thanks! I missed that. I had fixed it in this commit

ranocha · 2026-03-15T09:14:25Z

test/test_tree_2d_advection.jl

+    @test size(Trixi.get_u(sol)) == (4, 4, 256)
+    @test size(Trixi.get_coordinates(sol)) == (4, 4, 256)


We should also add more tests for other mesh types.

…fixes DGMulti tests

ShahuK283 · 2026-03-26T13:21:25Z

Hi! @ranocha , @jlchan
Let me know if this updated approach looks good!
The Downgrade and Trixi2Vtk checks are failing with HTTP/2 429 (Too Many Requests) errors; other CI have passed

jlchan

Thank you! It's looking good, I have a few suggestions for organization. When moving the tests to test_visualization.jl it would also be nice if we could consolidate them into a loop over a single test since some of the visualization tests are identical.

jlchan · 2026-03-27T04:29:05Z

docs/src/visualization.md

+
+If you want to extract the raw nodal coordinates and solution arrays to build your own custom plots or perform external data analysis, you can use the `get_coordinates` and `get_u` functions. 
+
+These functions use multiple dispatch to automatically reshape the flat ODE state vectors into intuitive, multidimensional tensors based on the underlying mesh type.


I think the "multidimensional tensors" comment is true for TreeMesh, not DGMultiMesh

jlchan · 2026-03-27T04:29:24Z

docs/src/visualization.md

+coords = Trixi.get_coordinates(sol)
+u_nodal = Trixi.get_u(sol)
+
+# The arrays are now ready to be used with external tools like Makie.jl or Plots.jl


Could you include an example of a Plots.jl command?

jlchan · 2026-03-27T04:31:26Z

src/auxiliary/solution_interface.jl

+function get_coordinates(mesh, equations, solver, cache)
+    return cache.elements.node_coordinates
+end
+


Can you add a comment about the layout of the coordinates for TreeMesh vs DGMultiMesh?

jlchan · 2026-03-27T04:34:10Z

test/test_tree_2d_advection.jl

+@testset "Nodal API" begin
+    trixi_include(@__MODULE__,
+                  joinpath(examples_dir(), "tree_2d_dgsem", "elixir_advection_basic.jl"))
+
+    semi = sol.prob.p
+
+    coords = Trixi.get_coordinates(sol)
+    @test size(coords) == (2, 4, 4, 256)
+    @test coords == semi.cache.elements.node_coordinates
+
+    u_nodal = Trixi.get_u(sol)
+    @test size(u_nodal) == (1, 4, 4, 256)
+    @test u_nodal == Trixi.wrap_array(sol.u[end], semi)
+end
+


Can you move this to test_visualization.jl instead?

jlchan · 2026-03-27T04:34:15Z

test/test_unstructured_2d.jl

+
+    @testset "Nodal API" begin
+        coords = Trixi.get_coordinates(sol)
+        @test size(coords) == size(semi.cache.elements.node_coordinates)
+        @test coords == semi.cache.elements.node_coordinates
+
+        u_nodal = Trixi.get_u(sol)
+        @test size(u_nodal) == size(Trixi.wrap_array(sol.u[end], semi))
+        @test u_nodal == Trixi.wrap_array(sol.u[end], semi)
+    end


Can you move this to test_visualization.jl instead?

jlchan · 2026-03-27T04:34:31Z

test/test_structured_2d.jl

+
+    @testset "Nodal API" begin
+        coords = Trixi.get_coordinates(sol)
+        @test size(coords) == size(semi.cache.elements.node_coordinates)
+        @test coords == semi.cache.elements.node_coordinates
+
+        u_nodal = Trixi.get_u(sol)
+        @test size(u_nodal) == size(Trixi.wrap_array(sol.u[end], semi))
+        @test u_nodal == Trixi.wrap_array(sol.u[end], semi)
+    end


Can you move this to test_visualization.jl instead?

jlchan · 2026-03-27T04:34:46Z

test/test_dgmulti_2d.jl

+
+    @testset "Nodal API" begin
+        semi = sol.prob.p
+
+        coords = Trixi.get_coordinates(sol)
+        @test coords == semi.mesh.md.xyz
+
+        u_nodal = Trixi.get_u(sol)
+        @test size(u_nodal) == size(Trixi.wrap_array(sol.u[end], semi))
+        @test u_nodal == Trixi.wrap_array(sol.u[end], semi)
+    end


Can you move this to test_visualization.jl instead?

jlchan reviewed Mar 9, 2026

View reviewed changes

Add public API for nodal solution extraction returning StructArrays (t…

badf9c4

…rixi-framework#1717)

ShahuK283 force-pushed the feature/1717-nodal-api branch from d7ee1bd to badf9c4 Compare March 10, 2026 02:05

DanielDoehring and others added 3 commits March 12, 2026 16:19

Merge branch 'main' into feature/1717-nodal-api

172b6c2

Fix load order, use AbstractSemidiscretization, export API, and clean up

f3af42d

Merge branch 'feature/1717-nodal-api' of https://github.com/ShahuK283…

6040b64

…/Trixi.jl into feature/1717-nodal-api

Trigger CI to fix caching error

957a823

ShahuK283 added 3 commits March 14, 2026 01:02

Fix formatting and add nodal API tests using trixi_include

ffef126

Remove tspan override to fix Nodal API test

a470cfb

Update Nodal API tests to expect 3D StructArrays

9f0d160

jlchan requested changes Mar 14, 2026

View reviewed changes

ranocha requested changes Mar 15, 2026

View reviewed changes

ShahuK283 added 2 commits March 25, 2026 02:34

Finalize Nodal API: auto-formatted, addresses reviewer feedback, and …

705b570

…fixes DGMulti tests

Fix formatting spaces to pass CI

88f3dc0

ShahuK283 marked this pull request as ready for review March 26, 2026 13:26

jlchan requested changes Mar 27, 2026

View reviewed changes

This was referenced Mar 30, 2026

Support for purely parabolic PDEs via SemidiscretizationParabolic #2874

Merged

Interface to avoid exposure of solver internals in usage of get_node_variable #2902

Open

		@test size(Trixi.get_u(sol)) == (4, 4, 256)
		@test size(Trixi.get_coordinates(sol)) == (4, 4, 256)


		If you want to extract the raw nodal coordinates and solution arrays to build your own custom plots or perform external data analysis, you can use the `get_coordinates` and `get_u` functions.

		These functions use multiple dispatch to automatically reshape the flat ODE state vectors into intuitive, multidimensional tensors based on the underlying mesh type.

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ShahuK283 commented Mar 9, 2026

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Test nodal API

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