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Io simulations#17
amrueda wants to merge 141 commits intomainfrom
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@amrueda amrueda commented Jul 14, 2025

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amrueda and others added 30 commits December 19, 2024 17:51
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
DanielDoehring and others added 30 commits September 1, 2025 16:59
…mework#2505)

* example linear newton krylov

* Nonlinear example

* comment

* Update test/Project.toml

* Update test/Project.toml

* check different sciml

* v

* v

* v

* v

* v

* v

* v

* v

* v

* v

* Update test/Project.toml

* Update Project.toml

* ci

* compat

* v

* v

* v

* v

* v

* v

* Update test/Project.toml

Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>

* Update test/Project.toml

Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>

* Update test/Project.toml

* Update test/Project.toml

* Update test/test_parabolic_2d.jl

* up

* Update test/test_parabolic_2d.jl

* Update test/test_parabolic_2d.jl

* tolerances

* ci vals

* ode solver tols

* Update test/test_parabolic_2d.jl

---------

Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
* uType <: AbstractVector for code verbosity

* revert for ssp

---------

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Michael Schlottke-Lakemper <michael@sloede.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.34.0 to 1.35.7.
- [Release notes](https://github.com/crate-ci/typos/releases)
- [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md)
- [Commits](crate-ci/typos@v1.34.0...v1.35.7)

---
updated-dependencies:
- dependency-name: crate-ci/typos
  dependency-version: 1.35.7
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 4 to 5.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v4...v5)

---
updated-dependencies:
- dependency-name: actions/download-artifact
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Daniel Doehring <daniel.doehring@rwth-aachen.de>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
…atrixColorings` (trixi-framework#2532)

* Elixir for implicit solver using sparse jacobian

* Docstring for new semidiscretize

* PR comments

* Making the hacks into an extension

* Apply suggestions from code review

* work

* packages

* reduce time

* work

* use sparse ode

* comment

* be more explicit

* try nonlinear

* comment

* comment

* exchange solver

* work

* comment

* comments

* comment

* rename

* comments

* Moving the ext back into the elixirs

* Adding CI test

* Adding CI test for implicit_sparse_jacobian elixir

* Update examples/tree_1d_dgsem/elixir_euler_convergence_implicit_sparse_jacobian.jl

* Update examples/tree_1d_dgsem/elixir_euler_convergence_implicit_sparse_jacobian.jl

* Apply suggestions from code review

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian.jl

* comments on constant jacs

* move dir

* comment

* order

* restart file

* Apply suggestions from code review

* compat

* remove redundant comments

* Elixir for implicit solver using sparse jacobian

* Docstring for new semidiscretize

* PR comments

* Making the hacks into an extension

* Apply suggestions from code review

* work

* packages

* reduce time

* work

* use sparse ode

* comment

* be more explicit

* try nonlinear

* comment

* comment

* exchange solver

* work

* comment

* comments

* comment

* rename

* comments

* Moving the ext back into the elixirs

* Adding CI test

* Adding CI test for implicit_sparse_jacobian elixir

* CI tests for both

* Other 2 CI tests

* Uncomment commented tests and delete 1D convergence_implicit elixir

* Replace the test that I accidentally overwrote

* Unit test

* Update test/test_unit.jl

* Update Project.toml

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian.jl

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian.jl

* revisit

* unit test

* repeat comment

* linear structure

* fmzt

* fix unit test

* Apply suggestions from code review

* Spellcheck

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian.jl

* comment

* add sparse arrays

* try module

* rm

* try more specific overload

* simplify

* v

* v

* Update examples/structured_2d_dgsem/elixir_euler_convergence_implicit_sparse_jacobian.jl

Co-authored-by: Marco Artiano <57838732+MarcoArtiano@users.noreply.github.com>

* Update examples/structured_2d_dgsem/elixir_euler_convergence_implicit_sparse_jacobian.jl

* Update examples/structured_2d_dgsem/elixir_euler_convergence_implicit_sparse_jacobian.jl

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian.jl

* correct comment

* simplify

* kwargs

* adapt

* shorten

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian_restart.jl

* fmt

* simplify

* try different warning

* warning

* test

* up

* revert

* move comment

* compat

* v

* v

* v

* try plots

* v

* Update test/Project.toml

* module replace

* typo

* error tol

* switch spars detec backend

* fmt

* clean up

* simplify

* test no colorvec

* add finite diff

* typo

* docs

* add

* fmt

* correct type

* test non-including finite diff

* bring back

* fix

* ext

* typo

* reduce docs deps

* red project

* shorten

* typo

* comment

* com

* weak dep

* Update examples/tree_2d_dgsem/elixir_advection_implicit_sparse_jacobian_restart.jl

* Apply suggestions from code review

* mention

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* tspan

* shorten

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* comment

* import

* Update test/test_structured_2d.jl

* fmt

* Update docs/literate/src/files/differentiable_programming.jl

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* comments

* Update src/semidiscretization/semidiscretization.jl

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

---------

Co-authored-by: Steve <steve.bairos@rwth-aachen.de>
Co-authored-by: Marco Artiano <57838732+MarcoArtiano@users.noreply.github.com>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
* Single out `u_mean` computation into function

* revisit

* shorten

* fmt

* shorten

* debug

* Update src/callbacks_stage/positivity_zhang_shu_dg1d.jl

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* re-order

* node_vol

* mesh type respect

* real for treemesh

* fix

* Update src/callbacks_stage/positivity_zhang_shu_dg1d.jl

Co-authored-by: Benjamin Bolm <74359358+bennibolm@users.noreply.github.com>

* refactor

* comment

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

---------

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
Co-authored-by: Benjamin Bolm <74359358+bennibolm@users.noreply.github.com>
* small refactor kennedy gruber

* fix
…compat) (trixi-framework#2512)

* CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat)

* Update Project.toml

* Update Project.toml

---------

Co-authored-by: CompatHelper Julia <compathelper_noreply@julialang.org>
Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
* Yet another docu formatting

* fix
* Finally x code blocks in list :crossed-fingers:

* Single space after numbers
* Subsonic boundary treatment for constant state

* Add Section number, following Andrew's suggestion

* Suggestion from Daniel

* Apply suggestions from code review

Co-authored-by: Daniel Doehring <doehringd2@gmail.com>

* Update examples/tree_2d_dgsem/elixir_euler_subsonic_constant.jl

* Update examples/tree_2d_dgsem/elixir_euler_subsonic_constant.jl

---------

Co-authored-by: Daniel Doehring <doehringd2@gmail.com>
…rixi-framework#2562)

* Clarify `direction` instead of `normal_direction` for `TreeMesh` BCs

* Update examples/tree_1d_dgsem/elixir_burgers_shock.jl

Co-authored-by: Arpit Babbar <arpitbabbar@gmail.com>

* Update examples/tree_1d_dgsem/elixir_burgers_rarefaction.jl

---------

Co-authored-by: Arpit Babbar <arpitbabbar@gmail.com>
* Schulz-Rinne (2D) Riemann Problem

* work

* p

* comment

* clean up

* clean up

* hllc comment

* comment

* improve comment

* Update examples/tree_2d_dgsem/elixir_euler_riemannproblem_quadrants_amr.jl

Co-authored-by: Arpit Babbar <arpitbabbar@gmail.com>

* cfl

* cfl increase

* correct signature

---------

Co-authored-by: Arpit Babbar <arpitbabbar@gmail.com>
* `PlotData2D` for coupled semidiscretization

* Update src/visualization/types.jl

---------

Co-authored-by: Simon Candelaresi <10759273+SimonCan@users.noreply.github.com>
* add comment to new subsonic elixir

* add comments to other new elixir

* remove Trixi.flux

* duplicate

---------

Co-authored-by: Daniel Doehring <daniel.doehring@rwth-aachen.de>
* Hard-coded scalar scalar advection equation

* db
* Examples with IMEX integrator

* imex

* revisit

* mention imex

* main project toml

* shorten test

* version

* Update test/Project.toml

* Update test/Project.toml

* Update test/Project.toml

* Update test/Project.toml

* Update test/Project.toml

* Update test/Project.toml

* Update test/test_parabolic_1d.jl

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

---------

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
* use all macros provided by TrixiTest

* bump TrixiBase version

* add import Trixi

* replace test_nowarn_mod by trixi_test_nowarn

* replace @test_nowarn_mod trixi_include by @test_trixi_include

* unified use of EXAMPLES_DIR

* fmt

* temporarily swtich to branch of TrixiTest

* lots of local usings

* get sources right

* compat for TrixiTest

* use escaped version as in TrixiTest

* switch to branch in CI

* use reexported SVector

* fix url

* both test and main project?

* no

* fix

* try deving

* path keyword

* without cache and buildpkg

* yet another try

* some fixes

* next

* fmt

* fixes

* Trixi.jl maxiters warning

* fix

* try 1.11 and sources

* fix sources

* fixes

* fmt

* ugly workaround for @unpack macro

* Apply suggestions from code review

Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>

* compat bound from TrixiBase.jl

* yet another EXAMPLES_DIR

* use native unpack syntax

* adapt new test

---------

Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com>
Co-authored-by: Hendrik Ranocha <ranocha@users.noreply.github.com>
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