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Adding Acoustic Helmholtz equation to the tutorial #232

Merged
merged 10 commits into from
Feb 3, 2025
Merged

Adding Acoustic Helmholtz equation to the tutorial #232

merged 10 commits into from
Feb 3, 2025

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bayswiss
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Both the helmholtz.md introduction file (where the variational formulation is derived) and helmholtz.ipynb (implementation) have been written to be consistent with the rest of the tutorial. I tried to maintain paragraph titles and structure to keep it coherent with the others.

The code works in parallel, and I have already checked for typos. I am not perfect, though, so some minor fixes may still be needed.

I hope this is appreciated.

@bayswiss
Acoustic Helmholtz scripts
a2b32bb 
helmholtz.md contains the mathematical derivation of the variational formulation, while the helmholtz_code scripts contain the implementation.
@bayswiss
Merge pull request #1 from bayswiss/bayswiss-patch-1
9e90ff4 
Acoustic Helmholtz scripts
@bayswiss
Fix
44f42ec
@bayswiss
equations rendering bug fixed
669a64e
@bayswiss
Update helmholtz.md
4153f24 
Equations rendering second fix, missing spaces
@jorgensd
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jorgensd commented Jan 6, 2025

Hi @bayswiss,

I'll have a look at the PR this week:)

@bayswiss
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bayswiss commented Jan 6, 2025

Hi @bayswiss,

I'll have a look at the PR this week:)

Nice. Thank you Jorgen!

@jorgensd
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@bayswiss better late than never?:)
Here are my thoughts: bayswiss#2

@jorgensd jorgensd added the enhancement New feature or request label Jan 19, 2025
@jorgensd
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@bayswiss I’ll make one more change tomorrow to make it backwards compatible so we can publish it in 0.9

@bayswiss
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@bayswiss I’ll make one more change tomorrow to make it backwards compatible so we can publish it in 0.9

Perfect. Thank you for your work, as always!

@jorgensd jorgensd merged commit 2a13c0e into jorgensd:main Feb 3, 2025
1 check passed
jorgensd added a commit that referenced this pull request Feb 4, 2025
@bayswiss @jorgensd
Adding Acoustic Helmholtz equation to the tutorial (#232)
459ee5b 
* Acoustic Helmholtz scripts

helmholtz.md contains the mathematical derivation of the variational formulation, while the helmholtz_code scripts contain the implementation.

* Fix

* equations rendering bug fixed

* Update helmholtz.md

Equations rendering second fix, missing spaces

* Major updates to helmholtz

* Add to toc

* Updates to helmholtz

* Update to work in parallel

---------

Co-authored-by: jorgensd <dokken92@gmail.com>
jorgensd added a commit that referenced this pull request Feb 4, 2025
@jorgensd @mleoni-pf
@juliusgh @rossbm1 @MPenaR @dependabot @bayswiss
Dokken/bump release (#249)
ce168fa 
* Update elasticity_scaling.md (#242)

* Improve workflow handling (#118)

* Create common action for all workflows and split them into multiple files

* Dokken/update fspace and wmtgs (#127)

* fix runs-on

* Minor improvements in linearelasticity.md (#124)

* Fix various things on release branch

* Try adding trame

* Revert fundamentals

* Membrane code

* More updates due to autoformatting

* Lagrange -> CG back conversion

* Change to github image

---------

Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>

* Update petsc arches

* Fix bounding boxes and more (#135)

* Start fixing code for nightly build

* rerun all files

* Try fixing subdomains

* Fix meshio

* PETSc python API update (#137)

* Resolve #136

* Fixes related to: FEniCS/dolfinx#2703

* Update changelog

* Make sure all notebooks run. Change to pathlib in some examples

* Api changes related to: FEniCS/dolfinx#2763 (#142)

* Bump version numbers

* Bump version numbers (#149)

* Fix petsc arch

* Prepare v0.7.1 (#154)

* Merge branch 'main' into release and bump versions

* Delete obsolete file

* Temporary shift path in nightly test

* Make sure there are no warnigns in build

* Tabulation

* Updates compatible with nightly branch of DOLFINx (#156)

* Replace VectorElement and FiniteElement with `basix.ufl.element`.
Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`

* More updates

* And more

* Last vector element updates

* Bump pyvista and dolfinx to v0.7.2 (#159)

* Bump pyvista and dolfinx to v0.7.2

* remove -r

* Add further pyvista deps

* Bump versions

* Update petsc solver and pc links. Resolves #143 (#160)

* Fix typo and issue Issue on page /fem.html #122 (#161)

* Compute entity-cell connectivity before calling locate_dofs_topological.
Remove soon to be deprecated pyvista syntax for updating time dependent fields.
Fix range->np.arange conversion

* Update backend in workflow

* Fix broken link (#140) + http:// to https:// (#162)

* Run book build prior to parallel run

* Add back write frame

* Fix wrong link

* Fix typo in changelog

* Merge main into release (#189)

* Merge main into release

* Apply suggestions from code review

* Various fixes when reading through the diff

* Further fixes

* add missing checkout (#191)

* add missing checkout

* Add test docker on release PR and release (only push on tag

* Remove unused import

* Update text to resolve #194 (#195)

* Dokken/update nonlin options (#203)

* Update options for non-linear solver to sensible choice, ref #200

* Update docker path

* Update python file as well

* Update config ptr (#207)

* Pressure correction equation fix (#196)

* Update fundamentals.md (#199)

on line 110, updated a typesetting error in equation (3)

* Change from vector to petsc_vec (#206)

* dolfinx.fem.Form changed to dolfinx.fem.form (#213)

* Update compiler_parameters.ipynb

In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell.

* jupytext sync

* Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem

* Update book_stable.yml

* Update test_stable.yml

* Fix python path in test

* Fix CI (#227)

* Bump docker/build-push-action from 5 to 6 (#221)

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@v5...v6)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  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>

* Bump actions/configure-pages from 4 to 5 (#222)

Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5.
- [Release notes](https://github.com/actions/configure-pages/releases)
- [Commits](actions/configure-pages@v4...v5)

---
updated-dependencies:
- dependency-name: actions/configure-pages
  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>

* Update book_stable.yml (#225)

* Update book_stable.yml

* Update test_stable.yml

* resolve #224 (#226)

* Update test_stable.yml

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update test_stable.yml (#235)

* Add libgl flag to ci (#238)

* Update elasticity_scaling.md

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>
Co-authored-by: Jørgen S. Dokken <dokken@simula.no>
Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>
Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com>
Co-authored-by: Manuel Pena <mpena991@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update navierstokes.md (#247)

* Improve workflow handling (#118)

* Create common action for all workflows and split them into multiple files

* Dokken/update fspace and wmtgs (#127)

* fix runs-on

* Minor improvements in linearelasticity.md (#124)

* Fix various things on release branch

* Try adding trame

* Revert fundamentals

* Membrane code

* More updates due to autoformatting

* Lagrange -> CG back conversion

* Change to github image

---------

Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>

* Update petsc arches

* Fix bounding boxes and more (#135)

* Start fixing code for nightly build

* rerun all files

* Try fixing subdomains

* Fix meshio

* PETSc python API update (#137)

* Resolve #136

* Fixes related to: FEniCS/dolfinx#2703

* Update changelog

* Make sure all notebooks run. Change to pathlib in some examples

* Api changes related to: FEniCS/dolfinx#2763 (#142)

* Bump version numbers

* Bump version numbers (#149)

* Fix petsc arch

* Prepare v0.7.1 (#154)

* Merge branch 'main' into release and bump versions

* Delete obsolete file

* Temporary shift path in nightly test

* Make sure there are no warnigns in build

* Tabulation

* Updates compatible with nightly branch of DOLFINx (#156)

* Replace VectorElement and FiniteElement with `basix.ufl.element`.
Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`

* More updates

* And more

* Last vector element updates

* Bump pyvista and dolfinx to v0.7.2 (#159)

* Bump pyvista and dolfinx to v0.7.2

* remove -r

* Add further pyvista deps

* Bump versions

* Update petsc solver and pc links. Resolves #143 (#160)

* Fix typo and issue Issue on page /fem.html #122 (#161)

* Compute entity-cell connectivity before calling locate_dofs_topological.
Remove soon to be deprecated pyvista syntax for updating time dependent fields.
Fix range->np.arange conversion

* Update backend in workflow

* Fix broken link (#140) + http:// to https:// (#162)

* Run book build prior to parallel run

* Add back write frame

* Fix wrong link

* Fix typo in changelog

* Merge main into release (#189)

* Merge main into release

* Apply suggestions from code review

* Various fixes when reading through the diff

* Further fixes

* add missing checkout (#191)

* add missing checkout

* Add test docker on release PR and release (only push on tag

* Remove unused import

* Update text to resolve #194 (#195)

* Dokken/update nonlin options (#203)

* Update options for non-linear solver to sensible choice, ref #200

* Update docker path

* Update python file as well

* Update config ptr (#207)

* Pressure correction equation fix (#196)

* Update fundamentals.md (#199)

on line 110, updated a typesetting error in equation (3)

* Change from vector to petsc_vec (#206)

* dolfinx.fem.Form changed to dolfinx.fem.form (#213)

* Update compiler_parameters.ipynb

In the text it was mentioned that `dolfinx.fem.Form` was used to compile the form, instead of `dolfinx.fem.form`. Not matching the code cell.

* jupytext sync

* Form -> form in both py and ipynb and LinearProblem -> fem.petsc.LinearProblem

* Update book_stable.yml

* Update test_stable.yml

* Fix python path in test

* Fix CI (#227)

* Bump docker/build-push-action from 5 to 6 (#221)

Bumps [docker/build-push-action](https://github.com/docker/build-push-action) from 5 to 6.
- [Release notes](https://github.com/docker/build-push-action/releases)
- [Commits](docker/build-push-action@v5...v6)

---
updated-dependencies:
- dependency-name: docker/build-push-action
  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>

* Bump actions/configure-pages from 4 to 5 (#222)

Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5.
- [Release notes](https://github.com/actions/configure-pages/releases)
- [Commits](actions/configure-pages@v4...v5)

---
updated-dependencies:
- dependency-name: actions/configure-pages
  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>

* Update book_stable.yml (#225)

* Update book_stable.yml

* Update test_stable.yml

* resolve #224 (#226)

* Update test_stable.yml

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Update test_stable.yml (#235)

* Add libgl flag to ci (#238)

* Update navierstokes.md

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: Jørgen Schartum Dokken <dokken92@gmail.com>
Co-authored-by: Jørgen S. Dokken <dokken@simula.no>
Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>
Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com>
Co-authored-by: Manuel Pena <mpena991@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Adding Acoustic Helmholtz equation to the tutorial  (#232)

* Acoustic Helmholtz scripts

helmholtz.md contains the mathematical derivation of the variational formulation, while the helmholtz_code scripts contain the implementation.

* Fix

* equations rendering bug fixed

* Update helmholtz.md

Equations rendering second fix, missing spaces

* Major updates to helmholtz

* Add to toc

* Updates to helmholtz

* Update to work in parallel

---------

Co-authored-by: jorgensd <dokken92@gmail.com>

* Make helmholtz backwards compatible (#248)

* Native arm build (#240)

* Try new publish workflow

* Fix platform choice

* Update workflow to merge artifacts to one place

* Set retention days to minimum

* Fix name

* change name to pattern

* Minor improvements

* Try new strategy

* Remove duplicate tag

* Revert platform tags

* Use correct dockerfile

* remove first login

* Add merge skip if not pushing on release or tagging

* Set push to false as we don't need the images before merging.

* Remove push

* Remove conditional to check that simpler code runs

* Add back pushtrue

* Revert comment

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: mleoni-pf <160495781+mleoni-pf@users.noreply.github.com>
Co-authored-by: Julius Herb <43179176+juliusgh@users.noreply.github.com>
Co-authored-by: rossbm1 <120818149+rossbm1@users.noreply.github.com>
Co-authored-by: Manuel Pena <mpena991@gmail.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Antonio Baiano Svizzero <107617271+bayswiss@users.noreply.github.com>
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@bayswiss @jorgensd