Festim

Latest version: v1.3.1

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1.3.1

This PR includes a couple of bug fixes that were identified right after the 1.3 release.

Upgrading FESTIM is only required if you are using `SurfaceFlux` in combination with the Soret effect.

* Fix SurfaceFlux with Soret by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/831
* allowed_meshes property for derived quantities by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/832
* Fixed Simulation.exports setter by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/836
* Correct units for cylindrical and spherical fluxes by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/835


**Full Changelog**: https://github.com/festim-dev/FESTIM/compare/v1.3...v1.3.1

1.3

We encourage users to upgrade their FESTIM version with


pip install -U festim


🌟 Highlights 🌟

* **Custom solver**
Users can now use a custom newton solver and have a finer control on the solver parameters (pre-conditioners, linear solvers...)
* **Kinetic surface model**
Similar to the model of Pick & Sonnenberg for surface dynamics, it is now possible to have a kinetic surface model in 1D simulations

New features
* Custom solver by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/734
* `SurfaceKinetics` BC by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/791
* Units in title for derived quantities by jhdark in https://github.com/festim-dev/FESTIM/pull/736
* Cylindrical and spherical versions of `SurfaceFlux` by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/689
* Soret effect in cylindrical and spherical coordinates by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/823

Bug fixes

* Fix bug with XDMF export in mode last by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/796
* Fixing the timer to stop at the end of a simulation. by Allentro in https://github.com/festim-dev/FESTIM/pull/713
* Fix bug with trap id is None by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/810

QoL improvements
* Temperature can be given as float or sp.Expr by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/770
* Error message when temperature is not defined by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/768
* Add error message when no final time is provided in transient simulations by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/769
* IC improvements for Heat Transfer by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/774
* Reset derived quantities data by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/772
* Error if temperature BC or source with `F.Temperature` by JonathanGSDUFOUR in https://github.com/festim-dev/FESTIM/pull/812

Documentation
* Test documentation code blocks by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/780
* Update the information in the XDMF section by XinShen-CHN in https://github.com/festim-dev/FESTIM/pull/801
* Add `DissociationFlux` to API documentation by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/707
* Add roadmap to README and change layout by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/709
* Update citation and add missing publications by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/717
* Adding copy button to the documentation by Allentro in https://github.com/festim-dev/FESTIM/pull/716
* Adds NumFOCUS sponsorship by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/763
* Map of institutions in documentation by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/761
* Additional buttons in header by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/762
* Update docstrings for `Temperature` by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/771
* Documentation: stepsize and Newton Solver by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/777
* Documentation guide by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/779
* SALOME meshing guide by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/776
* Fix user map + new institutions by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/786
* Move icons to header in docs by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/794
* Fix attributes typo in docs by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/795
* Docs fixes by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/797
* `SurfaceKinetics` docs and form by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/805
* Add ornl by jbae11 in https://github.com/festim-dev/FESTIM/pull/809
* List of maintainers in docs by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/815
* Radioactive decay in Theory by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/816
* Filter method docs by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/817
* Theory and UG for the `SurfaceKinetics` BC by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/808
* Fixed the typo in `ExtrinsicTrap` docstring[Issue 825] by muddi900 in https://github.com/festim-dev/FESTIM/pull/826

Misc
* Old comment on cylindrical flux by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/722
* Small refactoring of tests by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/726
* Fix codecov upload by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/757
* added TotalVolume to allowed cartesian quantities by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/766
* Fix units for "retention" with TotalVolume and TotalSurface by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/767
* Fix warnings + remove warnings in test by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/773
* Assign traps ids before by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/822
* No python version in CI by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/827
* Fixing typo Ellapsed -> Elapsed by Allentro in https://github.com/festim-dev/FESTIM/pull/714

New Contributors
* XinShen-CHN made their first contribution in https://github.com/festim-dev/FESTIM/pull/801
* jbae11 made their first contribution in https://github.com/festim-dev/FESTIM/pull/809
* muddi900 made their first contribution in https://github.com/festim-dev/FESTIM/pull/826

**Full Changelog**: https://github.com/festim-dev/FESTIM/compare/v1.2.1...v1.3

1.2.1

Fix for backward compatibility related to the recent refactoring of `DerivedQuantities` `Exports` `Traps` and `Materials` 725

**Full Changelog**: https://github.com/festim-dev/FESTIM/compare/v1.2...v1.2.1

1.2

New features
* TXTExport features by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/676
* Radioactive decay by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/679
* Soret coefficient as a function of temperature by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/690
* RaiseError when DirichletBC is set with another BC by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/692
* `max_stepsize` attribute for `festim.Stepsize` by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/698
* Warn about derived quantities in non cartesian by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/688

Bug fixes
* Fix bug with calculations on small timescales by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/682
* Bug in `test_unused_thermal_cond` due to pytest update by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/691

Documentation
* Updating getting_started link in README.md by Allentro in https://github.com/festim-dev/FESTIM/pull/696
* Fix workshop link in documentation by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/678
* Improve docs by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/681
* Documentation: getting started to installation by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/687
* Small update of Docs by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/699

Refactoring
* F.Materials -> subclass of list by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/694
* F.Exports -> subclass of list by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/695
* `F.Traps` and `F.DerivedQuantities` -> subclasses of list by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/697

New Contributors
* Allentro made their first contribution in https://github.com/festim-dev/FESTIM/pull/696

**Full Changelog**: https://github.com/festim-dev/FESTIM/compare/v1.1.1...v1.2

1.1.1

What's Changed
* Fix bug is_steady_state with TemperatureFromXDMF by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/674


**Full Changelog**: https://github.com/festim-dev/FESTIM/compare/v1.1...v1.1.1

1.1

What's Changed
* Fix build documentation by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/630
* Updated Documentation by Rajdeep1311 in https://github.com/festim-dev/FESTIM/pull/631
* Export data with TXTExport into single file by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/628
* MeshFromVertices in parallel by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/634
* Code of Conduct by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/649
* Fix README links by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/648
* Update README.md by tadash10 in https://github.com/festim-dev/FESTIM/pull/651
* PointValue class by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/655
* InitialCondition for HeatTransferProblem by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/662
* Update Codecov upload step by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/667
* Update theory.rst by KulaginVladimir in https://github.com/festim-dev/FESTIM/pull/664
* Fix TOC in Theory by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/670
* Update metadata of documentation by RemDelaporteMathurin in https://github.com/festim-dev/FESTIM/pull/669

New Contributors
* Rajdeep1311 made their first contribution in https://github.com/festim-dev/FESTIM/pull/631
* KulaginVladimir made their first contribution in https://github.com/festim-dev/FESTIM/pull/628
* tadash10 made their first contribution in https://github.com/festim-dev/FESTIM/pull/651

**Full Changelog**: https://github.com/festim-dev/FESTIM/compare/v1.0...v1.1

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