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V2.2.01 (#336)
## [2.2.01] 2025-04-16 ### Changed - Fix a bug that led to instabilities in the RKL scheme with very small grid spacings (#323) - Fix a bug that prevented Idefix from running with Sycl backend (required on Intel GPUs) (#331) - Fix an error that led to incorrect electrical current regularisation around the polar axis in non-Ideal MHD (#333) - Improve div(B) checks with a dimensionless implementation, avoiding too large divB errors in grids with large stretch factors (#334) ### Added - Time-Implicit drag for multiple dust species, preventing small time steps for strongly coupled dust grains (#321) - Collisionless heat flux added to the Braginskii module (#317) - New global `idfx::DumpArray` debugging function to dump any Idefix array into a numpy array that can read from python (#318) - Automatic benchmark plots in the documentation (#319) - More CI tests of grid coarsening (#329) - Dump outputs based on wallclock time (#335) --------- Co-authored-by: Victor Réville <victorreville@gmail.com> Co-authored-by: Hal Bal <vreville@irap.omp.eu> Co-authored-by: Jean Kempf <jean.kempf@irap.omp.eu> Co-authored-by: Victor Réville <47865059+vreville@users.noreply.github.com> Co-authored-by: Marc Coiffier <marc.coiffier@univ-grenoble-alpes.fr> Co-authored-by: pre-commit-ci-lite[bot] <117423508+pre-commit-ci-lite[bot]@users.noreply.github.com>
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‎.github/workflows/idefix-ci-jobs.yml‎

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run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang -all $TESTME_OPTIONS
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- name: Orszag Tang 3D+restart tests
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run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang3D -all $TESTME_OPTIONS
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- name: Axis Flux tube
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run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/AxisFluxTube -all $TESTME_OPTIONS
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ParabolicMHD:
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runs-on: self-hosted
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run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sphBragTDiffusion -all $TESTME_OPTIONS
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- name: Spherical anisotropic viscosity
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run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sphBragViscosity -all $TESTME_OPTIONS
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- name: Collisionless thermal conduction
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run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/clessTDiffusion -all $TESTME_OPTIONS
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Examples:
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needs: [Fargo, Dust, Planet, ShearingBox, SelfGravity]
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run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/lookupTable -all $TESTME_OPTIONS
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- name: Dump Image
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run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/dumpImage -all $TESTME_OPTIONS
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- name: Column density
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run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/columnDensity -all $TESTME_OPTIONS

‎.gitignore‎

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doc/source/_public/*
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doc/source/api/*
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doc/source/xml/*
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doc/env/*
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# compiled files
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**/__pycache__

‎CHANGELOG.md‎

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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [2.2.01] 2025-04-16
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### Changed
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- Fix a bug that led to instabilities in the RKL scheme with very small grid spacings (#323)
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- Fix a bug that prevented Idefix from running with Sycl backend (required on Intel GPUs) (#331)
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- Fix an error that led to incorrect electrical current regularisation around the polar axis in non-Ideal MHD (#333)
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- Improve div(B) checks with a dimensionless implementation, avoiding too large divB errors in grids with large stretch factors (#334)
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### Added
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- Time-Implicit drag for multiple dust species, preventing small time steps for strongly coupled dust grains (#321)
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- Collisionless heat flux added to the Braginskii module (#317)
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- New global `idfx::DumpArray` debugging function to dump any Idefix array into a numpy array that can read from python (#318)
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- Automatic benchmark plots in the documentation (#319)
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- More CI tests of grid coarsening (#329)
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- Dump outputs based on wallclock time (#335)
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## [2.2.00] 2025-01-17
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### Changed
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‎CMakeLists.txt‎

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set(Idefix_VERSION_MAJOR 2)
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set(Idefix_VERSION_MINOR 2)
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set(Idefix_VERSION_PATCH 00)
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set(Idefix_VERSION_PATCH 01)
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project (idefix VERSION 2.2.00)
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project (idefix VERSION 2.2.01)
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option(Idefix_MHD "enable MHD" OFF)
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option(Idefix_MPI "enable Message Passing Interface parallelisation" OFF)
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option(Idefix_HIGH_ORDER_FARGO "Force Fargo to use a PPM reconstruction scheme" OFF)

‎doc/python_requirements.txt‎

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m2r2==0.3.2
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sphinx-copybutton==0.5.2
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#sphinxcontrib-applehelp==1.0.7
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matplotlib==3.10.0

‎doc/source/bench.json‎

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‎doc/source/conf.py‎

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extensions = [
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"sphinx_rtd_theme",
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'sphinx_git',
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'matplotlib.sphinxext.plot_directive',
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"breathe",
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"exhale",
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"m2r2",

‎doc/source/faq.rst‎

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I want to use a lookup table from a CSV file in my idefix_loop. How could I proceed?
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Use the ``LookupTable`` class (see :ref:`LookupTableClass`)
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I want to compute a cumulative sum (e.g a column density) on the fly. How could I proceed?
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Use the ``Column`` class (see :class:`::Column`)

‎doc/source/index.rst‎

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Clément Robert
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gitlab integration, linter
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Jean Kempf & François Rincon
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anisotropic diffusion
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Jean Kempf, Victor Reville, François Rincon
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anisotropic diffusion and collisionless thermal conduction
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Marc Coiffier
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Continuous integration, automatic benchmarking
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========================
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About this documentation

‎doc/source/modules/braginskii.rst‎

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===================
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Equations solved and methods
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----------------------------
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The ``Braginskii`` module implements the anisotropic heat and momentum fluxes specific
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cell interface by a simple arithmetic average
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However in the same paper, the authors showed that this implementation can lead to
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unphysical heat flux from high to low temperature regions.
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unphysical heat flux from low to high temperature regions.
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So we implemented slope limiters for the computation of these transverse heat fluxes,
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Only the van Leer and the Monotonized Central (MC) limiters are available
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.. _braginskiiParameterSection:
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Saturation with collisionless heat flux
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---------------------------------------
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The ``Braginskii`` module can include a collisionless saturation of the Braginskii heat flux, typically due to supra-thermal electrons.
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The heat flux is then computed as follows:
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:math:`q = \alpha (q_B + q_\perp) + (1-\alpha)\beta*p*v`,
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where :math:`\alpha \in [0,1]` controls the transition between the Braginskii heat flux and the collisionless heat flux
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and :math:`\beta` controls the amplitude of the collisionless heat flux (typically :math:`\beta \in [1,4]`, see Hollweg 1976).
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.. note::
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As a result, even with :math:`\kappa_\perp = 0`, the heat flux is no longer necessarilly strictly aligned with the magnetic field.
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.. note::
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The collisionless heat flux is a hyperbolic term and the diffusion coefficient is set proportional to :math:`\alpha`.
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This saturation has been thought to be used mostly using the userdef function that takes four userdef arrays as input.
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starting with the keyword `bragTDiffusion` or/and *bragViscosity*. The following tables summarise the different options
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| Column | Entry name | Parameter type | Comment |
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| 0 | bragModule | string | | Activates Braginskii diffusion. Can be ``bragTDiffusion`` or ``bragViscosity``. |
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| 0 | bragTDiffusion | string | | Activates Braginskii thermal diffusion. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 1 | integration | string | | Specifies the type of scheme to be used to integrate the parabolic term. |
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| | | | | Can be ``rkl`` or ``explicit``. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 2 | slope limiter | string | | Choose the type of limiter to be used to compute anisotropic transverse flux terms. |
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| | | | | Can be ``mc``, ``vanleer`` or ``nolimiter``. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 3 | saturation mode | string | | Include or not collisionless saturation. Can be ``nosat`` or ``wcless``. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 4 | diffusivity type | string | | Specifies the type of diffusivity wanted. Can be ``constant`` or ``userdef``. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 5 | parallel diffusivity | real | | Mandatory if the diffusivity type is ``constant``. Not needed otherwise. |
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| | | | | Value of the parallel diffusivity. Should be a real number. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 6 | normal diffusivity | real | | When bragModule ``bragTDiffusion`` and diffusivity type ``constant``, |
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| | | | | value of the normal diffusivity. Should be a real number. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 7 | alpha collisionless | real | | If the diffusivity type is ``constant`` and saturation is ``wcless``. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| 8 | beta collisionless | real | | If the diffusivity type is ``constant`` and saturation is ``wcless``. |
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+--------+-----------------------+-------------------------+---------------------------------------------------------------------------------------+
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| Column | Entry name | Parameter type | Comment |
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+========+=======================+=========================+=======================================================================================+
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| 0 | bragViscosity | string | | Activates Braginskii viscosity. |
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(diffusion along the polar axis has not been directly tested).
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The collisionless saturation has been tested in 1D and 2D spherical geometry.

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