changes.rst

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Changes since 4.2.0
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List of the main bugfixes in the new 4.2.1 release - May 2023

**KERNEL**

- Fix emp initial value if salinity relaxation is not used (:mergereq:`221`)
- TKE boundary condition in GLS was wrong with iceshelves cavities (:gitlab:`/commit/bad665bd`)
- Model initialization in coupled configurations fixed (:mergereq:`151`)
- ABL model was not working with waves options (:mergereq:`144`)
- Spitz 12 configuration namelists have been updated (:mergereq:`!175`)
- Bugfixes in the OSMOSIS vertical mixing scheme and the associated diagnostics (:mergereq:`172`, :mergereq:`168`)
- CPL_OASIS test case has been updated (:mergereq:`111`)

**Sea-ice SI3**

- Surface roughness can now be ice-thickness dependant in GLS and TKE scheme (:mergereq:`49`)
- A bug in Rothrock ice strength has been fixed (:mergereq:`139`)

**High Performance Computing (HPC)**

- Enable NEMO compilation using single-precision variable (:mergereq:`171`)
- Fix NEMO compilation when using MPI2 option (:mergereq:`97`) and bugfix in configurations without MPI use (:mergereq:`167`)
- Demonstration of mixed-precision compilation using key_single (ORCA2 only) (:mergereq:`261`)

**AGRIF zooms**

- Correct freshwater budget computation when using  AGRIF zooms (:mergereq:`162`)
- Fixed issue with sea surface height (ssh) offset with sea-ice and AGRIF (:mergereq:`120`, :mergereq:`128`, :mergereq:`149`)

**Tracers and biogeochemistry TOP**

- PISCES consolidation and robustness (reproducibility, bugfix corrections, memory optimisation)
- Extension of passive-tracer conservation to the Euler-forward time-stepping option (:mergereq:`187`) and generic accuracy of the restart mechanism for configurations with Euler-forward time integration (:mergereq:`96`) 
- Bugfix on offline transport in TOP when using  linear surface option (:mergereq:`141`)
- Boundary conditions were missing in 1D configurations with TOP (:mergereq:`103`)
- Improve the use of multiple BDY segments and tracer inputs fields within TOP (:mergereq:`231`)

**Input Output Manager**

- Enable the use of XIOS3 to create outputs and handle restart files by means of `key_xios3` (:mergereq:`267`)

**Diagnostics**

- Some dia_ar5_hst outputs were wrong (:mergereq:`140`)

###################
Changes since 4.0.7
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List of the main additions to the 4.2.0 release - February 2022

This section is an overview of the major NEMO upgrades as included in the 4.2.0 release. 

If you are willing to port an existing configuration in order to start using this new release, it is sugggested to also look at the 4.2 `Migration Guide`_ .

.. _`Migration guide`: https://sites.nemo-ocean.io/user-guide/migration.html

**KERNEL**

- New vertical scale factors management (improving computational performance and reducing memory footprint) via added keys: 
   - key_qco (Quasi Eulerian Coordinates) 
   - key_linssh (Linear Sea Surface Height)
- New HPG schemes (improvements and new option)
- Preparatory stages for new RK3 time stepping scheme, includes: 
   - time-pointer changes
   - DO LOOP macros
   - changes in main arrays dimensions)
- Full Shallow Water setup

**AIR SEA INTERACTIONS**

- Currents feedbacks
- Mass-flux convection scheme (still not compatible with TOP & PISCES)
- Bulk improvements 
- Atmospheric Boundary layer model (1D vertical as for now) & tools improvements
- Wave forcing improvements

**AGRIF zooms**

- Improvement of Agrif for global configurations (periodic, north fold zoom, HPC), 
- Allow AGRIF for multiple vertical grids
- Updated Nesting Tools to set up the AGRIF zooms

**Sea-ice SI3**

- EAP & VP rheology (V&V to complete)
- Melt ponds (preliminary implementation)
- (Updated Reference Manual will be made available to users by March 2022)

**ENHANCEMENTS**

- Ocean column properties in NEMO-ICB
- OSMOSIS (awaiting improvements)
- Update internal tidal mixing 

**Tracers and biogeochemistry TOP**

- Ice sheet iron sources
- Scheme for vertical penetration of visible light
- (Updated Reference Manual will be made available to users by March 2022)

**DATA interface**

- OBS modifications

**Input Output Manager**

- Use XIOS to read & write restart file (allowing to produce a unique restart file while using domain decomposition)

**High Performance Computing (HPC)**

- MPI Communication cleanup & improvements using MPI3
- Reduction in memory footprint
- Improved computational performance of solar penetration scheme
- Additional improvements in preparation (requiring further developments before producing performance gains):
   - Extra Halo extension (namelist activation but keep nn_hls=1 for now)
   - Mixed precision preparatory phase
   - Loop fusion (activated via key_loop_fusion not currently recommended)
   - Tiling (namelist activation but keep ln_tile=.false. for now)

**VERIFICATION & VALIDATION**

- Tests cases now available with most  new developments
- SETTE validation script improvements
- OASIS test case for ocean atmosphere coupled interface


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Known Issues
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- Simulations are not reproductible when using a halo size of 2 points (MR !34 for details)
- Domain attributes are missing in multiple file output (Issue #14)
- SI3 manual is not yet available (coming soon !)