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Restructured dynamical core, variables array-agnostic and 3-dimension…
…al, modular netCDF output (#525) * PrognosticVariables with LowerTriangularArray * WIP: initial indexing changes * WIP: indexing not working yet * WIP indexing (probably) working * WIP: zeros, ones, rand, ... * WIP: copyto! * copyto! working * LTA N-1 dim change tests passing * adjusting for size(alms) * fast cartesian indexing + broadcasting * clean up explicit arithmetics functions * code cleanup broadcasting * remove add! tests * show LowerTriangularMatrix * fix LTA plot * PrognosticVariables new structure * DiagnosticVariables new structure * zeros for Vector{Particle} * no set vars tests due to new structure * SpectralGrid with Spectral/GridVariable2D/3D types * progn/diagn prettier printing * fill!(::Tendencies, x) instead of zero_tendencies! * prognostic variables as NTuple{2, LowerTriangularArray} * BarotropicModel without layer structure * N-dimensional transform! spec->grid * n-dim transform! also grid -> spectral * CartesianIndex{0} and broadcast tests * LTA tests fixed * SpectralTransform adjusted to ndim-1 LTA, still WIP * n-dim leapfrogging * n-dimensional UV_from_vor! * BarotropicModel with n-dim formulation * define prognostic_variables(::ModelSetup) * shallow water model with new array structure * First working shallow water model with new variable structure * Spectral gradients with better size checks * horizontal diffusion with nlayers * implicit, land, ocean adapted to new structure * First half of the primitive equation dynamical core restructured * surface pressure tendency, vertical velocity and linear pres gradient restructured * vertical advection to new structure * vor, div, temp, humid tendencies, implicit and diffusion * physics_tendencies_only! renaming * Further size calls for LTA corrected * replace spectral/gridded functions with transform * transform and gradient tests passing * more tests adapted * extending tests adapted * nlayers instead of nlev; starting to adjust docs * docs rework contiues * benchmark suite nlayers spectral grid call * further docs updated * doc add section about batched transforms * typo in docs * docs: another typo * changelog updated * New 4D Variable Structure: nlayers instead of nlev; starting to adjust docs (#566) * nlayers instead of nlev; starting to adjust docs * docs rework contiues * benchmark suite nlayers spectral grid call * further docs updated * doc add section about batched transforms * typo in docs * docs: another typo * changelog updated * linting * nlayers kwarg in README * more type stable `global_diagnostics` in analysis docs * spectral! -> transform! * NF=Float32 for SpectralGrid --------- Co-authored-by: Milan <[email protected]> * all merged * rename ModelSetup to AbstractModel * NetCDF output modularised (#573) * NetCDF output modularised * docstrings everywhere * precipitation output bugs corrected * changelog added * parameters.txt pulls automatically all show strings from model components * include precip and clouds into standard output for primitive wet * show output tweaks * netcdf output tests adapted and extended * gremlins removed * particle tracker test adapted * bugs in netcdf output tests * include previous bugfix changelog * benchmarks nlayer/nlev fixed * add @inbounds back in * constrain to julia 1.10 * CI with prelease for 1.11 * add dependabot.yml * update CI.yml * move dependabot * Tuple instead of vector of different grids, latter fails in 1.9 * CI with 1.9 again * grid creation with Grid(grid.data) to avoid double nesting * define JLArray method for julia v1.9 * set compat to Julia 1.9 again * JetStreamForcing adapted * bug: wrote restart even without output * output show with restart information * RandomWaves initial conditions adapted * docs: extensions/forcing_drag adapted * transforms with singleton dimensions possible * test real to real transform * Transfroms: More number format flexibility tests * docs build errors addressed * first version NetCDFOutput new documentation * docs: particle advection with 2D shallow water model nlayers=1 * make nlayers>1 warn an error for 2D models * Improved error message for `ismatching` * docs speedytransforms * docs: add variables to netcdf * docs misc * docs: extending netCDF output * custom netcdf output * docs: custom netcdf output finished * Set! function for PrognosticVariables and ICs for new structure (#563) * export set! * reworking UV from vordiv tests with set! * move radius keyword into spectral gradient kernels * set! linting * spectral gradients: typo corrected * @inbounds in dynamics tendencies * FLoops dependency removed * allocation free vertical velocity * (almost) non-allocating vertical advection * general vertical advection stencil via ntuple --------- Co-authored-by: Max <[email protected]>
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