├── .github └── workflows │ └── checks.yml ├── .gitignore ├── .readthedocs.yml ├── CITATION.cff ├── CONTRIBUTORS.md ├── LICENSE.txt ├── README.md ├── documentation ├── Makefile ├── clean_examples.sh ├── execute_examples.sh ├── generate_examples.sh ├── make.bat ├── notes │ └── joss_paper │ │ ├── Makefile │ │ ├── joss.bib │ │ ├── paper.md │ │ └── timing_results.pdf └── source │ ├── conf.py │ ├── files │ ├── diagnostic.rst │ ├── examples.rst │ ├── examples │ │ ├── DDV.rst │ │ ├── DDV2016.ipynb │ │ ├── Hamiltonetal.rst │ │ ├── Hamiltonetal2023.ipynb │ │ ├── Lietal.rst │ │ ├── Lietal2017.ipynb │ │ ├── RP.rst │ │ ├── RP1982.ipynb │ │ ├── VSPD.rst │ │ ├── VSPD2019.ipynb │ │ ├── diffeq.rst │ │ ├── diffeq_example.ipynb │ │ ├── manual.rst │ │ ├── manual_basis.ipynb │ │ ├── tgls.rst │ │ └── tgls_example.ipynb │ ├── figures │ │ └── compuflow.png │ ├── general_information.rst │ ├── model │ │ ├── atmosphere.rst │ │ ├── figures │ │ │ ├── atmoro.png │ │ │ ├── atmoro.svg │ │ │ ├── energybalance.png │ │ │ ├── energybalance.svg │ │ │ ├── energybalance_detail.png │ │ │ ├── energybalance_detail.svg │ │ │ ├── model_variables_duck.png │ │ │ ├── model_variables_duck.svg │ │ │ ├── model_variables_maosoam_duck.png │ │ │ ├── model_variables_maosoam_duck.svg │ │ │ ├── visualise_basisfunctions_atmosphere.png │ │ │ └── visualise_basisfunctions_ocean.png │ │ ├── li_model.rst │ │ ├── maooam_model.rst │ │ ├── ocean.rst │ │ ├── oro_model.rst │ │ └── ref.bib │ ├── model_description.rst │ ├── references.rst │ ├── technical │ │ ├── configuration.rst │ │ ├── diagnostics.rst │ │ ├── functions.rst │ │ ├── inner_products.rst │ │ ├── integrators.rst │ │ ├── misc.rst │ │ ├── tensors.rst │ │ └── toolbox.rst │ ├── technical_description.rst │ ├── user_guide.rst │ └── user_guide │ │ ├── figures │ │ ├── maooam_run-Copy1_63_1.png │ │ └── maooam_run-Copy1_70_0.png │ │ ├── vid_diag.rst │ │ └── vid_multi.rst │ └── index.rst ├── environment.yml ├── misc └── figs │ └── readme.gif ├── model_test ├── test_aotensor.py ├── test_aotensor.ref ├── test_aotensor_6x6.py ├── test_aotensor_6x6.ref ├── test_aotensor_jacobian.py ├── test_aotensor_jacobian.ref ├── test_aotensor_sym.py ├── test_aotensor_sym_dynT.py ├── test_aotensor_sym_ground.py ├── test_base.py ├── test_base_symbolic.py ├── test_inner_products.py ├── test_inner_products_6x6.py ├── test_inprod_analytic.ref ├── test_inprod_analytic_6x6.ref └── test_tlad.py ├── notebooks ├── diagnostics │ ├── eddy_heat_flux.ipynb │ └── vertical_wind_velocity.ipynb ├── diffeq_test.ipynb ├── ground_heat.ipynb ├── introduction_qgs.ipynb ├── lyapunov │ ├── CLV_methods_comparison.ipynb │ ├── maooam_model_lyapunov.ipynb │ └── simple_model_lyapunov.ipynb ├── manual_ocean_basis_setting.ipynb ├── maooam_T4.ipynb ├── maooam_dynamic_temperature.ipynb ├── maooam_run.ipynb ├── maosoam_run.ipynb ├── simple_run.ipynb └── symbolic_outputs │ ├── symbolic_output_land_atmosphere-AUTO.ipynb │ └── symbolic_output_land_atmosphere.ipynb ├── pyproject.toml ├── qgs ├── __init__.py ├── basis │ ├── __init__.py │ ├── base.py │ └── fourier.py ├── diagnostics │ ├── __init__.py │ ├── base.py │ ├── differential.py │ ├── eddy.py │ ├── misc.py │ ├── multi.py │ ├── streamfunctions.py │ ├── temperatures.py │ ├── util.py │ ├── variables.py │ ├── vorticity.py │ └── wind.py ├── functions │ ├── __init__.py │ ├── sparse_mul.py │ ├── symbolic_mul.py │ ├── symbolic_tendencies.py │ ├── tendencies.py │ └── util.py ├── inner_products │ ├── __init__.py │ ├── analytic.py │ ├── base.py │ ├── definition.py │ └── symbolic.py ├── integrators │ ├── __init__.py │ ├── integrate.py │ ├── integrator.py │ └── statistics.py ├── params │ ├── __init__.py │ ├── parameter.py │ └── params.py ├── plotting │ ├── __init__.py │ └── util.py ├── tensors │ ├── __init__.py │ ├── atmo_thermo_tensor.py │ ├── qgtensor.py │ └── symbolic_qgtensor.py └── toolbox │ ├── __init__.py │ └── lyapunov.py ├── qgs_maooam.py ├── qgs_rp.py └── requirements.txt /.github/workflows/checks.yml: 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