├── .github └── workflows │ ├── docs.yml │ ├── lint.yml │ ├── pr.yml │ ├── push.yml │ ├── schedule_future.yml │ ├── schedule_main.yml │ ├── test.yml │ └── website.yml ├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── docs ├── 404.html ├── Gemfile ├── Gemfile.lock ├── Makefile ├── _config.yml ├── _includes │ └── navbar.html ├── _layouts │ ├── home.html │ └── page.html ├── about_gusto.md ├── assets │ ├── css │ │ └── style.scss │ ├── home.html │ ├── images │ │ ├── gusto_galewsky_banner.png │ │ ├── gusto_galewsky_grey_on_white.png │ │ ├── gusto_galewsky_white_on_grey.png │ │ ├── gusto_grey_on_blank.png │ │ ├── gusto_grey_on_white.png │ │ ├── gusto_logo_square.png │ │ ├── gusto_navbar.png │ │ ├── gusto_white_on_blank.png │ │ ├── gusto_white_on_grey.png │ │ ├── shallow_water_galewsky.jpg │ │ └── shallow_water_pangea.jpg │ └── page.html ├── index.markdown ├── server.py └── source │ ├── _static │ ├── GitHub_Logo.png │ └── bibliography.bib │ ├── conf.py │ ├── gusto.fml.rst │ ├── gusto.recovery.rst │ └── index.rst ├── examples ├── boussinesq │ ├── skamarock_klemp_compressible.py │ ├── skamarock_klemp_incompressible.py │ ├── skamarock_klemp_linear.py │ └── test_boussinesq_examples.py ├── compressible_euler │ ├── dcmip_3_1_gravity_wave.py │ ├── dry_bryan_fritsch.py │ ├── schaer_mountain.py │ ├── skamarock_klemp_nonhydrostatic.py │ ├── straka_bubble.py │ ├── test_compressible_euler_examples.py │ └── unsaturated_bubble.py └── shallow_water │ ├── linear_thermal_galewsky_jet.py │ ├── linear_williamson_2.py │ ├── moist_convective_williamson_2.py │ ├── moist_thermal_equivb_gw.py │ ├── moist_thermal_williamson_5.py │ ├── shallow_water_1d_wave.py │ ├── test_shallow_water_examples.py │ ├── thermal_williamson_2.py │ ├── williamson_2.py │ └── williamson_5.py ├── figures ├── boussinesq │ ├── skamarock_klemp_compressible_bouss_final.png │ ├── skamarock_klemp_compressible_bouss_initial.png │ ├── skamarock_klemp_incompressible_bouss_final.png │ ├── skamarock_klemp_incompressible_bouss_initial.png │ ├── skamarock_klemp_linear_bouss_final.png │ └── skamarock_klemp_linear_bouss_initial.png ├── compressible_euler │ ├── dcmip_3_1_gravity_wave_final.png │ ├── dcmip_3_1_gravity_wave_initial.png │ ├── dry_bryan_fritsch.png │ ├── schaer_mountain_final.png │ ├── schaer_mountain_initial.png │ ├── skamarock_klemp_nonhydrostatic_final.png │ ├── skamarock_klemp_nonhydrostatic_initial.png │ ├── skamarock_klemp_nonhydrostatic_trbdf2_final.png │ ├── straka_bubble.png │ ├── unsaturated_bubble_final.png │ └── unsaturated_bubble_initial.png └── shallow_water │ ├── linear_thermal_galewsky_final.png │ ├── linear_thermal_galewsky_initial.png │ ├── linear_williamson_2_final.png │ ├── linear_williamson_2_initial.png │ ├── moist_convective_williamson_2_final.png │ ├── moist_convective_williamson_2_initial.png │ ├── moist_thermal_equivb_gw_final.png │ ├── moist_thermal_equivb_gw_initial.png │ ├── moist_thermal_williamson_5_final.png │ ├── moist_thermal_williamson_5_initial.png │ ├── shallow_water_1d_wave.png │ ├── thermal_williamson_2_final.png │ ├── thermal_williamson_2_initial.png │ ├── williamson_2_final.png │ ├── williamson_2_initial.png │ ├── williamson_5_final.png │ └── williamson_5_initial.png ├── gusto ├── __init__.py ├── complex_proxy │ ├── __init__.py │ ├── common.py │ ├── mixed.py │ ├── mixed_impl.py │ ├── vector.py │ └── vector_impl.py ├── core │ ├── __init__.py │ ├── configuration.py │ ├── conservative_projection.py │ ├── coord_transforms.py │ ├── coordinates.py │ ├── domain.py │ ├── equation_configuration.py │ ├── fields.py │ ├── function_spaces.py │ ├── io.py │ ├── kernels.py │ ├── labels.py │ ├── logging.py │ └── meshes.py ├── diagnostics │ ├── __init__.py │ ├── compressible_euler_diagnostics.py │ ├── diagnostics.py │ └── shallow_water_diagnostics.py ├── equations │ ├── __init__.py │ ├── active_tracers.py │ ├── advection_diffusion_equations.py │ ├── boussinesq_equations.py │ ├── common_forms.py │ ├── compressible_euler_equations.py │ ├── diffusion_equations.py │ ├── prognostic_equations.py │ ├── shallow_water_equations.py │ ├── thermodynamics.py │ └── transport_equations.py ├── initialisation │ ├── __init__.py │ ├── hydrostatic_initialisation.py │ └── numerical_integrator.py ├── physics │ ├── __init__.py │ ├── boundary_and_turbulence.py │ ├── chemistry.py │ ├── held_suarez_forcing.py │ ├── microphysics.py │ ├── physics_parametrisation.py │ └── shallow_water_microphysics.py ├── recovery │ ├── __init__.py │ ├── averaging.py │ ├── recovery.py │ ├── recovery_kernels.py │ ├── recovery_options.py │ └── reversible_recovery.py ├── rexi │ ├── __init__.py │ ├── rexi.py │ └── rexi_coefficients.py ├── solvers │ ├── __init__.py │ ├── linear_solvers.py │ ├── parameters.py │ └── preconditioners.py ├── spatial_methods │ ├── __init__.py │ ├── augmentation.py │ ├── diffusion_methods.py │ ├── limiters.py │ ├── spatial_methods.py │ └── transport_methods.py ├── time_discretisation │ ├── __init__.py │ ├── explicit_runge_kutta.py │ ├── imex_runge_kutta.py │ ├── implicit_runge_kutta.py │ ├── multi_level_schemes.py │ ├── sdc.py │ ├── time_discretisation.py │ └── wrappers.py └── timestepping │ ├── __init__.py │ ├── semi_implicit_quasi_newton.py │ ├── split_timestepper.py │ ├── timestepper.py │ └── tr_bdf2_quasi_newton.py ├── integration-tests ├── adjoints │ ├── test_diffusion_sensitivity.py │ ├── test_moist_thermal_williamson_5_sensitivity.py │ └── test_shallow_water_sensitivity.py ├── balance │ ├── test_boussinesq_balance.py │ ├── test_compressible_balance.py │ ├── test_saturated_balance.py │ └── test_unsaturated_balance.py ├── conftest.py ├── data │ ├── boussinesq_compressible_chkpt.h5 │ ├── boussinesq_incompressible_chkpt.h5 │ ├── dry_compressible_chkpt.h5 │ ├── linear_sk_rexi_chkpt.h5 │ ├── linear_sw_wave_chkpt.h5 │ ├── linear_sw_wave_rexi_chkpt.h5 │ ├── moist_compressible_chkpt.h5 │ ├── simult_SIQN_order0_chkpt.h5 │ ├── simult_SIQN_order1_chkpt.h5 │ ├── sw_fplane_chkpt.h5 │ └── update_kgos.py ├── diffusion │ └── test_diffusion.py ├── equations │ ├── test_advection_diffusion.py │ ├── test_boussinesq.py │ ├── test_coupled_transport.py │ ├── test_dry_compressible.py │ ├── test_forced_advection.py │ ├── test_linear_sw_wave.py │ ├── test_moist_compressible.py │ ├── test_sw_fplane.py │ ├── test_sw_linear_triangle.py │ ├── test_sw_triangle.py │ └── test_thermal_sw.py ├── model │ ├── test_IMEX.py │ ├── test_TR-BDF2.py │ ├── test_checkpointing.py │ ├── test_conservative_transport_with_physics.py │ ├── test_mean_mixing_ratio.py │ ├── test_multi_checkpoint.py │ ├── test_nc_outputting.py │ ├── test_nonsplit_physics.py │ ├── test_passive_tracer.py │ ├── test_prescribed_transport.py │ ├── test_sdc.py │ ├── test_simultaneous_SIQN.py │ ├── test_split_timestepper.py │ └── test_time_discretisation.py ├── physics │ ├── test_boundary_layer_mixing.py │ ├── test_held_suarez_friction.py │ ├── test_held_suarez_relaxation.py │ ├── test_instant_rain.py │ ├── test_precipitation.py │ ├── test_saturation_adjustment.py │ ├── test_source_sink.py │ ├── test_static_adjustment.py │ ├── test_suppress_vertical_wind.py │ ├── test_surface_fluxes.py │ ├── test_sw_saturation_adjustment.py │ ├── test_terminator_toy.py │ └── test_wind_drag.py ├── rexi │ ├── test_linear_compressible_boussinesq.py │ ├── test_linear_sw.py │ └── test_rexi_approximations.py └── transport │ ├── test_advective_then_flux.py │ ├── test_dg_transport.py │ ├── test_embedded_dg_advection.py │ ├── test_limiters.py │ ├── test_mixed_fs_options.py │ ├── test_recovered_transport.py │ ├── test_split_dg_transport.py │ ├── test_subcycling.py │ ├── test_supg_transport.py │ ├── test_tracer_conservative_transport.py │ ├── test_vector_recovered_space.py │ ├── test_vorticity_transport.py │ └── test_zero_limiter.py ├── plotting ├── boussinesq │ └── plot_skamarock_klemp_boussinesq.py ├── compressible_euler │ ├── plot_dcmip_3_1_gravity_wave.py │ ├── plot_dry_bryan_fritsch.py │ ├── plot_schaer_mountain.py │ ├── plot_skamarock_klemp_nonhydrostatic.py │ ├── plot_straka_bubble.py │ └── plot_unsaturated_bubble.py ├── plot_1D_profile.py ├── plot_hovmoller.py ├── plot_stats.py ├── plotting.py └── shallow_water │ ├── plot_linear_thermal_galewsky_jet.py │ ├── plot_linear_williamson_2.py │ ├── plot_moist_convective_williamson_2.py │ ├── plot_moist_thermal_equivb_gravity_wave.py │ ├── plot_moist_thermal_williamson_5.py │ ├── plot_shallow_water_1d_wave.py │ ├── plot_thermal_williamson_2.py │ ├── plot_williamson_2.py │ └── plot_williamson_5.py ├── pyproject.toml ├── requirements.txt ├── setup.cfg └── unit-tests ├── complex_proxy ├── test_complex_mixed.py └── test_complex_vector.py ├── diagnostic_tests ├── test_cumulative_sum.py ├── test_dewpoint_temperature.py └── test_wetbulb_temperature.py ├── kernel_tests ├── test_clip_zero_kernel.py ├── test_limit_midpoints_kernel.py ├── test_max_kernel.py └── test_min_kernel.py ├── recovery_tests ├── test_average_kernel.py ├── test_conservative_recovery.py ├── 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